Patent Application
20230101432
The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled 761612000740SeqList.TXT, created Jan. 3, 2019, which is 5,783 kilobytes in size. The information in the electronic format of the Sequence Listing is incorporated by reference in its entirety.
The present disclosure provides multi-domain immunomodulatory proteins, nucleic acids encoding such immunomodulatory proteins, cells engineered to express the immunomodulatory proteins and infectious agents containing nucleic acid encoding the immunomodulatory proteins. The immunomodulatory proteins bind both an inhibitory receptor and a receptor involved in activation signaling cascades in an immune cell, such as a T cell. The immunomodulatory proteins, engineered cells and infectious agents provide therapeutic utility for a variety of immunological diseases or conditions. Compositions and methods for making and using such proteins are provided.
Modulation of the immune response by intervening in the processes that occur in the immunological synapse (IS) formed by and between antigen-presenting cells (APCs) or target cells and lymphocytes is of increasing medical interest. Currently, biologics used to enhance or suppress immune responses have generally been limited to immunoglobulins (e.g., anti-PD-1 antibodies) or soluble receptors against a single cell surface molecule (e.g., Fc-CTLA4). Improved therapeutic agents that can modulate the IS are needed. Provided are embodiments that meet such needs.
Provided are immunomodulatory proteins containing at least one inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor; and at least one activating receptor binding molecule (ARBM) that binds to (i) an activating receptor (ii) a ligand of the activating receptor, wherein the inhibitory receptor and the activating receptor are expressed on the same immune cell; the IRBM and ARBM are different polypeptides in which (a) one of the at least one of the IRBM or ARBM is a not an antibody or an antigen-binding antibody fragment; and/or (b) the at least one of the IRBM or the at least one of the ARBM contains a non-antibody immunoglobulin superfamily (IgSF) domain; and the IRBM exhibits higher binding activity, optionally higher binding affinity, for the inhibitory receptor than the ARBM exhibits for the activating receptor or a ligand of the activating receptor.
Provided are immunomodulatory proteins containing at least one inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor; and at least one activating receptor binding molecule (ARBM) that binds to (i) an activating receptor or (ii) a ligand of an activating receptor, wherein the inhibitory receptor and the activating receptor are expressed on the same immune cell; the IRBM and ARBM are different polypeptides in which (a) one of the at least one of the IRBM or ARBM is a not an antibody or an antigen-binding antibody fragment; and/or (b) the at least one of the IRBM or the at least one of the ARBM contains a non-antibody immunoglobulin superfamily (IgSF) domain; and the immunomodulatory protein is a monomeric polypeptide and/or contains a single polypeptide chain.
In some of any of the provided embodiments, the ARBM binds to a ligand of an activating receptor. In some examples, the ligand of an activating receptor is CD80, CD86, ICOSL or an MHC molecule. In some embodiments, the ARBM binds to an activating receptor.
Provided are immunomodulatory proteins containing at least one inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor; and at least one activating receptor binding molecule (ARBM) that binds to an activating receptor, wherein the inhibitory receptor and the activating receptor are expressed on the same immune cell; and the IRBM and ARBM are different polypeptides in which (a) one of the at least one of the IRBM or ARBM is a not an antibody or an antigen-binding antibody fragment; and/or (b) the at least one of the IRBM or the at least one of the ARBM contains a non-antibody immunoglobulin superfamily (IgSF) domain. In some of any such embodiments, the immune cell is a T cell.
In some of any of the provided embodiments, the activating receptor contains an immunoreceptor tyrosine-based activation motif (ITAM) or interacts with an adaptor protein comprising a binding domain specific to a phosphotyrosine residue. In some embodiments, the activating receptor is selected from a TCR, CD3, CD4, CD8, CD28, ICOS or CD2. In some embodiments, the activating receptor is CD28. In some embodiments, the activating receptor is CD2.
Provided are immunomodulatory proteins containing at least one inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor, wherein the inhibitory receptor is PD-1 and at least one activating receptor binding molecule (ARBM) that binds to an activating receptor or to a ligand of the activating receptor, wherein the IRBM and ARBM are different polypeptides. Provided are immunomodulatory proteins containing at least one inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor, wherein the inhibitory receptor is TIGIT and at least one activating receptor binding molecule (ARBM) that binds to an activating receptor or to a ligand of the activating receptor, wherein the IRBM and ARBM are different polypeptides. In some of any such embodiments, the activating receptor contains an immunoreceptor tyrosine-based activation motif (ITAM) or interacts with an adaptor protein comprising a binding domain specific to a phosphotyrosine residue. In some embodiments, the activating receptor is selected from a TCR, CD3, CD4, CD8, CD28, ICOS or CD2. In some examples, the activating receptor is CD28. In some embodiments, the activating receptor is CD2.
Provided are immunomodulatory proteins comprising at least one inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor; and at least one activating receptor binding molecule (ARBM) that binds to an activating receptor or to a ligand of the activating receptor, wherein the activating receptor is CD28, wherein the IRBM and ARBM are different polypeptides.
Provided are immunomodulatory proteins comprising at least one inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor; and at least one activating receptor binding molecule (ARBM) that binds to an activating receptor or to a ligand of the activating receptor, wherein the activating receptor is CD2, wherein the IRBM and ARBM are different polypeptides.
In some of any of the provided embodiments, the inhibitory receptor and the activating receptor are expressed on the same immune cell. In some embodiments, the immune cell is a T cell.
In some of any of the provided embodiments, one of the at least one of the IRBM or ARBM is a not an antibody or an antigen-binding antibody fragment; and/or the at least one of the IRBM or the at least one of the ARBM contains a non-antibody immunoglobulin superfamily (IgSF) domain.
In some of any of the provided embodiments, the IRBM exhibits higher binding activity, optionally higher binding affinity, for the inhibitory receptor than the ARBM exhibits for the activating receptor or a ligand of the activating receptor. In some embodiments, the IRBM exhibits 1.2-fold, 1.5-fold, 2.0-fold, 2.5-fold, 3.0-fold, 4.0-fold, 5.0-fold, 6.0-fold, 7.0-fold, 8.0-fold, 9.0-fold, 10.0 fold or higher binding activity, optionally higher binding affinity, for the inhibitory receptor than the ARBM exhibits for the activating receptor or a ligand of the activating receptor.
In some of any such embodiments, the at least one of the IRBM and the at least one of the ARBM is not an antibody or an antigen-binding antibody fragment. In some embodiments, the at least one of the IRBM or the at least one of the ARBM contains a non-antibody immunoglobulin superfamily (IgSF) domain. In some embodiments, the at least one of the IRBM and the at least one of the ARBM each individually contains at least one non-antibody IgSF domain.
In some of any of the provided embodiments, the ARBM binds to a ligand of the activating receptor and the ligand of the activating receptor is CD80 or CD86. In some embodiments, the ARBM is an antibody that specifically binds to the ligand of an activating receptor or is an antigen-binding antibody fragment. In some embodiments, the ARBM contains at least one IgSF domain of a binding partner of the ligand of the activating receptor. In some such embodiments, the binding partner of a ligand of an activating receptor is a wild-type CTLA-4 or is a variant thereof that binds to the ligand of the activating receptor, optionally wherein the ligand is CD80 or CD86. In some cases, the wild-type protein is a human protein. In some embodiments, the ARBM is not the full-length sequence of the binding partner; and/or the ARBM only contains the extracellular domain or an IgSF domain or specific binding fragment thereof of the binding partner. In some embodiments, the IgSF domain is an IgV domain. In some of any such embodiments, the binding partner of the ligand of an activating receptor is a CTLA-4 polypeptide or a variant thereof and the ARBM contains (i) the sequence of amino acids set forth in SEQ ID NO: 36, 2655 or 2947, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 36, 2655 2947; or (iii) a specific binding fragment of (i) or (ii). In some embodiments, the binding partner is a variant of a CTLA-4 polypeptide and the variant exhibits increased binding activity, optionally binding affinity, to the ligand of the activating receptor compared to the binding of unmodified or wild-type binding partner to the same ligand. In some cases, the binding activity, optionally binding affinity, to the ligand of the activating receptor is increased more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold or 60-fold.
In some of any of the provided embodiments, the ARBM is an antibody that specifically binds to the activating receptor or is an antigen-binding antibody fragment.
In some of any of the provided embodiments, the ARBM contains at least one IgSF domain of a binding partner of the activating receptor. In some of any such embodiments, the ARBM is not the full-length sequence of the binding partner; and/or the ARBM only contains the extracellular domain or at least one IgSF domain or specific binding fragment thereof of the binding partner. In some embodiments, the IgSF domain is an IgV domain or an IgC domain. In some aspects, the at least one IgSF domain contains an IgV domain or specific binding fragment thereof, an IgC domain or a specific binding fragment thereof, or both. In some embodiments, the at least one IgSF domain consists of an IgV domain or specific binding fragment thereof, an IgC domain or a specific binding fragment thereof, or both.
In some embodiments, the activating receptor is CD28. In some embodiments, the binding partner of the activating receptor is selected from a wild-type ICOSL, CD80 or CD86 or is a variant thereof that binds to the activating receptor. In some cases, the wild-type protein is a human protein. In some of any such embodiments, the binding partner of the activating receptor is a ICOSL polypeptide or a variant thereof and the ARBM contains (i) the sequence of amino acids set forth in SEQ ID NO:32, 2056, or 2244, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 32, 2056, or 2244; or (iii) a specific binding fragment of (i) or (ii). In some of any such embodiments, the activating receptor is CD28 and the binding partner of the activating receptor is a CD80 polypeptide or a variant thereof and the ARBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 28, 1005, 1079, 2615, 2654, or 3580, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:28, 1005, 1079, 2615, 2654, or 3580; or (iii) a specific binding fragment of (i) or (ii). In some of any such embodiments, the binding partner of the activating receptor is a CD86 polypeptide or a variant thereof and the ARBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 29 or 1195, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:29 or 1195; or (iii) a specific binding fragment of (i) or (ii).
In some embodiments, the activating receptor is CD2. In some embodiments, the binding partner of the activating receptor is CD58 or is a variant thereof that binds to the activating receptor. In some cases, the wild-type protein is a human protein. In some of any such embodiments, the binding partner of the activating receptor is a CD58 polypeptide or a variant thereof and the ARBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 2946, 3239 or 3650, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:2946, 3239 or 3650; or (iii) a specific binding fragment of (i) or (ii).
In some of any such embodiments, the binding partner is a variant of the activating receptor and the variant exhibits increased binding activity, optionally binding affinity, to the activating receptor compared to the binding of unmodified or wild-type binding partner to the same activating receptor. In some examples, the binding activity, optionally binding affinity, to the activating receptor is increased more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold or 60-fold.
In some of any of the provided embodiments, the inhibitory receptor includes an immunoreceptor tyrosine-based inhibitory motif (ITIM). In some embodiments, the inhibitory receptor is PD-1, TIGIT or CTLA-4. In some embodiments, the IRBM is an antibody that specifically binds to the inhibitory receptor or is an antigen-binding antibody fragment. In some embodiments, the IRBM contains at least one IgSF domain of a binding partner of the inhibitory receptor. In some examples, the binding partner of the inhibitory receptor is selected from a wild-type CD112, CD155, PD-L1 or PD-L2 or is a variant thereof that binds to the inhibitory receptor. In some instances, the wild-type protein is a human protein.
In some embodiments, the IRBM is not the full-length sequence of the binding partner; and/or the IRBM only contains the extracellular domain or an IgSF domain or specific binding fragment thereof of the binding partner, optionally wherein the IgSF domain is an IgV domain or an IgC domain. In some aspects, the at least one IgSF domain includes an IgV domain or specific binding fragment thereof, an IgC domain or a specific binding fragment thereof, or both. In some embodiments, the at least one IgSF domain consists of an IgV domain or specific binding fragment thereof, an IgC domain or a specific binding fragment thereof, or both.
In some of any such embodiments, the inhibitory receptor is a TIGIT. In some embodiments, the binding partner of the inhibitory receptor is a CD155 polypeptide or a variant thereof and the IRBM contains (i) the sequence of amino acids set forth in SEQ ID NO: 47, 310 or 353, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 47, 310 or 353; or (iii) a specific binding fragment of (i) or (ii). In some embodiments, the binding partner of the inhibitory receptor is a CD112 polypeptide or a variant thereof and the IRBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 48, 666 or 761, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 48, 666 or 761; or (iii) a specific binding fragment of (i) or (ii).
In some of any such embodiments, the inhibitory receptor is PD-1. In some embodiments, the binding partner of the inhibitory receptor is a PD-L1 polypeptide or a variant thereof and the IRBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 30, 55, 309 or 1728, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 30, 55, 309 or 1728; or (iii) a specific binding fragment of (i) or (ii). In some embodiments, the binding partner of the inhibitory receptor is a PD-L2 polypeptide or a variant thereof and the IRBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 31, 1203 or 1263, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 31, 1203 or 1263; or (iii) a specific binding fragment of (i) or (ii).
In some of any of the provided embodiments, the IRBM contains at least one IgSF domain of a binding partner of the inhibitory receptor. In some of any of the provided embodiments, the IRBM is not the full-length sequence of the binding partner; and/or the IRBM only contains the extracellular domain or an IgSF domain or specific binding fragment thereof of the binding partner. In some embodiments, the IgSF domain is an IgV domain or an IgC domain. In some embodiments, the at least one IgSF domain contains an IgV domain or specific binding fragment thereof, an IgC domain or a specific binding fragment thereof, or both. In some embodiments, the at least one IgSF domain consists of an IgV domain or specific binding fragment thereof, an IgC domain or a specific binding fragment thereof, or both.
In some of any of the provided embodiments, the inhibitory is PD-1 and the binding partner of the inhibitory receptor is selected from a wild-type PD-L1 or PD-L2 or is a variant thereof that binds to the inhibitory receptor. In some cases, the wild-type protein is a human protein. In some embodiments, the binding partner of the inhibitory receptor is a PD-L1 polypeptide or a variant thereof and the IRBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 30, 55, 309 or 1728, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 30, 55, 309 or 1728; or (iii) a specific binding fragment of (i) or (ii); or the binding partner of the inhibitory receptor is a PD-L2 polypeptide or a variant thereof and the IRBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 31, 1203 or 1263, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 31, 1203 or 1263; or (iii) a specific binding fragment of (i) or (ii).
In some of any of the provided embodiments, the inhibitory is TIGIT and the binding partner of the inhibitory receptor is selected from a wild-type CD155 or CD112 or is a variant thereof that binds to the inhibitory receptor. In some cases, the wild-type protein is a human protein. In some embodiments, the binding partner of the inhibitory receptor is a CD155 polypeptide or a variant thereof and the IRBM contains (i) the sequence of amino acids set forth in SEQ ID NO: 47, 310 or 353, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 47, 310 or 353; or (iii) a specific binding fragment of (i) or (ii). In some embodiments, the binding partner of the inhibitory receptor is a CD112 polypeptide or a variant thereof and the IRBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 48, 666 or 761, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 48, 666 or 761; or (iii) a specific binding fragment of (i) or (ii).
In some of any such embodiments, the binding partner is a variant and the variant exhibits increased binding activity, optionally binding affinity, to the inhibitory receptor compared to the binding of unmodified or wild-type binding partner to the same inhibitory receptor. In some examples, the binding activity, optionally binding affinity, to the inhibitory receptor is increased more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold or 60-fold.
In some of any of the provided embodiments, the ARBM binds to an activating receptor that is CD28 and the IRBM binds to an inhibitory receptor that is PD-1. In some of any of the provided embodiments, the ARBM binds to an activating receptor that is CD28 and the IRBM binds to an inhibitory receptor that is TIGIT.
In some of any of the provided embodiments, the ARBM binds to an activating receptor that is CD28 and the ARBM contains at least one IgSF domain of a binding partner of CD28.
In some of any such embodiments, the binding partner of CD28 is ICOSL or is a variant thereof that binds to CD28. In some aspects, the binding partner is a variant of ICOSL and the variant exhibits increased binding activity, optionally binding affinity, to CD28 compared to the binding of unmodified or wild-type ICOSL to CD28. In some embodiments, the binding activity, optionally binding affinity, to CD28 is increased more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold or 60-fold. In some embodiments, the ARBM contains (i) the sequence of amino acids set forth in SEQ ID NO: 32, 2056, or 2244, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 32, 2056, or 2244; or (iii) a specific binding fragment of (i) or (ii). In some of any such embodiments, the ARBM is a variant ICOSL and the one or more amino acid modifications in a variant ICOSL can be any described herein, such as set forth in Section I.B.1.a. In some embodiments, the one or more amino acid modifications include any set forth in Table 7. In some embodiments, the ARBM is a variant ICOSL and the variant ICOSL contains one or more amino acid modifications at one or more position corresponding to 52, 57, 100, 110, or 198 with reference to numbering set forth in SEQ ID NO: 32, 2056, or 2244. In some cases, the variant ICOSL contains one or more amino acid modifications selected from N52H, N52D, N52S, N52K, S54A, S54P, N57Y, Q100P, Q100R, V110A, V110D, C198R, or a conservative amino acid substitution thereof, with reference to numbering set forth in SEQ ID NO: 32, 2056, or 2244. In some embodiments, the variant ICOSL contains one or more amino acid modifications selected from M10V, M10I, V11E, S13G, E16V, S18R, A20V, S25G, F27S, F27C, N30D, Y33del, Q37R, K42E, T43A, Y47H, N52A, N52C, N52D, N52G, N52H, N52L, N52K, N52M, N52P, N52Q, N52R, N52S, N52T, N52V, N52Y, S54A, S54P, N57A, N57E, N57F, N57H, N57K, N57L, N57M, N57P, N57Q, N57S, N57T, N57V, N57W, N57Y, R61S, R61C, Y62F, L67P, A71T, G72R, L74Q, R75Q, D77G, F78L, L80P, N84Q, D89G, E90A, K92R, F93L, H94E, H94D, L96F, L96I, V97A, L98F, S99G, Q100A, Q100D, Q100E, Q100G, Q100K, Q100L, Q100M, Q100N, Q100R, Q100P, Q100S, Q100T, Q100V, L102R, G103E, V107A, V107I, S109G, 5109N, V110D, V110N, V110A, E111del, T113E, H115R, H115Q, V116A, A117T, N119Q, F120I, F120S, S121G, V122A, V122M, S126T, S126R, H129P, S130G, S132F, Q133H, E135K, F138L, T139S, C140D, C140del, 5142F, I143V, I143T, N144D, Y146C, V151A, Y152C, Y152H, W153R, I154F, N155H, N155Q, K156M, D158G, L161P, L161M, L166Q, N168Q, F172S, L173S, M175T, T1905, T190A, S192G, V193M, N194D, C198R, N201S, L203P, L203F, N207Q, L208P, V210A, S212G, D217V, I218T, 1218N, E220G, R221G, R221I, I224V, T225A, N227K or a conservative amino acid modification thereof, with reference to numbering of reference to numbering of SEQ ID NO:32, 2056 or 2244.
In some of any such embodiments, the variant ICOSL polypeptide contains the amino acid modification(s) N52S, N52S, N52D, N52Y/N57Y/F138L/L203P, N52H/N57Y/Q100P, N52S/Y146C/Y152C, N52H/C198R, N52H/C140del/T225A, N52H/C198R/T225A, N52H/K92R, N52H/599G, N57Y, N57Y/Q100P, N52S/S130G/Y152C, N52S/Y152C, N52S/C198R, N52Y/N57Y/Y152C, N52Y/N57Y/H129P/C198R, N52H/L161P/C198R, N52S/T113E, S54A, N52D/554P, N52K/L208P, N52S/Y152H, N52H/I143T, N52S/L80P, N52S/D158G, N52D/Q133H, N52H/N57Y/Q100R/V110D/C198R/S212G, N52H/N57Y/Q100R/C198R, N52H/N57Y/L74Q/V110D/S192G, N52H/Q100R, N52H/S121G/C198R, A20V/N52H/N57Y/Q100R/S109G, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100R/V122A, N52H/N57Y/Q100R/F172S, N52H/N57Y/Q100R, N52S/F120S/N227K, N52S/N194D, N52S/F120S, N52S/G72R, N52S/A71T/A117T/T190A/C198R, N52H/N57Y/Q100R/V107I/V110D/S132F/I154F/C198R/R221G, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/C198R, N52H/N57Y/Q100R/V110D/C198R, F27S/N52H/N57Y/V110N, N52S/H94E/L96I/S109N/L166Q, S18R/N52S/F93L/I143V/R221G, V11E/N30D/N52H/N57Y/H94E/L96I/L98F/N194D/V210A/I218T, N52S/H94E/L96I/V122M, N52H/N57Y/H94E/L96I/F120I/S126T/W153R/I218N, M10V/S18R/N30D/N52S/S126R/T139S/L203F, S25G/N30D/N52S/F120S/N227K, N52H/N57Y/Q100R/V110D/F172S/C198R, S25G/F27C/N52H/N57Y/Q100R/V110D/E135K/L173S/C198R, N52H/N57Y/V110A/C198R/R221I, N52H/N57Y/Q100R/L102R/V110D/H115R/C198R, N52H/N57Y/Q100R/V110D/N144D/F172S/C198R, N52S/H94E/L98F/Q100R, N52S/E90A, N52S/F120S/I143V/I224V, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52Y/N57Y/Q100P/F172S, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/F172S/C198R, N52S/H115R/F120S/I143V/C198R, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100P/H115R/F172S/C198R, N52H/N57Y/Q100P/F172S/C198R, N52H/N57Y/Q100P/H115R, N52H/N57Y/Q100P/H115R/C198R, N52H/Q100R/C198R, N52H/Q100R/H115R/F172S, N52H/Q100R/H115X/F172S/C198R, N52H/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S, Q100R, N52Y/F138L/L203P, N57Y/Q100R/C198R, N57Y/F138L/L203, N52H, N57Y, N57Y/Q100P, Q100R/F138L, N52H/N57Y/Q100R/H115R, N52H/N57Y/Q100R/F172S, N52H/N57Y/Q100R/H115R/F172S/I224V, N52H/N57Y/Q100R/H115R/F172S, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/I143V/F172S/C198R, N52H/N57Y/Q100R/L102R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/N194D, N52H/N57Y/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/H115R, N52H/Q100R/H115R/I143T/F172S, N52H/N57Y/Q100P/H115R/F172S, E16V/N52H/N57Y/Q100R/V110D/H115R/C198R, N30D/K42E/N52S/H115R/C198R/R221I, N52S/E90A/H115R, N30D/K42E/N52S/H115R, N52S/H115R/F172S/C198R, N119Q, N207Q, N52Q/N207X, N168X/N207X, N52Q/N168Q, N84Q/N207Q, N119Q/N168Q, N119Q/N207Q, N119Q/N155X, N52Q/N119Q, N52Q/N84Q/N207Q, N119Q/N155Q/N168Q, N52Q/N84Q/N155X/N168X, N52Q/N84Q/N119Q/N168Q, N52A/N57F/Q100S, N52A/N57H/Q100S, N52A/N57Y/Q100A, N52D/N57A/Q100A, N52D/Q100S, N52G/Q100A, N52H/Q100A, N52M/N57H/Q100S, N52M/N57W/Q100P, N52Q/N57F, N52Q/N57S/Q100A, N52R/N57L/Q100A, N52R/N57Y/Q100P, N52R/N57Y/Q100S, N52S/N57A/Q100A, N52S/N57H/Q100E, N52S/N57L/Q100S, N52S/N57M/Q100S, N52S/N57Y/Q100S, N52S/N57Y/Q100M, N52S/N57Y/Q100V, N52T/N57H/Q100S, N52T/N57H/Q100A, N52T/N57Y/Q100A, N52V/N57L/Q100A, N52H/N57Y/Q100K, N52K/N57Y/Q100R, N52L/N57H/Q100R, N52R/N57F/Q100N, N52R/N57F/Q100P, N52R/N57F/Q100R, N52R/N57F/Q100T, N52R/N57L/Q100S, N52R/N57W/Q100K, N52R/N57W, N52G/N57V, N52L/N57V, N52S/N57L/Q100G, N52T/N57K/Q100P. In some cases, the variant ICOSL polypeptide contains the modification(s) N52H/N57Y/Q100R/F172S, N52H/N57Y/Q100R, N52H/N57Y/Q100R/V122A, N52H/Q100R, N52H/N57Y/Q100P, N52H/N57Y/V110A/C198R/R221I, N52Y/N57Y/I38L/L203P, N52S/N194D or N52D.
In some of any of the provided embodiments, the ARBM contains the sequence of amino acids set forth in any of SEQ ID NOs: 2022-2055, 2074, 2076-2121, 2137-2154, 2160-2197, 2200-2206, 2208-2243, 2299-2346, or a specific binding fragment thereof. In some of any of the provided embodiments, the ARBM includes the sequence of amino acids set forth in any of SEQ ID NOs: 2057-2073, 2075, 2122-2136, 2155-2159, 2189-2199, 2207, 2245-2298, 2347-2518, or a specific binding fragment thereof.
In some of any of the provided embodiments, the binding partner of CD28 is CD80 or CD86. In some embodiments, the ARBM contains (i) the sequence of amino acids set forth in SEQ ID NO: 28, 1005, 1079, 2615, 2654 or 3580, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 28, 1005, 1079, 2615, 2654 or 3580; or (iii) a specific binding fragment of (i) or (ii). In some of any of the provided embodiments, the ARBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 29 or 1195, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 29 or 1195; or (iii) a specific binding fragment of (i) or (ii). In some of any such embodiments, the ARBM is a variant CD80 and the one or more amino acid modifications can include any described herein, such as set forth in Section I.B.1.b. In some embodiments, the one or more amino acid modifications include any set forth in Table 8. In some of any such embodiments, the ARBM is a variant CD86 and the one or more amino acid modifications can be any described herein, such as set forth in Section I.B.1.c. In some embodiments, the one or more amino acid modifications include any set forth in Table 9.
In some of any of the provided embodiments, the ARBM binds to an activating receptor that is CD28 and the IRBM binds to an inhibitory receptor that is PD-1. In some of any of the provided embodiments, the ARBM binds to an activating receptor that is CD28 and the IRBM binds to an inhibitory receptor that is TIGIT.
In some of any of the provided embodiments, the ARBM binds to an activating receptor that is CD2 and the ARBM contains at least one IgSF domain of a binding partner of CD2. In some embodiments the binding partner of CD2 is CD58 or is a variant thereof.
In some of any of the provided embodiments, the ARBM comprises (i) the sequence of amino acids set forth in SEQ ID NO: 2946, 3239 or 3650, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 2946, 3239 or 3650; or (iii) a specific binding fragment of (i) or (ii). In some embodiments, the binding partner of CD2 is a wild-type human CD58. In some embodiments, the ARBM is set forth in SEQ ID NO:2946, 3239 or 3650 or is a specific binding fragment thereof that binds to CD2.
In some of any of the provided embodiments, the ARBM binds to a ligand of an activating receptor that is CD80 or CD86 and the IRBM binds to an inhibitory receptor that is PD-1. In some embodiments, the ARBM contains at least one IgSF domain of a binding partner of the ligand of the activating receptor. In some examples, the binding partner is CTLA-4 or is a variant thereof that binds to CD80 or CD86. In some of any such embodiments, the binding partner is a variant of CTLA-4 and the variant exhibits increased binding activity, optionally binding affinity, to CD80 or CD86 compared to the binding of unmodified or wild-type CTLA-4 to CD80 or CD86. In some cases, the binding activity, optionally binding affinity, to CD80 or CD86 is increased more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold or 60-fold. In some embodiments, the ARBM contains (i) the sequence of amino acids set forth in SEQ ID NO: 36, 2655 or 2947, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 36, 2655 or 2947; or (iii) a specific binding fragment of (i) or (ii). In some of any such embodiments, the ARBM is a variant CTLA-4 and the one or more amino acid modifications can include any described herein, such as set forth in Section I.B.5.b. In some embodiments, the one or more amino acid modifications include any set forth in Table 10. In some embodiments, the variant CTLA-4 contains one or more modification at one or more position selected from 6, 10, 12, 14, 15, 16, 18, 19, 20, 22, 24, 26, 27, 28, 29, 30, 31, 33, 35, 37, 38, 41, 42, 43, 45, 46, 47, 48, 53, 54, 55, 56, 58, 59, 61, 63, 64, 65, 67 69, 71, 72, 73, 75, 76, 82, 85, 86, 87, 89, 91, 93, 95, 96, 97, 98, 99, 105, 106, 108, 110, 113, 115, 116, 117, 118, 119, 120, 121 or 122 with reference to numbering set forth in SEQ ID NO:36 or 2655. In some embodiments, the variant CTLA-4 contains one or more amino acid modifications selected from A6T, V10A, L12F, L12H, L12P, S14N, S15P, R16C, R16G, R16H, I18A, I18F, I18N, I18T, I18V, A19V, S20N, V22A, V221, E24Q, A26D, A26S, A26T, S27P, P28L, G29R, G29W, K30R, A31Y, E33M, E33V, R35K, T37S, V38I, Q41L, A42S, A42T, A42V, D43N, Q45H, V46E, T47A, E48R, T53S, Y54F, M55R, M55T, M55V, M56K, M56L, M56R, M56T, M56V, N58D, N58S, E59D, E59G, T61A, T61I, T61N, T61R, T61S, L63H, L63P, D64E, D64N, D64V, D65G, I67N, I67T, I67V, T69A, T69I, T69S, T71A, T71I, S72G, S72T, S73R, N75D, Q76R, Q82H, Q82R, R85G, A86T, M87A, M87K, M87T, M87V, T89A, T89M, T89S, L91R, I93L, I93V, K95R, V96I, E97Q, L98Q, L98R, M99I, M99L, Y105F, Y105L, L106E, L106I, L106R, I108F, 1108V, N110K, N110S, N110Y, Y115N, V116A, I117E, I117L, I117M, I117T, I18T, or I18V, or a conservative amino acid substitution thereof, with reference to numbering set forth in SEQ ID NO: 36 or 2655.
In some of any such embodiments, the variant CTLA-4 contains the amino acid modification(s) A31Y/L106E, A6T/A26T/M55T/M99L/Y105L, V10A/G29W/T53S/M56K/L63P/L98Q/Y105L/P121S, V10A/L63P/D64V/S72G/L98Q/M99L/Y105L, V10A/L63P/L98Q/Y105L, L12F/R16H/G29W/M56T/L98Q/Y105L, L12F/A26T/L63P/L98Q/Y105L/L106R, L12F/K30R/S72G/Q82R/L98Q/M99L/Y105L, L12H/I18V/A42T/M55T/N58D/L98R/Y105L/L106I/P121S, L12H/E33M/L98Q/Y105L, L12H/M55T/E59D/L63P/M99L, L12H/L63P/S72G/L98Q/Y105L, L12I/M55T/M56V/I67T/M99L/L106R/I108F, L12P/R16H/A26T/T61S/L63P/M87V/L98Q/M99L/Y105L/L106I/I117L, L12P/I18T/A26T/M55T/T69S/S72G/M99L/Y105L, L12P/A26T, L12P/A26T/L63P, L12P/A26T/L63P/S72G/T89M/L98Q/M99L/Y105L, L12P/G29W/L63P/S72G/L98Q/Y105L, L12P/G29W/L63P/S72G/L98Q/Y105L/L106I, L12P/A26T/L63P/L98Q/M99L/Y105L, L12P/A26T/L63P/L98Q/Y105L, L12P/A26T/L63P/L98Q/Y105L/L106I, L12P/G29W/D43N/N58S/L63P/L98Q/M99L/Y105L, L12P/M56V/L63P/V96I/L98Q/M99L/Y105L/Y115H, L12P/L63P/S72G/L98Q/M99L/Y105L, L12P/L63P/S72G/L98Q/M99L/Y105L/L106N, L12P/L63P/S72G/L98Q/M99L/Y105L/L106N/I117L, S14N/R16C/I18T/M56K/T61A/L63P/A86T/M99L, S15P/I18V/M56T/L98Q/M99L/Y105L, R16C/G29W/E33V/M55T/L63P/L98Q/Y105L, I18A/L63P/S72G/L98Q/Y105L, I18F/L63P/L98Q/M99L/Y105L/P121S, I18N/A26T/L63H/T89A/L98Q/M99L/Y105L, I18N/L63P/S72T/M87T/L98Q/Y105L/N110S, I18T/A26S/M55T/M56V/L63P/S72G/L98Q/M99L/Y105L/I117K, I18T/A26T/L63P/S72G/L98Q/Y105L, I18T/A26T/L63P/Q82R/L98Q/Y105L, I18T/G29R/L63P/S72G/L98Q/M99L/Y105L, I18T/G29W/L63P/L98Q/Y105L, I18T/E48R/L63P/T69S/L98Q/Y105L/N110Y, I18T/T61R/L63P/S72G/L98Q/M99L/Y105L, I18T/L63P/S72G/M87K/L98Q/M99L/Y105L, I18T/L63P/S72G/L98Q/M99L/Y105L, I18T/L63P/S72G/L98Q/Y105L/I108V, I18V/A26T/L63P/D64E/L98Q/Y105L/L106R/N110K, I18V/G29W/L63P/S72G/L98Q/Y105L, A19V/G29W/R35K/L63P/L98Q/M99L/Y105L, S20N/A26T/L63P/L98Q/M99L/Y105L, V22A/L63P/L98Q/M99L/Y105L/P119H, V22I/L63P/L98Q/Y105L/I117M, E24Q/L63P/S72G/L98Q/M99L/Y105L, A26D/S72G/L98Q/M99L/Y105L, A26T/A42V/Q45H/I67N/M87K/E97Q/M99L, A26T/V46E/L63P/D65G/L98Q, A26T/T47A/M56K/L63P/S72G/Q82R/L98Q/M99L/Y105L, A26T/T53S/M56K/L63P/L98Q/Y105L, A26T/T53S/L63P/L98Q/Y105L/L106I/I117L, A26T/Y54F/M56K/M99L/Y105L, A26T/M55R/L98Q/M99L/Y105L, A26T/M55T/L63P/S72G/L98Q/M99L/Y105L, A26T/M55T/L63P/L98Q/M99L/Y105L, A26T/L63P/D65G/L98Q/M99L/Y105L, A26T/L63P/M87V/N110K/I117E, A26T/L63P/S72G/L98Q/M99L/Y105L, A26T/L63P/S72G/L98Q/Y105L/L106I/I117L, A26T/L63P/L98Q/M99L/Y105L, A26T/167N/S72G/L98Q/M99L/Y105L, S27P/M56K/L63P/S72G/S73R/T89A/M99L/Y105L/I117M, P28L/E33V/L63P/S72G/L98Q/M99L/Y105L, P28L/E33V/L63P/S72G/L98R/M99L/Y105L, G29W/T53S/M56K/N58S/L63P/M87V/L98Q/Y105L, G29W/T53S/M56K/N58S/L63P/M87V/L98Q/Y105L/I108V, G29W/T53S/M56K/N58S/L63P/M87V/L98Q/Y105L/P121S, G29W/T53S/M56K/T61N/L63P/L98Q/Y105L, G29W/T53S/M56K/L63P/Q82H/L98Q/M99I/Y105L, G29W/T53S/M56K/L63P/L98Q/Y105L, G29W/T53S/L63P/S72G/L98Q/Y105L, G29W/M55V/E59G/L63P/L98Q/Y105L, G29W/M56T/L63P/L98Q/Y105L/L106I/I117L, G29W/N58D/167V/L98Q/M99L/Y105L, G29W/N58S/L63P/D64N/L98Q/M99L/Y105L, G29W/N58S/L63P/T69I/L98Q/M99L/Y105L, G29W/N58S/L63P/S72G/L98Q/Y105L, G29W/N58S/L63P/S72G/L98Q/Y105L/L106I, G29W/N58S/L63P/S72G/L98Q/Y105L/L106V, G29W/N58S/L63P/S72G/M87V/L98Q/Y105L, G29W/N58S/L63P/Q82R/L98Q/Y105L, G29W/N58S/L63P/M87T/L98Q/M99L/Y105L, G29W/N58S/L63P/L98Q/Y105L, G29W/E59G/L63P/L98Q/Y105L, G29W/T61I/L63P/S72G/L98Q/M99L/Y105L, G29W/L63P/D65G/S72G/L98Q/Y105L, G29W/L63P/167V/S72G/L98Q/Y105L, G29W/L63P/S72G/L98Q/Y105L/L106I, G29W/L63P/S72G/L98Q/Y105L/L106I/I117L, G29W/L63P/S72G/L98Q/Y105L/I117L, G29W/L63P/S72G/L98Q/Y105L/P121S, G29W/L63P/L98Q/M99L/Y105L, G29W/S72G/Q76R/L98Q/Y105L/L106I/Q113H, G29W/M87K/T89S/L98Q/M99L/Y105L/I108V/I117L, G29W/M87K/I93V/L98Q/M99L/Y105L, G29W/L98Q/M99L/Y105L, E33M/A42T/L98Q/Y105L, E33M/L63P/S72G/L98Q/Y105L, E33M/L63P/S72G/L98Q/Y105L/I108F, E33M/L63P/S72G/L98Q/Y105L/I117L, E33M/Q82H/L98Q/M99L/Y105L, E33V/A42S/M55T/L98Q/M99L/Y105L, T37S/M56V/L98Q/Y105L, V38I/L63P/S72G/L98Q/M99L/Y105L, Q41L/Y54F/M56K/M99L/I108F, T53S/M56V/L98Q/Y105L, M55T/L63P/T71I/M99L/Y105L, M55T/S72G/L98Q/M99L/Y105L, M55T/E97Q/M99L/Y105F, M56K/L63P/N75D/V96I/M99L/Y105L/L106I, M56L/L63P/L98Q/Y105L/L106I/I117L, M56R/L63P/L98Q/M99L/Y105L, M56T/L91R/L98Q/Y105L, M56V/E59G/L63P/S72G/M87K/I93V/L98Q/M99L/Y105L/I117E, T61A/L63P/S72G/L98Q/M99L/Y105L, L63P/T69A/L98Q/M99L/Y105L/L106R/V116A, L63P/S72G/M87A/L98Q/Y105L, L63P/S72G/I93L/L98Q/M99L/Y105L, L63P/S72G/L98Q/M99L/Y105L, L63P/S72G/L98Q/M99L/Y105L/L106I/I117L, L63P/S72G/L98Q/Y105L, L63P/S72G/L98Q/Y105L/L106I/I117L, L63P/S72G/Y105L, L63P/M87K/M99L/L106R, L63P/Q82H/L98Q/M99L/Y105L, L63P/K95R, L63P/L98Q, L63P/L98Q/M99L/Y105L, L63P/L98Q/M99L/Y105L/L106I, L63P/L98Q/M99L/Y105L/I108V, L63P/L98Q/M99L/Y105L/I117M, L63P/L98Q/Y105L, L63P/L98Q/V116A, L63P/L98R/N110K, L63P/M99L/Y105L/I108F, I67V/S72G/Q82H/T89A/L98Q/M99L/Y105L, S72G/R85G/L98Q/M99L/Y105L/L106I, S72G/L98Q/M99L/Y105L/I117T, L98Q/M99L/Y105L, L98Q/M99L/Y105L/L106I/I117T, L98Q/M99L/Y105L/L106I/Y115N, L98Q/Y105L, and L98R/N110K, with reference to numbering set forth in SEQ ID NO:36 or 2655. In some embodiments, the variant CTLA-4 polypeptide contains the modification(s) A31Y/L106E, with reference to numbering set forth in SEQ ID NO:36 or 2655.
In some of any of the provided embodiments, the ARBM includes the sequence of amino acids set forth in any of 2519, 2520, 2948-3041, 3043-3048, 3050-3099, 3230, 3231, or a specific binding fragment thereof. In some of any of the provided embodiments, the ARBM includes the sequence of amino acids set forth in any of SEQ ID NOs: 3100-3229, 3232 or 3233, or a specific binding fragment thereof.
In some of any of the provided embodiments, the IRBM contains at least one IgSF domain of a binding partner of PD-1. In some embodiments, the binding partner of PD-1 is PD-L1 or PD-L2 or is a variant of PD-L1 or PD-L2 that binds to PD-1. In some embodiments, the binding partner is a variant of PD-L1 or PD-L2 and the variant exhibits increased binding activity, optionally binding affinity, to PD-1 compared to the binding of unmodified or wild-type PD-L1 or PD-L2, respectively, to PD-1. In some embodiments, the binding activity, optionally binding affinity, to PD-1 is increased more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold or 60-fold. In some embodiments, the IRBM contains (i) the sequence of amino acids set forth in SEQ ID NO: 30, 55, 309 or 1728, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 30, 55, 309 or 1728; or (iii) a specific binding fragment of (i) or (ii). In some embodiments, the IRBM includes (i) the sequence of amino acids set forth in SEQ ID NO: 31, 1203 or 1263, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 31, 1203 or 1263; or (iii) a specific binding fragment of (i) or (ii). In some of any such embodiments, the one or more amino acid modifications is a variant PD-L1 and can include any described herein, such as set forth in Section I.A.1.a. In some embodiments, IRBM is a variant PD-L1 and the one or more amino acid modifications include any set forth in Table 2. In some of any such embodiments, the IRBM is a variant PD-L2 and the one or more amino acid modifications can include any described herein, such as set forth in Section I.A.1.b. In some embodiments, the one or more amino acid modifications include any set forth in Table 3.
In some of any such embodiments, the IRBM is a variant of PD-L1 and the variant PD-L1 contains one or more amino acid modifications at one or more positions corresponding to 6, 10, 11, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 33, 35, 36, 40, 41, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 60, 64, 65, 68, 71, 72, 73, 74, 75, 78, 79, 83, 85, 89, 90, 93, 97, 98, 99, 101, 102, 103, 104, 106, 110, 111, 112, 113, 117, 119, 120, 121, 124, 129, 130, 131, 134, 137, 138, 144, 148, 149, 150, 155, 158, 160, 163, 165, 167, 170, 171, 173, 175, 176, 177, 179, 180, 183, 185, 188, 189, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 206, 207, 213, or 221, with reference to numbering set forth in SEQ ID NO: 30, 309 or 1728. In some of any such embodiments, the variant PD-L1 contains one or more amino acid modifications selected from P6S, Y10F, V11A, V11E, Y14S, G15A, S16G, N17D, M18I, M18T, M18V, T19A, T19I, I20L, C22R, K23E, K23N, K23R, E26A, E27D, E27G, K28E, K28I, K28N, K28R, A33D, L35P, I36S, I36T, E40G, M41K, M41V, D43G, D43V, K44E, N45D, N45I, N45T, I46V, I47T, F49S, V50A, H51N, H51R, H51Y, G52R, G52V, E53G, E53V, E54G, D55G, D55N, D55S, D55V, L56Q, K57E, K57R, V58A, V58D, H60R, R64S, Q65L, R68L, K71E, D72G, Q73R, L74P, S75P, N78I, N78S, A79T, I83T, D85E, Q89R, D90G, V93E, M97I, M97K, M97L, I98L, I98T, I98V, S99G, G101D, G101G-ins (G101GG), G102D, A103V, D104G, K106E, K106R, V110M, K111E, K111T, V112A, N113Y, N117S, 1119T, N120S, Q121L, L124S, V129A, V129D, T130A, S131F, E134G, C137R, Q138R, K144E, K144Q, I148V, W149R, T150A, Q155H, S158G, K160M, T163I, K163N, N165Y, K167R, K167T, E170G, K171R, F173I, F173L, K173Y, V175A, S177C, L179P, R180S, T183A, T183I, T185A, I188V, F189L, F189S, T192S, F193S, R194G, R194W, R195G, R195S, R195T, L196S, D197G, P198S, P198T, E199G, E200K, E200N, N201D, N201Y, H202Q, T203A, A204T, L206F, V207A, L213P, or T221L or a conservative amino acid substitution thereof, with reference to numbering set forth in SEQ ID NO: 30, 309 or 1728.
In some embodiments, the variant PD-L1 polypeptide contains the amino acid modification(s) K28N/M41V/N45T/H51N/K57E, I20L/I36T/N45D/147T, I20L/M41K/K44E, P6S/N45T/N78I/183T, N78I, M41K/N78I, N45T/N78I, I20L/N45T, N45T, M41K, I20L/I36T/N45D, N17D/N45T/V50A/D72G, I20L/F49S, N45T/V50A, I20L/N45T/N78I, I20L/N45T/V50A, M41V/N45T, M41K/N45T, A33D/S75P/D85E, M18I/M41K/D43G/H51R/N78I, V11E/I20L/I36T/N45D/H60R/S75P, A33D/V50A, S16G/A33D/K71E/S75P, E27G/N45T/M97I, E27G/N45T/K57R, A33D/E53V, D43G/N45D/V58A, E40G/D43V/N45T/V50A, Y14S/K28E/N45T A33D/N78S, A33D/N78I, A33D/N45T, A33D/N45T/N78I, E27G/N45T/V50A, N45T/V50A/N78S, I20L/N45T/V110M, I20L/I36T/N45T/V50A, N45T/L74P/S75P, N45T/S75P, S75P/K106R, S75P, A33D/S75P, A33D/S75P/D104G, A33D/S75P, I20L/E27G/N45T/V50A, I20L/E27G/D43G/N45D/V58A/N78I, I20L/D43G/N45D/V58A/N78I, I20L/A33D/D43G/N45D/V58A/N78I, I20L/D43G/N45D/N78I, E27G/N45T/V50A/N78I, N45T/V50A/N78I, V11A/I20L/E27G/D43G/N45D/H51Y/S99G, I20L/E27G/D43G/N45T/V50A, I20L/K28E/D43G/N45D/V58A/Q89R, I20L/I36T/N45D, I20L/K28E/D43G/N45D/E53G/V58A/N78I, A33D/D43G/N45D/V58A/S75P, K23R/D43G/N45D, I20L/D43G/N45D/V58A/N78I/D90G/G101D, D43G/N45D/L56Q/V58A/G101GG, I20L/K23E/D43G/N45D/V58A/N78I, I20L/K23E/D43G/N45D/V50A/N78I, T19I/E27G/N45I/V50A/N78I/M97K, I20L/M41K/D43G/N45D, K23R/N45T/N78I, I20L/K28E/D43G/N45D/V58A/Q89R/G101G-ins (G101GG), K57R/S99G, K57R/S99G/F189L, M18V/M97L/F193S/R195G/E200K/H202Q, I36S/M41K/M97L/K144Q/R195G/E200K/H202Q/L206F, C22R/Q65L/L124S/K144Q/R195G/E200N/H202Q/T221L, M18V/I98L/L124S/P198T/L206F, S99G/N117S/I148V/K171R/R180S, I36T/M97L/A103V/Q155H, K28I/S99G, R195S, A79T/S99G/T185A/R195G/E200K/H202Q/L206F, K57R/S99G/L124S/K144Q, K57R/S99G/R195G, D55V/M97L/S99G, E27G/I36T/D55N/M97L/K111E, E54G/M97L/S99G, G15A/I36T/M97L/K111E/H202Q, G15A/I36T/V129D, G15A/I36T/V129D/R195G, G15A/V129D, I36S/M97L, I36T/D55N/M97L/K111E/A204T, I36T/D55N/M97L/K111E/V129A/F173L, I36T/D55S/M97L/K111E/I148V/R180S, I36T/G52R/M97L/V112A/K144E/V175A/P198T, I36T/I46V/D55G/M97L/K106E/K144E/T185A/R195G, I36T/I83T/M97L/K144E/P198T, I36T/M97L/K111E, I36T/M97L/K144E/P198T, I36T/M97L/Q155H/F193S/N201Y, I36T/M97L/V129D, L35P/I36S/M97L/K111E, M18I/I36T/E53G/M97L/K144E/E199G/V207A, M18T/I36T/D55N/M97L/K111E, M18V/M97L/T176N/R195G, M97L/S99G, N17D/M97L/S99G, S99G/T185A/R195G/P198T, V129D/H202Q, V129D/P198T, V129D/T150A, V93E/V129D, Y10F/M18V/S99G/Q138R/T203A, N45D, K160M/R195G, N45D/K144E, N45D/P198S, N45D/P198T, N45D/R195G, N45D/R195S, N45D/S131F, N45D/V58D, V129D/R195S, I98T/F173Y/L196S, N45D/E134G/L213P, N45D/F173I/S177C, N45D/I148V/R195G, N45D/K111T/R195G, N45D/N113Y/R195S, N45D/N165Y/E170G, N45D/Q89R/I98V, N45D/S131F/P198S, N45D/S75P/P198S, N45D/V50A/R195T, E27D/N45D/T183A/I188V, F173Y/T183I/L196S/T203A, K23N/N45D/S75P/N120S, N45D/G102D/R194W/R195G, N45D/G52V/Q121L/P198S, N45D/I148V/R195G/N201D, N45D/K111T/T183A/I188V, N45D/Q89R/F189S/P198S, N45D/S99G/C137R/V207A, N45D/T163I/K167R/R195G, N45D/T183A/T192S/R194G, N45D/V50A/I119T/K144E, T19A/N45D/K144E/R195G, V11E/N45D/T130A/P198T, V26A/N45D/T163I/T185A, K23N/N45D/L124S/K167T/R195G, K23N/N45D/Q73R/T163I, K28E/N45D/W149R/S158G/P198T, K28R/N45D/K57E/I98V/R195S, K28R/N45D/V129D/T163N/R195T, M41K/D43G/N45D/R64S/R195G, M41K/D43G/N45D/R64S/S99G, N45D/R68L/F173L/D197G/P198S, N45D/V50A/I148V/R195G/N201D, M41K/D43G/K44E/N45D/R195G/N201D, or N45D/V50A/L124S/K144E/L179P/R195G, with reference to numbering set forth in SEQ ID NO: 30, 309 or 1728. In some embodiments, the variant PD-L1 contains the modification(s) D43G/N45D/L56Q/V58A/G101G-ins.
In some of any of the provided embodiments, the IRBM contains the sequence of amino acids set forth in any of SEQ ID NOs: 56-120, 1725, 1729-1818, 1819-1907, 1943-2008 or a specific binding fragment thereof. In some of any of the provided embodiments, the IRBM contains the sequence of amino acids set forth in any of SEQ ID NOs: 121-185, 244-308, 1726-1727, 1908-1937.
In some of any of the provided embodiments, the IRBM is a variant of PD-L2 and the variant PD-L2 contains one or more amino acid modifications at one or more positions corresponding to 2, 12, 13, 15, 18, 20, 23, 24, 28, 31, 32, 33, 36, 37, 39, 44, 45, 46, 47, 48, 58, 59, 65, 67, 69, 71, 72, 73, 74, 75, 76, 77, 82, 85, 86, 89, or 91, with reference to SEQ ID NO:31 and 1263. In some of any such embodiments, the variant PD-L2 contains one or more amino acid modifications selected from F2L, I12V, I13V, H15Q, N18D, T20A, N24S, C23S, G28V, N24D, V31A, V31M, N32D, L33P, L33H, L33F, I36V, T37A, S48C, S39I, E44D, N45S, D46E, T47A, E58G, E59G, K65R, S67L, H69L, P71S, Q72H, V73A, Q74R, R76G, D77N, Q82R, I85F, I86T, V89D, or W91R, with reference to numbering set forth in SEQ ID NO:31 and 1263. In some of any such embodiments, the variant PD-L2 contains the amino acid modification(s) H15Q, N24D, E44D, V89D, Q82R/V89D, E59G/Q82R, S39I/V89D, S67L/V89D, S67L/I85F, S67L/I86T, H15Q/K65R, H15Q/Q72H/V89D, H15Q/S67L/R76G, H15Q/R76G/185F, H15Q/T47A/Q82R, H15Q/Q82R/V89D, H15Q/C23S/I86T, H15Q/S39I/I86T, E44D/V89D/W91R, I13V/S67L/V89D, H15Q/S67L/I86T, I13V/H15Q/S67L/I86T, I13V/H15Q/E44D/V89D, I13V/S39I/E44D/Q82R/V89D, I13V/E44D/Q82R/V89D, I13V/Q72H/R76G/I86T, I13V/H15Q/R76G/185F, H15Q/S39I/R76G/V89D, H15Q/S67L/R76G/185F, H15Q/T47A/Q72H/R76G/I86T, H15Q/T47A/Q72H/R76G, I13V/H15Q/T47A/Q72H/R76G, H15Q/E44D/R76G/185F, H15Q/S39I/S67L/V89D, H15Q/N32D/S67L/V89D, N32D/S67L/V89D, H15Q/S67L/Q72H/R76G/V89D, H15Q/Q72H/Q74R/R76G/I86T, G28V/Q72H/R76G/I86T, I13V/H15Q/S39I/E44D/S67L, E44D/S67L/Q72H/Q82R/V89D, H15Q/V89D, H15Q/T47A, I13V/H15Q/Q82R, I13V/H15Q/V89D, I13V/S67L/Q82R/V89D, I13V/H15Q/Q82R/V89D, H15Q/V31M/S67L/Q82R/V89D, I13V/H15Q/T47A/Q82R, I13V/H15Q/V31A/N45S/Q82R/V89D, H15Q/T47A/H69L/Q82R/V89D, I13V/H15Q/T47A/H69L/R76G/V89D, I12V/I13V/H15Q/T47A/Q82R/V89D, I13V/H15Q/R76G/D77N/Q82R/V89D, I13V/H15Q/T47A/R76G/V89D, I13V/H15Q/T47A/Q82R/V89D, I13V/H15Q/N24D/Q82R/V89D, I13V/H15Q/I36V/T47A/S67L/V89D, H15Q/T47A/K65R/S67L/Q82R/V89D, H15Q/L33P/T47A/S67L/P71S/V89D, I13V/H15Q/Q72H/R76G/I86T, H15Q/T47A/S67L/Q82R/V89D, F2L/H15Q/D46E/T47A/Q72H/R76G/Q82R/V89D, I13V/H15Q/L33F/T47A/Q82R/V89D, I13V/H15Q/T47A/E58G/S67L/Q82R/V89D, H15Q/N24S/T47A/Q72H/R76G/V89D, I13V/H15Q/E44V/T47A/Q82R/V89D, H15Q/N18D/T47A/Q72H/V73A/R76G/I86T/V89D, I13V/H15Q/T37A/E44D/S48C/S67L/Q82R/V89D, H15Q/L33H/S67L/R76G/Q82R/V89D, I13V/H15Q/T47A/Q72H/R76G/I86T, H15Q/S39I/E44D/Q72H/V75G/R76G/Q82R/V89D, H15Q/T47A/S67L/R76G/Q82R/V89D, or I13V/H15Q/T47A/S67L/Q72H/R76G/Q82R/V89D, with reference to numbering set forth in SEQ ID NO:31 and 1263. In some embodiments, the variant PD-L2 contains the modification(s) H15Q/T47A/K65R/S67L/Q82R/V89D.
In some of any of the provided embodiments, the IRBM contains the sequence of amino acids set forth in any of SEQ ID NOs: 1204-1280 or a specific binding fragment thereof. In some of any of the provided embodiments, the IRBM contains the sequence of amino acids set forth in any of SEQ ID NOs: 1283-1331, 1333-1407, 1309-1432.
In some of any of the provided embodiments, the IRBM contains at least one IgSF domain of a binding partner of TIGIT. In some embodiments, the binding partner of TIGIT is CD155 or CD122 or is a variant of CD155 or CD122 that binds to PD-1. In some embodiments, the binding partner is a variant of CD155 or CD112 and the variant exhibits increased binding activity, optionally binding affinity, to TIGIT compared to the binding of unmodified or wild-type CD155 or CD112, respectively, to TIGIT. In some embodiments, the binding activity, optionally binding affinity, to TIGIT is increased more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold or 60-fold. In some of any of the provided embodiments, the IRBM comprises (i) the sequence of amino acids set forth in SEQ ID NO: 47, 310 or 353, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 47, 310 or 353; or (iii) a specific binding fragment of (i) or (ii). In some of any of the provided embodiments, the IRBM comprises (i) the sequence of amino acids set forth in SEQ ID NO: 48, 666 or 761, (ii) a sequence of amino acids that has at least 85%, 86%, 87%, 88%%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 48, 666 or 761; or (iii) a specific binding fragment of (i) or (ii). In some of any such embodiments, the IRBM is a variant CD155 and the one or more amino acid modification can be any described herein, such as set forth in Section I.A.2.a. In some embodiments, the IRBM is a variant CD155 and the one or more amino acid modifications include any set forth in Table 4. In some of any such embodiments, the IRBM is a variant CD112 and the one or more amino acid modification can be any described herein, such as set forth in Section I.A.2.b. In some embodiments, the one or more amino acid modifications include any set forth in Table 5.
In some of any of the provided embodiments, the variant CD155 comprises one or more amino acid modifications selected from P18F, P18S, S67A, L104M, L104Q, G111D or G111R. In some embodiments, the variant CD155 polypeptide comprises the amino acid modification(s) P18F/T26M/L44V/Q62K/L79P/F91S/L104M/G111D, P18S/T45S/T61K/S65W/S67A/F91S/G111R, P18S/L79P/L104M/T107M, P18S/S65W/S67A/M90V/V95A/L104Q/G111R, P18S/S65W/S67A/L104Q/G111R.
In some of any of the provided embodiments, the IRBM comprises the sequence of amino acids set forth in any of SEQ ID NOs: 312-331, 375-471, 1551-1575, 1577-1622. In some of any of the provided embodiments, the IRBM comprises the sequence of amino acids set forth in any of SEQ ID NOs: 332-352, 354-374, 472-665, 1505-1550, 1575, 1576, 1623-1714.
In some of any of the provided embodiments, the ARBM or IRBM is a specific binding fragment of any of the above IgSF domain and has a length of at least 50, 60, 70, 80, 90, 100, 110 or more amino acids.
In some of any of the provided embodiments, the ARBM or IRBM is a variant of any of the above IgSF domains and the variant contains one or more amino acid modifications at one or more positions in an IgSF domain of an unmodified or wild-type IgSF domain, such as an IgSF domain of a binding partner of an activating receptor, a binding partner of a ligand of an activating receptor or a binding partner of an inhibitory receptor. In some embodiments, the one or more amino acid modification is an amino acid substitution, insertion or deletion. In some embodiments, the variant contains up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications, optionally amino acid substitutions, insertions and/or deletions.
In some of any of the provided embodiments, the ARBM contains an IgV domain or a specific binding fragment thereof. In some embodiments, the at least one ARBM in a provided immunomodulatory protein contains only one ARBM.
In some of any such embodiments, the IRBM contains at least one IgSF domain that is an IgV domain or a specific binding fragment thereof. In some embodiments, the at least one IRBM in a provided immunomodulatory protein contains only one IRBM. In some embodiments, the at least one IRBM in a provided immunomodulatory protein contains 2, 3, 4, 5 or more IRBMs, optionally wherein each IRBM is the same. In some embodiments, each IRBM of a provided immunomodulatory protein is linked directly or indirectly via a linker, optionally wherein the linker is a peptide linker.
In some of any of the provided embodiments, the at least one IRBM and the at least one ARBM are linked direct or indirectly via a linker. In some instances, the embodiments is a peptide linker.
In some of any such embodiments, the peptide linker is selected from GSGGS (SEQ ID NO: 2523), GGGGS (G4S; SEQ ID NO: 1942), GSGGGGS (SEQ ID NO: 1941), GGGGSGGGGS (2×GGGGS; SEQ ID NO: 240), GGGGSGGGGSGGGGS (3×GGGGS; SEQ ID NO: 239), GGGGSSA (SEQ ID NO: 2524) or combinations thereof.
In some embodiments, the at least one IRBM is amino-terminal to the at least one ARBM in the polypeptide. In some embodiments, the at least one IRBM is carboxy-terminal to the at least one ARBM in the polypeptide. In some embodiments, the immunomodulatory protein contains at least two IRBM. In some of any such embodiments, at least one IRBM is amino-terminal to the at least one ARBM in the polypeptide and at least one IRBM is carboxy-terminal to the at least one ARBM in the polypeptide.
In some of any of the provided embodiments, the immunomodulatory protein is a multi-domain protein in which the ARBM contains at least one IgSF domain of CTLA-4 or a variant thereof, e.g affinity-modified domain thereof, and the IRBM contains at least one IgSF domain of PD-L1 or a variant thereof, e.g affinity-modified domain thereof.
In some of any of the provided embodiments, the immunomodulatory protein a multi-domain protein in which the ARBM contains at least one IgSF domain of ICOS-L or a variant thereof, e.g affinity-modified domain thereof, and the IRBM contains at least one IgSF domain of PD-L1 or a variant thereof, e.g affinity-modified domain thereof.
In some of any of the provided embodiments, the immunomodulatory protein a multi-domain protein in which the ARBM contains at least one IgSF domain of ICOS-L or a variant thereof, e.g affinity-modified domain thereof, and the IRBM contains at least one IgSF domain of PD-L2 or a variant thereof, e.g affinity-modified domain thereof.
In some of any of the provided embodiments, the immunomodulatory protein is a multi-domain protein in which the ARBM contains at least one IgSF domain of CD58 or a variant thereof, e.g affinity-modified domain thereof, and the IRBM contains at least one IgSF domain of PD-L1 or a variant thereof, e.g affinity-modified domain thereof.
In some of any of the provided embodiments, the immunomodulatory protein is a multi-domain protein in which the ARBM contains at least one IgSF domain of CTLA-4 or a variant thereof, e.g affinity-modified domain thereof, and the IRBM contains at least one IgSF domain of CD155 or a variant thereof, e.g affinity-modified domain thereof.
In some of any of the provided embodiments, the immunomodulatory protein is a multi-domain protein in which the ARBM contains at least one IgSF domain of CD58 or a variant thereof, e.g affinity-modified domain thereof, and the IRBM contains at least one IgSF domain of CD155 or a variant thereof, e.g affinity-modified domain thereof.
In some of any of the provided embodiments, the immunomodulatory protein is a multi-domain protein in which the ARBM contain at least one IgSF domain of ICOSL or a variant thereof, e.g affinity-modified domain thereof, and the IRBM contains at least one IgSF domain of CD155 or a variant thereof, e.g affinity-modified domain thereof.
In some of any of the provided embodiments, the immunomodulatory protein is an immunomodulatory protein set forth in any of Tables E2, E3A, E3B, E4 or E5.
In some embodiments, the immunomodulatory protein is a monomer and/or contains a single polypeptide chain. In some embodiments, the immunomodulatory protein comprises the sequence of amino acids set forth in any of SEQ ID NOS: 2563, 2567, 2569, 2571, 2573, 2575, 2577, 2579, 2581, 2583, 2585, 2587, 2589, 2591, 2593, 2595, 2597, 2599, 2601, 2603, 2605, 2607, 2609, 2612, 2614, 2619, 2621, 2623, 2625, 2627, 2629, 2631, 2633, 2635, 2637, 2639, 2641, 2643, 2645, 2647, 2649, 2651, 2653, 3496, 3497, 3498, 3499, 3500, 3501, 3502, 3535, 3656, 3658, or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID Nos: 2563, 2567, 2569, 2571, 2573, 2575, 2577, 2579, 2581, 2583, 2585, 2587, 2589, 2591, 2593, 2595, 2597, 2599, 2601, 2603, 2605, 2607, 2609, 2612, 2614, 2619, 2621, 2623, 2625, 2627, 2629, 2631, 2633, 2635, 2637, 2639, 2641, 2643, 2645, 2647, 2649, 2651, 2653, 3496, 3497, 3498, 3499, 3500, 3501, 3502, 3535, 3656, 3658 and retains the same or similar activity.
In some of any such embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS:2541, 2543, 2563, 2567, 2569, 2579, 2583, 2585, 2587, 2589, 2591, 2595, 2597, 2599, 2601, 2603, 2605, 2607, 2609, 2631, 2643, 2651, or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity thereto and retains the same or similar activity.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 2583, 2587, 2603, 2651, or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity thereto and retains the same or similar activity.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 2541, 2533, 2651, 3522, 3523, 3664, 3666, 3668, 3674, 3766 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 3522, 3523, 3664, 3666, 3668, 3674, 3766 and retains the same or similar activity. In some embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in SEQ ID NO:3522 or 3666 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3522 or 3566. In some embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in SEQ ID NO:3523 or 3668 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3523 or 3568. In some embodiments the immunomodulatory proteins binds CD80 or CD86 and binds PD-1.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 2583, 2587, 2603, 3678 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 2583, 2587, 2603, 3678 and retains the same or similar activity. In some embodiments the immunomodulatory proteins binds CD28 and binds PD-1.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 3680, 3682, 3684, 3686, 3688 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 3680, 3682, 3684, 3686, 3688 and retains the same or similar activity. In some embodiments the immunomodulatory proteins binds CD2 and binds PD-1.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 3652, 3654, or 3664 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 3652, 3654, or 3664 and retains the same or similar activity. In some embodiments the immunomodulatory proteins binds CD80 or CD86 and binds TIGIT.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 3656 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 3656 and retains the same or similar activity. In some embodiments the immunomodulatory proteins binds CD28 and binds TIGIT.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 3660 or 3662 or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 3660 or 3662 and retains the same or similar activity. In some embodiments the immunomodulatory proteins binds CD2 and binds TIGIT.
In some of any of the provided embodiments, the ARBM and IRBM are linked by a linker and the linker is or includes a multimerization domain. In some embodiments, the multimerization domain promotes dimerization, trimerization, tetramerization, or pentamerization. In some embodiments, the immunomodulatory protein is a dimer, trimer, tetramer, or a pentamer.
In some embodiments, the immunomodulatory protein is a dimer, optionally wherein each polypeptide of the dimer is linked to a multimerization domain. In some aspects, the multimerization domain is an Fc domain. In some of any such embodiments, the Fc domain is an IgG, optionally an IgG1, IgG2 or IgG4, Fc domain. In some cases, the Fc domain is an IgG1 Fc domain. In some embodiments, the Fc domain is a human Fc domain.
In some of any such embodiments, the Fc domain exhibits reduced binding affinity to an Fc receptor and/or reduced effector function, optionally as compared to a native IgG1 Fc domain. In some aspects, the Fc domain contains one or more amino acid substitution that reduces binding to an Fc receptor and or effector function, optionally wherein the one or more amino acid substitutions are in a native IgG1 Fc domain. In some examples, the one or more amino acid substitutions in the Fc domain are selected from E233P, L234A, L234V, L235A, L235E, G236del, G237A, S267K, N297G, V302C and K447del, each by EU numbering. In some embodiments, the Fc contains the amino acid substitutions L234A, L235E an G237A by EU numbering. In some embodiments, the Fc contains the amino acid substitutions R292C, N297G and V302C by EU numbering.
In some embodiments, the immunomodulatory protein contains a first polypeptide chain comprising the at least one ARBM, the at least one IRBM and a first multimerization domain, optionally wherein the first multimerization domain is a first Fc domain, and a second polypeptide chain comprising the at least one ARBM, the at least one IRBM and a second multimerization domain, optionally wherein the second multimerization domain is a second Fc domain, wherein the first and second multimerization domains. In some embodiments the first and second Fc domains are able to interact to form a dimer comprising the first and second polypeptides. In some embodiments, the at least one IRBM is amino-terminal to the at least one ARBM in the first and/or second polypeptide.
In some embodiments, the first and second multimerization domain, optionally the first and second Fc domain, are the same. In some embodiments, the immunomodulatory protein is a homodimer.
In some embodiments, the Fc domain contains the sequence of amino acids set forth in any of SEQ ID NOs:187 or 3538 or a sequence of amino acids that exhibits at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any of SEQ ID NOs: 187 or 3538. In some embodiments, the Fc domain contains the sequence of amino acids set forth in any of SEQ ID NOs:1155, 1157, 1158, 1159, 1938, 1939 or 1940 or a sequence of amino acids that exhibits at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any of SEQ ID NOs: 1155, 1157, 1158, 1159, 1938, 1939 or 1940. In some embodiments, the Fc domain contains the sequence of amino acids set forth in any of SEQ ID NOs:1158, 1715 or 3579 or a sequence of amino acids that exhibits at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any of SEQ ID NOs: 1158, 1715 or 3579.
In some of any such embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 2529, 2530, 2531, 2533, 2535, 2537, 2539, 2541, 2543, 3516, 3517, 3518, 3519, 3520, 3521, 3522, 3523, 3524, 3652, 3654, 3660, 3662, 3664, 3666, 3668, 3670, 3672, 3674, 3676, 3680, or 3682 ora sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 2529, 2530, 2531, 2533, 2535, 2537, 2539, 2541, 2543, 3516, 3517, 3518, 3519, 3520, 3521, 3522, 3523, 3524, 3652, 3654, 3660, 3662, 3664, 3666, 3668, 3670, 3672, 3674, 3676, 3680, or 3682 and retains the same activity.
In some embodiments, the immunomodulatory includes a first polypeptide chain containing (i) one of the at least one ARBM or the at least one IRBM and (ii) a first multimerization domain, optionally wherein the first multimerization domain is a first Fc domain and a second polypeptide chain comprising (i) the other of the at least one ARBM or the at least one IRBM and (b) a second multimerization domain, optionally wherein the second multimerization domain is a second Fc domain, wherein the first and second multimerization domains, optionally the first and second Fc domains, interact to form a dimer comprising the first and second polypeptides. In some embodiments, the first and second multimerization domains, optionally the first and second Fc domains, are different. In some of any of the provided embodiments, the immunomodulatory protein is a heterodimer.
In some embodiments, each polypeptide of the dimer is linked to an Fc domain and wherein the Fc domains contain a knob-into-hole modification or contain a charge mutation to reduce or prevent self-association due to charge repulsion.
In some embodiments, the Fc domain contains a knob-into-hole modification wherein one of the Fc domains contains a knob modification comprising the amino acid substitution T366W and the other one of the Fc domain contains a hole modification selected from T366S, L368A and/or Y407V, each by EU numbering. In some examples, the Fc domain containing the knob modification further contains the amino acid substitution S354C and the Fc domain comprising the hole modification further contains the amino acid substitution Y349C, each by EU numbering. In some embodiments, one of the Fc domains includes the sequence set forth in any of SEQ ID NO:1153 or 2558 or a sequence of amino acids that exhibits at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any of SEQ ID NO: 1153 or 2558 and contains the knob-into-hole modifications, optionally amino acid substitutions T366W and/or S354C, and the other Fc domain includes the sequence set forth in SEQ ID NO: 1154 or 2559 or a sequence of amino acids that exhibits at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any of SEQ ID NOs: 1154 or 2559 and contains the knob-into-hole modifications, optionally Y349C, T366S, L368A and/or Y407V.
In some embodiments, the Fc domain includes a charge mutation wherein one of the Fc domains contains the amino acid substitution E356K, E357K and/or D399K and the other of the Fc domains contains the amino acid substitution K370D, K392D and/or K409D. In some cases, one of the Fc domains contains the sequence set forth in SEQ ID NO:2544 or a sequence of amino acids that exhibits at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 2544 and includes the charge mutation, optionally the amino acid substitution E356K, E357K and/or D399K, and the other of the Fc domains includes the sequence set forth in SEQ ID NO:2544 or a sequence of amino acids that exhibits at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 2544 and contains the charge mutation, optionally the amino acid substitution K370D, K392D and/or K409D.
In some of any such embodiments, the immunomodulatory protein contains a first and second polypeptide comprising the sequence of amino acids set forth in SEQ ID NOs: 2547 and 2549, SEQ ID Nos: 2547 and 2551, SEQ ID Nos: 2553 and 2549, SEQ ID Nos: 2553 and 2551, SEQ ID Nos: 2547 and 2555, SEQ ID Nos: 2547 and 2557, SEQ ID Nos: 2553 and 2555 and SEQ ID Nos: 2553 and 2557, SEQ ID Nos: 2526 and 2528, SEQ ID Nos: 2526 and 2561, SEQ ID Nos: 3513 and 3514 or SEQ ID Nos: 3515 and 3514, or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to each of SEQ ID NOs: 2547 and 2549, SEQ ID Nos: 2547 and 2551, SEQ ID Nos: 2553 and 2549, SEQ ID Nos: 2553 and 2551, SEQ ID Nos: 2547 and 2555, SEQ ID Nos: 2547 and 2557, SEQ ID Nos: 2553 and 2555 and SEQ ID Nos: 2553 and 2557, SEQ ID Nos: 2526 and 2528, SEQ ID Nos: 2526 and 2561, SEQ ID Nos: 3513 and 3514 or SEQ ID Nos: 3515 and 3514 and retains the same activity.
In some embodiments, the ARBM and IRBM are linked by a multimerization domain that promotes dimerization, trimerization, tetramerization, or pentamerization. In some embodiments, the multimerization domain is a portion of a cartilage oligomeric protein (COMP), such as set forth in SEQ ID NO:3503. In some embodiments, the multimerization domain is a vasodilatory-stimulated phosphoprotein (VASP) tetramerization domain, such as set forth in SEQ ID NO:3504. In some embodiments, the multimerization domain is a ZymoZipper (ZZ) domain, such as set forth in SEQ ID NO:3505.
In some of any of the provided embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS: 3507, 3509 or 3678, or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 3507, 3509 or 3678 and retains the same activity.
In some embodiments, the immunomodulatory protein contains the sequence of amino acids set forth in any of SEQ ID NOS:2541, 2533, or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NOS:2541 or 2533 and retains the same activity.
Provided herein is an immunomodulatory protein that contains the sequence of amino acids set forth in any of SEQ ID NOS: 3506, 3508, 3510 or 3511, or a sequence that exhibits at least 85% 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 3506, 3508, 3510 or 3511 and retains the same activity.
In some of any of the provided embodiments, the immunomodulatory protein further contains a detectable moiety, optionally wherein the detectable moiety is a peptide capable of detection, optionally wherein the peptide capable of detection is a flag tag or a his tag.
In some of any of the provided embodiments, the IRBM has a dissociation constant for binding the inhibitory receptor of from 0.001 nM to 1000 nM, from or from about 0.01 nM to about 500 nM, from or from about 0.01 nM to about 400 nM, from or from about 0.01 nM to about 100 nM, from or from about 0.01 nM to about 50 nM, from or from about 0.01 nM to about 10 nM, from or from about 0.01 nM to about 1 nM, from or from about 0.01 nM to about 0.1 nM, is from or from about 0.1 nM to about 500 nM, from or from about 0.1 nM to about 400 nM, from or from about 0.1 nM to about 100 nM, from or from about 0.1 nM to about 50 nM, from or from about 0.1 nM to about 10 nM, from or from about 0.1 nM to about 1 nM, from or from about 0.5 nM to about 200 nM, from or from about 1 nM to about 500 nM, from or from about 1 nM to about 100 nM, from or from about 1 nM to about 50 nM, from or from about 1 nM to about 10 nM, from or from about 2 nM to about 50 nM, from or from about 10 nM to about 500 nM, from or from about 10 nM to about 100 nM, from or from about 10 nM to about 50 nM, from or from about 50 nM to about 500 nM, from or from about 50 nM to about 100 nM or from or from about 100 nM to about 500 nM.
In some of any of the provided embodiments, the ARBM has a dissociation constant for binding the activating receptor or a ligand of the activating receptor of from or from about 0.001 nM to 1000 nM, from or from about 0.01 nM to about 500 nM, from or from about 0.01 nM to about 400 nM, from or from about 0.01 nM to about 100 nM, from or from about 0.01 nM to about 50 nM, from or from about 0.01 nM to about 10 nM, from or from about 0.01 nM to about 1 nM, from or from about 0.01 nM to about 0.1 nM, is from or from about 0.1 nM to about 500 nM, from or from about 0.1 nM to about 400 nM, from or from about 0.1 nM to about 100 nM, from or from about 0.1 nM to about 50 nM, from or from about 0.1 nM to about 10 nM, from or from about 0.1 nM to about 1 nM, from or from about 0.5 nM to about 200 nM, from or from about 1 nM to about 500 nM, from or from about 1 nM to about 100 nM, from or from about 1 nM to about 50 nM, from or from about 1 nM to about 10 nM, from or from about 2 nM to about 50 nM, from or from about 10 nM to about 500 nM, from or from about 10 nM to about 100 nM, from or from about 10 nM to about 50 nM, from or from about 50 nM to about 500 nM, from or from about 50 nM to about 100 nM or from or from about 100 nM to about 500 nM.
In some of any of the provided embodiments, the immunomodulatory protein attenuates, decreases or reduces an immune response. In some embodiments, the immune response is a T cell response. In some embodiments, a reduced, decreased or attenuated T cell response includes one or more of cell cycle inhibition, reduced cell survival, reduced cell proliferation, reduced cytokine production (e.g. IFN-gamma or IL-2), or reduced T-cell cytotoxicity. In some embodiments, the reduced activity is observed in vitro in a primary T cell activation assays, such as in a Jurkat reporter assay, SEB assay or mixed lymphocyte reaction (MLR) assay. In some embodiments, the activity is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% compared to the activity in the same assay in the absence of the immunomodulatory protein. In some embodiments, the activity is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% compared to the activity in the same assay presence of a control in which the control is a protein that is known or suspected not to modulate T cell activity, e.g. an Fc only control. In some embodiments, the activity is reduced to a level that is greater than the reduction observed by a reference immunomodulatory protein containing only the ARBM or containing only the IRBM, such as is reduced by greater than or greater than about 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold 5.0-fold or more compared to the reference immunomodulatory protein.
In some of any such embodiments, upon contact of the immunomodulatory protein with the immune cell, the immunomodulatory protein proximalizes association of the inhibitory receptor and activating receptor by the immune cell. In some cases, upon contact of the immunomodulatory protein with the immune cell, the immunomodulatory protein recruits a cytoplasmic protein tyrosine phosphatase to the intracellular region of the inhibitory receptor, optionally wherein the protein tyrosine phosphatase is a SHP-1 or SHP-2. In some of any such embodiments, the immune cell is a T cell. In some embodiments, contact of the immunomodulatory protein and immune cell is in vitro or in vivo.
In some of any of the provided embodiments, binding of the IRBM of the immunomodulatory protein to the inhibitory receptor on the immune cell blocks or antagonizes binding between the inhibitory receptor and its cognate ligand. In some such embodiments, the cognate ligand is expressed on an antigen presenting cell. In some such embodiments, the immune cell is a T cell.
In some of any of the provided embodiments, binding of the ARBM of the immunomodulatory protein to the activating receptor on the immune cell blocks or antagonizes binding between the activating receptor and its cognate ligand. In some such embodiments, the cognate ligand is expressed on an antigen presenting cell. In some such embodiments, the immune cell is a T cell.
In some of any of the provided embodiments, binding of the ARBM of the immunomodulatory protein to the ligand of an activating receptor, in which said activating receptor is expressed on the immune cell, blocks or antagonizes binding between the activating receptor and the ligand. In some such embodiments, the ligand is expressed on an antigen presenting cell. In some such embodiments, the immune cell is a T cell.
In some of any of the provided embodiments, the immunomodulatory protein increases an immune response. In some embodiments, the immune response is a T cell response. In some embodiments, an increased T cell response includes one or more of increased cell activation, increased cell differentiation, increased or greater cell survival, increased cell proliferation, increased cytokine production (e.g. IFN-gamma or IL-2), or increased T-cell cytotoxicity. In some embodiments, the increased activity is observed in vitro in a primary T cell activation assays, such as in a Jurkat reporter assay, SEB assay or mixed lymphocyte reaction (MLR) assay. In some embodiments, the activity is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% compared to the activity in the same assay in the absence of the immunomodulatory protein. In some embodiments, the activity is increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% compared to the activity in the same assay in the presence of a control in which the control is a protein that is known or suspected not to modulate T cell activity, e.g. an Fc only control. In some embodiments, the activity is increased to a level that is greater than the reduction observed by a reference immunomodulatory protein containing only the ARBM or containing only the IRBM, such as is increased by greater than or greater than about 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold 5.0-fold or more compared to the reference immunomodulatory protein.
Provided are nucleic acid molecules encoding any of the provided immunomodulatory proteins. In some cases, the nucleic acid molecule is a synthetic nucleic acid. In some cases, the nucleic acid molecule is a cDNA. In some of any of the provided embodiments, the nucleic acid includes any having a DNA SEQ ID NO set forth in any of Tables E2, E3A, E3B, E4 or E5.
Provided are vectors containing any of the provided nucleic acid molecules. In some cases, the vector is an expression vector. In some embodiments, the vector is a mammalian expression vector or a viral vector.
Provided are cells containing any of the provided nucleic acid molecules. Provided are cells containing any of the provided vectors. In some cases, the cell is a mammalian cell. In some embodiments, the cell is a human cell.
Provided are methods of producing an immunomodulatory protein including introducing any of the provided nucleic acid molecules or vectors into a host cell under conditions to express the protein in the cell. In some cases, the method further includes isolating or purifying the immunomodulatory protein from the cell.
Provided are methods of engineering a cell expressing an immunomodulatory protein including introducing a nucleic acid molecule encoding a polypeptide or polypeptides of any of the provided immunomodulatory proteins into a host cell under conditions in which the polypeptide is expressed in the cell.
Provided are engineered cells expressing any of the provided immunomodulatory proteins, nucleic acid molecules, or vectors. In some cases, the immunomodulatory protein is capable of being secreted from the engineered cell. In some embodiments, the immunomodulatory protein does not contain a cytoplasmic signaling domain or transmembrane domain and/or is not capable of mediating or modulating an intracellular signal when secreted from a cell. In some embodiments, the cell is an immune cell. In some embodiments, the immune cell is a lymphocyte. In some embodiments, the lymphocyte is a T cell. In some examples, the T cell is a CD4+ and/or CD8+ T cell. In some examples, the T cell is a regulatory T cell (Treg). In some embodiments, the engineered cell is a primary cell. In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is a human cell. In some embodiments, the engineered cell further contains a chimeric antigen receptor (CAR). In some embodiments, the engineered cell further contains an engineered T-cell receptor (TCR).
Provided are infectious agents containing a nucleic acid molecule encoding any of the provided immunomodulatory proteins. In some embodiments, the infectious agent is a bacterium or a virus.
Also provided are pharmaceutical compositions containing any of the provided immunomodulatory proteins. Also provided are pharmaceutical compositions containing any of the provided engineered cells. Also provided are pharmaceutical compositions containing any of the provided infectious agents. In some embodiments, the pharmaceutical composition further contains a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition is sterile.
Provided are articles of manufacture containing any of the provided pharmaceutical compositions in a vial or container. In some cases, the vial or container is sealed.
Provided are kits containing any of the provided pharmaceutical compositions and instructions for use. Also provided are kits containing any of the provided articles of manufacture and instructions for use.
Provided are methods of modulating an immune response in a subject including administering any of the provided immunomodulatory proteins to the subject. Provided are methods of modulating an immune response in a subject including administering any of the provided pharmaceutical compositions to the subject. Also provided are methods of modulating an immune response in a subject, including administering any of the provided engineered cells. In some cases, the engineered cells are autologous to the subject. In some embodiments, the engineered cells are allogenic to the subject.
In some of any of the provided embodiments, modulating the immune response treats a disease or condition in the subject. In some cases, the immune response is decreased. Also provided are methods of treating a disease or condition in a subject including administering any of the provided immunomodulatory proteins to the subject. Also provided are methods of treating a disease or condition in a subject including administering any of the provided pharmaceutical compositions to the subject. In some embodiments, the disease or condition is an inflammatory or autoimmune disease or condition, or is a disease or condition associated with an overactive immune response. In some embodiments, the disease or condition is an Antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis, a vasculitis, an autoimmune skin disease, transplantation, a Rheumatic disease, a thyroiditis, an inflammatory gastrointestinal disease, an inflammatory eye disease, an inflammatory neurological disease, an inflammatory pulmonary disease, an inflammatory endocrine disease, an autoimmune hematological disease, an autoimmune demyelinating disease, or an autoimmune disease involving a systemic autoimmune disorder.
In some examples, the disease or condition is selected from among inflammatory bowel disease, transplant, Crohn's disease, ulcerative colitis, asthma, autoimmune asthma, rheumatoid arthritis, psoriasis, lupus erythematosus, celiac disease, type I diabetes mellitus, Guillain-Barre syndrome, Chronic inflammatory demyelinating polyneuropathy, Graves' disease, Hashimoto's thyroiditis, DeQuervains thyroiditis, myasthenia gravis, Vasculitis, autoimmune hemolytic anemia, autoimmune atrophic gastritis of pernicious anemia, autoimmune encephalomyelitis, autoimmune orchitis, Goodpasture's disease, autoimmune thrombocytopenia, sympathetic opthalmia, primary biliary cirrhosis, chronic aggressive hepatitis, membranous glomerulopathy, primary idiopathic myxedema, scleroderma, chronic hepatitis, Addison's disease, hypogonadism, pernicious anemia, vitiligo, alopecia areata, autoimmune enteropathy syndrome, idiopathic thrombocytic purpura, acquired splenic atrophy, idiopathic diabetes insipidus, infertility due to antispermatazoan antibodies, sensoneural hearing loss, Sjogren's syndrome, polymyositis, multiple sclerosis, transverse myelitis, ataxic sclerosis, pemphigus, progressive systemic sclerosis, dermatomyositis, polyarteritis nodosa, hemolytic anemia, glomerular nephritis, and idiopathic facial paralysis. In some cases, the disease or condition is a vasculitis that is a giant cell arteritis (GCA).
In some embodiments, the immunomodulatory protein increases an immune response in the subject. In some embodiments, the disease or condition is a cancer.
Provided herein are multi-domain immunomodulatory proteins that are capable of binding to two or more protein cell surface molecules to modulate, e.g. suppress, immunological immune responses. In some embodiments, the cell surface molecules are cell surface proteins expressed by immune cells, such as T lymphocytes, that engage with one or more other immune receptor or ligand, e.g. on antigen-presenting cells, to induce inhibitory or activating signals. For example, the interaction of certain receptors on lymphocytes with their cognate cell surface ligands to form an immunological synapse (IS) between antigen-presenting cells (APCs) or target cells and lymphocytes can provide costimulatory or inhibitory signals that can regulate the immune system. In some aspects, the multi-domain immunomodulatory proteins provided herein can alter the interaction of cell surface protein ligands with their receptors and/or alter the cell signal(s) induced in a cell to thereby modulate immune cells, such as T cell, activity. In some embodiments, the immunomodulatory proteins provided herein can be used for the treatment of diseases or conditions that are associated with a dysregulated immune response, such as autoimmune symptoms or an autoimmune disease.
In general, antigen specific T-cell activation generally requires two distinct signals. The first signal is provided by the interaction of the T-cell receptor (TCR) with major histocompatibility complex (MHC) associated antigens present on antigen presenting cells (APCs). The second signal is costimulatory to TCR engagement and is necessary for T cell proliferation, differentiation and/or survival, including, in some cases, to avoid T-cell apoptosis or anergy. In some embodiments, under normal physiological conditions, the T cell-mediated immune response is initiated by antigen recognition by the T cell receptor (TCR) and is regulated by a balance of co-stimulatory activating signals and inhibitory signals (i.e., immune checkpoint proteins).
Among activating receptors on T cells are the costimulatory receptor CD28, which binds to costimulatory ligands CD80 (also called B7-1) and CD86 (also called B7-2), and promotes activation of naïve T cells in the presence of a TCR signal. T cell activation, however, can be attenuated by engagement of inhibitory receptors, such as PD-1, CTLA-4 or TIGIT. For example, CTLA-4 competes with CD28 for binding of CD80 and CD86 to induce negative regulation of T cell activation. When CTLA-4 binds CD80 and/or CD86, and prevents CD28 from binding its cognate ligands, T cells do not effectively transmit the activating signaling cascade, and T cell activation and effector function can be eliminated or attenuated. In some cases, engagement of PD-1, expressed on NK cells and T cells, by its ligands PD-L1 and PD-L2, negatively regulate immune activation to inhibit activation, including by inhibiting cytolytic activity, proliferation and/or cytokine production. Similarly, TIGIT, which also can be expressed on NK cells and T cells, can suppress or inhibit the cytolytic activity of NK cells and T cells, T cell proliferation and/or proinflammatory cytokine production via engagement by its ligands CD112 or CD155. Inhibitory receptor ligands are, in some cases, expressed on antigen presenting cells, such that the ability to negatively regulate an immune response is often dependent on cells expressing activating or inhibitory receptors being present in the same space at the same time.
The immune system relies on immune checkpoints to prevent autoimmunity (i.e., self-tolerance) and to protect tissues from excessive damage during an immune response, for example during an attack against a pathogenic infection. In some cases, however, the immune system can become dysregulated and an abnormal immune response can be mounted against a normal body part or tissue, resulting in an autoimmune disease or condition or autoimmune symptoms. In other cases an unwanted immune response can be mounted to a foreign tissue, such as a transplant, resulting in transplant rejection.
In some aspects, immunotherapy that alters immune cell activity, such as T cell activity, can treat certain diseases and conditions in which the immune response is dysregulated. In particular, inhibition or attenuation of an immune response, such as a T cell response, could be desirable to reduce or prevent unwanted autoimmune symptoms and/or transplant rejection. Therapeutic approaches that seek to modulate interactions in the IS, however, are not entirely satisfactory. In some cases, therapies to intervene and alter the immunomodulatory effects of immune cell, e.g. T cell, activation are constrained by the spatial orientation requirements as well as size limitations imposed by the confines of the immunological synapse. In some aspects, existing therapeutic drugs, including antibody drugs, may not be able to interact simultaneously with the multiple target proteins involved in modulating these interactions. For example, soluble receptors and antibodies generally bind competitively (e.g., to no more than one target species at a time) and therefore lack the ability to simultaneously bind multiple targets. And while bispecific antibodies, as well as modalities comprising dual antigen binding regions, can bind to more than one target molecule simultaneously, the three-dimensional configuration typical of these modalities often precludes them intervening in key processes occurring in the IS in a manner consistent with their temporal and spatial requirements. Additionally, pharmacokinetic differences between drugs that independently target one of these receptors can create difficulties in properly maintaining a desired blood concentration of a drug combination targeting two different targets throughout the course of treatment.
Further, in some cases, existing therapeutic drugs may only have the ability to antagonize but not agonize an immune response. For example, the inhibitory receptor PD-1 has proven to be an effective inhibitory checkpoint receptor that regulates T cell activation. Therapeutic molecules that antagonize PD-1/PD-L1 interactions have proven to be efficacious in stimulating patient immune responses towards tumors. Therapeutic molecules targeting PD-1 or its ligands, however, have not been demonstrated to do the reverse, such as to mediate an inhibitory signal intrinsically into the T cell to attenuate an immune response. Such a therapeutic molecule would be desirable for use in treating inflammatory or autoimmune diseases or conditions.
Thus, there is a need for therapeutic molecules that have the specificity and affinity of antibodies or soluble receptors but, in addition, attenuate immune responses intrinsically through an immune cell, such as a T cell. It is contemplated herein that the inability for molecules targeting inhibitory receptors, such as PD-1, to deliver negative signals into a cell is due to the inability of such molecules to proximalize signaling of an inhibitory and activating receptor in the cell. Inhibitory receptors contain an immunoreceptor tyrosine-based inhibitory motif (ITIM), which when phosphorylated upon engagement of the inhibitor receptor by a ligand, can recruit phosphotyrosine phosphatases, such as a SHP-1 or SHP-2. Recruiting phosphatases can attenuate activating signaling cascades when the ITIM bearing receptors are in close proximity to the activating receptor (see
The provided embodiments are based on findings that strategies that physically proximalize the inhibitory and the activating receptor of the surface of the same immune cell, such as a T cell, include the uses of reagents that can bind both the inhibitory and activating receptor. In some embodiments, binding of both the inhibitory and activating receptor can keep the ITIM and ITAM signaling components in close proximity, including, in some cases for extended periods of time, and thereby favor phosphatase dependent dephosphorylation of the activating receptor signaling cascades to attenuate immune responses.
Provided are therapeutic molecules that, in some embodiments, bind both T-cell activation signaling components, such as the activating receptor or its ligand, and inhibitory receptors. In some cases, the inhibitory receptor is an ITIM containing receptor and the activating receptor is a molecule that contains an ITAM and/or that associates or interacts with an adaptor protein involved in or regulating a tyrosine phosphorylation signaling cascade in the cell (e.g. T cell). In some embodiments, the provided immunomodulatory proteins contain at least two binding molecules: (1) an activating receptor binding molecule (ARBM) that is specific for an activating receptor or a ligand of the activating receptor and (2) an inhibitory receptor binding molecule (IRBM) that is specific for an inhibitory receptor. In some embodiments, the ARBM and IRBM are distinct or different polypeptides that independently bind different target cell surface molecules. In some aspects, the binding can occur simultaneously or in a non-competitive manner. In some embodiments, the activating receptor and inhibitory receptor are expressed on the same cell, e.g. a T cell, such that interactions of the ARBM and IRBM with their target cell surface molecules can physically proximalize the inhibitory receptor and activating receptor on the surface of the immune cells, e.g. T cell. In some cases, the close proximity of the inhibitory and activating receptors induced by binding of the immunomodulatory protein to its target cell surface molecules recruits a cytoplasmic protein tyrosine phosphatase to the intracellular region of the inhibitory receptor and/or favors phosphatase dependent phosphorylation of the activating receptor signaling cascades. In some embodiments, binding of the immunomodulatory protein to a target cell expressing the activating receptor and inhibitor receptor, such as a T cells, can lead to attenuation of immune responses, such as attenuation of T cell responses.
In some embodiments, the provided multi-domain immunomodulatory proteins can interact with the activating receptor/ligand in cis or in trans (
In particular aspects, the provided immunomodulatory proteins provide an immunotherapy platform using binding domains of wild-type or affinity modified native immune ligands or receptors as the IRBM and/or ARBM component. In some aspects, the binding domain is or includes an immunoglobulin superfamily (IgSF) domain of an IgSF family member. In some aspects, the IgSF domain excludes those found in antibodies (i.e., immunoglobulins), such that the provided embodiments include embodiments that relate to immunomodulatory proteins containing non-immunoglobulin (i.e., non-antibody) IgSF domains. Wild-type mammalian IgSF family members that are not immunoglobulins (i.e. antibodies) are known as are their nucleic and amino acid sequences. In some embodiments, the non-immunoglobulin IgSF family members, and the corresponding IgSF domains present therein, are of mouse, rat, cynomolgus monkey, or human origin. In some embodiments, the IgSF family members are members of an IgSF subfamily such as: Signal-Regulatory Protein (SIRP) Family, Triggering Receptor Expressed On Myeloid Cells Like (TREML) Family, Carcinoembryonic Antigen-related Cell Adhesion Molecule (CEACAM) Family, Sialic Acid Binding Ig-Like Lectin (SIGLEC) Family, Butyrophilin Family, B7 family, CD28 family, V-set and Immunoglobulin Domain Containing (VSIG) family, V-set transmembrane Domain (VSTM) family, Major Histocompatibility Complex (MHC) family, Signaling lymphocytic activation molecule (SLAM) family, Leukocyte immunoglobulin-like receptor (LIR), Nectin (Nec) family, Nectin-like (NECL) family, Poliovirus receptor related (PVR) family, Natural cytotoxicity triggering receptor (NCR) family, or Killer-cell immunoglobulin-like receptors (KIR) family. For purposes herein, the IgSF domain is one whose binding partner is an activating receptor or a ligand of an activating receptor or is an inhibitory receptor.
In some embodiments, non-immunoglobulin IgSF family members, and the corresponding IgSF domains present therein, of an immunomodulatory proteins provided herein, are affinity-modified compared to a mammalian IgSF member. The affinity-modified IgSF domains include IgSF domains that are modified, such as by one or more amino acid substitution, to bind with tunable affinities to one or more of their cognate binding partner. An IgSF domain can be affinity modified to independently increase or decrease specific binding affinity or avidity to each of the multiple cognate binding partners to which it binds. By this mechanism, specific binding to each of multiple cognate binding partners is independently tuned to a particular affinity or avidity. Exemplary affinity-modified or variant IgSF domains having altered, such as increased, binding activity to one or more cognate binding partners are known (e.g. International published PCT App. Nos. WO 2016/168771, WO 2017/181148 and WO 2017/181152) or are described.
In some aspects, the provided immunomodulatory proteins containing one or more IgSF domain based on an immune system molecule, such as human immune system molecule, themselves are more likely to retain their ability to normally assemble into key pathways of the immune synapse and maintain normal interactions and regulatory functions, in part, because they are based on natural components of the immune synapse. Further, the relatively small molecular weight of individual IgSF domain may be beneficial in bringing two receptors together in close enough proximity, such as to induce or mediate phosphatase regulatory activity. Such features may not be possible with antibodies, including next-generation bispecific regents, due to the relatively large size of antibodies as well as from the fact that antibodies are not natural components of the immune synapse.
In some embodiments, the provided immunomodulatory proteins are single polypeptide fusions or monomers containing the IRBM or ARBM, which in some cases, can be tagged with a detectable moiety, such as a flag and/or his tag. In some aspects, such single polypeptide fusion or monomer formats minimize the size of the immunomodulatory protein and/or avoid steric issues that may result from other formats, including those involving larger molecules, such as dimeric molecules, e.g. molecules containing a multimerization domain, such as an Fc domain. In some cases, such polypeptide fusions can be made in various orientations, e.g. IRBM-ARBM or ARBM-IRBM, to create optimal binding pairs. Further, in some aspects, multiple IRBM and/or ARBM, such as independently two or more, such as 2, 3, 4, 5 or more IRBM or ARBM binding domain, e.g. IgSF domain, can be configured in a single polypeptide molecule to increase or improve binding affinity or avidity of one or both components, e.g. IRBM-IRBM-IRBM-ARBM.
In some aspects, the immunomodulatory proteins are provided as a dimeric protein. Generally, such formats are generated as a heterodimer, e.g. heterodimeric Fc fusion protein, such as to avoid dimeric binding of the activating receptor (e.g. CD28), which could result in unwanted firing of activating receptor. In some aspects, a heterodimeric immunomodulatory protein, while larger, may exhibit pharmacodynamics advantages, such as increased half-life.
In some aspects, the immunomodulatory proteins provided herein have therapeutic utility by attenuating immunological activity in a mammal with a disease or disorder in which modulation of the immune system response is beneficial. In some embodiments, the disease or condition is an inflammatory or autoimmune disease or condition.
All publications, including patents, patent applications scientific articles and databases, mentioned in this specification are herein incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, including patent, patent application, scientific article or database, were specifically and individually indicated to be incorporated by reference. If a definition set forth herein is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications and other publications that are herein incorporated by reference, the definition set forth herein prevails over the definition that is incorporated herein by reference.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. Further various embodiments of the invention as discussed below are frequently provided. Thus, the headings, the order of presentation of the various aspects and embodiments, and the separate disclosure of each independent attribute is not meant to be a limitation to the scope of the present disclosure.
Unless defined otherwise, all terms of art, notations and other technical and scientific terms or terminology used herein are intended to have the same meaning as is commonly understood by one of ordinary skill in the art to which the claimed subject matter pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art.
Unless defined otherwise, all technical and scientific terms, acronyms, and abbreviations used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Unless indicated otherwise, abbreviations and symbols for chemical and biochemical names are per IUPAC-IUB nomenclature. Unless indicated otherwise, all numerical ranges are inclusive of the values defining the range as well as all integer values in-between.
As used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly indicates otherwise.
The term “about” as used herein refers to the usual error range for the respective value readily known to the skilled person in this technical field. Reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se. For example, description referring to “about X” includes description of “X”.
As used herein, an “activating receptor” refers to a cell surface molecule in which engagement or ligation of the molecule results in the direct or indirect activation of one or more tyrosine kinases in an immune cell and/or culminates in the induction or potentiation of one or more effector cell functions in an immune cell in which it is expressed. An activating receptor generally contains an extracellular portion, a transmembrane domain and cytoplasmic region. In some embodiments, the cytoplasmic region contains an intracellular signaling domain that contains an immunoreceptor tyrosine-based activation motif (ITAM; defined by the sequence YXX(L/I)X6-8YXX(L/I)) or that otherwise is capable of interacting with or associating with one or more accessory proteins, such as one or more adaptor proteins, involved in or regulating tyrosine phosphorylation in a signal transduction pathway. In some cases, an activating receptor interacts with or associates with an adaptor protein that contains an ITAM or an adaptor protein that contains one or more protein-binding domains, such as e.g., Src homology 2 (SH2) and SH3 domains, that bind specific amino acid sequences, e.g phosphotyrosine residues, within a protein in a signal transduction pathway. Examples of adaptor proteins include, but are not limited to, Lck, Fyn, ZAP70, SLP76, PI3K, Grb2, PKCΘ and SHC1. Thus, it is understood that the activating receptor itself need not possess intrinsic enzymatic activity but may indirectly mediate enzymatic activities via accessory or adaptor proteins. In some embodiments, an activating receptor is a cell surface molecule on a T cell. Typically, engagement of an activating receptor initiates, mediates or potentiates activation of a cell resulting in a measurable morphological, phenotypic, and/or functional changes in the cell, such as a T cell, including cell proliferation, cytolytic activity, cytokine production or secretion, or expression of cell surface molecules such as receptors or adhesion molecules. In some embodiments, an activating receptor includes a T cell receptor (TCR), CD3, CD4, CD8, CD28, ICOS, or CD2.
The term “activating receptor binding molecule” or ARBM refers to a protein that specifically binds to an activating receptor or a ligand of an activating receptor.
The term “affinity-modified” as used in the context of an immunoglobulin superfamily domain, means a mammalian immunoglobulin superfamily (IgSF) domain having an altered amino acid sequence (relative to the corresponding wild-type parental or unmodified IgSF domain) such that it has an increased or decreased binding activity, such as binding affinity or avidity, to at least one of its binding partners (alternatively “counter-structures”) compared to the parental wild-type or unmodified (i.e., non-affinity modified) IgSF control domain. In some embodiments, the affinity-modified IgSF domain can contain 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more amino acid differences, such as amino acid substitutions, in a wild-type or unmodified IgSF domain. An increase or decrease in binding activity, e.g. binding affinity or avidity, can be determined using well known binding assays, including flow cytometry. Larsen et al., American Journal of Transplantation, Vol 5: 443-453 (2005). See also, Linsley et al., Immunity, 1: 7930801 (1994). An increase in a protein's binding activity, e.g. affinity or avidity, to its binding partner(s) is to a value at least 10% greater than that of the wild-type IgSF domain control and in some embodiments, at least 20%, 30%, 40%, 50%, 100%, 200%, 300%, 500%, 1000%, 5000%, or 10000% greater than that of the wild-type IgSF domain control value. A decrease in a protein's binding activity, e.g. affinity or avidity, to at least one of its binding partner is to a value no greater than 90% of the control but no less than 10% of the wild-type IgSF domain control value, and in some embodiments no greater than 80%, 70% 60%, 50%, 40%, 30%, or 20% but no less than 10% of the wild-type IgSF domain control value. An affinity-modified protein is altered in primary amino acid sequence by substitution, addition, or deletion of amino acid residues. The term “affinity-modified IgSF domain” is not be construed as imposing any condition for any particular starting composition or method by which the affinity-modified IgSF domain was created. Thus, the affinity-modified IgSF domains of the present invention are not limited to wild-type IgSF domains that are then transformed to an affinity-modified IgSF domain by any particular process of affinity modification. An affinity-modified IgSF domain polypeptide can, for example, be generated starting from wild-type mammalian IgSF domain sequence information, then modeled in silico for binding to its binding partner, and finally recombinantly or chemically synthesized to yield the affinity-modified IgSF domain composition of matter. In but one alternative example, an affinity-modified IgSF domain can be created by site-directed mutagenesis of a wild-type IgSF domain. Thus, affinity modified IgSF domain denotes a product and not necessarily a product produced by any given process. A variety of techniques including recombinant methods, chemical synthesis, or combinations thereof, may be employed.
The term “allogeneic” as used herein means a cell or tissue that is removed from one organism and then infused or adoptively transferred into a genetically dissimilar organism of the same species.
The term “autologous” as used herein means a cell or tissue that is removed from the same organism to which it is later infused or adoptively transferred. An autologous cell or tissue can be altered by, for example, recombinant DNA methodologies, such that it is no longer genetically identical to the native cell or native tissue which is removed from the organism. For example, a native autologous T-cell can be genetically engineered by recombinant DNA techniques to become an autologous engineered cell expressing a immunomodulatory protein (which can be secreted from the engineered cell), which in some cases involves engineering a T-cell or TIL (tumor infiltrating lymphocyte). The engineered cell can then be infused into a patient from which the native T-cell was isolated. In some embodiments, the organism is human or murine.
As used herein, “bind,” “bound” or grammatical variations thereof refers to the participation of a molecule in any attractive interaction with another molecule, resulting in a stable association in which the two molecules are in close proximity to one another. Binding includes, but is not limited to, non-covalent bonds, covalent bonds (such as reversible and irreversible covalent bonds), and includes interactions between molecules such as, but not limited to, proteins, nucleic acids, carbohydrates, lipids, and small molecules, such as chemical compounds including drugs.
As used herein, binding activity refer to characteristics of a molecule, e.g. a polypeptide, relating to whether or not, and how, it binds one or more binding partners. A binding activity can include any measure of binding of one molecule for a binding partner. Binding activities include the ability to bind the binding partner(s), the affinity with which it binds to the binding partner (e.g. high affinity), the avidity with which it binds to the binding partner, the strength of the bond with the binding partner and/or specificity or selectivity for binding with the binding partner.
The term “binding affinity” as used herein means the specific binding affinity of a protein for its binding partner (i.e., its counter-structure) under specific binding conditions. The binding affinity refers to the strength of the interaction between two or more molecules, such as binding partners, typically the strength of the noncovalent interactions between two binding partners. An increase or attenuation in binding affinity of an affinity-modified IgSF domain, or an immunomodulatory protein containing an affinity-modified IgSF domain, to a binding partner is determined relative to the binding affinity of the unmodified IgSF domain (e.g., the native or wild-type IgSF domain). Methods for determining binding affinity, or relative binding affinity, are known in art, solid-phase ELISA immunoassays, ForteBio Octet, Biacore measurements or flow cytometry. See, for example, Larsen et al., American Journal of Transplantation, vol. 5: 443-453 (2005); Linsley et al., Immunity, Vol 1 (9): 793-801 (1994). In some embodiments, binding affinity can be measured by flow cytometry, such as based on a Mean Fluorescence Intensity (MFI) in a binding assay.
The term “binding avidity” as used herein means the specific binding avidity, of a protein for its binding partner (i.e., its counter-structure) under specific binding conditions. In biochemical kinetics avidity refers to the accumulated strength of multiple affinities of individual non-covalent binding interactions, such as between an IgSF domain and its binding partner (i.e., its counter-structure). As such, avidity is distinct from affinity, which describes the strength of a single interaction.
The term “biological half-life” refers to the amount of time it takes for a substance, such as an immunomodulatory protein, to lose half of its pharmacologic or physiologic activity or concentration. Biological half-life can be affected by elimination, excretion, degradation (e.g., enzymatic degradation/digestion) of the substance, or absorption and concentration in certain organs or tissues of the body. In some embodiments, biological half-life can be assessed by determining the time it takes for the blood plasma concentration of the substance to reach half its steady state level (“plasma half-life”). Conjugates that can be used to derivatize and increase the biological half-life of a protein are known in the art and include, but are not limited to, multimerization domains (e.g. Fc), polyethylene glycol (PEG), hydroxyethyl starch (HES), XTEN (extended recombinant peptides; see, WO2013130683), human serum albumin (HSA), bovine serum albumin (BSA), lipids (acylation), and poly-Pro-Ala-Ser (PAS), polyglutamic acid (glutamylation).
The term “cell surface counter-structure” (alternatively “cell surface binding partner”) as used herein is a counter-structure (alternatively is a binding partner) expressed on a mammalian cell. Typically, the cell surface binding partner is a transmembrane protein. In some embodiments, the cell surface binding partner is a receptor.
The terms “binding partner” or “counter-structure” in reference to a protein, such as an IgSF domain or an affinity-modified IgSF domain, refers to at least one molecule (typically a native mammalian protein) to which the referenced protein specifically binds under specific binding conditions. In some aspects, an affinity-modified IgSF domain, or an immunomodulatory protein containing an affinity-modified IgSF domain, specifically binds to the binding partner of the corresponding native or wild-type IgSF domain but with increased or attenuated affinity. A “cell surface binding partner” is a binding partner expressed on a mammalian cell. Typically, the cell surface binding partner is a transmembrane protein. In some embodiments, the cell surface binding partner is a receptor or a ligand of a receptor expressed on and by cells, such as mammalian cells, forming the immunological synapse, for example immune cells.
The term “cis” with reference to binding to cell surface molecules refers to binding to two or more different cell surface molecules, each of which is present on the surface of the same cell. In some embodiments, cis means that the two or more cell surface molecules are exclusively on one or exclusively the other (but not both) of the two mammalian cells forming the IS.
The term “competitive binding” as used herein means that a protein is capable of specifically binding to at least two binding partners but that specific binding of one binding partner inhibits, such as prevents or precludes, simultaneous binding of the second binding partner. Thus, in some cases, it is not possible for a protein to bind the two binding partners at the same time. Generally, competitive binders contain the same or overlapping binding site for binding but this is not a requirement. In some embodiments, competitive binding causes a measurable inhibition (partial or complete) of specific binding of a protein to one of its binding partner due to specific binding of a second binding partner. A variety of methods are known to quantify competitive binding such as ELISA (enzyme linked immunosorbent assay) or Forte-Bio Octet experimental systems.
The term “conservative amino acid substitution” as used herein means an amino acid substitution in which an amino acid residue is substituted by another amino acid residue having a side chain R group with similar chemical properties (e.g., charge or hydrophobicity). Examples of groups of amino acids that have side chains with similar chemical properties include 1) aliphatic side chains: glycine, alanine, valine, leucine, and isoleucine; 2) aliphatic-hydroxyl side chains: serine and threonine; 3) amide-containing side chains: asparagine and glutamine; 4) aromatic side chains: phenylalanine, tyrosine, and tryptophan; 5) basic side chains: lysine, arginine, and histidine; 6) acidic side chains: aspartic acid and glutamic acid; and 7) sulfur-containing side chains: cysteine and methionine. Conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, glutamate-aspartate, and asparagine-glutamine.
The term, “corresponding to” with reference to positions of a protein, such as recitation that nucleotides or amino acid positions “correspond to” nucleotides or amino acid positions in a disclosed sequence, such as set forth in the Sequence Listing, refers to nucleotides or amino acid positions identified upon alignment with the disclosed sequence based on structural sequence alignment or using a standard alignment algorithm, such as the GAP algorithm. By aligning the sequences, one skilled in the art can identify corresponding residues, for example, using conserved and identical amino acid residues as guides.
The term “cytokine” includes, e.g., but is not limited to, interleukins, interferons (IFN), chemokines, hematopoietic growth factors, tumor necrosis factors (TNF), and transforming growth factors. In general, these are small molecular weight proteins that regulate maturation, activation, proliferation, and differentiation of cells of the immune system.
The terms “decreased,” “reduced,” “suppressed” or “inhibits,” which can be used interchangeably, as used herein in the context of an immunological activity of a mammalian lymphocyte in the presence of a provided immunomodulatory protein means to decrease one or more activities of the lymphocyte, as compared to a control, such as an untreated control or a control involving treatment with another molecule, such as a molecule containing an individual IgSF domain of an immunomodulatory protein or an alternative molecule, was employed under the same conditions. A decreased activity can refer to one or more of cell cycle inhibition, reduced cell survival, reduced cell proliferation, reduced cytokine production, or reduced T-cell cytotoxicity, such as by a statistically significant amount. In some embodiments, reference to reduced immunological activity means to reduce interferon gamma (IFN-gamma) production compared to in the absence of treatment, such as by a statistically significant amount. In some embodiments, the immunological activity can be assessed in a mixed lymphocyte reaction (MLR) assay. Methods of conducting MLR assays are known in the art. Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56. Other methods of assessing activities of lymphocytes are known in the art, including any assay as described herein. In some embodiments, a decrease can be by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, 90%, or 100%, as compared to a control value, such as an untreated control value or a non-zero control value.
The terms “derivatives” or “derivatized” refer to modification of an immunomodulatory protein by covalently linking it, directly or indirectly, so as to alter such characteristics as half-life, bioavailability, immunogenicity, solubility, toxicity, potency, or efficacy while retaining or enhancing its therapeutic benefit. Derivatives can be made by glycosylation, pegylation, lipidation, or Fc-fusion. In some embodiments, the immunomodulatory protein is not derivatized. In some embodiments, the immunomodulatory protein is not conjugated to a half-life extending moiety, such as an Fc domain.
As used herein, “domain” (typically a sequence of three or more, generally 5 or 7 or more amino acids, such as 10 to 200 amino acid residues) refers to a portion of a molecule, such as a protein or encoding nucleic acid, that is structurally and/or functionally distinct from other portions of the molecule and is identifiable. For example, domains include those portions of a polypeptide chain that can form an independently folded structure within a protein made up of one or more structural motifs and/or that is recognized by virtue of a functional activity, such as binding activity. A protein can have one, or more than one, distinct domains. For example, a domain can be identified, defined or distinguished by homology of the primary sequence or structure to related family members, such as homology to motifs. In another example, a domain can be distinguished by its function, such as an ability to interact with a biomolecule, such as a cognate binding partner. A domain independently can exhibit a biological function or activity such that the domain independently or fused to another molecule can perform an activity, such as, for example binding. A domain can be a linear sequence of amino acids or a non-linear sequence of amino acids. Many polypeptides contain a plurality of domains. Such domains are known, and can be identified by those of skill in the art. For exemplification herein, definitions are provided, but it is understood that it is well within the skill in the art to recognize particular domains by name. If needed appropriate software can be employed to identify domains. It is understood that reference to amino acids, including to a specific sequence set forth as a SEQ ID NO used to describe domain organization of an IgSF domain are for illustrative purposes and are not meant to limit the scope of the embodiments provided. It is understood that polypeptides and the description of domains thereof are theoretically derived based on homology analysis and alignments with similar molecules. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. ECD or IgV) also can be included in a sequence of an IgSF domain, such as to ensure proper folding of the domain when expressed. Thus, the exact locus can vary, and is not necessarily the same for each protein. Hence, the specific IgSF domain, such as specific IgV domain or IgC domain, can be several amino acids (1-10, such as 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids) longer or shorter.
The term “ectodomain,” “extracellular domain,” or “ECD,” which are used interchangeably herein, refers to the region of a membrane protein, such as a transmembrane protein, that lies outside the vesicular membrane (e.g., the space outside of a cell). Ectodomains often interact with specific ligands or specific cell surface receptors, such as via a binding domain that specifically binds to the ligand or cell surface receptor. Ectodomains of members of the immunoglobulin superfamily contain immunoglobulin domains.
The terms “effective amount” or “therapeutically effective amount” refer to a quantity and/or concentration of a therapeutic composition of the invention, such as containing an immunomodulatory protein or engineered cells expressing an immunomodulatory protein, that when administered ex vivo (by contact with a cell from a patient) or in vivo (by administration into a patient) either alone (i.e., as a monotherapy) or in combination with additional therapeutic agents, yields a statistically significant inhibition of disease progression as, for example, by ameliorating or eliminating symptoms and/or the cause of the disease. An effective amount for treating a disease or disorder, such as an immune system disease or disorder, may be an amount that relieves, lessens, or alleviates at least one symptom or biological response or effect associated with the disease or disorder, prevents progression of the disease or disorder, or improves physical functioning of the patient. In the case of cell therapy, the effective amount is an effective dose or number of cells administered to a patient. In some embodiments the patient is a human patient.
The term “endodomain” as used herein refers to the region found in some membrane proteins, such as transmembrane proteins, that extends into the interior space defined by the cell surface membrane. In mammalian cells, the endodomain is the cytoplasmic region of the membrane protein. In cells, the endodomain interacts with intracellular constituents and can be play a role in signal transduction and thus, in some cases, can be an intracellular signaling domain. The endodomain of a cellular transmembrane protein is alternately referred to as a cytoplasmic domain, which, in some cases, can be a cytoplasmic signaling domain.
The term “enhanced” or “increased,” which can be used interchangeably, as used herein in the context of increasing immunological activity of a mammalian lymphocyte in the presence of a molecule means to increase one or more activities of the lymphocyte. An increased activity can be one or more of an increase cell survival, cell proliferation, cytokine production, or T-cell cytotoxicity, such as by a statistically significant amount. In some embodiments, reference to increased immunological activity means to increase interferon gamma (IFN-gamma) production, such as by a statistically significant amount. Typically, the increase is relative to or compared to a control, such as an untreated control or a control involving treatment with another molecule. Methods of assessing activities of lymphocytes are known in the art, including any assay as described herein. In some embodiments an enhancement can be an increase of at least 10%, 20%, 30%, 40%, 50%, 75%, 100%, 200%, 300%, 400%, or 500% greater than a non-zero control value.
The term “engineered cell” as used herein refers to a mammalian cell that has been genetically modified by human intervention such as by recombinant DNA methods or viral transduction. In some embodiments, the engineered cell is an immune cell, such as a lymphocyte (e.g. T cell, B cell, NK cell) or an antigen presenting cell (e.g. dendritic cell). The cell can be a primary cell from a patient or can be a cell line. In some embodiments, an engineered cell is capable of expressing and secreting a immunomodulatory protein as described herein.
The term “engineered T-cell” as used herein refers to a T-cell such as a T helper cell, cytotoxic T-cell (alternatively, cytotoxic T lymphocyte or CTL), natural killer T-cell, regulatory T-cell, memory T-cell, or gamma delta T-cell, that has been genetically modified by human intervention such as by recombinant DNA methods. In some embodiments, an engineered T-cell is capable of expressing and secreting an immunomodulatory protein as described herein.
As used herein, a fusion protein refers to a polypeptide encoded by a nucleic acid sequence containing a coding sequence for two or more proteins, in some cases 2, 3, 4, 5 or more protein, in which the coding sequences are in the same reading frame such that when the fusion construct is transcribed and translated in a host cell, the protein is produced containing the two or more proteins. Each of the two or more proteins can be adjacent to another protein in the construct or separated by a linker polypeptide that contains, 1, 2, 3, or more, but typically fewer than 20, 15, 10, 9, 8, 7, or 6 amino acids. The protein product encoded by a fusion construct is referred to as a fusion polypeptide.
The term “half-life extending moiety” refers to a moiety of a polypeptide fusion or chemical conjugate that extends the half-life of a protein circulating in mammalian blood serum compared to the half-life of the protein that is not so conjugated to the moiety. In some embodiments, half-life is extended by greater than or greater than about 1.2-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold, 5.0-fold, or 6.0-fold. In some embodiments, half-life is extended by more than 6 hours, more than 12 hours, more than 24 hours, more than 48 hours, more than 72 hours, more than 96 hours or more than 1 week after in vivo administration compared to the protein without the half-life extending moiety. The half-life refers to the amount of time it takes for the protein to lose half of its concentration, amount, or activity. Half-life can be determined for example, by using an ELISA assay or an activity assay. Exemplary half-life extending moieties include an Fc domain, a multimerization domain, polyethylene glycol (PEG), hydroxyethyl starch (HES), XTEN (extended recombinant peptides; see, WO2013130683), human serum albumin (HSA), bovine serum albumin (BSA), lipids (acylation), and poly-Pro-Ala-Ser (PAS), and polyglutamic acid (glutamylation).
An Fc (fragment crystallizable) region or domain of an immunoglobulin molecule (also termed an Fc polypeptide) corresponds largely to the constant region of the immunoglobulin heavy chain, and is responsible for various functions, including the antibody's effector function(s). The Fc domain contains part or all of a hinge domain of an immunoglobulin molecule plus a CH2 and a CH3 domain. The Fc domain can form a dimer of two polypeptide chains joined by one or more disulfide bonds. In some embodiments, the Fc is a variant Fc that exhibits reduced (e.g. reduced greater than 30%, 40%, 50%, 60%, 70%, 80%, 90% or more) activity to facilitate an effector function. In some embodiments, reference to amino acid substitutions in an Fc region is by EU numbering system unless described with reference to a specific SEQ ID NO. EU numbering is known and is according to the most recently updated IMGT Scientific Chart (IMGT®, the international ImMunoGeneTics information System®, http://www.imgt.org/IMGTScientificChart/Numbering/Hu_IGHGnber.html (created: 17 May 2001, last updated: 10 Jan. 2013) and the EU index as reported in Kabat, E. A. et al. Sequences of Proteins of Immunological interest. 5th ed. US Department of Health and Human Services, NIH publication No. 91-3242 (1991).
An immunoglobulin Fc fusion (“Fc-fusion”), such as an immunomodulatory Fc fusion protein, is a molecule comprising one or more polypeptides operably linked to an Fc region of an immunoglobulin. An Fc-fusion may comprise, for example, the Fc region of an antibody (which facilitates effector functions and pharmacokinetics) operably linked to an ARBM or IRBM of the provided immunomodulatory proteins. An immunoglobulin Fc region may be linked indirectly or directly to the ARBM and/or IRBM. Various linkers are known in the art and can optionally be used to link an Fc to a fusion partner to generate an Fc-fusion. Fc-fusions of identical species can be dimerized to form Fc-fusion homodimers, or using non-identical species to form Fc-fusion heterodimers. In some embodiments, the Fc is a mammalian Fc such as a murine or human Fc.
The term “host cell” refers to any cell that can be used to express a protein encoded by a recombinant expression vector. A host cell can be a prokaryote, for example, E. coli, or it can be a eukaryote, for example, a single-celled eukaryote (e.g., a yeast or other fungus), a plant cell (e.g., a tobacco or tomato plant cell), an animal cell (e.g., a human cell, a monkey cell, a hamster cell, a rat cell, a mouse cell, or an insect cell) or a hybridoma. Examples of host cells include Chinese hamster ovary (CHO) cells or their derivatives such as Veggie CHO and related cell lines which grow in serum-free media or CHO strain DX-B11, which is deficient in DHFR.
The term “immunological synapse” or “immune synapse” (abbreviated “IS”) as used herein means the interface between a mammalian cell that expresses MHC I (major histocompatibility complex) or MHC II, such as an antigen-presenting cell or tumor cell, and a mammalian lymphocyte such as an effector T cell or Natural Killer (NK) cell.
The term “immunoglobulin” (abbreviated “Ig”) as used herein is synonymous with the term “antibody” (abbreviated “Ab”) and refers to a mammalian immunoglobulin protein including any of the five human classes: IgA (which includes subclasses IgA1 and IgA2), IgD, IgE, IgG (which includes subclasses IgG1, IgG2, IgG3, and IgG4), and IgM. The term is also inclusive of immunoglobulins that are less than full-length, whether wholly or partially synthetic (e.g., recombinant or chemical synthesis) or naturally produced, including any fragment thereof containing at least a portion of the variable heavy (VH) chain and/or variable light (VL) chain region of the immunoglobulin molecule that is sufficient to form an antigen binding site and, when assembled, to specifically bind antigen. The antibody also can include all or a portion of the constant region. Such fragments include antigen binding fragment (Fab), variable fragment (Fv) containing VH and VL, the single chain variable fragment (scFv) containing VH and VL linked together in one chain, as well as other antibody V region fragments, such as Fab′, F(ab)2, F(ab′)2, dsFv diabody, Fc, and Fd polypeptide fragments. Hence, it is understood that reference to an antibody herein includes full-length antibody and antigen-binding fragments. The term antibody also includes antibody compositions with polyepitopic specificity, multispecific antibodies (e.g., bispecific antibodies), diabodies, and single-chain molecules. Bispecific antibodies, homobispecific and heterobispecific, are included within the meaning of the term. Antibodies include polyclonal antibodies or monoclonal antibodies. Antibody also includes synthetic antibodies or recombinantly produced antibodies. For the structure and properties of the different classes of antibodies, see e.g., Basic and Clinical Immunology, 8th Edition, Daniel P. Sties, Abba I. Ten and Tristram G. Parsolw (eds), Appleton & Lange, Norwalk, Conn., 1994, page 71 and Chapter 6.
The terms “full-length antibody,” “intact antibody” or “whole antibody” are used interchangeably to refer to an antibody in its substantially intact form, as opposed to an antibody fragment. A full-length antibody is an antibody typically having two full-length heavy chains (e.g., VH-CH1-CH2-CH3 or VH-CH1-CH2-CH3-CH4) and two full-length light chains (VL-CL) and hinge regions, such as antibodies produced from mammalian species (e.g. human, mouse, rat, rabbit, non-human primate, etc.) by antibody secreting B cells and antibodies with the same domains that are produced synthetically. Specifically whole antibodies include those with heavy and light chains including an Fc region. The constant domains may be native sequence constant domains (e.g., human native sequence constant domains) or amino acid sequence variants thereof. In some cases, the intact antibody may have one or more effector functions.
An “antibody fragment” comprises a portion of an intact antibody, the antigen binding and/or the variable region of the intact antibody. Antibody fragments, include, but are not limited to, Fab fragments, Fab′ fragments, F(ab′)2 fragments, Fv fragments, disulfide-linked Fvs (dsFv), Fd fragments, Fd′ fragments; diabodies; linear antibodies (see U.S. Pat. No. 5,641,870, Example 2; Zapata et al., Protein Eng. 8(10): 1057-1062 [1995]); single-chain antibody molecules, including single-chain Fvs (scFv) or single-chain Fabs (scFab); antigen-binding fragments of any of the above and multispecific antibodies from from antibody fragments.
“Fv” is composed of one heavy- and one light-chain variable region domain linked by non-covalent association. From the folding of these two domains emanate six complementarity determining regions (CDR) (3 in each from the heavy and light chain) that contribute the amino acid residues for antigen binding and confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although, in some cases, at a lower affinity than the entire binding site.
“dsFv” refers to an Fv with an engineered intermolecular disulfide bond, which stabilizes the VH-VL pair.
An “Fd fragment” is a fragment of an antibody containing a variable domain (VH) and one constant region domain (CH1) of an antibody heavy chain.
A “Fab fragment” is an antibody fragment that results from digestion of a full-length immunoglobulin with papain, or a fragment having the same structure that is produced synthetically, e.g., by recombinant methods. A Fab fragment contains a light chain (containing a VL and CL) and another chain containing a variable domain of a heavy chain (VH) and one constant region domain of the heavy chain (CH1).
A “F(ab′)2 fragment” is an antibody fragment that results from digestion of an immunoglobulin with pepsin at pH 4.0-4.5, or a fragment having the same structure that is produced synthetically, e.g., by recombinant methods. The F(ab′)2 fragment essentially contains two Fab fragments where each heavy chain portion contains an additional few amino acids, including cysteine residues that form disulfide linkages joining the two fragments.
A “Fab′ fragment” is a fragment containing one half (one heavy chain and one light chain) of the F(ab′)2 fragment.
An “Fd′ fragment” is a fragment of an antibody containing one heavy chain portion of a F(ab′)2 fragment.
An “Fv′ fragment” is a fragment containing only the VH and VL domains of an antibody molecule.
An “scFv fragment” refers to an antibody fragment that contains a variable light chain (VL) and variable heavy chain (VH), covalently connected by a polypeptide linker in any order. The linker is of a length such that the two variable domains are bridged without substantial interference. Exemplary linkers are (Gly-Ser)n residues with some Glu or Lys residues dispersed throughout to increase solubility.
“Diabodies” are dimeric scFv; diabodies typically have shorter peptide linkers than scFvs, and preferentially dimerize.
The term “immunoglobulin superfamily” or “IgSF” as used herein means the group of cell surface and soluble proteins that are involved in the recognition, binding, or adhesion processes of cells. Molecules are categorized as members of this superfamily based on shared structural features with immunoglobulins (i.e., antibodies); they all possess a domain known as an immunoglobulin domain or fold. Many “non-antibody IgSF” members include cell surface proteins or receptors that are not antibodies. Members of the IgSF include cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins. They are commonly associated with roles in the immune system. Proteins in the immunological synapse are often members of the IgSF. IgSF can also be classified into “subfamilies” based on shared properties such as function. Such subfamilies typically include from 4 to 30 IgSF members.
The terms “IgSF domain” or “immunoglobulin domain” or “Ig domain” or “IgD” as used herein refers to a structural domain or domains of IgSF proteins. Ig domains are named after the immunoglobulin molecules. They contain about 70-110 amino acids and are categorized according to their size and function. Ig-domains possess a characteristic Ig-fold, which has a sandwich-like structure formed by two sheets of antiparallel beta strands. Interactions between hydrophobic amino acids on the inner side of the sandwich and highly conserved disulfide bonds formed between cysteine residues in the B and F strands, stabilize the Ig-fold. In some cases, one end of the Ig domain has a section called the complementarity determining region, which, in some aspects, is involved in the specificity of antibodies for their ligands. The Ig like domains can be classified (into classes) as: IgV, IgC1, IgC2, or IgI. Most Ig domains are either variable (IgV) or constant (IgC). IgV domains with 9 beta strands are generally longer than IgC domains with 7 beta strands. Ig domains of some members of the IgSF resemble IgV domains in the amino acid sequence, yet are similar in size to IgC domains. These are called IgC2 domains, while standard IgC domains are called IgC1 domains. T-cell receptor (TCR) chains contain two Ig domains in the extracellular portion; one IgV domain at the N-terminus and one IgC1 domain adjacent to the cell membrane. A “non-antibody IgSF domain” refers to IgSF domain or domains present in proteins other than antibodies, which typically are present in the extracellular portion or domain of certain cell surface proteins. Thus, the extracellular domain (ECD) of IgSF family members contains one or more Ig domains; hence, the term Ig domain is also used with reference to the ECD of such protein molecules.
The term “immunological activity” as used herein in the context of mammalian lymphocytes, such as T cells, refers to one or more of activation, cell survival, cell proliferation, cytokine production (e.g. interferon-gamma), or T-cell cytotoxicity activities. Assays for determining enhancement or suppression of immunological activity include MLR (mixed lymphocyte reaction) assays measuring interferon-gamma cytokine levels in culture supernatants (Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56), SEB (staphylococcal enterotoxin B), T cell stimulation assays (Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56), and anti-CD3 T cell stimulation assays (Li and Kurlander, J Transl Med. 2010: 8: 104). Since T cell activation is associated with secretion of IFN-gamma cytokine, detecting IFN-gamma levels in culture supernatants from these in vitro human T cell assays can be assayed using commercial ELISA kits (Wu et al, Immunol Lett 2008 Apr. 15; 117(1): 57-62). Assays also include assays to assess cytotoxicity, including a standard 51Cr-release assay (see e.g. Milone et al., (2009) Molecular Therapy 17: 1453-1464) or flow based cytotoxicity assays, or an impedance based cytotoxicity assay (Peper et al. (2014) Journal of Immunological Methods, 405:192-198). Assays to assess immunological activity of immunomodulatory proteins can be compared to control proteins with a known activity.
An “immunomodulatory protein” or “immunomodulatory polypeptide” is a protein that modulates immunological activity. By “modulation” or “modulating” an immune response is meant that immunological activity is either enhanced or suppressed. An immunomodulatory protein can be a single polypeptide chain or a multimer (dimers or higher order multimers) of at least two polypeptide chains covalently bonded to each other by, for example, interchain disulfide bonds. Thus, monomeric, dimeric, and higher order multimeric proteins are within the scope of the defined term. Multimeric proteins can be homomultimeric (of identical polypeptide chains) or heteromultimeric (of different polypeptide chains). Secretable immunomodulatory proteins are a type of immunomodulatory protein.
As used herein, an “inhibitory receptor” refers to a cell surface molecule in which engagement of the molecule transmits a negative signal to an immune cell and/or downregulates or reduces activation of an immune cell. In some embodiments, transmission of an inhibitory signal to an immune cell can result in unresponsiveness or anergy or programmed cell death in the immune cell. An inhibitory receptor generally contains an extracellular portion, a transmembrane domain and a cytoplasmic region that directly or indirectly activates or recruits phosphatases. In some embodiments, the cytoplasmic region contains an immunoreceptor tyrosine-based inhibition motif (ITIM), which is a conserved sequence of amino acids (S/I/V/LxYxxI/V/L) that is found in the cytoplasmic tails of many inhibitory receptors of the immune system. In some aspects, engagement of an ITIM-containing receptor, such as with a ligand, results in phosphorylation of the ITIM motif to recruit SH2-domain containing phosphatases, such as the phosphotyrosine phosphatases SHP-1 and SHP-2 or the inositol-phosphatase called SHIP. In some aspects, the phosphatases can dephosphorylate kinases associated with ITAM-mediated cell activation, thereby attenuating signaling and effector functions mediated by an activating receptor, such as inhibition or reduction of proliferation, cytokine production or secretion or cytotoxic activity. In some embodiments, an inhibitory receptor includes PD-1, CTLA-4 or TIGIT.
The term “inhibitory receptor binding molecule” or IRBM refers to a protein that specifically binds to an inhibitory receptor.
The term “lymphocyte” as used herein means any of three subtypes of white blood cell in a mammalian immune system. They include natural killer cells (NK cells) (which function in cell-mediated, cytotoxic innate immunity), T cells (for cell-mediated, cytotoxic adaptive immunity), and B cells (for humoral, antibody-driven adaptive immunity). T cells include T helper cells, cytotoxic T-cells, natural killer T-cells, memory T-cells, regulatory T-cells, or gamma delta T-cells. Innate lymphoid cells (ILC) are also included within the definition of lymphocyte.
The term “lymphocyte” as used herein means any of three subtypes of white blood cell in a mammalian immune system. They include natural killer cells (NK cells) (which function in cell-mediated, cytotoxic innate immunity), T cells (for cell-mediated, cytotoxic adaptive immunity), and B cells (for humoral, antibody-driven adaptive immunity). T cells include: T helper cells, cytotoxic T-cells, natural killer T-cells, memory T-cells, regulatory T-cells, or gamma delta T-cells. Innate lymphoid cells (ILC) are also included within the definition of lymphocyte.
The terms “mammal,” “subject,” or “patient” specifically includes reference to at least one of a: human, chimpanzee, rhesus monkey, cynomolgus monkey, dog, cat, mouse, or rat.
The term “membrane protein” as used herein means a protein that, under physiological conditions, is attached directly or indirectly to a lipid bilayer. A lipid bilayer that forms a membrane can be a biological membrane such as a eukaryotic (e.g., mammalian) cell membrane or an artificial (i.e., man-made) membrane such as that found on a liposome. Attachment of a membrane protein to the lipid bilayer can be by way of covalent attachment, or by way of non-covalent interactions such as hydrophobic or electrostatic interactions. A membrane protein can be an integral membrane protein or a peripheral membrane protein. Membrane proteins that are peripheral membrane proteins are non-covalently attached to the lipid bilayer or non-covalently attached to an integral membrane protein. A peripheral membrane protein forms a temporary attachment to the lipid bilayer such that under the range of conditions that are physiological in a mammal, peripheral membrane protein can associate and/or disassociate from the lipid bilayer. In contrast to peripheral membrane proteins, integral membrane proteins form a substantially permanent attachment to the membrane's lipid bilayer such that under the range of conditions that are physiological in a mammal, integral membrane proteins do not disassociate from their attachment to the lipid bilayer. A membrane protein can form an attachment to the membrane by way of one layer of the lipid bilayer (monotopic), or attached by way of both layers of the membrane (polytopic). An integral membrane protein that interacts with only one lipid bilayer is an “integral monotopic protein”. An integral membrane protein that interacts with both lipid bilayers is an “integral polytopic protein” alternatively referred to herein as a “transmembrane protein”.
As used herein, modification is in reference to modification of a sequence of amino acids of a polypeptide or a sequence of nucleotides in a nucleic acid molecule and includes deletions, insertions, and replacements of amino acids and nucleotides, respectively. Methods of modifying a polypeptide are routine to those of skill in the art, such as by using recombinant DNA methodologies.
The terms “modulating” or “modulate” as used herein in the context of an immune response, such as a mammalian immune response, refer to any alteration, such as an increase or decrease, of an existing or potential immune responses that occurs as a result of administration of an immunomodulatory protein or as a result of administration of engineered cells expressing an immunomodulatory protein, such as a secretable immunomodulatory protein of the present invention. Such modulation includes any induction, or alteration in degree or extent, or suppression of immunological activity of an immune cell. Immune cells include B cells, T cells, NK (natural killer) cells, NK T cells, professional antigen-presenting cells (APCs), and non-professional antigen-presenting cells, and inflammatory cells (neutrophils, macrophages, monocytes, eosinophils, and basophils). Modulation includes any change imparted on an existing immune response, a developing immune response, a potential immune response, or the capacity to induce, regulate, influence, or respond to an immune response. Modulation includes any alteration in the expression and/or function of genes, proteins and/or other molecules in immune cells as part of an immune response. Modulation of an immune response or modulation of immunological activity includes, for example, the following: elimination, deletion, or sequestration of immune cells; proliferation, induction, survival or generation of immune cells that can modulate the functional capacity of other cells such as autoreactive lymphocytes, antigen presenting cells, or inflammatory cells; induction of an unresponsive state in immune cells (i.e., anergy); enhancing or suppressing the activity or function of immune cells, including but not limited to altering the pattern of proteins expressed by these cells. Examples include altered production and/or secretion of certain classes of molecules such as cytokines, chemokines, perforins, granzymes, growth factors, transcription factors, kinases, costimulatory molecules, or other cell surface receptors or any combination of these modulatory events. Modulation can be assessed, for example, by an alteration of an immunological activity.
The term, a “multimerization domain” refers to a sequence of amino acids that promotes stable interaction of a polypeptide molecule with one or more additional polypeptide molecules, each containing a complementary multimerization domain (e.g. a first multimerization domain and a second multimerization domain), which can be the same or a different multimerization domain. The interactions between complementary multimerization domains, e.g. interaction between a first multimerication domain and a second multimerization domain, form a stable protein-protein interaction to produce a multimer of the polypeptide molecule with the additional polypeptide molecule. In some cases, the multimerization domain is the same and interacts with itself to form a stable protein-protein interaction between two polypeptide chains. Generally, a polypeptide is joined directly or indirectly to the multimerization domain. Exemplary multimerization domains include the immunoglobulin sequences or portions thereof, leucine zippers, hydrophobic regions, hydrophilic regions, and compatible protein-protein interaction domains. The multimerization domain, for example, can be an immunoglobulin constant region or domain, such as, for example, the Fc domain or portions thereof from IgG, including IgG1, IgG2, IgG3 or IgG4 subtypes, IgA, IgE, IgD and IgM and modified forms thereof.
The term “non-competitive binding” as used herein means the ability of a protein to specifically bind simultaneously to at least two binding partners. In some embodiments, the binding occurs under specific binding conditions. Thus, the protein is able to bind to at least two different binding partners at the same time although the binding interaction need not be for the same duration such that, in some cases, the protein is specifically bound to only one of the binding partners. In some embodiments, the simultaneous binding is such that binding of one binding partner does not substantially inhibit simultaneous binding to a second binding partner. In some embodiments, non-competitive binding means that binding a second binding partner to its binding site on the protein does not displace the binding of a first binding partner to its binding site on the protein. Methods of assessing non-competitive binding are well known in the art such as the method described in Perez de La Lastra et al., Immunology, 1999 April: 96(4): 663-670. In some cases, in non-competitive interactions, the first binding partner specifically binds at an interaction site that does not overlap with the interaction site of the second binding partner such that binding of the second binding partner does not directly interfere with the binding of the first binding partner. Thus, any effect on binding of the binding partner by the binding of the second binding partner is through a mechanism other than direct interference with the binding of the first binding partner. For example, in the context of enzyme-substrate interactions, a non-competitive inhibitor binds to a site other than the active site of the enzyme. Non-competitive binding encompasses uncompetitive binding interactions in which a second binding partner specifically binds at an interaction site that does not overlap with the binding of the first binding partner but binds to the second interaction site only when the first interaction site is occupied by the first binding partner.
The terms “nucleic acid” and “polynucleotide” are used interchangeably to refer to a polymer of nucleic acid residues (e.g., deoxyribonucleotides or ribonucleotides) in either single- or double-stranded form. Unless specifically limited, the terms encompass nucleic acids containing known analogues of natural nucleotides and that have similar binding properties to it and are metabolized in a manner similar to naturally-occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary nucleotide sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues. The term nucleic acid or polynucleotide encompasses cDNA or mRNA encoded by a gene.
The terms “in operable combination,” “in operable order” and “operably linked” as used herein refer to the linkage of nucleic acid sequences in such a manner or orientation that the segments are arranged so that they function in concert for their intended purposes. In some embodiments, the term refers to linkage of nucleic acids to produce a nucleic acid molecule capable of directing the transcription of a given gene and/or to produce a desired protein molecule that is functional. For example, segments of a DNA sequence, e.g. a coding sequence and a regulatory sequence(s), are linked in such a way as to permit gene expression when the appropriate molecules (e.g. transcriptional activator proteins) are bound to the regulatory sequence.
The term “pharmaceutical composition” refers to a composition suitable for pharmaceutical use in a mammalian subject, often a human. A pharmaceutical composition typically comprises an effective amount of an active agent (e.g., an immunomodulatory protein or engineered cells expressing and/or secreting an immunomodulatory protein of the present invention) and a carrier, excipient, or diluent. The carrier, excipient, or diluent is typically a pharmaceutically acceptable carrier, excipient or diluent, respectively.
The terms “polypeptide” and “protein” are used interchangeably herein and refer to a molecular chain of two or more amino acids linked through peptide bonds. The terms do not refer to a specific length of the product. Thus, “peptides,” and “oligopeptides,” are included within the definition of polypeptide. The terms include post-translational modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like. The terms also include molecules in which one or more amino acid analogs or non-canonical or unnatural amino acids are included as can be synthesized, or expressed recombinantly using known protein engineering techniques. In addition, proteins can be derivatized as described herein by well-known organic chemistry techniques.
The term “primary T-cell assay” as used herein refers to an in vitro assay to measure interferon-gamma (“IFN-gamma”) expression. A variety of such primary T-cell assays are known in the art. In some embodiments, the assay used is anti-CD3 coimmobilization assay. In this assay, primary T cells are stimulated by anti-CD3 immobilized with or without additional recombinant proteins. Culture supernatants are harvested at timepoints, usually 24-72 hours. In another embodiment, the assay used is a mixed lymphocyte reaction (MLR). In this assay, primary T cells are simulated with allogenic APC. Culture supernatants are harvested at timepoints, usually 24-72 hours. Human IFN-gamma levels are measured in culture supernatants by standard ELISA techniques. In some cases, commercial kits are available from vendors and the assay can be performed according to manufacturer's recommendation.
The term “purified” as applied to nucleic acids, such as encoding immunomodulatory proteins, or proteins (e.g. immunomodulatory proteins) generally denotes a nucleic acid or polypeptide that is substantially free from other components as determined by analytical techniques well known in the art (e.g., a purified polypeptide or polynucleotide forms a discrete band in an electrophoretic gel, chromatographic eluate, and/or a media subjected to density gradient centrifugation). For example, a nucleic acid or polypeptide that gives rise to essentially one band in an electrophoretic gel is “purified.” A purified nucleic acid or protein is at least about 50% pure, usually at least about 75%, 80%, 85%, 90%, 95%, 96%, 99% or more pure (e.g., percent by weight or on a molar basis).
The term “recombinant” indicates that the material (e.g., a nucleic acid or a polypeptide) has been artificially (i.e., non-naturally) altered by human intervention. The alteration can be performed on the material within, or removed from, its natural environment or state. For example, a “recombinant nucleic acid” is one that is made by recombining nucleic acids, e.g., during cloning, affinity modification, DNA shuffling or other well-known molecular biological procedures. A “recombinant DNA molecule,” is comprised of segments of DNA joined together by means of such molecular biological techniques. The term “recombinant protein” or “recombinant polypeptide” as used herein refers to a protein molecule (e.g., an immunomodulatory protein) which is expressed using a recombinant DNA molecule. A “recombinant host cell” is a cell that contains and/or expresses a recombinant nucleic acid or that is otherwise altered by genetic engineering, such as by introducing into the cell a nucleic acid molecule encoding a recombinant protein, such as a immunomodulatory protein provided herein. Transcriptional control signals in eukaryotes comprise “promoter” and “enhancer” elements. Promoters and enhancers consist of short arrays of DNA sequences that interact specifically with cellular proteins involved in transcription. Promoter and enhancer elements have been isolated from a variety of eukaryotic sources including genes in yeast, insect and mammalian cells and viruses (analogous control elements, i.e., promoters, are also found in prokaryotes). The selection of a particular promoter and enhancer depends on what cell type is to be used to express the protein of interest.
The term “recombinant expression vector” as used herein refers to a DNA molecule containing a desired coding sequence (e.g., encoding an immunomodulatory protein) and appropriate nucleic acid sequences necessary for the expression of an operably linked coding sequence in a particular cell. Nucleic acid sequences necessary for expression in prokaryotes include a promoter, optionally an operator sequence, a ribosome binding site and possibly other sequences. Eukaryotic cells are known to utilize promoters, enhancers, and termination and polyadenylation signals. A secretory signal peptide sequence can also, optionally, be encoded by the recombinant expression vector, operably linked to the coding sequence so that the expressed protein can be secreted by the recombinant host cell, such as for its expression as a secretable protein or for more facile isolation or purification of the immunomodulatory protein from the cell, if desired. The term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. Among the vectors are viral vectors, such as lentiviral vectors.
The term “selectivity” refers to the preference of a subject protein, or polypeptide, for specific binding of one substrate, such as one binding partner, compared to specific binding for another substrate, such as a different binding partner of the subject protein. Selectivity can be reflected as a ratio of the binding activity (e.g. binding affinity) of a subject protein and a first substrate, such as a first binding partner, (e.g., Kd1) and the binding activity (e.g. binding affinity) of the same subject protein with a second binding partner (e.g., Kd2).
The term “sequence identity” as used herein refers to the sequence identity between genes or proteins at the nucleotide or amino acid level, respectively. “Sequence identity” is a measure of identity between proteins at the amino acid level and a measure of identity between nucleic acids at nucleotide level. The protein sequence identity may be determined by comparing the amino acid sequence in a given position in each sequence when the sequences are aligned. Similarly, the nucleic acid sequence identity may be determined by comparing the nucleotide sequence in a given position in each sequence when the sequences are aligned. Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software, FASTA and TFASTA. The BLAST algorithm calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Center for Biotechnology Information (NCBI) website. In some cases, a percent sequence identity can be determined as the percentage of amino acid residues (or nucleotide residues) in a candidate sequence that are identical with the amino acid residues (or nucleotide residues) in a reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
The term “soluble” as used herein in reference to proteins, means that the protein is not a membrane protein. In some cases, a soluble protein contains only an extracellular domain of an IgSF family member or members, or a portion thereof containing an IgSF domain or domains or specific-binding fragments thereof, but does not contain a transmembrane domain. In some cases, solubility of a protein can be improved by linkage or attachment, directly or indirectly via a linker, to an Fc domain, which, in some cases, also can improve the stability and/or half-life of the protein. In some aspects, a soluble protein is an Fc fusion protein.
The term “specifically binds” as used herein means the ability of a protein, under specific binding conditions, to bind to a target protein such that its affinity or avidity is at least 10 times as great, but optionally 50, 100, 250 or 500 times as great, or even at least 1000 times as great as the average affinity or avidity of the same protein to a collection of random peptides or polypeptides of sufficient statistical size. A specifically binding protein need not bind exclusively to a single target molecule but may specifically bind to more than one target molecule. In some cases, a specifically binding protein may bind to a protein that has similarity in structural conformation with the target protein (e.g., paralogs or orthologs). Those of skill will recognize that specific binding to a molecule having the same function in a different species of animal (i.e., ortholog) or to a molecule having a substantially similar epitope as the target molecule (e.g., paralog) is possible and does not detract from the specificity of binding which is determined relative to a statistically valid collection of unique non-targets (e.g., random polypeptides). Thus, an immunomodulatory protein of the invention, or an ARBM or IRBM thereof, may specifically bind to more than one distinct species of target molecule due to cross-reactivity. Solid-phase ELISA immunoassays, ForteBio Octet or Biacore measurements can be used to determine specific binding between two proteins. Generally, interactions between two binding proteins have dissociation constants (Kd) less than about 1×10−5 M, and often as low as about 1×10−12 M. In certain aspects of the present disclosure, interactions between two binding proteins have dissociation constants of less than about 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M, or 1×10−11 M or less.
The term “specific binding fragment” or “fragment” as used herein in reference to a protein means a polypeptide that is shorter than a full-length protein or a specific domain or region thereof and that specifically binds in vitro and/or in vivo to a binding partner of the full-length protein or of the specific domain or region. In some cases, a specific binding fragment is in reference to a fragment of a full-length IgSF family member or a full-length IgSF domain thereof (e.g. IgV or IgC), but that still binds to a binding partner of the IgSF family member or of an IgSF domain of an IgSF family member. In some embodiments, the specific binding fragment is at least 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% the sequence length of the full-length sequence or of a domain or region of an IgSF family member. In some embodiments, the specific binding fragment can have an amino acid length of at least 50 amino acids, such as at least 60, 70, 80, 90, 100, or 110 amino acids. The specific binding fragment can be altered in sequence to form an affinity modified IgSF domain.
As used herein, a “subject” is a mammal, such as a human or other animal, and typically is human. The subject can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects.
The terms “surface expresses” or “surface expression” in reference to a mammalian cell expressing a polypeptide means that the polypeptide is expressed as a membrane protein. In some embodiments, the membrane protein is a transmembrane protein.
As used herein, “synthetic,” with reference to, for example, a synthetic nucleic acid molecule or a synthetic gene or a synthetic peptide refers to a nucleic acid molecule or polypeptide molecule that is produced by recombinant methods and/or by chemical synthesis methods.
The term “trans” with reference to binding to cell surface molecules refers to binding to two different cell surface molecules, each of which is present on the surface of a different cell. In some embodiments, trans means that with respect to two different cell surface molecules, the first is exclusively present on one of the two mammalian cells forming the IS and the second is present exclusively on the second of the two mammalian cells forming the IS.
The term “transmembrane protein” as used herein means a membrane protein that substantially or completely spans a lipid bilayer such as those lipid bilayers found in a biological membrane such as a mammalian cell, or in an artificial construct such as a liposome. The transmembrane protein comprises a transmembrane domain (“transmembrane domain”) by which it is integrated into the lipid bilayer and by which the integration is thermodynamically stable under physiological conditions. Transmembrane domains are generally predictable from their amino acid sequence via any number of commercially available bioinformatics software applications on the basis of their elevated hydrophobicity relative to regions of the protein that interact with aqueous environments (e.g., cytosol, extracellular fluid). A transmembrane domain is often a hydrophobic alpha helix that spans the membrane. A transmembrane protein can pass through the both layers of the lipid bilayer once or multiple times.
The terms “treating,” “treatment,” or “therapy” of a disease or disorder as used herein mean slowing, stopping or reversing the disease or disorders progression, as evidenced by decreasing, cessation or elimination of either clinical or diagnostic symptoms, by administration of an immunomodulatory protein or engineered cells of the present invention either alone or in combination with another compound as described herein. “Treating,” “treatment,” or “therapy” also means a decrease in the severity of symptoms in an acute or chronic disease or disorder or a decrease in the relapse rate as for example in the case of a relapsing or remitting autoimmune disease course or a decrease in inflammation in the case of an inflammatory aspect of an autoimmune disease. “Preventing,” “prophylaxis,” or “prevention” of a disease or disorder as used in the context of this invention refers to the administration of an immunomodulatory protein or engineered cells expressing an immunomodulatory protein of the present invention, either alone or in combination with another compound, to prevent the occurrence or onset of a disease or disorder or some or all of the symptoms of a disease or disorder or to lessen the likelihood of the onset of a disease or disorder.
The term “variant” (also “modified” or mutant,” which can be used interchangeably) as used in reference to a variant protein or polypeptide, such as a variant of an IgSF family member or IgSF domain thereof, means a protein, such as a mammalian (e.g., human or murine) protein created by human intervention. The variant is a polypeptide having an altered or modified amino acid sequence, such as by one or more amino acid substitutions, deletions, additions or combinations thereof, relative to an unmodified or wild-type protein or to a domain (e.g. IgSF domain, such as an IgV domain) thereof. A variant polypeptide can contain 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more amino acid differences, such as amino acid substitutions. A variant polypeptide generally exhibits at least 50%, 60%, 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to a corresponding form of a wild-type or unmodified protein (e.g. an IgSF family member), such as a mature sequence thereof (lacking the signal sequence) or a portion thereof containing the extracellular domain or an IgSF domain thereof. Non-naturally occurring amino acids as well as naturally occurring amino acids are included within the scope of permissible substitutions or additions. A variant protein is not limited to any particular method of making and includes, for example, chemical synthesis, recombinant DNA techniques, or combinations thereof. A variant protein, such as a variant IgSF domain, of the invention specifically binds to at least one or more binding partners. In some embodiments, the altered amino acid sequence results in an altered (i.e., increased or decreased) binding activity, such as binding affinity or avidity, to the one or more binding partners.
The term “wild-type” or “natural” or “native,” which are used interchangeably, as used herein is used in connection with biological materials such as nucleic acid molecules, proteins, IgSF members, host cells, and the like, refers to those which are found in nature and not modified by human intervention
Provided herein are multi-domain immunomodulatory proteins that contain one or more inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor and one or more activating receptor binding molecule (ARBM) that binds to an activating receptor or a ligand of an activating receptor. In some embodiments, the activating receptor comprises an immunoreceptor tyrosine-based activation motif (ITAM) or interacts with an adaptor protein involved in signal transduction pathways in an immune cell, such as a T cell, to transduce activation signals. In some embodiments, the inhibitory receptor comprises an immunoreceptor tyrosine-based inhibitory motif (ITIM). In some embodiments, the inhibitory receptor and the activating receptor are expressed on the same immune cell. In some embodiments, the activating receptor and inhibitory receptor are both expressed on a T cell.
In some embodiments, the provided multi-domain immunomodulatory proteins can be generated in a cis binding strategy to target an inhibitory receptor and activating receptor on the same immune cell, such as the same T cell, which, in some cases, proximalize or cluster the inhibitory receptor and the activating receptor on the surface of the same cell. In such embodiments, the IRBM binds to the inhibitory receptor and the ARBM binds to the activating receptor.
In other embodiments, the provided multi-domain immunomodulatory proteins can be generated in a trans binding strategy to target an inhibitory receptor and a ligand of an activating receptor, each present on different immune cells in an immune synapse. For example, in some embodiments, the IRBM binds to the inhibitory receptor on a T cell and the ARBM binds to a ligand of the activating receptor on an antigen-presenting cell (APC). In the trans strategy, localization of the ligand on the APC during immune synapse formation may be sufficient for signaling by its cognate activating receptor, such that the presence of the immunomodulatory protein could antagonize such as a signal and instead present an inhibitory ligand to recruit the inhibitory receptor to the immune synapse.
In some embodiments, the ARBM can be any binding molecule that binds to an activating receptor or a ligand thereof. In some embodiments, the IRBM can be any binding molecule that binds to an inhibitory receptor. In some embodiments, the one or more IRBM and/or ARBM independently include an antibody or an antigen-binding antibody fragment. In some aspects, the IRBM and/or ARBM can be a human antibody and/or an antibody that binds a human protein.
In some embodiments, at least one of the IRBM or ARBM is not an antibody or antigen-binding fragment. In some embodiments, at least one of the IRBM or ARBM is or contains a non-antibody immunoglobulin superfamily (IgSF) domain (IgD) of an IgSF member, or is a specific binding fragment of such an IgSF domain. In some embodiments, the at least one of the IRBM or ARBM can be a variant IgD (hereinafter called “vIgD”) in which is contained one or more amino acid modifications (e.g. substitutions) in an IgD. In some aspects, the vIgD is an affinity-modified domain that exhibits increased binding activity, such as increased binding affinity, for the activating receptor (or ligand of the activating receptor) or inhibitory receptor compared to the binding activity of the unmodified or wild-type IgD for the same molecule. In some embodiment, both the IRBM and ARBM contain one or more IgD or vIgD of an IgSF member, in which, typically, the IgD or vIgD of the IRBM and ARBM are from, or derived from, a different IgSF member.
In some embodiments, the multi-domain immunomodulatory protein provided herein are soluble proteins and/or do not contain a portion that includes a transmembrane domain. Those of skill will appreciate that cell surface proteins, including proteins of the IgSF, typically have an intracellular domain, a transmembrane domain, and extracellular domain (ECD), and that a soluble form of such proteins can be made using the extracellular domain or an immunologically active subsequence thereof. Thus, in some embodiments, the ARBM or IRBM lacks a transmembrane domain or a portion of the transmembrane domain of an IgSF member. In some embodiments, the ARBM or IRBM lacks the intracellular (cytoplasmic) domain or a portion of the intracellular domain of an IgSF member. In some embodiments, the ARBM or IRBM only contains the ECD domain or a portion thereof containing an IgSF domain, such an IgV domain, or specific binding fragments thereof. In some cases, the ARBM and IRBM independently can include the extracellular domain of an IgSF family member or an IgSF domain or specific binding fragment thereof of an IgSF family member. In some aspects, the IgSF domain is an IgV domain or an IgC domain. In some aspects, the IgSF domain is an IgV domain or an IgC domain. In some aspects, the IRBM and/or ARBM is an IgSF domain of a IgSF family member that is a human protein and/or binds a human protein.
In some embodiments, the ARBM can bind to an activating receptor with at least a certain binding activity, such as binding affinity, as measured by any of a number of known methods. In some embodiments, the IRBM can bind to an inhibitory receptor with at least a certain binding activity, such as binding affinity, as measured by any of a number of known methods. In some embodiments, the affinity is represented by an equilibrium dissociation constant (KD) or is represented by EC50. A variety of assays are known for assessing binding activity, including binding affinity, and/or determining whether a binding molecule (e.g., an ARBM or IRBM) specifically binds to a particular binding partner. In some embodiments, a BIAcore® instrument can be used to determine the binding kinetics and constants of a complex between two proteins using surface plasmon resonance (SPR) analysis (see, e.g., Scatchard et al., Ann. N.Y. Acad. Sci. 51:660, 1949; Wilson, Science 295:2103, 2002; Wolff et al., Cancer Res. 53:2560, 1993; and U.S. Pat. Nos. 5,283,173, 5,468,614, or the equivalent). Other suitable assays for measuring the binding of one protein to another include, for example, immunoassays such as enzyme linked immunosorbent assays (ELISA) and radioimmunoassays (RIA), or determination of binding by monitoring the change in the spectroscopic or optical properties of the proteins through fluorescence, UV absorption, circular dichroism, or nuclear magnetic resonance (NMR). Other exemplary assays include, but are not limited to, Western blot, ELISA, analytical ultracentrifugation, spectroscopy, flow cytometry, sequencing and other methods for detection of expressed nucleic acids or binding of proteins.
In some embodiments, the ARBM and IRBM independently exhibit a binding affinity for a binding partner with a KD (i.e., an equilibrium dissociation constant of a particular binding interaction with units of M; equal to the ratio of the off-rate [koff or kd] to the on-rate [kon or ka] for this association reaction, assuming bimolecular interaction) of equal to or less than 10−5 M. For example, the equilibrium dissociation constant KD ranges from 10−6 M to 10−12 M, such as 10−7 M to 10−11 M, 10−8 M to 10−10 M, or 10−9 M to 10−10 M. The on-rate (association rate constant; kon or ka; units of 1/Ms) and the off-rate (dissociation rate constant; koff or kd; units of 1/s) can be determined using any of the assay methods known in the art, for example, surface plasmon resonance (SPR).
In some embodiments, the IRBM exhibits a binding affinity for an inhibitory receptor that is from or from about 0.001 nM to 1000 nM, such as from or from about 0.01 nM to about 500 nM, from or from about 0.01 nM to about 400 nM, from or from about 0.01 nM to about 100 nM, from or from about 0.01 nM to about 50 nM, from or from about 0.01 nM to about 10 nM, from or from about 0.01 nM to about 1 nM, from or from about 0.01 nM to about 0.1 nM, is from or from about 0.1 nM to about 500 nM, from or from about 0.1 nM to about 400 nM, from or from about 0.1 nM to about 100 nM, from or from about 0.1 nM to about 50 nM, from or from about 0.1 nM to about 10 nM, from or from about 0.1 nM to about 1 nM, from or from about 0.5 nM to about 200 nM, from or from about 1 nM to about 500 nM, from or from about 1 nM to about 100 nM, from or from about 1 nM to about 50 nM, from or from about 1 nM to about 10 nM, from or from about 2 nM to about 50 nM, from or from about 10 nM to about 500 nM, from or from about 10 nM to about 100 nM, from or from about 10 nM to about 50 nM, from or from about 50 nM to about 500 nM, from or from about 50 nM to about 100 nM or from or from about 100 nM to about 500 nM. In certain embodiments, the binding affinity of the IRBM for the inhibitory receptor is at or less than or about 400 nM, 300 nM, 200 nM, 100 nM, 50 nM, 40 nM, 30 nM, 25 nM, 20 nM, 19 nM, 18 nM, 17 nM, 16 nM, 15 nM, 14 nM, 13 nM, 12 nM, 11 nM, 10 nM, 9 nM, 8 nM, 7 nM, 6 nM, 5 nM, 4 nM, 3 nM, 2 nM, or 1 nM or less.
In some embodiments, the ARBM exhibits a binding affinity for an activating receptor or a ligand of an activating receptor that is from or from about 0.001 nM to about 1000 nM, such as from or from about 0.01 nM to about 500 nM, from or from about 0.01 nM to about 400 nM, from or from about 0.01 nM to about 100 nM, from or from about 0.01 nM to about 50 nM, from or from about 0.01 nM to about 10 nM, from or from about 0.01 nM to about 1 nM, from or from about 0.01 nM to about 0.1 nM, is from or from about 0.1 nM to about 500 nM, from or from about 0.1 nM to about 400 nM, from or from about 0.1 nM to about 100 nM, from or from about 0.1 nM to about 50 nM, from or from about 0.1 nM to about 10 nM, from or from about 0.1 nM to about 1 nM, from or from about 0.5 nM to about 200 nM, from or from about 1 nM to about 500 nM, from or from about 1 nM to about 100 nM, from or from about 1 nM to about 50 nM, from or from about 1 nM to about 10 nM, from or from about 2 nM to about 50 nM, from or from about 10 nM to about 500 nM, from or from about 10 nM to about 100 nM, from or from about 10 nM to about 50 nM, from or from about 50 nM to about 500 nM, from or from about 50 nM to about 100 nM or from or from about 100 nM to about 500 nM. In certain embodiments, the binding affinity of the ARBM for the activating receptor or a ligand of the activating receptor is at or less than or about 400 nM, 300 nM, 200 nM, 100 nM, 50 nM, 40 nM, 30 nM, 25 nM, 20 nM, 19 nM, 18 nM, 17 nM, 16 nM, 15 nM, 14 nM, 13 nM, 12 nM, 11 nM, 10 nM, 9 nM, 8 nM, 7 nM, 6 nM, 5 nM, 4 nM, 3 nM, 2 nM, or 1 nM or less.
In some embodiments, the IRBM exhibits higher affinity for the inhibitory receptor than the ARBM exhibits for the activating receptor or a ligand of the activating receptor. For example, in some embodiments, the IRBM exhibits 1.2-fold, 1.5-fold, 2.0-fold, 2.5-fold, 3.0-fold, 4.0-fold, 5.0-fold, 6.0-fold, 7.0-fold, 8.0-fold, 9.0-fold, 10.0 fold or higher affinity for the inhibitory receptor than the ARBM exhibits for the activating receptor or a ligand of the activating receptor.
In some embodiments, the provided multi-domain immunomodulatory proteins can include the ARBM and IRBM in various configurations or formats, including formats with one or more further moieties. In some embodiments, the provided immunomodulatory proteins include polypeptides in which the one or more IRBM is N-terminal to the ARBM. In some embodiments, the one or more IRBM is C-terminal to the ARBM. The one or more ARBM and the one or more IRBM can be linked directly or indirectly, via a linker. In some embodiments, the immunomodulatory proteins can be formatted as multimeric molecules via fusion with a multimerization domain, such as an Fc protein. In some embodiments, the multi-domain immunomodulatory proteins can be formatted as multimeric molecules, e.g., dimeric, trimer, tetrameric, or pentameric molecules. In some embodiments, the immunomodulatory proteins are formatted as a monomeric molecules containing single polypeptide fusions of the one or more ARBM and the one or more IRBM. In some aspects, the configurations can be chosen to effect spatial proximalization of ITIM bearing inhibitory receptors with activating receptors on immune cells, such as T cells, to make possible attenuation of T cell activation and/or tolerance induction.
In the subsections below, exemplary ARBM and IRBM components of the provided multi-domain immunomodulatory protein are described, as are exemplary formats for such immunomodulatory proteins.
A. Inhibitory Receptor Binding Molecule (IRBM)
In some embodiments, the provided immunomodulatory polypeptides contain an IRBM that binds to an inhibitory receptor. In some aspects, the inhibitory receptor includes an immunoreceptor tyrosine-based inhibitory motif (ITIM). In some embodiments, the inhibitory receptor target of the IRBM is CTLA-4, PD-1, or TIGIT, including any mammalian orthologs thereof. In some embodiments, the inhibitory receptor target is a human CTLA-4, human PD-1 or human TIGIT. In some embodiments, the inhibitory receptor is expressed on a T cell, such as a human T cell.
In some embodiments, the IRBM is an antibody or antigen-binding fragment that binds an inhibitory receptor. In some embodiments, the IRBM is an antibody or antigen-binding fragment that binds CTLA-4, PD-1 or TIGIT, such as a human CTLA-4, human PD-1 or human TIGIT.
In some embodiments, the IRBM is or contains a binding partner of an inhibitory receptor. For example, in some aspects, the IRBM is or contains an IgD of an IgSF family member that binds to an inhibitory receptor, such as a PD-1, TIGIT or CTLA-4 inhibitory receptor, or is a specific fragment or vIgD thereof that binds to the inhibitory receptor. Exemplary IgSF family members that are binding partners of or that bind to a PD-1 inhibitory receptor include, for example, PD-L1 and PD-L2, such as human PD-L1 or human PD-L2. Exemplary IgSF family members that are binding partners of or that bind to a TIGIT inhibitory receptor include, for example, CD155 or CD112, such as human CD155 or human CD112. In some embodiments, the IgSF binding partner of an inhibitory receptor is a molecule set forth in Table 1. In some examples, the IRBM is or contains an IgD of a wild-type PD-L1 or PD-L2 or is or contains a vIgD thereof, wherein the IRBM specifically binds to PD-1. In other examples, the IRBM is or contains an IgD of CD155 or CD112 or is or contains a vIgD thereof, wherein the IRBM specifically binds to TIGIT.
The first column of Table 1 provides the name and, optionally, the name of some possible synonyms for that particular domain. The second column provides the protein identifier of the UniProtKB database, a publicly available database accessible via the internet at uniprot.org. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases include the UniProt Knowledgebase (UniProtKB). UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR) and supported mainly by a grant from the U.S. National Institutes of Health (NIH). The third column provides the region where the indicated IgSF domain is located. The region is specified as a range where the domain is inclusive of the residues defining the range. Column 3 also indicates the domain class for the specified region. Column 4 provides the region where the indicated additional domains are located (signal peptide, S; extracellular domain, E; transmembrane domain, T; cytoplasmic domain, C). Column 5 indicates for some of the listed IgSF members, some of its cognate cell surface binding partners. It is understood that reference to amino acids, including to a specific sequence set forth as a SEQ ID NO used to describe domain organization, such as of an IgSF domain, are for illustrative purposes and are not meant to limit the scope of the embodiments provided. It is understood that polypeptides and the description of domains thereof are theoretically derived based on homology analysis and alignments with similar molecules. Thus, the exact locus can vary, and is not necessarily the same for each protein. Hence, the specific IgSF domain, such as specific IgV domain or IgC domain, can be several amino acids (such as one, two, three, four, five, six or more amino acids) longer or shorter.
In some embodiments, the IRBM is or contains a wild-type or unmodified IgD of a binding partner of an inhibitory receptor, such as a sequence that is or contains an ECD or an IgD domain or domains of a native binding partner of an inhibitory receptor or an ortholog thereof. In some embodiments, the IRBM is or comprises the extracellular domain (ECD), or a portion thereof containing one or more IgSF domains, of an IgSF member set forth in Table 1, e.g. human PD-L1, human PD-L2, human CD155 or human CD112. In some embodiments, the extracellular domain comprises an IgV domain or domains and, in some cases, an IgC (e.g. IgC1 and/or IgC2) domain or domains. In some embodiments, the IRBM is less than the full length sequence of the IgSF binding partner of the inhibitory receptor. For example, in some aspects, the IRBM is or only contains the extracellular domain (ECD) or specific binding fragment thereof of the binding partner. In some embodiments, the IRBM is or only contains the IgV domain or the IgC domain or specific binding fragment of the IgV domain or the IgC domain, or combinations thereof. In some embodiments, the IRBM can be an IgV only, the combination of the IgV and IgC, including the entire extracellular domain (ECD), or any combination of Ig domains. In some embodiments, the IRBM consists or consists essentially of the ECD or an IgD domain or domain thereof of a binding partner of an inhibitory receptor, such as consists or consists essentially of the ECD, IgV or IgC domain or domains. In some embodiments, the sequence of the IRBM containing an IgD of a binding partner of an inhibitory receptor is a mammalian sequence that includes, but is not limited to, human, mouse, cynomolgus monkey, or rat. In some embodiments, the sequence of IRBM containing an IgD is human. Table 1 provides exemplary residues that correspond to ECD, IgV, or IgC regions of various IgSF domains of binding partners of exemplary inhibitory receptors.
In some embodiments, the IRBM is or contains a vIgD that contains one or more amino acids modifications, such as one or more substitutions (alternatively, “mutations” or “replacements”), deletions or additions, in an IgD relative to a wild-type or unmodified IgD of a binding partner of the inhibitory receptor. In some aspects, the vIgD contains up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications, such as amino acid substitutions, deletions or additions in an IgD domain of an IgSF binding partner of an inhibitory receptor, e.g. in an IgD domain of a binding partner set forth in Table 1. The modifications (e.g., substitutions) can be in the IgV domain or the IgC domain. In some embodiments, the vIgD has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., substitutions) in the IgV domain or specific binding fragment thereof. In some embodiments, the vIgD has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., substitutions) in the IgC domain or specific binding fragment thereof. In some embodiments, the vIgD has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the wild-type or unmodified IgD or specific binding fragment thereof.
In some embodiments, the IRBM is a variant of a binding partner of an inhibitory receptor (e.g. variant of a molecule set forth in Table 1, e.g. human PD-L1, human PD-L2, human CD155 or human CD112), in which the IRBM is or comprises an ECD, or portion thereof, containing one or more vIgD of an IgSF binding partner of an inhibitory receptor. In some embodiments, the IRBM can comprise an IgV domain or an IgC domain or domains, or a specific binding fragment of the IgV domain or a specific binding fragment of the IgC domain or domains in which one or more of the IgSF domains (IgV or IgC) contains the one or more amino acid modifications (e.g. substitutions). In some embodiments, the IRBM can comprise an IgV domain and an IgC domain or domains, or a specific binding fragment of the IgV domain and a specific binding fragment of the IgC domain or domains, in which at least one of the IgV or IgC domain contains the amino acid modifications (e.g. substitutions). In some embodiments, the IRBM consists or consists essentially of the ECD containing a vIgD (e.g. IgV and/or IgC). In some embodiments, the IRBM contains only, such as consists or consists essentially of, an IgV domain or a specific binding fragment of the IgV domain, in which the one or more amino acid modifications (e.g. substitutions) are located in the IgV domain or specific binding fragment of the IgV domain. In some embodiments, the IRBM contains only, such as consists or consists essentially of, an IgC domain or a specific binding fragment of the IgC domain, in which the one or more amino acid modifications (e.g. substitutions) are located in an IgC domain or specific binding fragment of an IgC domain.
In some embodiments, the one or more amino acid modifications alter, such as increase, the binding activity, e.g. binding affinity, of the extracellular domain of the binding partner or an IgD domain thereof (e.g. IgV) for its cognate inhibitory receptor. In some embodiments, by virtue of the altered binding activity, such as binding affinity, the vIgD domain is an affinity-modified IgSF domain. Typically, the affinity-modified IgSF domain used in or as the IRBM is a human or murine affinity modified IgSF domain.
In some embodiments, an IRBM containing a vIgD has a binding activity, such as binding affinity, for the inhibitory receptor that is altered, e.g. increased, from that of an IRBM containing a wild-type or unmodified IgD sequence as determined by, for example, solid-phase ELISA immunoassays, flow cytometry or surface plasmon resonance (Biacore) assays. In some embodiments, the vIgD results in an increased binding activity, such as binding affinity, for the inhibitory receptor, relative to a wild-type or unmodified IgD. In some embodiments, the increase in binding activity, such as binding affinity, for the inhibitory receptor is at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 40%, 50%, 60%, 70%, 90%, 100%, 200% or more. In some embodiments, the increase in binding activity, such as binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions). In some embodiments, the equilibrium dissociation constant (Kd) of the IRBM to the inhibitory receptor can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less.
The use of the term “modification”, such as “substitution” does not imply that the present embodiments are limited to a particular method of making the immunomodulatory proteins. An IRBM that is or contains IgD or vIgDs can be made, for example, by de novo peptide synthesis and thus does not necessarily require a modification, such as a “substitution” in the sense of altering a codon to encode for the modification, e.g. substitution. This principle also extends to the terms “addition” and “deletion” of an amino acid residue which likewise do not imply a particular method of making. The means by which the vIgDs are designed or created is not limited to any particular method. In some embodiments, however, a wild-type or unmodified IgD encoding nucleic acid is mutagenized from wild-type or unmodified IgD genetic material and screened for desired specific binding activity, such as binding affinity, and/or alteration of IFN-gamma expression or other functional activity. In some embodiments, a vIgD is synthesized de novo utilizing protein or nucleic acid sequences available at any number of publicly available databases and then subsequently screened. The National Center for Biotechnology Information provides such information and its website is publicly accessible via the internet as is the UniProtKB database.
In some embodiments, the IRBM has (i) the sequence of amino acids set forth in SEQ ID NO: 3, 4, 20, 21 or a mature form thereof lacking the signal sequence, (ii) a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3, 4, 20 or 21 or the mature form thereof, or (iii) a portion of (i) or (ii) containing the extracellular domain or an IgV domain or IgC domain or specific binding fragments thereof. In some embodiments, the IRBM has (i) the sequence of amino acids (i) set forth in SEQ ID NO: 208, 209, 383 or 384, (ii) a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 208, 209, 383 or 384; or (iii) a portion of (i) or (ii) containing the extracellular domain or an IgV domain or IgC domain or specific binding fragment thereof.
In some embodiments, the IRBM is or comprises an extracellular domain or a portion thereof of an IgSF member that is a binding partner of an inhibitory receptor (e.g. Table 1). In some embodiments, the IRBM has or comprises the amino acid sequence set forth in SEQ ID NO: 30, 31, 47, 48, or an ortholog thereof. In some cases, the IRBM has or comprises (i) the sequence of amino acids set forth in SEQ ID NO: 30, 31, 47, 48, (ii) a sequence of amino acids that has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 30, 31, 47, 48, or (iii) is a specific binding fragment of the sequence of (i) or (ii) comprising an IgV domain or an IgC domain.
In some embodiments, the IRBM is or comprises an IgV domain or an IgC domain or domains, or a specific binding fragment thereof. In some embodiments, the IRBM has or comprises the amino acid sequence set forth in SEQ ID NO: 55, 309, 310, 353, 666, 761, 1203, 1263, or an ortholog thereof. For example, the IRBM has or comprises (i) the sequence of amino acids set forth in SEQ ID NO: 55, 309, 310, 353, 666, 761, 1203 or 1263, (ii) a sequence of amino acids that has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 55, 309, 310, 353, 666, 761, 1203 or 1263, or (iii) a specific binding fragment of the sequence of (i) or (ii).
1. PD-1 Binding Molecule
Provided are immunomodulatory proteins containing an IRBM that is or contains a binding molecule that binds to PD-1, such as to human PD-1. Programmed death 1 (PD-1) receptor or PD-1 is expressed on NK cells and T cells, including CD4+ and CD8+ T cells, whereby engagement of PD-1 can inhibit activation cell activation, proliferation, and/or expansion. In some embodiments, the IRBM of the immunomodulatory protein binds to the ectodomain of PD-1. In some embodiments, the IRBM binds to PD-1 on the surface of a cell, such as on the surface of a T cell.
In some embodiments, the provided immunomodulatory protein contains an IRBM that is or contains an antibody that binds PD-1 or is an antigen-binding antibody fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding antibody fragment binds human PD-1. For example, in some embodiments, the antibody is nivolumab, pembrolizumab, pidilizumab or BMS-936559 or an antigen binding fragment containing a VH chain region and/or VL chain region of nivolumab, pembrolizumab, pidilizumab or BMS-936559. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of nivolumab, pembrolizumab, pidilizumab or BMS-936559.
In some embodiments, the IRBM is or contains one or more IgD (e.g. IgV or IgC) or a specific binding fragment thereof, such as an unmodified or wild-type IgD or a vIgD or a specific binding fragment thereof, of an IgSF family member that binds PD-1. In some embodiments, the PD-1 is human PD-1. PD-1 is the T-cell costimulatory receptor for the ligands PD-L1 (also known as cluster of differentiation 274, CD274. B7 homolog 1 or B7-H1) and PD-L2 (also known as PDCD1L2, PDCD1LG2, cluster of differentiation 273, CD273. or B7-DC). PD-L1 and PD-L2 are normally expressed on the surface of T cells, B cells, and myeloid cells. PD-L1 and PD-L2 are negative regulators of immune activation and are capable of down-modulating the immune response via interactions with PD-1.
In some embodiment, the IRBM is or contains one or more IgD (e.g. IgV or IgC) that is an IgD of PD-L1 or PD-L2 polypeptide, such as a wild-type PD-L1 or PD-L2, e.g. a human PD-L1 or human PD-L2. In some aspects, the IRBM contains one or more IgD (e.g. IgV or IgC) that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified PD-L1 or PD-L2, which, in some aspects, result in increased binding of the IRBM to PD-1. Exemplary IgDs or vIgDs of PD-L1 or PD-L2 binding partners for inclusion as an IRBM in the provided immunomodulatory proteins are described. In some embodiments, the IRBM is or contains a vIgD polypeptide that exhibit increased binding activity, such as binding affinity, for PD-1 compared to a corresponding wild-type or unmodified IgD.
a. PD-L1 IgD or vIgD
Provided herein are immunomodulatory proteins containing an IRBM that is or contains one or more IgD, such as an unmodified or wild-type IgD or a vIgD, of PD-L1. In some embodiments, the IRBM is or contains one or more IgD domain of a wild-type or unmodified PD-L1, such as a mammalian PD-L1, e.g. a human PD-L1. In some embodiments, the IRBM is not the full length sequence of the PD-L1. In some aspects, the IRBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of PD-L1. In some embodiments, the IRBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the IRBM is or contains the ECD sequence set forth in SEQ ID NO:30 or 1728 or is a specific binding fragment thereof. In some embodiments, the IRBM is or contains the IgV sequence set forth in SEQ ID NO: 309 (containing residues 1-114 of SEQ ID NO:30) or set forth in SEQ ID NO:55, or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an IRBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified PD-L1. In some embodiments, modifications provided herein can be in an IRBM containing an unmodified IgD set forth in SEQ ID NO:30, 55, 309 or 1728 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 30, 55, 309 or 1728. In some embodiments, an IRBM containing a vIgD of PD-L1 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 30, 1728, 55 or 309.
In some embodiments, the vIgD is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for PD-1 relative to the binding activity of the wild-type or unmodified IgD for PD-1. In some embodiments, the increase in binding activity, e.g. binding affinity, for PD-1 is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions). In some embodiments, the equilibrium dissociation constant (Kd) of the IRBM to PD-1 can be less than 1×10−5 M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12M or less.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a PD-L1 ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:30 or 1728 or, where applicable, the unmodified IgV sequence set forth in SEQ ID NO: 309 (containing residues 1-114, respectively, of SEQ ID NO:30). It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs: 30, 309 or 1728. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the IRBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified PD-L1. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of PD-L1 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of PD-L1 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of PD-L1 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of PD-L1 or a specific binding fragment thereof and in an IgC domain or domains of PD-L1 or a specific binding fragment thereof.
In some embodiments, the IRBM is or contains a vIgD that has one or more amino acid modifications, e.g. substitutions, in an unmodified IgD of PD-L1 or a specific binding fragment thereof corresponding to position(s) 6, 10, 11, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 33, 35, 36, 40, 41, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 60, 64, 65, 68, 71, 72, 73, 74, 75, 78, 79, 83, 85, 89, 90, 93, 97, 98, 99, 101, 102, 103, 104, 106, 110, 111, 112, 113, 117, 119, 120, 121, 124, 129, 130, 131, 134, 137, 138, 144, 148, 149, 150, 155, 158, 160, 163, 165, 167, 170, 171, 173, 175, 176, 177, 179, 180, 183, 185, 188, 189, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 206, 207, 213, or 221, with reference to positions set forth in SEQ ID NO: 30 or 1728. In some embodiments, a polypeptide containing the vIgD exhibits altered, such as increased, binding activity, e.g. binding affinity, to PD-1 compared to a polypeptide containing the wild-type or unmodified PD-L1 IgD.
In some embodiments, the IRBM is or contains a vIgD of PD-L1 that has one or more amino acid modification selected from P6S, Y10F, V11A, V11E, Y14S, G15A, S16G, N17D, M18I, M18T, M18V, T19A, T19I, I20L, C22R, K23E, K23N, K23R, E26A, E27D, E27G, K28E, K28I, K28N, K28R, A33D, L35P, I36S, I36T, E40G, M41K, M41V, D43G, D43V, K44E, N45D, N45I, N45T, I46V, I47T, F49S, V50A, H51N, H51R, H51Y, G52R, G52V, E53G, E53V, E54G, D55G, D55N, D55S, D55V, L56Q, K57E, K57R, V58A, V58D, H60R, R64S, Q65L, R68L, K71E, D72G, Q73R, L74P, S75P, N78I, N78S, A79T, I83T, D85E, Q89R, D90G, V93E, M97I, M97K, M97L, I98L, I98T, I98V, S99G, G101D, G101G-ins (G101GG), G102D, A103V, D104G, K106E, K106R, V110M, K111E, K111T, V112A, N113Y, N117S, 1119T, N120S, Q121L, L124S, V129A, V129D, T130A, S131F, E134G, C137R, Q138R, K144E, K144Q, I148V, W149R, T150A, Q155H, S158G, K160M, T163I, K163N, N165Y, K167R, K167T, E170G, K171R, F173I, F173L, K173Y, V175A, S177C, L179P, R180S, T183A, T183I, T185A, I188V, F189L, F189S, T192S, F193S, R194G, R194W, R195G, R195S, R195T, L196S, D197G, P198S, P198T, E199G, E200K, E200N, N201D, N201Y, H202Q, T203A, A204T, L206F, V207A, L213P, OR T221L or a conservative amino acid substitution thereof.
In some embodiments, the IRBM is or contains a vIgD that has two or more amino acid modifications selected from P6S, Y10F, V11A, V11E, Y14S, G15A, S16G, N17D, M18I, M18T, M18V, T19A, T19I, I20L, C22R, K23E, K23N, K23R, E26A, E27D, E27G, K28E, K28I, K28N, K28R, A33D, L35P, I36S, I36T, E40G, M41K, M41V, D43G, D43V, K44E, N45D, N45I, N45T, I46V, I47T, F49S, V50A, H51N, H51R, H51Y, G52R, G52V, E53G, E53V, E54G, D55G, D55N, D55S, D55V, L56Q, K57E, K57R, V58A, V58D, H60R, R64S, Q65L, R68L, K71E, D72G, Q73R, L74P, S75P, N78I, N78S, A79T, I83T, D85E, Q89R, D90G, V93E, M97I, M97K, M97L, I98L, I98T, I98V, S99G, G101D, G101G-ins (G101GG), G102D, A103V, D104G, K106E, K106R, V110M, K111E, K111T, V112A, N113Y, N117S, 1119T, N120S, Q121L, L124S, V129A, V129D, T130A, S131F, E134G, C137R, Q138R, K144E, K144Q, I148V, W149R, T150A, Q155H, S158G, K160M, T163I, K163N, N165Y, K167R, K167T, E170G, K171R, F173I, F173L, K173Y, V175A, S177C, L179P, R180S, T183A, T183I, T185A, I188V, F189L, F189S, T192S, F193S, R194G, R194W, R195G, R195S, R195T, L196S, D197G, P198S, P198T, E199G, E200K, E200N, N201D, N201Y, H202Q, T203A, A204T, L206F, V207A, L213P, or T221L.
In some embodiments, the modification(s), e.g. substitutions(s), can be K28N/M41V/N45T/H51N/K57E, I20L/I36T/N45D/147T, I20L/M41K/K44E, P6S/N45T/N78I/183T, N78I, M41K/N78I, N45T/N78I, I20L/N45T, N45T, M41K, I20L/I36T/N45D, N17D/N45T/V50A/D72G, I20L/F49S, N45T/V50A, I20L/N45T/N78I, I20L/N45T/V50A, M41V/N45T, M41K/N45T, A33D/S75P/D85E, M18I/M41K/D43G/H51R/N78I, V11E/I20L/I36T/N45D/H60R/S75P, A33D/V50A, S16G/A33D/K71E/S75P, E27G/N45T/M97I, E27G/N45T/K57R, A33D/E53V, D43G/N45D/V58A, E40G/D43V/N45T/V50A, Y14S/K28E/N45T A33D/N78S, A33D/N78I, A33D/N45T, A33D/N45T/N78I, E27G/N45T/V50A, N45T/V50A/N78S, I20L/N45TN110M, I20L/I36T/N45T/V50A, N45T/L74P/S75P, N45T/S75P, S75P/K106R, S75P, A33D/S75P, A33D/S75P/D104G, A33D/S75P, I20L/E27G/N45T/V50A, I20L/E27G/D43G/N45D/V58A/N78I, I20L/D43G/N45D/V58A/N78I, I20L/A33D/D43G/N45D/V58A/N78I, I20L/D43G/N45D/N78I, E27G/N45T/V50A/N78I, N45T/V50A/N78I, V11A/I20L/E27G/D43G/N45D/H51Y/S99G, I20L/E27G/D43G/N45T/V50A, I20L/K28E/D43G/N45D/V58A/Q89R, I20L/I36T/N45D, I20L/K28E/D43G/N45D/E53G/V58A/N78I, A33D/D43G/N45D/V58A/S75P, K23R/D43G/N45D, I20L/D43G/N45D/V58A/N78I/D90G/G101D, D43G/N45D/L56Q/V58A/G101GG, I20L/K23E/D43G/N45D/V58A/N78I, I20L/K23E/D43G/N45D/V50A/N78I, T19I/E27G/N45I/V50A/N78I/M97K, I20L/M41K/D43G/N45D, K23R/N45T/N78I, I20L/K28E/D43G/N45D/V58A/Q89R/G101G-ins (G101GG), K57R/S99G, K57R/S99G/F189L, M18V/M97L/F193S/R195G/E200K/H202Q, I36S/M41K/M97L/K144Q/R195G/E200K/H202Q/L206F, C22R/Q65L/L124S/K144Q/R195G/E200N/H202Q/T221L, M18V/198L/L124S/P198T/L206F, S99G/N117S/I148V/K171R/R180S, I36T/M97L/A103V/Q155H, K28I/S99G, R195S, A79T/S99G/T185A/R195G/E200K/H202Q/L206F, K57R/S99G/L124S/K144Q, K57R/S99G/R195G, D55V/M97L/S99G, E27G/I36T/D55N/M97L/K111E, E54G/M97L/S99G, G15A/I36T/M97L/K111E/H202Q, G15A/I36T/V129D, G15A/I36TN129D/R195G, G15A/V129D, I36S/M97L, I36T/D55N/M97L/K111E/A204T, I36T/D55N/M97L/K111E/V129A/F173L, I36T/D55S/M97L/K111E/I148V/R180S, I36T/G52R/M97L/V112A/K144E/V175A/P198T, I36T/I46V/D55G/M97L/K106E/K144E/T185A/R195G, I36T/I83T/M97L/K144E/P198T, I36T/M97L/K111E, I36T/M97L/K144E/P198T, I36T/M97L/Q155H/F193S/N201Y, I36T/M97L/V129D, L35P/I36S/M97L/K111E, M18I/I36T/E53G/M97L/K144E/E199G/V207A, M18T/I36T/D55N/M97L/K111E, M18V/M97L/T176N/R195G, M97L/S99G, N17D/M97L/S99G, S99G/T185A/R195G/P198T, V129D/H202Q, V129D/P198T, V129D/T150A, V93E/V129D, Y10F/M18V/S99G/Q138R/T203A, N45D, K160M/R195G, N45D/K144E, N45D/P198S, N45D/P198T, N45D/R195G, N45D/R195S, N45D/S131F, N45D/V58D, V129D/R195S, I98T/F173Y/L196S, N45D/E134G/L213P, N45D/F173I/S177C, N45D/I148V/R195G, N45D/K111T/R195G, N45D/N113Y/R195S, N45D/N165Y/E170G, N45D/Q89R/I98V, N45D/S131F/P198S, N45D/S75P/P198S, N45D/V50A/R195T, E27D/N45D/T183A/I188V, F173Y/T183I/L196S/T203A, K23N/N45D/S75P/N120S, N45D/G102D/R194W/R195G, N45D/G52V/Q121L/P198S, N45D/I148V/R195G/N201D, N45D/K111T/T183A/I188V, N45D/Q89R/F189S/P198S, N45D/S99G/C137R/V207A, N45D/T163I/K167R/R195G, N45D/T183A/T192S/R194G, N45D/V50A/I119T/K144E, T19A/N45D/K144E/R195G, V11E/N45D/T130A/P198T, V26A/N45D/T163I/T185A, K23N/N45D/L124S/K167T/R195G, K23N/N45D/Q73R/T163I, K28E/N45D/W149R/S158G/P198T, K28R/N45D/K57E/I98V/R195S, K28R/N45D/V129D/T163N/R195T, M41K/D43G/N45D/R64S/R195G, M41K/D43G/N45D/R64S/S99G, N45D/R68L/F173L/D197G/P198S, N45D/V50A/I148V/R195G/N201D, M41K/D43G/K44E/N45D/R195G/N201D, or N45D/V50A/L124S/K144E/L179P/R195G.
In some embodiments, the IRBM contains a vIgD that has one or more amino acid modification, e.g. substitutions, in an unmodified PD-L1 or specific binding fragment thereof corresponding to position(s) 20, 27, 33, 36, 43, 45, 50, 58, 75, 78, 97, 99, 195, and/or 198 with reference to positions set forth in SEQ ID NO:36 or 2655. In some embodiments, the IRBM is or contains a vIgD of PD-L1 that has one or more amino acid modifications selected from I20L, E27D, E27G, A33D, I36S, I36T, D43G, D43V, N45D, N45I, N45T, V50A, V58A, V58D, S75P, N78I, N78S, M97I, M97K, M97L, S99G, R195G, R195S, R195T, P198S, and/or P198T, or a conservative amino acid substitution thereof.
In some embodiments, the IRBM is or contains an IgD (e.g. IgV) of wild-type PD-L1 set forth in Table 2 or a vIgD thereof comprising any of the modifications (e.g. substitutions) listed in Table 2. Table 2 also provides exemplary sequences by reference to SEQ ID NO for IRBMs containing an ECD or IgV domain of PD-L1. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. ECD or IgV) also can be included in a sequence of an IRBM, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 2 is not to be construed as limiting. For example, the particular domain, such as the ECD or IgV domain, can be several amino acids longer or shorter, such as 1-10, e.g. 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO.
In some embodiments, the IRBM is or contains a wild-type PD-L1 ECD set forth in SEQ ID NO:30 or 1728 or a variant ECD sequence set forth in any one of SEQ ID NOS: 56-120, 1725, 1729-1818, 1819-1907, 1943-2008. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the ECD sequences set forth in any one of SEQ ID NOS: 56-120, 1725, 1729-1818, 1819-1907, 1943-2008 and contains the amino acid modification(s), e.g. substitution(s), not present in the wild-type or unmodified PD-L1 ECD, e.g. not present in SEQ ID NO:30 or 1728. In some embodiments, the IRBM is or contains a specific binding fragment of any of the ECD sequences set forth in any one of SEQ ID NOS: 56-120, 1725, 1729-1818, 1819-1907, 1943-2008 and contains the amino acid modification(s), e.g. substitution(s), not present in a wild-type or unmodified PD-L1 ECD, e.g. not present in SEQ ID NO: 30 or 1728.
In some embodiments, the IRBM is or contains a wild-type PD-L1 IgV set forth in SEQ ID NO: 55 or 309 or a variant IgV sequence set forth in any one of SEQ ID NOS: 121-185, 244-308, 1726-1727, 1908-1937. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 121-185, 244-308, 1726-1727, 1908-1937 and contains the amino acid modification(s), e.g. substitution(s), not present in the wild-type or unmodified PD-L1, e.g. not present in SEQ ID NO:55 or 309. In some embodiments, the IRBM is or contains a specific binding fragment of any of the IgV sequences set forth in any one of SEQ ID NOS: 121-185, 244-308, 1726-1727, 1908-1937 and that contains the amino acid modification(s), e.g. substitution(s), not present in a wild-type or unmodified PD-L1 IgV, e.g. not present in SEQ ID NO:55 or 309.
b. PD-L2 IgD or vIgD
Provided herein are immunomodulatory proteins containing an IRBM that is or contains one or more IgD domain, such as an unmodified or wild-type IgD or a vIgD, of PD-L2. In some embodiments, the IRBM is or contains one or more IgD domain of a wild-type or unmodified PD-L2, such as a mammalian PD-L1, e.g. a human PD-L1. In some embodiments, the IRBM is not the full length sequence of the PD-L2. In some aspects, the IRBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of PD-L2. In some embodiments, the IRBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the IRBM is or contains the ECD sequence set forth in SEQ ID NO:31 or is a specific binding fragment thereof. In some embodiments, the IRBM is or contains the IgV sequence set forth in SEQ ID NO: 1203 or SEQ ID NO:1263 (containing residues 1-98 or 1-102, respectively, of SEQ ID NO:31), or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an IRBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified PD-L2. In some embodiments, modifications provided herein can be in an IRBM containing an unmodified IgD set forth in SEQ ID NO:31, 1203 or 1263 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 31, 1203 or 1263. In some embodiments, an IRBM containing a vIgD of PD-L2 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 31, 1203 or 1263.
In some embodiments, the vIgD is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for PD-1 relative to the binding activity of the wild-type or unmodified IgD for PD-1. In some embodiments, the increase in binding activity, e.g. binding affinity, for PD-1 is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions). In some embodiments, the equilibrium dissociation constant (Kd) of the IRBM to PD-1 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a PD-L2 ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:31 or, where applicable, the unmodified IgV sequence set forth in SEQ ID NO: 1263. It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs: 31 or 1263. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the IRBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified PD-L2. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of PD-L2 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of PD-L2 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of PD-L2 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of PD-L2 or a specific binding fragment thereof and in an IgC domain or domains of PD-L2 or a specific binding fragment thereof.
In some embodiments, the IRBM is or contains a vIgD that has one or more amino acid modifications, e.g. substitutions in an unmodified IgD of PD-L2 or specific binding fragment thereof corresponding to position(s) 2, 12, 13, 15, 18, 20, 23, 24, 28, 31, 32, 33, 36, 37, 39, 44, 45, 46, 47, 48, 58, 59, 65, 67, 69, 71, 72, 73, 74, 75, 76, 77, 82, 85, 86, 89, or 91 with reference to positions set forth in SEQ ID NO: 31. In some cases, a polypeptide containing the vIgD exhibits increased binding activity, e.g. binding affinity, to PD-1 compared to a polypeptide containing the wild-type or unmodified PD-L2 IgD.
In some embodiments, the IRBM is or contains a vIgD that has one or more amino acid modification, e.g. substitution, selected from F2L, I12V, I13V, H15Q, N18D, T20A, N24S, C23S, G28V, N24D, V31A, V31M, N32D, L33P, L33H, L33F, I36V, T37A, S48C, S39I, E44D, N45S, D46E, T47A, E58G, E59G, K65R, S67L, H69L, P71S, Q72H, V73A, Q74R, R76G, D77N, Q82R, I85F, I86T, V89D, or W91R, or a conservative amino acid substitution thereof.
In some embodiments, the IRBM is or contains a vIgD that has two or more amino acid modification, e.g. substitution, selected from F2L, I12V, I13V, H15Q, N18D, T20A, N24S, C23S, G28V, N24D, V31A, V31M, N32D, L33P, L33H, L33F, I36V, T37A, S48C, S39I, E44D, N45S, D46E, T47A, E58G, E59G, K65R, S67L, H69L, P71S, Q72H, V73A, Q74R, R76G, D77N, Q82R, I85F, I86T, V89D, W91R.
In some embodiments, the amino acid modification(s), e.g. substitution(s), is H15Q, N24D, E44D, V89D, Q82R/V89D, E59G/Q82R, S39I/V89D, S67L/V89D, S67L/I85F, S67L/I86T, H15Q/K65R, H15Q/Q72H/V89D, H15Q/S67L/R76G, H15Q/R76G/I85F, H15Q/T47A/Q82R, H15Q/Q82R/V89D, H15Q/C23S/I86T, H15Q/S39I/I86T, E44D/V89D/W91R, I13V/S67L/V89D, H15Q/S67L/I86T, I13V/H15Q/S67L/I86T, I13V/H15Q/E44D/V89D, I13V/S39I/E44D/Q82R/V89D, I13V/E44D/Q82R/V89D, I13V/Q72H/R76G/I86T, I13V/H15Q/R76G/I85F, H15Q/S39I/R76G/V89D, H15Q/S67L/R76G/I85F, H15Q/T47A/Q72H/R76G/I86T, H15Q/T47A/Q72H/R76G, I13V/H15Q/T47A/Q72H/R76G, H15Q/E44D/R76G/I85F, H15Q/S39I/S67L/V89D, H15Q/N32D/S67L/V89D, N32D/S67L/V89D, H15Q/S67L/Q72H/R76G/V89D, H15Q/Q72H/Q74R/R76G/I86T, G28V/Q72H/R76G/I86T, I13V/H15Q/S39I/E44D/S67L, E44D/S67L/Q72H/Q82R/V89D, H15Q/V89D, H15Q/T47A, I13V/H15Q/Q82R, I13V/H15Q/V89D, I13V/S67L/Q82R/V89D, I13V/H15Q/Q82R/V89D, H15Q/V31M/S67L/Q82R/V89D, I13V/H15Q/T47A/Q82R, I13V/H15Q/V31A/N45S/Q82R/V89D, H15Q/T47A/H69L/Q82R/V89D, I13V/H15Q/T47A/H69L/R76G/V89D, Il2V/I13V/H15Q/T47A/Q82R/V89D, I13V/H15Q/R76G/D77N/Q82R/V89D, I13V/H15Q/T47A/R76G/V89D, I13V/H15Q/T47A/Q82R/V89D, I13V/H15Q/N24D/Q82R/V89D, I13V/H15Q/I36V/T47A/S67L/V89D, H15Q/T47A/K65R/S67L/Q82R/V89D, H15Q/L33P/T47A/S67L/P71S/V89D, I13V/H15Q/Q72H/R76G/I86T, H15Q/T47A/S67L/Q82R/V89D, F2L/H15Q/D46E/T47A/Q72H/R76G/Q82R/V89D, I13V/H15Q/L33F/T47A/Q82R/V89D, I13V/H15Q/T47A/E58G/S67L/Q82R/V89D, H15Q/N24S/T47A/Q72H/R76G/V89D, I13V/H15Q/E44V/T47A/Q82R/V89D, H15Q/N18D/T47A/Q72H/V73A/R76G/I86T/V89D, I13V/H15Q/T37A/E44D/S48C/S67L/Q82R/V89D, H15Q/L33H/S67L/R76G/Q82R/V89D, I13V/H15Q/T47A/Q72H/R76G/I86T, H15Q/S39I/E44D/Q72H/V75G/R76G/Q82R/V89D, H15Q/T47A/S67L/R76G/Q82R/V89D, or I13V/H15Q/T47A/S67L/Q72H/R76G/Q82R/V89D.
In some embodiments, the IRBM contains a vIgD that has one or more amino acid modification, e.g. substitutions, in an unmodified PD-L2 or specific binding fragment thereof corresponding to position(s) 13, 15, 47, 67, 72, 76, 82, 86, and/or 89 with reference to positions set forth in SEQ ID NO:36 or 2655. In some embodiments, the IRBM is or contains a vIgD of PD-L1 that has one or more amino acid modifications selected from I13V, H15Q, T47A, S67L, Q72H, R76G, Q82R, I86T, and/or V89D, or a conservative amino acid substitution thereof.
In some embodiments, the IRBM is or contains an IgD (e.g. IgV) of wild-type PD-L2 set forth in Table 3 or a vIgD comprising any of the modifications (e.g. substitutions) listed in Table 3. Table 3 also provides exemplary sequences by reference to SEQ ID NO for IRBMs containing an ECD or IgV domain. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. IgV) also can be included in an IRBM, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 3 is not to be construed as limiting. For example, the particular domain, such as the ECD or IgV domain, can be several amino acids longer or shorter, such as 1-10, e.g. 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO.
In some embodiments, the IRBM is or contains a wild-type PD-L2 ECD set forth in SEQ ID NO:31 or a variant ECD sequence set forth in any one of SEQ ID NOS: 1204-1280. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the ECD sequences set forth in any one of SEQ ID NOS: 1204-1280 and contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified PD-L2, e.g. not present in SEQ ID NO:31. In some embodiments, the IRBM is or contains a specific binding fragment of any of the ECD set forth in any one of SEQ ID NOS: 1204-1280 and contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified PD-L2 ECD, e.g. not present in SEQ ID NO:31.
In some embodiments, the IRBM is or contains a wild-type PD-L2 IgV set forth in SEQ ID NO: 1203 or 1263 or a variant IgV set forth in any one of SEQ ID NOS: 1283-1331, 1333-1407, 1309-1432. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 1283-1331, 1333-1407, 1309-1432 and contains the amino acid substitution(s) not present in the wild-type or unmodified PD-L2 IgV, e.g. not present in SEQ ID NO:1203 or 1263. In some embodiments, the IRBM is or contains a specific binding fragment of any of the IgV sequences set forth in any one of SEQ ID NOS: 1283-1331, 1333-1407, 1309-1432 and that contains the amino acid modification(s), e.g., substitution(s) not present in the wild-type or unmodified PD-L2 IgV, e.g. not present in SEQ ID NO:1203 or 1263.
2. TIGIT-Binding Molecules
Provided are immunomodulatory proteins containing an IRBM that is or contains a binding molecule that binds to TIGIT, such as to human TIGIT. Engagement of TIGIT (T cell immunoreceptor with Ig and ITIM domains) inhibits or down-modulate immune responses. TIGIT, which can be expressed on NK cells and T cells, can suppress or inhibit the cytolytic activity of NK cells, T cell proliferation and/or proinflammatory cytokine production. In some embodiments, the IRBM of the immunomodulatory protein binds to the ectodomain of TIGIT. In some embodiments, the IRBM binds to TIGIT on the surface of a cell, such as on the surface of a T cell.
In some embodiments, the provided immunomodulatory protein contains an IRBM that is or contains an antibody that binds TIGIT or is an antigen-binding antibody fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding antibody fragment binds human TIGIT. For example, in some embodiments, the antibody is BMS-986207, OMP-313M32, or RG6058 (MTIG7192A), or an antigen binding fragment containing a VH chain region and/or VL chain region of BMS-986207, OMP-313M32, or RG6058 (MTIG7192A). In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of BMS-986207, OMP-313M32, or RG6058 (MTIG7192A).
In some embodiments, the IRBM is or contains one or more IgD (e.g. IgV or IgC) or a specific binding fragment thereof, such as an unmodified or wild-type IgD or a vIgD or a specific binding fragment thereof, of an IgSF family member that binds TIGIT. In some embodiments, the TIGIT is human TIGIT. The ligands CD155 (also known as the poliovirus receptor, PVR) and CD112 (also known as Nectin-2), which are normally expressed on the surface of APCs (e.g. dendritic cells) can bind TIGIT to inhibit or down-modulate immune responses.
In some embodiments, the IRBM is or contains one or more IgD (e.g. IgV or IgC) that is an IgD of a CD112 or CD155 polypeptide, such as a wild-type CD112 or CD155, e.g. a human CD112 or a human CD155. In some aspects, the IRBM contains one or more IgD (e.g. IgV or IgC) that is a vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified CD112 or CD155, which, in some aspects, result in increased binding to TIGIT. Exemplary IgDs or vIgDs of CD112 or CD155 binding partners for inclusion as an IRBM in the provided immunomodulatory proteins are described. In some embodiments, the IRBM is or contains a vIgD polypeptide that exhibit increased binding activity or affinity for TIGIT compared to a corresponding wild-type or unmodified IgD.
In some aspects, a vIgD of CD112 or CD155 may exhibit increased binding activity, e.g. binding affinity, to the activating receptor CD226. In such examples, such a vIgD may be used as an ARBM in the embodiments provided herein. In some embodiments, such an ARBM exhibits a greater binding activity, e.g. binding affinity, for CD226 than for TIGIT, such as a binding activity, e.g. binding affinity, that is at least 1.2-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold, 5.0-fold or 10.0-fold greater for CD226 than for TIGIT.
a. CD155 IgD or vIgD
Provided herein are immunomodulatory proteins containing an IRBM that is or contains one or more IgD domain, such as an unmodified or wild-type IgD or a vIgD, of CD155. In some embodiments, the IRBM is or contains one or more IgD domain of a wild-type or unmodified CD155, such as a mammalian CD155, e.g. a human CD155. In some embodiments, the IRBM is not the full length sequence of the CD155. In some aspects, the IRBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of CD155. In some embodiments, the IRBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the IRBM is or contains the ECD sequence set forth in SEQ ID NO:47 or is a specific binding fragment thereof. In some embodiments, the IRBM is or contains the IgV sequence set forth in SEQ ID NO: 310 or SEQ ID NO: 353, or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an IRBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified CD155. In some embodiments, modifications provided herein can be in an IRBM containing an unmodified IgD set forth in SEQ ID NO:37, 310 or 353 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 37, 310 or 353. In some embodiments, an IRBM containing a vIgD of CD155 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 37, 310 or 353.
In some embodiments, the vIgD is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for TIGIT relative to the binding affinity of the wild-type or unmodified IgD for TIGIT. In some embodiments, the increase in binding activity, e.g. binding affinity, for TIGIT is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions). In some embodiments, the equilibrium dissociation constant (Kd) of the IRBM to TIGIT can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less.
In some aspects, a vIgD of CD155 may exhibit increased binding activity, e.g. binding affinity, to the activating receptor CD226. In some embodiments, the increase in binding activity, e.g. binding affinity, for TIGIT is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, such a vIgD may be used as an ARBM in the embodiments provided herein. In some embodiments, the equilibrium dissociation constant (Kd) of the ARBM to CD226 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less. In some embodiments, such an ARBM exhibits a greater binding activity, e.g. binding affinity, for CD226 than for TIGIT, such as a binding activity, e.g. binding affinity, that is at least 1.2-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold, 5.0-fold or 10.0-fold greater for CD226 than for TIGIT.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a CD155 ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:47 or, where applicable, the unmodified IgV sequence set forth in SEQ ID NO: 353. It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs: 47 or 353. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the IRBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified CD155. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of CD155 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD155 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of CD155 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD155 or a specific binding fragment thereof and in an IgC domain or domains of CD155 or a specific binding fragment thereof.
In some embodiments, the IRBM is or contains a vIgD that has one or more amino acid modification, e.g. substitutions, in an unmodified IgD of CD155 or specific binding fragment thereof corresponding to position(s) 7, 8, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 64, 65, 67, 68, 69, 70, 72, 73, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 94, 95, 96, 97, 98, 99, 100, 102, 104, 106, 107, 108, 110, 111, 112, 113, 114, 115, or 116 with reference to positions set forth in SEQ ID NO: 47. In some embodiments, a polypeptide containing the vIgD exhibits altered, such as increased, binding activity, e.g. binding affinity, to TIGIT compared to a polypeptide containing the wild-type or unmodified CD155 IgD.
In some embodiments, the IRBM is or contains a vIgD of CD155 that has one or more amino acid modifications selected from G7E, D8G, V9A, V9D, V91, V9L, V10F, V10G, V10I, V11A, V11E, V11M, Q12H, Q12K, Q12L, A13E, A13R, T151, T155, Q16H, P18C, P18F, P18H, P18L, P185, P18T, P18Y, G19D, F20I, F205, F20Y, L21S, L21M, G22S, D23A, D23G, D23N, D23Y, S24A, S24P, V25A, V25E, T26M, C29R, Y30C, Y30F, Y30H, Q32L, Q32R, V33M, P34S, N35D, N35F, N35S, M36I, M36R, M36T, E37G, E37P, E37S, E37V, V38A, V38G, T39A, T39S, H40Q, H40R, H40T, V41A, V41M, S42A, S42C, S42G, S42L, S42N, S42P, S42Q, S42T, S42V, S42W, L44P, L44V, T45A, T45G, T45I, T45S, T45Q, T45V, W46C, W46R, A47E, A47G, A47V, R48Q, H49L, H49Q, H49R, G50S, E51G, E51K, E51V, S52A, S52E, S52G, S52K, 552L, S52M, S52P, S52Q, S52R, S52T, S52W, G53R, S54C, S54G, S54H, S54N, S54R, M55I, M55L, M55V, A56V, V57A, V57L, V57T, F58L, F58Y, H59E, H59N, N59R, Q60H, Q60K, Q60P, Q60R, T61A, T61G, T61K, T61M, T61R, T61S, Q62F, Q62H, Q62K, Q62L, Q62M, Q62R, Q62Y, P64S, S65A, 565C, 565G, S65D, 565T, 565Y, S65H, S65N, 565T, 565W, S67A, S67E, S67G, S67H, S67L, S67T, S67V, S67W, E68G, S69L, S69P, K70E, K70R, K70Q, L72Q, E73D, E73G, E73R, V75A, V75L, A76E, A76G, A76T, A77T, A77V, R78G, R78K, R78S, L79P, L79Q, L79V, G80D, G805, A81E, A81P, A81T, A81V, E82D, E82G, L83P, L83Q, R84W, N85D, N85Y, N87T, L88P, R89K, M901, M90L, M90V, F91S, F91P, F91T, G92A, G92E, G92W, R94H, V95A, E96D, D97G, E98D, E98S, G99D, G99Y, N100Y, T1025, L104E, L104M, L104N, L104P, L104Q, L104T, L104Y, V106A, V106I, V106L, T107A, T107L, T107M, T1075, T107V, F108H, F108L, F108Y, Q110R, G111D, G111R, S112I, S112N, S112V, R113G, R113W, S114N, S114T, V115A, V115M, D116G, or D116N, or a conservative amino acid substitution thereof.
In some embodiments, the IRBM is or contains a vIgD that has two or more amino acid modifications selected from G7E, D8G, V9A, V9D, V91, V9L, V10F, V10G, V10I, V11A, V11E, V11M, Q12H, Q12K, Q12L, A13E, A13R, T151, T15S, Q16H, P18C, P18F, P18H, P18L, P18S, P18T, P18Y, G19D, F20I, F20S, F20Y, L21S, L21M, G22S, D23A, D23G, D23N, D23Y, S24A, S24P, V25A, V25E, T26M, C29R, Y30C, Y30F, Y30H, Q32L, Q32R, V33M, P34S, N35D, N35F, N35S, M36I, M36R, M36T, E37G, E37P, E37S, E37V, V38A, V38G, T39A, T39S, H40Q, H40R, H40T, V41A, V41M, S42A, S42C, S42G, S42L, S42N, S42P, S42Q, S42T, S42V, S42W, L44P, L44V, T45A, T45G, T45I, T45S, T45Q, T45V, W46C, W46R, A47E, A47G, A47V, R48Q, H49L, H49Q, H49R, G50S, E51G, E51K, E51V, S52A, S52E, S52G, S52K, S52L, S52M, S52P, S52Q, S52R, S52T, S52W, G53R, S54C, S54G, S54H, S54N, S54R, M55I, M55L, M55V, A56V, V57A, V57L, V57T, F58L, F58Y, H59E, H59N, N59R, Q60H, Q60K, Q60P, Q60R, T61A, T61G, T61K, T61M, T61R, T61S, Q62F, Q62H, Q62K, Q62L, Q62M, Q62R, Q62Y, P64S, S65A, S65C, S65G, S65D, S65T, S65Y, S65H, S65N, S65T, S65W, S67A, S67E, S67G, S67H, S67L, S67T, S67V, S67W, E68D, E68G, S69L, S69P, K70E, K70R, K70Q, L72Q, E73D, E73G, E73R, V75A, V75L, A76E, A76G, A76T, A77T, A77V, R78G, R78K, R78S, L79P, L79Q, L79V, G80D, G80S, A81E, A81P, A81T, A81V, E82D, E82G, L83P, L83Q, R84W, N85D, N85Y, N87T, L88P, R89K, M901, M90L, M90V, F91S, F91T, F91P, G92A, G92E, G92W, R94H, V95A, E96D, D97G, E98D, E98S, G99D, G99Y, N100Y, T102S, L104E, L104M, L104N, L104P, L104Q, L104T, L104Y, V106A, V106I, V106L, T107A, T107L, T107M, T107S, T107V, F108H, F108L, F108Y, Q110R, G111D, G111R, S112I, S112N, S112V, R113G, R113W, S114N, S114T, V115A, V115M, D116G, or D116N.
In some embodiments, the amino acid modification(s), e.g. substitutions(s), is P18S/P64S/F91S, P18S/F91S/L104P, P18L/L79V/F91S, P18S/F91S, P18T/F91S, P18T/S42P/F91S, G7E/P18T/Y30C/F91S, P18T/F91S/G111D, P18S/F91P, P18T/F91S/F108L, P18S/F91S, P18T/T45A/F91S, P18T/F91S/R94H, P18S/Y30C/F91S, A81V/L83P, A13E/P18S/A56V/F91S, P18T/F91S/V115A, P18T/Q60K, S52M, T45Q/S52L/L104E/G111R, S42G, Q62F, S52Q, S42A/L104Q/G111R, S42A/S52Q/L104Q/G111R, S52W/L104E, S42C, S52W, S52M/L104Q, S42L/S52L/Q62F/L104Q, S42W, S42Q, S52L, S52R, L104E, G111R, S52E, Q62Y, T45Q/S52M/L104E, S42N/L104Q/G111R, S52M/V57L, S42N/S52Q/Q62F, S42A/S52L/L104E/G111R, S42W/S52Q/V57L/Q62Y, L104Q, S42L/S52Q/L104E, S42C/S52L, S42W/S52R/Q62Y/L104Q, T45Q/S52R/L104E, S52R/Q62F/L104Q/G111R, T45Q/S52L/V57L/L104E, S52M/Q62Y, Q62F/L104E/G111R, T45Q/S52Q, S52L/L104E, S42V/S52E, T45Q/S52R/G111R, S42G/S52Q/L104E/G111R, S42N/S52E/V57L/L104E, S42C/S52M/Q62F, S42L, S42A, S42G/S52L/Q62F/L104Q, S42N, P18T/S65A/S67V/F91S, P18F/T39A/T45Q/T61R/S65N/S67L/E73G/R78G, P18T/T45Q/T61R/S65N/S67L, P18F/S65A/S67V/F91S, P18F/T45Q/T61R/S65N/S67L/F91S/L104P, P18S/L79P/L104M, P18S/L104M, L79P/L104M, P18T/T45Q/L79P, P18T/T45Q/T61R/S65H/S67H, P18T/A81E, P18S/D23Y/E37P/S52G/Q62M/G80S/A81P/G99Y/S112N, A13R/D23Y/E37P/S42P/Q62Y/A81E, A13R/D23Y/E37P/G99Y/S112N, A13R/D23Y/E37P/Q62M/A77V/G80S/A81P/G99Y, P18L/E37S/Q62M/G80S/A81P/G99Y/S112N, P18S/L104T, P18S/Q62H/L79Q/F91S, T45Q/S52K/Q62F/L104Q/G111R, T45Q/S52Q/Q62Y/L104Q/G111R, T45Q/S52Q/Q62Y/L104E/G111R, V57A/T61M/S65W/S67A/E96D/L104T, P18L/V57T/T61S/S65Y/S67A/L104T, P18T/T45Q, P18L/V57A/T61M/S65W/S67A/L104T, T61M/S65W/S67A/L104T, P18S/V41A/S42G/T45G/L104N, P18H/S42G/T45I/S52T/G53R/S54H/V57L/H59E/T61S/S65D/E68G/L104N, P18S/S42G/T45V/F58L/S67W/L104N, P18S/T45I/L104N, P18S/S42G/T45G/L104N/V106A, P18H/H40R/S42G/T45I/S52T/G53R/S54H/V57L/H59E/T61S/S65D/E68G/L104Y/V106L/F108H, E37V/S42G/T45G/L104N, P18S/T45Q/L79P/L104T, P18L/Q62R, A13R/D23Y/E37P/S42L/S52G/Q62Y/A81E, P18L/H49R/L104T/D116N, A13R/D23Y/E37P/Q62M/G80S/A81P/L104T, S65T/L104T, A13R/D23Y/E37P/S52G/V57A/Q62M/K70E/L104T, P18L/A47V/Q62Y/E73D/L104T, H40T/V41M/A47V/S52Q/Q62L/S65T/E73R/D97G/E98S/L104T/D116N, P18L/S42P/T45Q/T61G/S65H/S67E/L104T/D116N, P18S/H40T/V41M/A47V/S52Q/Q62L/S65T/E73R/L104M/V106A, H40T/V41M/A47V/S52Q/Q62L/S65T/E68G/E73R/D97G/E98S/L104T, T45Q/S52E/L104E, T45Q/S52E/Q62F/L104E, P18F/T26M/L44V/Q62K/L79P/F91S/L104M/G111D, P18S/T45S/T61K/S65W/S67A/F91S/G111R, P18S/L79P/L104M/T107M, P18S/S65W/S67A/M90V/V95A/L104Q/G111R, P18S/A47G/L79P/F91S/L104M/T107A/R113W, P18T/D23G/S24A/N35D/H49L/L79P/F91S/L104M/G111R, V9L/P18S/Q60R/V75L/L79P/R89K/F91S/L104E/G111R, P18S/H49R/E73D/L79P/N85D/F91S/V95A/L104M/G111R, V11A/P18S/L79P/F91S/L104M/G111R, V11A/P18S/S54R/Q60P/Q62K/L79P/N85D/F91S/T107M, P18T/S52P/S65A/S67V/L79P/F91S/L104M/G111R, P18T/M36T/L79P/F91S/G111R, D8G/P18S/M361/V38A/H49Q/A76E/F91S/L104M/T107A/R113W, P18S/S52P/S65A/S67V/L79P/F91S/L104M/T107S/R113W, T151/P18T/L79P/F91S/L104M/G111R, P18F/T26M/L44V/Q62K/L79P/E82D/F91S/L104M/G111D, P18T/E37G/G53R/Q62K/L79P/F91S/E98D/L104M/T107M, P18L/K70E/L79P/F91S/V95A/G111R, V91/Q12K/P18F/S65A/S67V/L79P/L104T/G111R/S1121, P18F/S65A/S67V/F91S/L104M/G111R, V9I/V10I/P18S/F20S/T45A/L79P/F91S/L104M/F108Y/G111R/S112V, V9L/P18L/L79P/M901/F91S/T102S/L104M/G111R, P18C/T26M/L44V/M551/Q62K/L79P/F91S/L104M/T107M, V9I/P18T/D23G/L79P/F91S/G111R, P18F/L79P/M90L/F91S/V95A/L104M/G111R, P18T/M36T/S65A/S67E/L79Q/A81T/F91S/G111R, V9L/P18T/Q62R/L79P/F91S/L104M/G111R, P18S/S65W/S67A/L104Q/G111R, P18T/G19D/M36T/S54N/L79P/L83Q/F91S/T107M/F108Y, V9L/P18L/M55V/S69L/L79P/A81E/F91S/T 107M, P18F/H40Q/T61K/Q62K/L79P/F91S/L104M/T107V, P18S/Q32R/Q62K/R78G/L79P/F91S/T107A/R113W, Q12H/P18T/L21S/G22S/V57A/Q62R/L79P/F91S/T107M, V91/P18S/S24P/H49Q/F58Y/Q60R/Q62K/L79P/F91S/T107M, P18T/W46C/H49R/S65A/S67V/A76T/L79P/S87T/L104M, P18S/S42T/E51G/L79P/F91S/G92W/T107M, V10F/T15S/P18L/R48Q/L79P/F91S/T107M/V115M, P18S/L21M/Y30F/N35D/R84W/F91S/T107M/D116G, P18F/E51V/S54G/Q60R/L79Q/E82G/S87T/M901/F91S/G92R/T107M, Ql6H/P18F/F91S/T107M, P18T/D23G/Q60R/S67L/L79P/F91S/T107M/V115A, D8G/V9I/V11A/P18T/T26M/S52P/L79P/F91S/G92A/T107L/V115A, V9I/P18F/A47E/G50S/E68G/L79P/F91S/T107M, P18S/M551/Q62K/S69P/L79P/F91S/T107M, P18T/T39S/S52P/S54R/L79P/F91S/T107M, P18S/D23N/L79P/F91S/T107M/S114N, P18S/P34S/E51V/L79P/F91S/G111R, P18S/H59N/V75A/L79P/A81T/F91S/L104M/T107M, P18S/W46R/E68D/L79P/F91S/T107M/R113G, V9L/P18F/T45A/S65A/S67V/R78K/L79V/F91S/T107M/S114T, P18T/M55L/T61R/L79P/F91S/V106I/T107M, T151/P18S/V33M/N35F/T39S/M55L/R78S/L79P/F91S/T107M, P18S/Q62K/K70E/L79P/F91S/G92E/R113W, P18F/F201/T26M/A47V/E51K/L79P/F91S, P18T/D23A/Q60H/L79P/M90V/F91S/T107M, P18S/D23G/C29R/N35D/E37G/M551/Q62K/S65A/S67G/R78G/L79P/F91S/L104M/T107M/Q110R, A13E/P18S/M36R/Q62K/S67T/L79P/N85D/F91S/T107M, V9I/P18T/H49R/L79P/N85D/F91S/L104T/T107M, V9A/P18F/T61S/Q62L/L79P/F91S/G111R, D8E/P18T/T61A/L79P/F91S/T107M, P18S/V41A/H49R/S54C/L79S/N85Y/L88P/F91S/L104M/T107M, V11E/P18H/F20Y/V25E/N35S/H49R/L79P/F91S/T107M/G111R, V11A/P18F/D23A/L79P/G80D/V95A/T107M, P18S/K70R/L79P/F91S/G111R, V9L/V11M/P18S/N35S/S54G/Q62K/L79P/L104M/T107M/V115M, V9L/P18Y/V25A/V38G/M55V/A77T/L79P/M901/F91S/L104M, V10G/P18T/L72Q/L79P/F91S/T107M, P18S/H59R/A76G/R78S/L79P, V9A/P18S/M36T/S65G/L79P/F91S/L104T/G111R/S1121, P18T/S52A/V57A/Q60R/Q62K/S65C/L79P/F91T/N100Y/T107M, V11A/P18F/N35D/A47E/Q62K/L79P/F91S/G99D/T107M/S114N, V11A/P18T/N35S/L79P/S87T/F91S, V9D/V11M/Q12L/P18S/E37V/M551/Q60R/K70Q/L79P/F91S/L104M/T107M, or T15S/P18S/Y30H/Q32L/Q62R/L79P/F91S/T107M.
In some embodiments, the IRBM is or contains an IgD (e.g. IgV) of a wild-type CD155 polypeptide set forth in Table 4 or a vIgD thereof comprising any of the modifications (e.g. substitutions) listed in Table 4. Table 4 also provides exemplary sequences by reference to SEQ ID NO for IRBMs containing an ECD or IgV domain of CD155. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. ECD or IgV) also can be included in a sequence of an IRBM, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 4 is not to be construed as limiting. For example, the particular domain, such as the ECD or IgV domain, can be several amino acids longer or shorter, such as 1-10, e.g. 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO.
In some embodiments, the IRBM is or contains a wild-type ECD set forth in SEQ ID NO: 47 or a variant ECD sequence set forth in any one of SEQ ID NOS: 311-331, 375-471, 1551-1622. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the ECD sequences set forth in any one of SEQ ID NOS: 311-331, 375-471, 1551-1622 and contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified CD155 ECD, e.g. not present in SEQ ID NO:47. In some embodiments, the IRBM is or contains a specific binding fragment of any of the ECD sequences set forth in any one of SEQ ID NOS: 311-331, 375-471, 1551-1622 and that contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified CD155 ECD, e.g. not present in SEQ ID NO:47.
In some embodiments, the IRBM is or contains a wild-type CD155 IgV set forth in SEQ ID NO: 310 or 353 or a variant IgV set forth in any one of SEQ ID NOS: 332-352, 354-374, 472-665, 1505-1550, 1575-1576, 1623-1714. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 332-352, 354-374, 472-665, 1505-1550, 1575-1576, 1623-1714 and contains the amino acid modification(s), e.g. substitution(s), not present in the wild-type or unmodified CD155 IgV, e.g. not present in SEQ ID NO: 310 or 353. In some embodiments, the IRBM is or contains a specific binding fragment of any of the IgV sequences set forth in any one of SEQ ID NOS: 332-352, 354-374, 472-665, 1505-1550, 1575-1576, 1623-1714 and that contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified CD155 IgV, e.g. not present in SEQ ID NO: 310 or 353.
b. CD112 IgD or vIgD
Provided herein are immunomodulatory proteins containing an IRBM that is or contains one or more IgD domain, such as an unmodified or wild-type IgD or a vIgD, of CD112. In some embodiments, the IRBM is or contains one or more IgD domain of a wild-type or unmodified CD112, such as a mammalian CD112, e.g. a human CD112. In some embodiments, the IRBM is not the full length sequence of the CD112. In some aspects, the IRBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of CD112. In some embodiments, the IRBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the IRBM is or contains the ECD sequence set forth in SEQ ID NO:48 or is a specific binding fragment thereof. In some embodiments, the IRBM is or contains the IgV sequence set forth in SEQ ID NO: 666 or SEQ ID NO: 761, or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an IRBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified CD112. In some embodiments, modifications provided herein can be in an IRBM containing an unmodified IgD set forth in SEQ ID NO:48, 666 or 761 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 48, 666 or 761. In some embodiments, an IRBM containing a vIgD of CD112 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 48, 666 or 761.
In some embodiments, the vIgD is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for TIGIT relative to the binding affinity of the wild-type or unmodified IgD for TIGIT. In some embodiments, the increase in binding activity, e.g. binding affinity, for TIGIT is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions). In some embodiments, the equilibrium dissociation constant (Kd) of the IRBM to TIGIT can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less.
In some aspects, a vIgD of CD112 may exhibit increased binding activity, e.g. binding affinity, to the activating receptor CD226. In some embodiments, the increase in binding activity, e.g. binding affinity, for TIGIT is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, such a vIgD may be used as an ARBM in the embodiments provided herein. In some embodiments, the equilibrium dissociation constant (Kd) of the ARBM to CD226 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less. In some embodiments, such an ARBM exhibits a greater binding activity, e.g. binding affinity, for CD226 than for TIGIT, such as a binding activity, e.g. binding affinity, that is at least 1.2-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold, 5.0-fold or 10.0-fold greater for CD226 than for TIGIT.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a CD112 ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:48 or, where applicable, the unmodified IgV sequence set forth in SEQ ID NO: 666 or 761. It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs:48, 666 or 761. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the IRBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified CD112. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of CD112 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD112 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of CD112 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD112 or a specific binding fragment thereof and in an IgC domain or domains of CD112 or a specific binding fragment thereof.
In some embodiments, the IRBM is or contains a vIgD that has one or more amino acid modifications, e.g., substitutions in an unmodified IgD of CD112 or specific binding fragment there of corresponding to position(s) 9, 12, 15, 18, 19, 21, 22, 24, 27, 28, 29, 32, 30, 32, 33, 34, 35, 37, 38, 40, 42, 43, 45, 46, 47, 48, 51, 54, 56, 60, 64, 66, 67, 69, 74, 75, 76, 78, 79, 80, 81, 82, 83, 84, 85, 87, 90, 95, 96, 98, 99, 100, 101, 106, 108, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 121, 122, 124, or 125 with reference to positions set forth in SEQ ID NO: 48, 666 or 761. In some embodiments, a polypeptide containing the vIgD exhibits altered, such as increased, binding activity, e.g. binding affinity, to TIGIT compared toa polypeptide containing the wild-type or unmodified CD112 IgD.
In some embodiments, the IRBM is or contains a vIgD of CD112 that has one or more amino acid modification selected from P9R, P9S, R12W, L15V, T18S, T18A, V19A, L21V, P22L, H24R, P27A, P27L, P27S, P28S, V29M, V29A, P30S, L32P, Y33H, I34M, S35P, V37M, T38A, T38N, Q40R, P42L, P42S, D43G, P45S, A46T, N47K, N47S, H48Y, V51M, F54L, F54S, P56L, P60T, S64G, K66M, P67H, P67S, S69F, S69P, F74L, F74S, V75M, S76P, K78R, Q79R, S80G, T81I, T81S, G82S, Q83K, D84G, T85A, A87V, Q90R, A95T, A95V, L96P, G98D, G98S, L99M, T100A, V101A, V101M, N106I, N106Y, T108A, T1081, E110G, F111L, A112I, A112V, T113A, T113S, F114L, F114S, F114Y, P115S, K116E, G117D, S118F, S118T, S118Y, V119A, G121S, M1221, W124L, or L125A, or a conservative amino acid substitution thereof.
In some embodiments, the IRBM is or contains a vIgD that has two or more amino acid modification selected from P9R, P9S, R12W, L15V, T18S, T18A, V19A, L21V, P22L, H24R, P27A, P27L, P27S, P28S, V29M, V29A, P30S, L32P, Y33H, I34M, S35P, V37M, T38A, T38N, Q40R, P42L, P42S, D43G, P45S, A46T, N47K, N47S, H48Y, V51M, F54L, F54S, P56L, P60T, S64G, K66M, P67H, P67S, S69F, S69P, F74L, F74S, V75M, S76P, K78R, Q79R, S80G, T81I, T81S, G82S, Q83K, D84G, T85A, A87V, Q90R, A95T, A95V, L96P, G98D, G98S, L99M, T100A, V101A, V101M, N106I, N106Y, T108A, T1081, E110G, F111L, A112I, A112V, T113A, T113S, F114L, F114S, F114Y, P115S, K116E, G117D, S118F, S118T, S118Y, V119A, G121S, M1221, W124L, or L125A.
In some embodiments, the two or more amino acid modification(s), e.g. substitution(s), is Y33H/A112V/G117D, V19A/Y33H/S64G/S80G/G98S/N106Y/A112V, L32P/A112V, A95V/A112I, P28S/A112V, P27A/T38N/V101A/A112V, R12W/H48Y/F54S/S118F, R12W/Q79R/S118F, T113S/S118Y, N106I/S118Y, N106I/S118F, A95T/L96P/S118Y, Y33H/P67S/N106Y/A112V, N106Y/A112V, T18S/Y33H/A112V, P9S/Y33H/N47S/A112V, P42S/P67H/A112V, P27L/L32P/P42S/A112V, G98D/A112V, Y33H/S35P/N106Y/A112V, L32P/P42S/T100A/A112V, P27S/P45S/N106I/A112V, Y33H/N47K/A112V, Y33H/N106Y/A112V, K78R/D84G/A112V/F114S, Y33H/N47K/F54L/A112V, Y33H/A112V, A95V/A112V, R12W/A112V, R12W/P27S/A112V, Y33H/V51M/A112V, Y33H/A112V/S118T, Y33H/V101A/A112V/P115S, H24R/T38N/D43G/A112V, P27A/A112V, A112V/S118T, R12W/A112V/M1221, Q83K/N106Y/A112V, R12W/P27S/A112V/S118T, P28S/Y33H/A112V, P27S/Q90R/A112V, L15V/P27A/A112V/S118T, Y33H/N106Y/T108I/A112V, Y33H/P56L/V75M/V101M/A112V, N47K/Q79R/S118F, Q40R/P60T/A112V/S118T, F114Y/S118F, Y33H/K78R/S118Y, R12W/A46T/K66M/Q79R/N106I/T113A/S118F, Y33H/A112V/S118F, R12W/Y33H/N106I/S118F, L15V/Q90R/S118F, N47K/D84G/N106I/S118Y, L32P/S118F, Y33H/Q79R/A112V/S118Y, T18A/N106I/S118T, L15V/Y33H/N106Y/A112V/S118F, V37M/S118F, N47K/A112V/S118Y, A46T/A112V, P28S/Y33H/N106I/S118Y, P30S/Y33H/N47K/V75M/Q79R/N106I/S118Y, V19A/N47K/N106Y/K116E/S118Y, Q79R/T85A/A112V/S118Y, V101M/N106I/S118Y, Y33H/Q79R/N106I/A112V/S118T, Q79R/A112V, Y33H/A46T/Q79R/N106I/S118F, A112V/G121S, Y33H/Q79R/N106I/S118Y, Y33H/N106I/A112V, Y33H/A46T/V101M/A112V/S118T, L32P/L99M/N106I/S118F, L32P/T108A/S118F, R12W/Q79R/A112V, Y33H/N106Y/E110G/A112V, Y33H/N106I/S118Y, Q79R/S118F, Y33H/Q79R/G98D/V101M/A112V, N47K/T81S/V101M/A112V/S118F, G82S/S118Y, Y33H/A112V/S118Y, Y33H/N47K/Q79R/N106Y/A112V, Y33H/S118T, R12W/Y33H/Q79R/V101M/A112V, Y33H/Q83K/A112V/S118T, V29M/Y33H/N106I/S118F, Y33H/A46T/A112V, Y33H/Q79R/S118F, Y33H/N47K/F74L/S118F, R12W/V101M/N106I/S118Y, A46T/V101A/N106I/S118Y, N106Y/A112V/S118T, S76P/T81I/V101M/N106Y/A112V/S118F, P9R/L21V/P22L/I34M/S69F/F74L/A87V/A112V/L125A, Y33H/V101M/A112V, V29A/L32P/S118F, Y33H/V101M/N106I/A112V, R12W/Y33H/N47K/Q79R/S118Y, Y33H/A46T/A112V/S118T, Y33H/A112V/F114L/S118T, Y33H/T38A/A46TN101M/A112V, P28S/Y33H/S69P/N106I/A112V/S118Y, Y33H/P42L/N47K/V101M/A112V, Y33H/N47K/F74S/Q83K/N106I/F111L/A112V/S118T, Y33H/A112V/S118T/V119A, Y33H/N106I/A112V/S118F, Y33H/K66M/S118F/W124L, or N106I/A112V.
In some embodiments, the IRBM is or contains an IgD (e.g. IgV) of a wild-type CD112 polypeptide set forth in Table 5 or a vIgD thereof that comprises any of the modifications, e.g., substitutions, listed in Table 5. Table 5 also provides exemplary sequences by reference to SEQ ID NO for IRBMs containing an ECD or IgV domain of CD112. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g., ECD or IgV) also can be included in a sequence of a variant IgSF polypeptide, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 5 is not to be construed as limiting. For example, the particular domain, such as the ECD or IgV domain, can be several amino acids longer or shorter, such as 1-10, e.g., 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO.
In some embodiments, the IRBM is or contains a wild-type ECD set forth in SEQ ID NO: 48 or a variant ECD set forth in any one of SEQ ID NOS:667-713, 809-849, 1433-1456. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the ECD sequences set forth in any one of SEQ ID NOS: 667-713, 809-849, 1433-1456 and contains the amino acid modification, e.g., substitution(s) not present in the wild-type or unmodified CD112 ECD, e.g. not present in SEQ ID NO:48. In some embodiments, the IRBM is or contains a specific binding fragment of any of the ECD sequences set forth in any one of SEQ ID NOS: 667-713, 809-849, 1433-1456 and that contains the amino acid modification, e.g., substitution(s) not present in the wild-type or unmodified CD112 ECD, e.g. not present in SEQ ID NO:48.
In some embodiments, the IRBM is or contains a wild-type CD112 IgV set forth in SEQ ID NO: 666 or 761 or a variant IgV set forth in any one of SEQ ID NOS: 714-760, 762-808, 850-931, 1457-1504. In some embodiments, the IRBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 714-760, 762-808, 850-931, 1457-1504 and contains the amino acid modification, e.g., substitution(s) not present in the wild-type or unmodified CD112 IgV, e.g. not present in SEQ ID NO:666 or 761. In some embodiments, the IRBM is or comprises a specific binding fragment of any of the IgV sequences set forth in any one of SEQ ID NOS: 714-760, 762-808, 850-931, 1457-1504 and that contains the amino acid modification, e.g., substitution(s), not present in the wild-type or unmodified CD112 IgV, e.g. not present in SEQ ID NO:666 or 761.
3. CTLA-4 Binding Molecule
Provided herein are immunomodulatory proteins containing an IRBM that is or contains a binding molecule that binds to CTLA-4, such as to human CTLA-4. CTLA-4, is an inhibitory IgSF receptor that inhibits T cell responses through modulation of TCR/CD28 signaling. CTLA-4 is expressed on T cells, and particularly is expressed following T cell activation. CTLA-4, a co-inhibitory receptor, competes with CD28 for binding of CD80 and CD86 to induce negative regulation of T cell activation. When CTLA-4 binds CD80 and/or CD86 T cell activation and effector function can be eliminated or attenuated. In some embodiments, the IRBM of the immunomodulatory protein binds to the ectodomain of CTLA-4. In some embodiments, the IRBM binds to CTLA-4 on the surface of a cell, such as on the surface of a T cell.
In some embodiments, the provided immunomodulatory protein contains an IRBM that is or contains an antibody that binds CTLA-4 or is an antigen-binding antibody fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding antibody fragment binds human CTLA-4. For example, in some embodiments, the antibody is ipilimumab or tremelimumab or an antigen binding fragment containing a VH chain region and/or VL chain region of ipilimumab or tremelimumab. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of ipilimumab or tremelimumab.
In some embodiments, the IRBM is or contains one or more IgD (e.g. IgV or IgC) or a specific binding fragment thereof, such as an unmodified or wild-type IgD or a vIgD or a specific binding fragment thereof, of an IgSF family member that binds CTLA-4. In some embodiments, the CTLA-4 is human CTLA-4. In some embodiments, the IRBM is or contains one or more IgD (e.g. IgV or IgC) that is a vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified CD80 or CD86, which, in some aspects, result in increased binding to CTLA-4 and/or decreased binding to CD28. In some embodiments, the IRBM is or contains a vIgD polypeptide that exhibit increased binding activity, such as binding affinity, for CTLA-4 and decreased binding to CD28 compared to a corresponding wild-type or unmodified IgD of CD80 or CD86. In some embodiments, the IRBM binds to CTLA-4 with an equilibrium dissociation constant (Kd) of less than 1×10−5 M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less and does not substantially bind to CD28, such as exhibits a Kd for binding CD28 of greater than or greater than about 1×10−5 M, 1×10−4 M, 1×10−3M or more.
B. Activating Receptor Binding Molecule (ARBM)
In some embodiments, the provided immunomodulatory protein contains an ARBM that binds to an activating receptor or a ligand of an activating receptor. In some embodiments, the activating receptor is expressed on a T cell, such as a human T cell. In some embodiments, the ligand of an activating receptor is expressed on an APC, such as a dendritic cell.
In some aspects, the activating receptor comprises a cytoplasmic region containing an immunoreceptor tyrosine-based activation motif (ITAM) or a cytoplasmic region that interacts with one or more adaptor protein involved in a signal transduction pathway in a cell to induce, mediate or potentiate activation of an immune cell, such as a T cell. In some embodiment, the adaptor protein contains a binding domain specific to a phosphotyrosine residue in a cytoplasmic region of an activating receptor. In some embodiments, the activating receptor includes a component of a TCR complex or is a co-receptor or costimulatory molecule that augments or enhances TCR signaling. In some embodiments, the activating receptor is a TCR, CD3, CD4, CD8, CD28, ICOS or CD2, including any mammalian orthologs thereof. In some embodiments, the activating receptor target is a human TCR, human CD3, human CD4, human CD8, human CD28, human ICOS or human CD2. In some embodiments, the activating receptor is expressed on a T cell, such as a human T cell.
In some cases, the ARBM binds to a ligand of an activating receptor. In some embodiments, the ARBM binds to a ligand of a component of a TCR complex or a ligand of a co-receptor or costimulatory molecule that augments or enhances TCR signaling. In some embodiments, the ARBM binds to a ligand of a TCR, CD3, CD4, CD8, CD28, ICOS or CD2 molecule, including such molecules expressed on a T cell, e.g. a human T cell. In some embodiments, the ARBM binds to a ligand of CD28, such as a ligand of CD28 expressed on a T cell, e.g. a human T cell. In some embodiments, the ligand is a CD80 or a CD86, such as a human CD80 or human CD86. In some embodiments, the ARBM binds to a ligand of a CD4, a CD8 or a TCR, including such molecules expressed on a T cell, e.g. a human T cell. In some embodiments, the ligand is an MHC molecule, such as an MHC class I molecule or an MHC class II molecule. In some embodiments, the ligand is expressed on an APC.
In some embodiments, the ARBM is an antibody or antigen-binding fragment that binds to an activating receptor or binds to a ligand of an activating receptor. In some embodiments, the ARBM is an antibody or antigen-binding fragment that binds to a TCR, CD3, CD4, CD8, CD28, ICOS or CD2, including any mammalian orthologs thereof. In some embodiments, the antibody or antigen-binding fragment binds to a human TCR, human CD3, human CD4, human CD8, human CD28, human ICOS or human CD2, including such molecules expressed on a human T cell. In some embodiments, the antibody or antigen-binding fragment binds to CD80, CD86 or an MHC molecule (e.g. MHC class I or MHC class II). In some embodiments, the antibody or antigen-binding fragment binds to a human CD80, human CD86 or a human MHC molecule, including such molecules expressed on a human APC.
In some embodiments, the ARBM is a binding molecule that binds to CD4 or CD8. In some embodiments, the ARBM is a chemokine or cytokine. In some embodiments, the binding molecule is an IL-16 molecule, which is a chemoattractant that binds to CD4.
In some embodiments, the ARBM is or contains a binding partner of an activating receptor or a ligand of an activating receptor. In some aspects, the ARBM is or contains an IgD of an IgSF family member that binds to an activating receptor, such as binds to TCR, CD3, CD4, CD8, CD28, ICOS or CD2, or is a specific fragment or vIgD thereof that binds to the activating receptor. Exemplary IgSF family members that are binding partners of or that bind to a CD28 activating receptor include, for example, CD80, CD86 and ICOSL, such as human CD80, CD86 or ICOSL. Exemplary IgSF family members that are binding partners of or that bind to CD2 include, for example, LFA-3 (CD58) or CD48, such as human LFA-3 or human CD48. In some embodiments, the IgSF binding partner of an activating receptor is a molecule set forth in Table 6A. In some examples, the ARBM is or contains an IgD of a wild-type CD80, CD86 or ICOSL or is or contains a vIgD thereof, wherein the ARBM specifically binds to CD28. In other examples, the ARBM is or contains an IgD of LFA-3 or CD48 or is or contains a vIgD thereof, wherein the IRBM specifically binds to CD2.
In other aspects, the ARBM is or contains an IgD of an IgSF family member that binds to a ligand of an activating receptor, such as binds to CD80, CD86 or an MHC molecule, or is a specific fragment or vIgD thereof that binds to the ligand of the activating receptor. Exemplary IgSF family members that are binding partners of or that bind to CD80 or CD86 include, for example, CTLA-4, such as human CTLA-4. Exemplary IgSF family members that are binding partners of or that bind to an MHC molecule include, for example, a TCR, CD4, CD8 or LAG-3, such as a human TCR, human CD4, human CD8 or human LAG-3 In some embodiments, the IgSF binding partner of a ligand of an activating receptor is a molecule set forth in Table 6B. In some examples, the ARBM is or contains an IgD of a wild-type CTLA-4 or is or contains a vIgD thereof, wherein the ARBM specifically binds to CD80 or CD86. In other examples, the ARBM is or contains an IgD of a CD4 or CD8 or is or contains a vIgD thereof, wherein the IRBM specifically binds to an MHC molecule.
The first column of Tables 6A and 6B provides the name and, optionally, the name of some possible synonyms for that particular domain. The second column provides the protein identifier of the UniProtKB database, a publicly available database accessible via the internet at uniprot.org. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases include the UniProt Knowledgebase (UniProtKB). UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR) and supported mainly by a grant from the U.S. National Institutes of Health (NIH). The third column provides the region where the indicated IgSF domain is located. The region is specified as a range where the domain is inclusive of the residues defining the range. Column 3 also indicates the domain class for the specified region. Column 4 provides the region where the indicated additional domains are located (signal peptide, S; extracellular domain, E; transmembrane domain, T; cytoplasmic domain, C). Column 5 indicates for some of the listed IgSF members, some of its cognate cell surface binding partners. It is understood that reference to amino acids, including to a specific sequence set forth as a SEQ ID NO used to describe domain organization, such as of an IgSF domain, are for illustrative purposes and are not meant to limit the scope of the embodiments provided. It is understood that polypeptides and the description of domains thereof are theoretically derived based on homology analysis and alignments with similar molecules. Thus, the exact locus can vary, and is not necessarily the same for each protein. Hence, the specific IgSF domain, such as specific IgV domain or IgC domain, can be several amino acids (such as one, two, three, four, five, six or more amino acids) longer or shorter.
In some embodiments, the ARBM is or contains a wild-type or unmodified IgD of a binding partner of an activating receptor or a ligand of an activating receptor, such as a sequence that is or contains an ECD or an IgD domain or domains of a native binding partner of an inhibitory receptor or an ortholog thereof. In some embodiments, the ARBM is or comprises the extracellular domain (ECD), or a portion thereof containing one or more IgSF domains, of an IgSF member set forth in Table 6A, e.g. human CD80, human CD86, human ICOSL, human LFA-3 (CD58) or human CD48. In some embodiments, the ARBM is or comprises the extracellular domain (ECD), or a portion thereof containing one or more IgSF domains, of an IgSF member set forth in Table 6B, e.g. human CTLA-4, human CD4, human CD8a, human CD8b or human LAGS. In some embodiments, the extracellular domain comprises an IgV domain or domains and, in some cases, an IgC (e.g. IgC1 and/or IgC2) domain or domains. In some embodiments, the ARBM is less than the full length sequence of the IgSF binding partner of the activating receptor or a ligand of the activating receptor. For example, in some aspects, the ARBM is or only contains the extracellular domain (ECD) or specific binding fragment thereof of the binding partner. In some embodiments, the ARBM is or only contains the IgV domain or the IgC domain or specific binding fragment of the IgV domain or the IgC domain, or combinations thereof. In some embodiments, the ARBM can be an IgV only, the combination of the IgV and IgC, including the entire extracellular domain (ECD), or any combination of Ig domains. In some embodiments, the ARBM consists or consists essentially of the ECD or an IgD domain or domain thereof of a binding partner of an activating receptor or a ligand of an activating receptor, such as consists or consists essentially of the ECD, IgV or IgC domain or domains.
In some embodiments, the sequence of the ARBM containing an IgD of a binding partner of an activating receptor or a ligand of an activating receptor is a mammalian sequence that includes, but is not limited to, human, mouse, cynomolgus monkey, or rat. In some embodiments, the sequence of ARBM containing an IgD is human. Table 6A and Table 6B provide exemplary residues that correspond to ECD, IgV, or IgC regions of various IgSF domains of binding partners of exemplary activating receptors or ligands of activating receptors.
In some embodiments, the ARBM is or contains a vIgD that contains one or more amino acids modifications, such as one or more substitutions (alternatively, “mutations” or “replacements”), deletions or additions, in an IgD relative to a wild-type or unmodified IgD of a binding partner of the activating receptor or a ligand of the activating receptor. In some aspects, the vIgD contains up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications, such as amino acid substitutions, deletions or additions in an IgD domain of an IgSF binding partner of an activating receptor, e.g. in an IgD domain of a binding partner set forth in Table 6A, or a ligand of an activating receptor, e.g. in an IgD domain of a binding partner set forth in Table 6B. The modifications (e.g., substitutions) can be in the IgV domain or the IgC domain. In some embodiments, the vIgD has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., substitutions) in the IgV domain or specific binding fragment thereof. In some embodiments, the vIgD has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications (e.g., substitutions) in the IgC domain or specific binding fragment thereof. In some embodiments, the vIgD has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the wild-type or unmodified IgD or specific binding fragment thereof.
In some embodiments, the ARBM is a variant of a binding partner of an activating receptor (e.g. variant of a molecule set forth in Table 6A, e.g. human ICOSL, human CD80, human CD86 or human LFA-3 (CD58) or human CD48, in which the ARBM is or comprises an ECD, or portion thereof, containing one or more vIgD of an IgSF binding partner of an activating receptor. In some embodiments, the ARBM is a variant of a binding partner of a ligand of an activating receptor (e.g. variant of a molecule set forth in Table 6B, e.g. human CTLA-4, human CD4, human CD8a, human CD8b or human LAGS, in which the ARBM is or comprises an ECD, or portion thereof, containing one or more vIgD of an IgSF binding partner of a ligand of an activating receptor. In some embodiments, the ARBM can comprise an IgV domain or an IgC domain or domains, or a specific binding fragment of the IgV domain or a specific binding fragment of the IgC domain or domains in which one or more of the IgSF domains (IgV or IgC) contains the one or more amino acid modifications (e.g. substitutions). In some embodiments, the ARBM can comprise an IgV domain and an IgC domain or domains, or a specific binding fragment of the IgV domain and a specific binding fragment of the IgC domain or domains, in which at least one of the IgV or IgC domain contains the amino acid modifications (e.g. substitutions). In some embodiments, the ARBM consists or consists essentially of the ECD containing a vIgD (e.g. IgV and/or IgC). In some embodiments, the ARBM contains only, such as consists or consists essentially of, an IgV domain or a specific binding fragment of the IgV domain, in which the one or more amino acid modifications (e.g. substitutions) are located in the IgV domain or specific binding fragment of the IgV domain. In some embodiments, the ARBM contains only, such as consists or consists essentially of, an IgC domain or a specific binding fragment of the IgC domain, in which the one or more amino acid modifications (e.g. substitutions) are located in an IgC domain or specific binding fragment of an IgC domain.
In some embodiments, the one or more amino acid modifications alter, such as increase, the binding activity, e.g. binding affinity, of the extracellular domain of the binding partner or an IgD domain thereof (e.g. IgV) for its cognate receptor or ligand. In some embodiments, by virtue of the altered binding activity, e.g. binding affinity, the vIgD domain is an affinity-modified IgSF domain. Typically, the affinity-modified IgSF domain used in or as the ARBM is a human or murine affinity modified IgSF domain.
In some embodiments, an ARBM containing a vIgD has a binding activity, such as binding affinity, for an activating receptor or a ligand of an activating receptor that is altered, e.g. increased, from that of an ARBM containing a wild-type or unmodified IgD sequence as determined by, for example, solid-phase ELISA immunoassays, flow cytometry or surface plasmon resonance (Biacore) assays. In some embodiments, the vIgD results in an increased binding activity, such as binding affinity, for the activating receptor or ligand of the activating receptor, relative to a wild-type or unmodified IgD. In some embodiments, the increase in binding activity, such as binding affinity, is at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 40%, 50%, 60%, 70%, 90%, 100%, 200% or more. In some embodiments, the increase in binding activity, such as binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions). In some embodiments, the equilibrium dissociation constant (Kd) of the ARBM to the activating receptor or a ligand of the activating receptor can be less than 1×10−5 M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less.
The use of the term “modification”, such as “substitution” does not imply that the present embodiments are limited to a particular method of making the immunomodulatory proteins. An ARBM that is or contains IgD or vIgDs can be made, for example, by de novo peptide synthesis and thus does not necessarily require a modification, such as a “substitution” in the sense of altering a codon to encode for the modification, e.g. substitution. This principle also extends to the terms “addition” and “deletion” of an amino acid residue which likewise do not imply a particular method of making. The means by which the vIgDs are designed or created is not limited to any particular method. In some embodiments, however, a wild-type or unmodified IgD encoding nucleic acid is mutagenized from wild-type or unmodified IgD genetic material and screened for desired specific binding activity, e.g. binding affinity, and/or alteration of IFN-gamma expression or other functional activity. In some embodiments, a vIgD is synthesized de novo utilizing protein or nucleic acid sequences available at any number of publicly available databases and then subsequently screened. The National Center for Biotechnology Information provides such information and its website is publicly accessible via the internet as is the UniProtKB database.
In some embodiments, the ARBM has (i) the sequence of amino acids set forth in SEQ ID NO: 1, 2, 5, 9, 13-15, 3237, or a mature form thereof lacking the signal sequence, (ii) a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 1, 2, 5, 9, 13-15, 3237, or the mature form thereof, or (iii) is a portion of (i) or (ii) containing an IgV domain or IgC domain or specific binding fragments thereof. In some embodiments, the ARBM has (i) the sequence of amino acids (i) set forth in SEQ ID NO: 189, 190, 193, 197, 201, 394, 395 or 3238, (ii) a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 189, 190, 193, 197, 201, 394, 395 or 3238; or (iii) a portion of (i) or (ii) containing the extracellular domain or an IgV domain or IgC domain or specific binding fragment thereof.
In some embodiments, the ARBM is or comprises an extracellular domain or a portion thereof of an IgSF member that is a binding partner of an activating receptor (e.g. Table 6A). In some cases, the ARBM has or comprises (i) the sequence of amino acids set forth in SEQ ID NO: 28, 29, 32, or 3239, (ii) a sequence of amino acids that has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 28, 29, 32, or 3239 or (iii) is a specific binding fragment of the sequence of (i) or (ii) comprising an IgV domain or an IgC (e.g. IgC2) domain.
In some embodiments, the ARBM is or comprises an IgV domain or an IgC (e.g. IgC2) domain or domains, or a specific binding fragment thereof. In some embodiments, the ARBM has or comprises the amino acid sequence set forth in SEQ ID NO: 1005, 1079, 1195, 2056, 2244, 2615, 2654, 2655, 2946, 2947, or 3580, or an ortholog thereof. For example, the ARBM has or comprises (i) the sequence of amino acids set forth in SEQ ID NO: 1005, 1079, 1195, 2056, 2244, 2615, 2654, 2655, 2946, 2947, or 3580, (ii) a sequence of amino acids that has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 1005, 1079, 1195, 2056, 2244, 2615, 2654, 2655, 2946, 2947, or 3580 or (iii) a specific binding fragment of the sequence of (i) or (ii).
In some embodiments, the ARBM is or comprises an extracellular domain or a portion thereof of an IgSF member that is a binding partner of a ligand of an activating receptor (e.g. Table 6B). In some embodiments, the ARBM has or comprises the amino acid sequence set forth in SEQ ID NO: 36 or 40-42, or an ortholog thereof. In some cases, the ARBM has or comprises (i) the sequence of amino acids set forth in SEQ ID NO: 36 or 40-42 (ii) a sequence of amino acids that has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 36 or 40-42 or (iii) is a specific binding fragment of the sequence of (i) or (ii) comprising an IgV domain or an IgC (e.g. IgC2) domain.
In some embodiments, the ARBM has or comprises an IgV domain or an IgC domain or domains, or a specific binding fragment thereof. In some embodiments, the ARBM comprises the amino acid sequence set forth in SEQ ID NO: 2947, or an ortholog thereof. For example, the ARBM has or comprises (i) the sequence of amino acids set forth in SEQ ID NO: 2947, (ii) a sequence of amino acids that has at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to SEQ ID NO: 2947, or (iii) a specific binding fragment of the sequence of (i) or (ii).
1. CD28 Binding Molecules
Provided herein are immunomodulatory proteins containing an ARBM that is or contains a binding molecule that binds to CD28, such as to human CD28. In some embodiments, the ARBM of the immunomodulatory protein binds to the ectodomain of CD28. In some embodiments, the ARBM binds to CD28 on the surface of a cell, such as on the surface of a T cell.
CD28 is a T-cell costimulatory receptors that is engaged by ligands B7-1 (CD80) and B7-2 (CD86) both of which are present on APCs. In some cases, CD28 also can interact with ICOSL at a binding site that overlaps with the binding of ICOSL to the T-cell costimulatory receptor ICOS (Yao et al. (2011) Immunity, 34:729-740). In some cases, an affinity-modified ICOSL containing modifications in an IgSF domain can exhibit increased affinity to CD28 (see e.g., published International PCT App. No. WO 2017/181148). In some cases, the provided immunomodulatory proteins containing an ARBM can bind ICOS (inducible costimulator), which is another T-cell costimulatory receptor engaged by ICOS ligand (ICOSL) on APCs. Although CD28 and ICOS are related CD28 family activating receptors and share some intracellular signaling motifs, costimulatory effects between CD28 and ICOS differ. For example, CD28 is expressed on both unactivated and activated T cells and its signaling is involved in IL-2 production and subsequent T cell effector function. ICOS is generally not expressed on the surface of T cells until after T cell activation, and signaling through ICOS on activated T cells can, in some cases, support specialized T cell subset differentiation. Thus, in some cases, costimulation by CD28 and ICOS yields overlapping and complementary effects.
In some embodiments, the provided immunomodulatory protein contains an ARBM that is or contains an antibody that binds CD28 or is an antigen-binding antibody fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding antibody fragment binds human CD28. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of an anti-CD28 antibody or antigen-binding fragment.
In some embodiments, the ARBM is or contains one or more IgD (e.g. IgV or IgC) or a specific binding fragment thereof, such as an unmodified or wild-type IgD or a vIgD or a specific binding fragment thereof, of an IgSF family member that binds CD28. In some embodiments, the CD28 is human CD28. In some embodiment, the ARBM is or contains one or more IgD (e.g. IgV or IgC) that is an IgD of a CD80, CD86 or ICOSL polypeptide, such as a wild-type CD80, CD86 or ICOSL, e.g. a human CD80 or human CD86 or human ICOSL. In some aspects, the ARBM contains one or more IgD (e.g. IgV or IgC) that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified CD80, CD86 or ICOSL, which, in some aspects, result in increased binding of the ARBM to CD28. Exemplary IgDs or vIgDs of CD80, CD86 or ICOSL binding partners for inclusion as an ARBM in the provided immunomodulatory proteins are described. In some embodiments, the ARBM is or contains a vIgD polypeptide that exhibit increased binding activity, such as binding affinity, for CD28 compared to a corresponding wild-type or unmodified IgD.
a. ICOSL IgD or vIgD
Provided herein are immunomodulatory proteins containing an ARBM that is or contains one or more IgD, such as a wild-type or unmodified IgD or a vIgD, of ICOSL. In some embodiments, the ARBM is not the full length sequence of the ICOSL. In some aspects, the ARBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of ICOSL. In some embodiments, the ARBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:32 or is a specific binding fragment thereof. In some embodiments, the IRBM is or contains an IgV sequence of ICOSL, such as human ICOSL. In some embodiments, the IgV domain contains at least amino acids 1-111, 1-112, 1-113, 1-114, 1-115, 1-116, 1-117, 1-118, 1-119, 1-120, 1-121, 1-122, with reference to numbering set forth in SEQ ID NO:32. In some embodiments, the ARBM is or contain an IgV sequence set forth in SEQ ID NO:2056 or SEQ ID NO: 2244, or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an ARBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified ICOSL. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO:32, 2056 or 2244 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 32, 2056 or 2244. In some embodiments, an ARBM containing a vIgD of ICOSL has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 32, 2056 or 2244.
In some embodiments, the ARBM is or contains a vIgD that is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for CD28 relative to the binding activity of the wild-type or unmodified IgD for CD28. In some embodiments, the increase in binding activity, e.g. binding affinity, for CD28 is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions).
In some embodiments, the equilibrium dissociation constant (Kd) of the ARBM to CD28 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less. In some embodiments, the ARBM binds to CD28 with a Kd of from or from about 100 pm to 5000 pm, 100 pm to 2000 pm, 100 pm to 1500 pm, 100 pm to 1000 pm, 100 pm to 800 pm, 100 pm to 500 pm, 100 pm to 400 pm, 400 pm to 4000 pm, 400 pm to 2000 pm, 400 pm to 1500 pm, 400 pm to 1000 pm, 400 pm to 800 pm, 400 pm to 500 pm, 500 pm to 5000 pm, 500 pm to 2000 pm, 500 pm to 1500 pm, 500 pm to 1000 pm, 500 pm to 800 pm, 800 pm to 5000 pm, 800 pm to 2000 pm, 800 pm to 1500 pm, 800 pm to 1000 pm, 1000 pm to 5000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm, 1500 pm to 5000 pm, 1500 to 2000 pm to 2000 pm to 50000 pm. In some embodiments, the ABRM binds to CD28 with a Kd of less than 200 pM, 300 pM, 400 pM, 500 pM. In some embodiments, the ABRM binds to CD28 with a Kd of greater than or greater than about 500 pm but less than or less than about 2000 pm, such as from or from about 500 pm to 1500 pm, 500 pm to 1250 pm, 500 pm to 1000 pm, 500 pm to 750 pm, 750 pm to 1500 pm, 750 pm to 1250 pm, 750 pm to 1000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm or 1500 pm to 2000 pm.
In some embodiments, the ARBM binds to ICOS. In some embodiments, the variant ARBM binds to ICOS and to CD28. In some aspects, the equilibrium dissociation constant (Kd) for binding to ICOS can be less than 1×10−5 M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M. In some embodiments, the ARBM exhibits a greater binding activity, e.g. binding affinity, for CD28 than for ICOS, such as a binding activity, e.g. binding affinity, that is at least 1.2-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold, 5.0-fold or 10.0-fold greater for CD28 than for ICOS. In some embodiments, the ARBM exhibits a greater binding activity, e.g. binding affinity, for ICOS than for CD28, such as a binding activity, e.g. binding affinity, that is at least 1.2-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold, 5.0-fold or 10.0-fold greater for ICOS than for CD28.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a ICOSL ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:32 or, where applicable, the unmodified IgV sequence set forth in SEQ ID NO: 2056 or 2244. It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs: 32, 2056 or 2244. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the ARBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified ICOSL. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of ICOSL or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of ICOSL or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of ICOSL or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of ICOSL or a specific binding fragment thereof and in an IgC domain or domains of ICOSL or a specific binding fragment thereof.
In some embodiments, the ARBM is or contains a vIgD that has one or more amino acid modification, e.g. substitution, in an unmodified IgD of ICOSL or a specific binding fragment there of corresponding to position(s) 10, 11, 13, 16, 18, 20, 25, 27, 30, 33, 37, 42, 43, 47, 52, 54, 57, 61, 62, 67, 71, 72, 74, 77, 78, 75, 80, 84, 89, 90, 92, 93, 94, 96, 97, 98, 99, 100, 102, 103, 107, 109, 110, 111, 113, 115, 116, 117, 119, 120, 121, 122, 126, 129, 130, 132, 133, 135, 138, 139, 140, 142, 143, 144, 146, 151, 152, 153, 154, 155, 156, 158, 161, 166, 168, 172, 173, 175, 190, 192, 193, 194, 198, 201, 203, 207, 208, 210, 212, 217, 218, 220, 221, 224, 225, or 227 with reference to numbering of SEQ ID NO:32, 2056 or 2244.
In some embodiments, the ARBM is or contains a vIgD of ICOSL that has one or more amino acid modification, e.g. substitution, selected from M10V, M10I, V11E, S13G, E16V, S18R, A20V, S25G, F27S, F27C, N30D, Y33del, Q37R, K42E, T43A, Y47H, N52A, N52C, N52D, N52G, N52H, N52L, N52K, N52M, N52P, N52Q, N52R, N52S, N52T, N52V, N52Y, S54A, S54P, N57A, N57E, N57F, N57H, N57K, N57L, N57M, N57P, N57Q, N57S, N57T, N57V, N57W, N57Y, R61S, R61C, Y62F, L67P, A71T, G72R, L74Q, R75Q, D77G, F78L, L80P, N84Q, D89G, E90A, K92R, F93L, H94E, H94D, L96F, L96I, V97A, L98F, S99G, Q100A, Q100D, Q100E, Q100G, Q100K, Q100L, Q100M, Q100N, Q100R, Q100P, Q100S, Q100T, Q100V, L102R, G103E, V107A, V107I, S109G, S109N, V110D, V110N, V110A, E111del, T113E, H115R, H115Q, V116A, A117T, N119Q, F120I, F120S, S121G, V122A, V122M, S126T, S126R, H129P, S130G, S132F, Q133H, E135K, F138L, T139S, C140D, C140del, S142F, I143V, I143T, N144D, Y146C, V151A, Y152C, Y152H, W153R, I154F, N155H, N155Q, K156M, D158G, L161P, L161M, L166Q, N168Q, F172S, L173S, M175T, T1905, T190A, S192G, V193M, N194D, C198R, N201S, L203P, L203F, N207Q, L208P, V210A, S212G, D217V, 1218T, 1218N, E220G, R221G, R221I, I224V, T225A, N227K or a conservative amino acid modification, e.g. substitution thereof.
In some embodiments, the ARBM is or contains a vIgD of ICOSL that has two or more amino acid modification, e.g. substitution, selected from M10V, M10I, V11E, S13G, E16V, S18R, A20V, S25G, F27S, F27C, N30D, Y33del, Q37R, K42E, T43A, Y47H, N52A, N52C, N52D, N52G, N52H, N52L, N52K, N52M, N52P, N52Q, N52R, N52S, N52T, N52V, N52Y, S54A, S54P, N57A, N57E, N57F, N57H, N57K, N57L, N57M, N57P, N57Q, N57S, N57T, N57V, N57W, N57Y, R61S, R61C, Y62F, L67P, A71T, G72R, L74Q, R75Q, D77G, F78L, L80P, N84Q, D89G, E90A, K92R, F93L, H94E, H94D, L96F, L96I, V97A, L98F, S99G, Q100A, Q100D, Q100E, Q100G, Q100K, Q100L, Q100M, Q100N, Q100R, Q100P, Q100S, Q100T, Q100V, L102R, G103E, V107A, V107I, S109G, S109N, V110D, V110N, V110A, E111del, T113E, H115R, H115Q, V116A, A117T, N119Q, F120I, F120S, S121G, V122A, V122M, S126T, S126R, H129P, S130G, S132F, Q133H, E135K, F138L, T139S, C140D, C140del, S142F, I143V, I143T, N144D, Y146C, V151A, Y152C, Y152H, W153R, I154F, N155H, N155Q, K156M, D158G, L161P, L161M, L166Q, N168Q, F172S, L173S, M175T, T190S, T190A, S192G, V193M, N194D, C198R, N201S, L203P, L203F, N207Q, L208P, V210A, S212G, D217V, I218T, I218N, E220G, R221G, R221I, I224V, T225A or N227K.
In some embodiments, the amino acid modification(s), e.g. substitution(s) is N52Y/N57Y/F138L/L203P, N52H/N57Y/Q100P, N52S/Y146C/Y152C, N52H/C198R, N52H/C140D/T225A, N52H/C198R/T225A, N52H/K92R, N52H/S99G, N57Y/Q100P, N52S/G103E, N52S/S130G/Y152C, N52S/Y152C, N52S/C198R, N52Y/N57Y/Y152C, N52Y/N57Y/H129P/C198R, N52H/L161P/C198R, N52S/T113E, N52D/S54P, N52K/L208P, N52S/Y152H, N52D/V151A, N52H/I143T, N52S/L80P, F120S/Y152H/N201S, N52S/R75Q/L203P, N52S/D158G, N52D/Q133H, N52S/N57Y/H94D/L96F/L98F/Q100R, N52S/N57Y/H94D/L96F/L98F/Q100R/G103E/F120S, N52H/F78L/Q100R, N52H/N57Y/Q100R/V110D, N52H/N57Y/R75Q/Q100R/V110D, N52H/N57Y/Q100R, N52H/N57Y/L74Q/Q100R/V110D, N52H/Q100R, N52H/S121G, A20V/N52H/N57Y/Q100R/S109G, N52H/N57Y/Q100P, N52H/N57Y/R61S/Q100R/V110D/L173S, N52H/N57Y/Q100R/V122A, N52H/N57Y/Q100R/F172S, N52H/N57Y, N52S/F120S, N52S/V97A, N52S/G72R, N52S/A71T/A117T, N52S/E220G, Y47H/N52S/V107A/F120S, N52H/N57Y/Q100R/V110D/S132F/M175T, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/C198R, Q37R/N52H/N57Y/Q100R/V110N/S142F/C198R/D217V/R221G, N52H/N57Y/Q100R/V110D/C198R, N52H/N57Y/Q100R/V110D/V116A/L161M/F172S/S192G/C198R, F27S/N52H/N57Y/V110N, N52S/H94E/L96I/S109N/L166Q, S18R/N52S/F93L/I143V/R221G, A20T/N52D/Y146C/Q164L, V11E/N30D/N52H/N57Y/H94E/L96I/L98F/N194D/V210A/I218T, N52S/H94E/L96I/V122M, N52H/N57Y/H94E/L96I/F120I/S126T/W153R/I218N, M10V/S18R/N30D/N52S/S126R/T139S/L203F, S25G/N30D/N52S/F120S/N227K, N30D/N52S/L67P/Q100K/D217G/R221K/T225S, N52H/N57Y/Q100R/V110D/A117T/T190S/C198R, N52H/N57Y/Q100R/V110D/F172S/C198R, S25G/F27C/N52H/N57Y/Q100R/V110D/E135K/L173S/C198R, N52H/N57Y/V110A/C198R/R221I, M10I/S13G/N52H/N57Y/D77G/V110A/H129P/I143V/F172S/V193M, C198R, N52H/N57Y/R61C/Y62F/Q100R/V110N/F120S/C198R, N52H/N57Y/Q100R/V110D/H115R/C198R, N52H/N57Y/Q100R/V110D/N144D/F172S/C198R, N52S/H94E/L98F/Q100R, N52S/E90A, N30D/K42E/N52S, N52S/F120S/I143V/I224V, N52H/N57Y/Q100R/V110D/C198R/5212G, N52H/N57Y/Q100R/C198R, N52S/N194D, N52H/N57Y/Q100R/L102R/V110D/H115R/C198R, N52S/S54P, T38P/N52S/N57D, N52H/C140del/T225A, N52H/F78L/Q100R/C198R, N52H/N57Y/R75Q/Q100P/V110D, N52H/N57Y/L74Q/V110D/S192G, N52H/S121G/C198R, N52S/F120S/N227K, N52S/A71T/A117T/T190A/C198R, T43A/N52H/N57Y/L74Q/D89G/V110D/F172S, N52H/N57Y/Q100R/V110D/S132F/M175T, N52H/N57Y/Q100R/V107I/V110D/1154F/C198R/R221G, Q100R, F138L/L203P, N57Y/F138L/L203P, N57Y/Q100R/C198R, N57Y/F138L/L203P, Q100R/F138L, L203P, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/I143V/F172S/C198R, N52H/N57Y/Q100R/L102R/H115R/F172S/C198R, N52H/V122A/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/N194D, N52H/N57Y/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/H115R, N52H/N57Y/Q100R/H115R, N52H/N57Y/Q100R/H115R/F172S/1224V, N52H/N57Y/Q100R/H115R/F172S, N52H/N57Y/Q100R/F172S, N52H/Q100R/H115R/1143T/F172S, N52H/N57Y/Q100P/H115R/F172S, N52Y/N57Y/Q100P/F172S, E16V/N52H/N57Y/Q100R/V110D/H115R/C198R, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/F172S/C198R, N52S/E90A/H115R, N30D/K42E N52S/H115R, N30D/K42E/N52S/H115R/C198R/R221I, N30D/K42E/N52S/H115R/C198R, N30D/K42E/N52S/H115R/F172S/N194D, N52S/H115R/F120S/I143V/C198R, N52S/H115R/F172S/C198R, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100P H115R/F172S/C198R, N52H/N57Y/Q100P/F172S/C198R, N52H/N57Y/Q100P/H115R, N52H/N57Y/Q100P/H115R/C198R, N52H/Q100R/C198R, N52H/Q100R/H115R/F172S, N52H/Q100R/F172S/C198R, N52H/Q100R/H115Q/F172S/C198R, N52H/N57Y/Q100R/F172S/C198R, N52Q/N207Q, N168Q/N207Q, N52Q/N168Q, N84Q/N207Q, N155Q/N207Q, N119Q/N168Q, N119Q/N207Q, N119Q/N155Q, N52Q/N84Q, N52Q/N119Q, N84Q/N119Q, N52Q/N84Q/N168Q, N52Q/N84Q/N207Q, N84Q/N155Q/N168Q, N84Q/N168Q/N207Q, N84Q/N155H/N207Q, N155Q/N168Q/N207Q, N119Q/N155Q/N168Q, N119Q/N168Q/N207Q, N84Q/N119Q/N207Q, N119Q/N155H/N207Q, N84Q/N119Q/N155Q, N52Q/N119Q/N155Q, N52H/N84Q/N119Q, N52H/N84Q, N52H/N84Q/N168Q, N52H/N84Q/N207Q, N52H/N84Q/N168Q/N207Q, N52Q/N84Q/N155Q, N52Q/N84Q/N168Q, N52Q/N84Q/N155Q/N168Q, N52Q/N84Q/N119Q/N168Q, N84Q/N119Q/N155Q/N168Q, N84Q/N155Q/N168Q/N207Q, N84Q/N119Q/N155Q/N207Q, N52Q/N84Q/N119Q/N207Q, N52Q/N84Q/N119Q/N155Q, N52Q/N84Q/N119Q/N155Q/N207Q, N84Q/N119Q/N155Q/N168Q/N207Q, N52A/N57F/Q100S, N52A/N57H/Q100S, N52A/N57Y/Q100A, N52D/N57A/Q100A, N52D/Q100S, N52G/Q100A, N52H/Q100A, N52M/N57H/Q100S, N52M/N57W/Q100P, N52Q/N57F, N52Q/N57S/Q100A, N52R/N57L/Q100A, N52R/N57Y/Q100P, N52R/N57Y/Q100S, N52S/N57A/Q100A, N52S/N57H/Q100E, N52S/N57L/Q100S, N52S/N57M/Q100S, N52S/N57Y/Q100S, N52S/N57Y/Q100M, N52S/N57Y/Q100V, N52T/N57H/Q100S, N52T/N57H/Q100A, N52T/N57Y/Q100A, N52V/N57L/Q100A, N52H/N57Y/Q100K, N52K/N57Y/Q100R, N52L/N57H/Q100R, N52R/N57F/Q100N, N52R/N57F/Q100P, N52R/N57F/Q100R, N52R/N57F/Q100T, N52R/N57H/Q100K, N52R/N57L/Q100S, N52R/N57W/Q100K, N52R/N57W, N52R/N57Y/Q100R, N52C/N57E/Q100S, N52G/N57P/Q100D, N52G/N57V/Q100G, N52G/N57V, N52L/N57V, N52P/N57P, N52P/N57S/Q100G, N52S/N57L/Q100G, N52T/N57K/Q100P, N52V/N57T/Q100L, or N57Q/Q100P.
In some embodiments, the ARBM is or an IgD (e.g. IgV) of wild-type ICOSL set forth in Table 7 or a vIgD thereof comprising any of the modifications (e.g. substitutions) listed in Table 7. Table 7 also provides exemplary sequences by reference to SEQ ID NO for ARBMs containing an ECD or IgV domain of ICOSL. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. IgV) also can be included in a sequence of an ARBM, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 7 is not to be construed as limiting. For example, the particular domain, such as the ECD or IgV domain, can be several amino acids longer or shorter, such as 1-10, e.g. 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO. Mutations designated with an “X” indicate the designated position contains a Q or the wild-type residue set forth in the corresponding position of SEQ ID NO: 32.
In some embodiments, the ARBM is or contains a wild-type ICOSL ECD set forth in SEQ ID NO: 32 or a variant ECD sequence set forth in any one of SEQ ID NOS: 2022-2055, 2074, 2076-2121, 2137-2154, 2160-2197, 2200-2206, 2208-2243, 2299-2346. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any one of SEQ ID NOS: 2022-2055, 2074, 2076-2121, 2137-2154, 2160-2197, 2200-2206, 2208-2243, 2299-2346) and contains the amino acid modification(s), e.g. substitution(s) not present in the unmodified or wild-type ICOSL ECD, e.g. not present in SEQ ID NO:32. In some embodiments, the ARBM is or contains a specific binding fragment of any of the ECD sequences set forth in any one of SEQ ID NOS: 2022-2055, 2074, 2076-2121, 2137-2154, 2160-2197, 2200-2206, 2208-2243, 2299-2346) and contains the amino acid modification(s), e.g. substitution (s) not present in the wild-type or unmodified ICOSL ECD, e.g. not present in SEQ ID NO:32.
In some embodiments, the ARBM is or contains a wild-type ICOSL IgV set forth in SEQ ID NO: 2056 or 2244 or a variant IgV sequence set forth in any one of SEQ ID NOS: 2057-2073, 2075, 2122-2136, 2155-2159, 2189-2199, 2207, 2245-2298, 2347-2518. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 2057-2073, 2075, 2122-2136, 2155-2159, 2189-2199, 2207, 2245-2298, 2347-2518 and contains the amino acid modification(s) (e.g. substitution(s)) not present in the unmodified or wild-type ICOSL, e.g. not present in SEQ ID NO:2056 or 2244. In some embodiments, the ARBM is or contains a specific binding fragment of any of the IgV sequences set forth in any one of SEQ ID NOS: 2057-2073, 2075, 2122-2136, 2155-2159, 2189-2199, 2207, 2245-2298, 2347-2518 and that contains the amino acid substitution(s) not present in the unmodified or wild-type ICOSL, e.g. not present in SEQ ID NO:2056 or 2244.
In some embodiments, the ARBM is or contains a vIgD that contains one or more amino acid modifications (e.g. substitutions) corresponding to a position(s) selected from 52, 57, 100, 110, or 198. In some embodiments, the one or more amino acid modifications are selected from N52H, N52D, N52S, N52K, S54A, S54P, N57Y, Q100P, Q100R, V110A, V110D, C198R, or a conservative amino acid substitution thereof.
In some embodiments, the variant ICOSL polypeptide has one or more amino acid substitutions including N52S, N52S, N52D, N52Y/N57Y/F138L/L203P, N52H/N57Y/Q100P, N52S/Y146C/Y152C, N52H/C198R, N52H/C140del/T225A, N52H/C198R/T225A, N52H/K92R, N52H/S99G, N57Y, N57Y/Q100P, N52S/S130G/Y152C, N52S/Y152C, N52S/C198R, N52Y/N57Y/Y152C, N52Y/N57Y/H129P/C198R, N52H/L161P/C198R, N52S/T113E, S54A, N52D/S54P, N52K/L208P, N52S/Y152H, N52H/I143T, N52S/L80P, N52S/D158G, N52D/Q133H, N52H/N57Y/Q100R/V110D/C198R/S212G, N52H/N57Y/Q100R/C198R, N52H/N57Y/L74Q/V110D/S192G, N52H/Q100R, N52H/S121G/C198R, A20V/N52H/N57Y/Q100R/S109G, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100R/V122A, N52H/N57Y/Q100R/F172S, N52H/N57Y/Q100R, N52S/F120S/N227K, N52S/N194D, N52S/F120S, N52S/G72R, N52S/A71T/A117T/T190A/C198R, N52H/N57Y/Q100R/V107I/V110D/S132F/1154F/C198R/R221G, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/C198R, N52H/N57Y/Q100R/V110D/C198R, F27S/N52H/N57Y/V110N, N52S/H94E/L96I/S109N/L166Q, S18R/N52S/F93L/I143V/R221G, V11E/N30D/N52H/N57Y/H94E/L96I/L98F/N194D/V210A/I218T, N52S/H94E/L96I/V122M, N52H/N57Y/H94E/L96I/F120I/S126T/W153R/I218N, M10V/S18R/N30D/N52S/S126R/T139S/L203F, S25G/N30D/N52S/F120S/N227K, N52H/N57Y/Q100R/V110D/F172S/C198R, S25G/F27C/N52H/N57Y/Q100R/V110D/E135K/L173S/C198R, N52H/N57Y/V110A/C198R/R221I, N52H/N57Y/Q100R/L102R/V110D/H115R/C198R, N52H/N57Y/Q100R/V110D/N144D/F172S/C198R, N52S/H94E/L98F/Q100R, N52S/E90A, N52S/F120S/I143V/I224V, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52Y/N57Y/Q100P/F172S, E16V/N52H/N57Y/Q100R/V110D/H115R/Y152C/K156M/F172S/C198R, N52S/H115R/F120S/I143V/C198R, N52H/N57Y/Q100P/C198R, N52H/N57Y/Q100P/H115R/F172S/C198R, N52H/N57Y/Q100P/F172S/C198R, N52H/N57Y/Q100P/H115R, N52H/N57Y/Q100P/H115R/C198R, N52H/Q100R/C198R, N52H/Q100R/H115R/F172S, N52H/Q100R/H115X/F172S/C198R, N52H/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S, Q100R, N52Y/F138L/L203P, N57Y/Q100R/C198R, N57Y/F138L/L203, N52H, N57Y, N57Y/Q100P, Q100R/F138L, N52H/N57Y/Q100R/H115R, N52H/N57Y/Q100R/F172S, N52H/N57Y/Q100R/H115R/F172S/1224V, N52H/N57Y/Q100R/H115R/F172S, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/Q100R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/I143V/F172S/C198R, N52H/N57Y/Q100R/L102R/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/F172S/N194D, N52H/N57Y/H115R/F172S/C198R, N52H/N57Y/Q100R/H115R/C198R, N52H/N57Y/H115R, N52H/Q100R/H115R/1143T/F172S, N52H/N57Y/Q100P/H115R/F172S, E16V/N52H/N57Y/Q100R/V110D/H115R/C198R, N30D/K42E/N52S/H115R/C198R/R221I, N52S/E90A/H115R, N30D/K42E/N52S/H115R, N52S/H115R/F172S/C198R, N119Q, N207Q, N52Q/N207X, N168X/N207X, N52Q/N168Q, N84Q/N207Q, N119Q/N168Q, N119Q/N207Q, N119Q/N155X, N52Q/N119Q, N52Q/N84Q/N207Q, N119Q/N155Q/N168Q, N52Q/N84Q/N155X/N168X, N52Q/N84Q/N119Q/N168Q, N52A/N57F/Q100S, N52A/N57H/Q100S, N52A/N57Y/Q100A, N52D/N57A/Q100A, N52D/Q100S, N52G/Q100A, N52H/Q100A, N52M/N57H/Q100S, N52M/N57W/Q100P, N52Q/N57F, N52Q/N57S/Q100A, N52R/N57L/Q100A, N52R/N57Y/Q100P, N52R/N57Y/Q100S, N52S/N57A/Q100A, N52S/N57H/Q100E, N52S/N57L/Q100S, N52S/N57M/Q100S, N52S/N57Y/Q100S, N52S/N57Y/Q100M, N52S/N57Y/Q100V, N52T/N57H/Q100S, N52T/N57H/Q100A, N52T/N57Y/Q100A, N52V/N57L/Q100A, N52H/N57Y/Q100K, N52K/N57Y/Q100R, N52L/N57H/Q100R, N52R/N57F/Q100N, N52R/N57F/Q100P, N52R/N57F/Q100R, N52R/N57F/Q100T, N52R/N57L/Q100S, N52R/N57W/Q100K, N52R/N57W, N52G/N57V, N52L/N57V, N52S/N57L/Q100G, N52T/N57K/Q100P.
b. CD80 IgD or vIgD
Provided herein are immunomodulatory proteins containing an ARBM that is or contains one or more IgD, such as a wild-type or unmodified IgD or a vIgD, of CD80. In some embodiments, the ARBM is not the full length sequence of the CD80. In some aspects, the ARBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of CD80. In some embodiments, the ARBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:28 or a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgV sequence set forth in SEQ ID NOs: 1005, 1079, 2615, 2654, or 3580, or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an ARBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified CD80. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO: 28, 1005, 1079, 2615, 2654, or 3580 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 28, 1005, 1079, 2615, 2654, or 3580. In some embodiments, an ARBM containing a vIgD of CD80 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 28, 1005, 1079, 2615, 2654, or 3580.
In some embodiments, the ARBM is or contains a vIgD that is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for CD28 relative to the binding activity of the wild-type or unmodified IgD for CD28. In some embodiments, the increase in binding activity, e.g. binding affinity, for CD28 is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions).
In some embodiments, the equilibrium dissociation constant (Kd) of the ARBM to CD28 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less. In some embodiments, the ARBM binds to CD28 with a Kd of from or from about 100 pm to 5000 pm, 100 pm to 2000 pm, 100 pm to 1500 pm, 100 pm to 1000 pm, 100 pm to 800 pm, 100 pm to 500 pm, 100 pm to 400 pm, 400 pm to 4000 pm, 400 pm to 2000 pm, 400 pm to 1500 pm, 400 pm to 1000 pm, 400 pm to 800 pm, 400 pm to 500 pm, 500 pm to 5000 pm, 500 pm to 2000 pm, 500 pm to 1500 pm, 500 pm to 1000 pm, 500 pm to 800 pm, 800 pm to 5000 pm, 800 pm to 2000 pm, 800 pm to 1500 pm, 800 pm to 1000 pm, 1000 pm to 5000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm, 1500 pm to 5000 pm, 1500 to 2000 pm to 2000 pm to 50000 pm. In some embodiments, the ABRM binds to CD28 with a Kd of less than 200 pM, 300 pM, 400 pM, 500 pM. In some embodiments, the ABRM binds to CD28 with a Kd of greater than or greater than about 500 pm but less than or less than about 2000 pm, such as from or from about 500 pm to 1500 pm, 500 pm to 1250 pm, 500 pm to 1000 pm, 500 pm to 750 pm, 750 pm to 1500 pm, 750 pm to 1250 pm, 750 pm to 1000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm or 1500 pm to 2000 pm.
In some aspects, a vIgD of CD80 may exhibit increased binding activity, e.g. binding affinity, to the inhibitory receptor CTLA-4. In some embodiments, the increase in binding activity, e.g. binding affinity, for CTLA-4 is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, such a vIgD may be used as an IRBM in the embodiments provided herein. In some embodiments, the equilibrium dissociation constant (Kd) of the IRBM to CTLA-4 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less. In some embodiments, such an IRBM exhibits a greater binding activity, e.g. binding affinity, for CTLA-4 than for CD28, such as a binding activity, e.g. binding affinity, that is at least 1.2-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold, 5.0-fold or 10.0-fold greater for CTLA-4 than for CD28.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a CD80 ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:28 or, where applicable, the unmodified IgV sequence set forth in SEQ ID NO: 1005, 1079, 2615, 2654, or 3580. It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs: 28, 1005, 1079, 2615, 2654, or 3580. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the ARBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified CD80. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of CD80 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD80 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of CD80 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD80 or a specific binding fragment thereof and in an IgC domain or domains of CD80 or a specific binding fragment thereof.
In some embodiments, the ARBM is or contains a vIgD that has one or more amino acid modifications (e.g., substitutions) in an unmodified IgD of CD80 or specific binding fragment thereof corresponding to position(s) 4, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 46, 47, 48, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 99, 102, 103, 104, 107, 108, 109, 110, 114, 115, 116, 117, 118, 120, 121, 122, 126, 127, 128, 129, 130, 133, 137, 140, 142, 143, 144, 148, 149, 152, 154, 160, 162, 164, 168, 169, 174, 175, 177, 178, 183, 185, 188, 190, 192, 193 or 199 with reference to numbering of SEQ ID NO: 28, 1005, 1079, 2615, 2654, or 3580.
In some embodiments, the ARBM is or contains a vIgD of CD80 that has one or more amino acid modifications, e.g. substitutions, selected from among V4M, E7D, K9E, E10R, V11S, A12G, A12T, A12V, T13N, T13A, T13R, L14A, S15V, S15F, 515P, C165, C16G, C16L, C16R, G17W, H18L, H18R, H18Y, V20A, V20I, V20L, S21P, V22A, V22I, V22D, V22L, E23D, E23G, E24D, E24G, L25P, L25S, A26E, A26P, A26S, A26T, Q27H, Q27L, Q27R, T28A, T28S, R29C, R29D, R29H, R29V, 130F, 130T, 130V, Y31F, Y31H, Y31L, Y31S, Q33E, Q33H, Q33K, Q33L, Q33R, K34E, E35D, E35G, K36E, K36G, K36R, K37E, K37Q, M38I, M38L, M38T, M38V, L40M, T41A, T41G, T41D, T41I, T41S, M42I, M42T, M42V, M431, M43L, M43Q, M43R, M43T, M43V, S44P, D46E, D46V, M471, M47L, M47T, M47V, N48H, N48D, N48H, N48I, N48K, N48R, N48S, N48T, W50G, P51A, E52G, Y53C, Y53F, K54M, K54E, K54N, K54R, N55D, N55I, T57A, T57I, I58V, F59L, F59S, D60V, I61N, I61V, T62A, T62N, T62S, N63S, N64S, L65H, L65P, S66H, I67F, I67L, I67T, I67V, V68A, V68E, V68L, V68M, I69F, I69T, L70M, L70P, L70R, L70Q, A71D, A71G, L72V, L72P, R73H, R73S, P74L, P74S, D76G, D76H, E77A, E77G, E77K, G78A, T79A, T791, T79L, T79P, Y80N, E81A, E81G, E81K, E81R, E81V, C82R, V83A, V83I, V84A, V84I, L85E, L85I, L85M, L85R, L85Q, K86E, K86M, Y87H, Y87N, E88D, E88G, E88V, K89E, K89N, K89R, D90K, D90L, D90N, A91E, A91G, A91S, A91T, F92L, F92N, F92P, F92S, F92V, F92Y, K93I, K93E, K93Q, K93R, K93V, R94G, R94L, R94F, R94Q, R94W, E95D, E95K, E95V, H96R, L97M, L97R, L97Q, E99D, E99G, L1025, 5103L, S103P, V104A, V104L, D107N, F108L, P1095, P109H, T110A, D115G, S114T, F1165, F116L, E117V, E117G, 1118V, 1118A, 1118T, T120S, S121P, N122S, I126L, I126V, I127T, C128Y, C128R, 5129L, S129P, T130A, G133D, P137L, 5140T, L1425, E143G, N144D, N144S, L1485, N149D, N149S, N152T, T1541, T154A, E160G, E162G, Y164H, S168G, K169E, K1691, K1695, M174T, M174V, T175A, N177S, H178R, L183H, K185E, H188D, H188Q, R1905, N192D, Q193L, or T1995 or a conservative amino acid modification, e.g. substitution thereof.
In some embodiments, the ARBM is or contains a vIgD of CD80 that has two or more amino acid modifications, e.g. substitutions, selected from among V4M, E7D, K9E, E10R, V11S, A12G, A12T, A12V, T13N, T13A, T13R, L14A, S15V, S15F, S15P, C16S, C16G, C16L, C16R, G17W, H18L, H18R, H18Y, V20A, V20I, V20L, S21P, V22A, V22I, V22D, V22L, E23D, E23G, E24D, E24G, L25P, L25S, A26E, A26P, A26S, A26T, Q27H, Q27L, Q27R, T28A, T28S, R29C, R29D, R29H, R29V, 130F, 130T, 130V, Y31F, Y31H, Y31L, Y31S, Q33E, Q33H, Q33K, Q33L, Q33R, K34E, E35D, E35G, K36E, K36G, K36R, K37E, K37Q, M38I, M38L, M38T, M38V, L40M, T41A, T41G, T41D, T41I, T41S, M42I, M42T, M42V, M43I, M43L, M43Q, M43R, M43T, M43V, S44P, D46E, D46V, M47I, M47L, M47T, M47V, N48H, N48D, N48H, N48I, N48K, N48R, N48S, N48T, W50G, P51A, E52G, Y53C, Y53F, K54M, K54E, K54N, K54R, N55D, N55I, T57A, T57I, I58V, F59L, F59S, D60V, I61N, I61V, T62A, T62N, T62S, N63S, N64S, L65H, L65P, S66H, I67F, I67L, I67T, I67V, V68A, V68E, V68L, V68M, I69F, I69T, L70M, L70P, L70R, L70Q, A71D, A71G, L72V, L72P, R73H, R73S, P74L, P74S, D76G, D76H, E77A, E77G, E77K, G78A, T79A, T79I, T79L, T79P, Y80N, E81A, E81G, E81K, E81R, E81V, C82R, V83A, V83I, V84A, V84I, L85E, L85I, L85M, L85R, L85Q, K86E, K86M, Y87H, Y87N, E88D, E88G, E88V, K89E, K89N, K89R, D90K, D90L, D90N, A91E, A91G, A91S, A91T, F92L, F92N, F92P, F92S, F92V, F92Y, K93I, K93E, K93Q, K93R, K93V, R94G, R94L, R94F, R94Q, R94W, E95D, E95K, E95V, H96R, L97M, L97R, L97Q, E99D, E99G, L102S, S103L, S103P, V104A, V104L, D107N, F108L, P109S, P109H, T110A, D115G, S114T, F116S, F116L, E117V, E117G, 1118V, 1118A, 1118T, T120S, S121P, N122S, I126L, I126V, I127T, C128Y, C128R, S129L, S129P, T130A, G133D, P137L, S140T, L142S, E143G, N144D, N144S, L148S, N149D, N149S, N152T, T1541, T154A, E160G, E162G, Y164H, S168G, K169E, K1691, K169S, M174T, M174V, T175A, N177S, H178R, L183H, K185E, H188D, H188Q, R190S, N192D, Q193L, or T199S.
In some embodiments, the one or more amino acid modification(s), e.g. substitution(s) is 130F/L70P, Q27H/T41S/A71D, I30T/L70R, T13R/C16R/L70Q/A71D, T57I, M43I/C82R, V22L/M38V/M47T/A71D/L85M, 130V/T571/L70P/A71D/A91T, V22I/L70M/A71D, N55D/L70P/E77G, T57A/I69T, N55D/K86M, L72P/T791, T79P, E35D/M471/L65P/D90N, L25S/E35D/M471/D90N, A71D, T13A/I61N/A71D, K34E/T41A/L72V, T41S/A71D/V84A, E35D/A71D, E35D/M47I, K36R/G78A, S44P/A71D, Q27H/M431/A71D/R73S, Q33R/K54N/T57I/167V/A71D, E35D/T57I/L70Q/A71D, M42I/I61V/A71D, P51A/A71D, H18Y/M471/T571/A71G, V201/M47V/T571/V841, V201/M47V/A71D, A71D/L72V/E95K, V22L/E35G/A71D/L72P, E35D/A71D, E35D/I67L/A71D, Q27H/E35G/A71D/L72P/T79I, T13R/M42V/M471/A71D, E35D, E35D/M471/L70M, E35D/A71D/L72V, E35D/M43L/L70M, A26P/E35D/M43I/L85Q/E88D, E35D/D46V/L85Q, Q27L/E35D/M471/T57I/L70Q/E88D, M47V/I69F/A71D/V831, E35D/T57A/A71D/L85Q, H18Y/A26T/E35D/A71D/L85Q, E35D/M47L, E23D/M42V/M431/158V/L70R, V68M/L70M/A71D/E95K, N551/T571/I69F, E35D/M43I/A71D, T41S/T571/L70R, H18Y/A71D/L72P/E88V, V20I/A71D, E23G/A26S/E35D/T62N/A71D/L72V/L85M, A12T/E24D/E35D/D46V/161V/L72P/E95V, V22L/E35D/M43L/A71G/D76H, E35G/K54E/A71D/L72P, L70Q/A71D, A26E/E35D/M47L/L85Q, D46E/A71D, Y31H/E35D/T41S/V68L/K93R/R94W, A26E/Q33R/E35D/M47L/L85Q/K86E, A26E/Q33R/E35D/M47L/L85Q, E35D/M47L/L85Q, A26E/Q33L/E35D/M47L/L85Q, A26E/Q33L/E35D/M47L, H18Y/A26E/Q33L/E35D/M47L/L85Q, Q33L/E35D/M47I, H18Y/Q33L/E35D/M471, Q33L/E35D/D46E/M47I, Q33R/E35D/D46E/M47I, H18Y/E35D/M47L, Q33L/E35D/M47V, Q33L/E35D/M47V/T79A, Q33L/E35D/T41S/M47V, Q33L/E35D/M47I/L85Q, Q33L/E35D/M47I/T62N/L85Q, Q33L/E35D/M47V/L85Q, A26E/E35D/M43T/M47L/L85Q/R94Q, Q33R/E35D/K37E/M47V/L85Q, V22A/E23D/Q33L/E35D/M47V, E24D/Q33L/E35D/M47V/K54R/L85Q, S15P/Q33L/E35D/M47L/L85Q, E7D/E35D/M47I/L97Q, Q33L/E35D/T41S/M43I, E35D/M47I/K54R/L85E, Q33K/E35D/D46V/L85Q, Y31S/E35D/M47L/T79L/E88G, H18L/V22A/E35D/M47L/N48T/L85Q, Q27H/E35D/M47L/L85Q/R94Q/E95K, Q33K/E35D/M47V/K89E/K93R, E35D/M47I/E77A/L85Q/R94W, A26E/E35D/M43I/M47L/L85Q/K86E/R94W, Q27H/Q33L/E35D/M47V/N55D/L85Q/K89N, H18Y/V20A/Q33L/E35D/M47V/Y53F, V22A/E35D/V68E/A71D, Q33L/E35D/M47L/A71G/F92S, V22A/R29H/E35D/D46E/M47I, Q33L/E35D/M431/L85Q/R94W, H18Y/E35D/V68M/L97Q, Q33L/E35D/M47L/V68M/L85Q/E88D, Q33L/E35D/M43V/M47I/A71G, E35D/M47L/A71G/L97Q, E35D/M47V/A71G/L85M/L97Q, H18Y/Y31H/E35D/M47V/A71G/L85Q, E35D/D46E/M47V/L97Q, E35D/D46V/M47I/A71G/F92V, E35D/M47V/T62A/A71G/V83A/Y87H/L97M, Q33L/E35D/N48K/L85Q/L97Q, E35D/L85Q/K93T/E95V/L97Q, E35D/M47V/N48K/V68M/K89N, Q33L/E35D/M47I/N48D/A71G, R29H/E35D/M43V/M47I/149V, Q27H/E35D/M471/L85Q/D90G, E35D/M471/L85Q/D90G, E35D/M47I/T62S/L85Q, A26E/E35D/M47L/A71G, E35D/M47I/Y87Q/K89E, V22A/E35D/M47I/Y87N, H18Y/A26E/E35D/M47L/L85Q/D90G, E35D/M47L/A71G/L85Q, E35D/M47V/A71G/E88D, E35D/A71G, E35D/M47V/A71G, 130V/E35D/M47V/A71G/A91V, I30V/Y31C/E35D/M47V/A71G/L85M, V22D/E35D/M47L/L85Q, H18Y/E35D/N48K, E35D/T41S/M47V/A71G/K89N, E35D/M47V/N48T/L85Q, E35D/D46E/M47V/A71D/D90G, E35D/D46E/M47V/A71D, E35D/T41S/M431/A71G/D90G, E35D/T41S/M43I/M47V/A71G, E35D/T41S/M43I/M47L/A71G, H18Y/V22A/E35D/M47V/T62S/A71G, H18Y/A26E/E35D/M47L/V68M/A71G/D90G, E35D/K37E/M47V/N48D/L85Q/D90N, Q27H/E35D/D46V/M47L/A71G, V22L/Q27H/E35D/M47I/A71G, E35D/D46V/M47L/V68M/L85Q/E88D, E35D/T41S/M43V/M471/L70M/A71G, E35D/D46E/M47V/N63D/L85Q, E35D/M47V/T62A/A71D/K93E, E35D/D46E/M47V/V68M/D90G/K93E, E35D/M43I/M47V/K89N, E35D/M47L/A71G/L85M/F92Y, E35D/M42V/M47V/E52D/L85Q, V22D/E35D/M47L/L70M/L97Q, E35D/T41S/M47V/L97Q, E35D/Y53H/A71G/D90G/L97R, E35D/A71D/L72V/R73H/E81K, Q33L/E35D/M43I/Y53F/T62S/L85Q, E35D/M38T/D46E/M47V/N48S, Q33R/E35D/M47V/N48K/L85M/F92L, E35D/M38T/M43V/M47V/N48R/L85Q, T28Y/Q33H/E35D/D46V/M47I/A71G, L70Q/A91G, L70Q/A91G/T130A, L70Q/A91G/II18A/T120S/T130A, V4M/L70Q/A91G/T120S/T130A, L70Q/A91G/T120S/T130A, V20L/L70Q/A91S/T120S/T130A, S44P/L70Q/A91G/T130A, L70Q/A91G/E117G/T120S/T130A, A91G/T120S/T130A, L70R/A91G/T120S/T130A, L70Q/E81A/A91G/T120S/1127T/T130A, L70Q/Y87N/A91G/T130A, T28S/L70Q/A91G/E95K/T120S/T130A, N63S/L70Q/A91G/T120S/T130A, K36E/I67T/L70Q/A91G/T120S/T130A/N152T, E52G/L70Q/A91G/T120S/T130A, K37E/F59S/L70Q/A91G/T120S/T130A, A91G/S103P, K89E/T130A, A91G, D60V/A91G/T120S/T130A, K54M/A91G/T120S, M38T/L70Q/E77G/A91G/T120S/T130A/N152T, R29H/E52G/L70R/E88G/A91G/T130A, Y31H/T41G/L70Q/A91G/T120S/T130A, V68A/T110A, S66H/D90G/T110A/F116L, R29H/E52G/T120S/T130A, A91G/L102S, I67T/L70Q/A91G/T120S, L70Q/A91G/T110A/T120S/T130A, M38V/T41D/M431/W50G/D76G/V83A/K89E/T120S/T130A, V22A/L70Q/S121P, A12V/S15F/Y31H/T41G/T130A/P137L/N152T, 167F/L70R/E88G/A91G/T120S/T130A, E24G/L25P/L70Q/T120S, A91G/F92L/F108L/T120S, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118T/N149S, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/N144 S/N149S, R29D/Y31L/Q33H/K36G/M38I/T41A/M42T/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/L148S/N149S, E24G/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/F59L/E81V/L85R/K89N/A91T/F92P/K93V/R94L/H96R/N149S/C182S, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/N149 S, R29V/M43Q/E81R/L851/K89R/D90L/A91E/F92N/K93Q/R94G, T41I/A91G, K89R/D90K/A91G/F92Y/K93R/N122S/N177S, K89R/D90K/A91G/F92Y/K93R, K36G/K37Q/M38I/F59L/E81V/L85R/K89N/A91T/F92P/K93V/R94L/E99G/T130A/N149S, E88D/K89R/D90K/A91G/F92Y/K93R, K36G/K37Q/M38I/L40M, K36G, R29H/Y31H/T41G/Y87N/E88G/K89E/D90N/A91G/P109S, A12T/H18L/M43V/F59L/E77K/P109S/1118T,
R29V/Y31F/K36G/M38L/M43Q/E81R/V831/L851/K89R/D90L/A91E/F92N/K93Q/R94G, V68M/L70P/L72P/K86E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T120S/1127T/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T120S/T130A/M174T, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/F59L/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T120S/1127T/T130A/H188D, H18R/R29D/Y31L/Q33H/K36G/K37E/M381/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A/E143G/K169E/M174V/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T120S/1127T/T130A/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L85R/K89N/A91T/F92P/K93V/R94L/T120S/1127 T/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/F108L/T 120S/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T130A/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A/K169E, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T120S/1127T/C128Y/T130A/H188D, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94F/T130A/K169E, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T130A, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/T130A/K169E, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K931/R94L/L97R/T 130A, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K931/R94L/L97R/T 130A/L148S, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/I11 8V/T120S/1127T/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/161N/E81V/L85R/K89N/A91T/F92P/K93V/R94F/V 104A/T120S/T130A, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/F92P/K93V/R94F/I118V/T130A, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/T62S/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/K169E/T175A, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/F116S/T130A/H188D, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 120S/1127T/T130A/L142S/H188D, C16S/H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 110A/H188D, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/A91G/T120S/1127T/T130A/H188D, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/L70Q/D76G/A91G/S103L/T120S/1127T/T130A, DELTAQ33/Y53C/L85R/K89N/A91T/F92P/K93V/R94L/T120S/1127T/T130A/K169E, T62S/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T120S/T130A/K169E, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/S129L/H188D, K9E/E10R/V11S/A12G/T13N/K14A/S15V/C16L/G17W/H18Y/Y53C/L70Q/D90G/T 130A/N149D/N152T/H188D, H18L/R29D/Y31L/Q33H/K36G/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/I118V/T 120S/1127T/T130A/H188D, K89E/K93E/T130A, S21P/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/N481/V68A/E81V/L85R/K89N/A91T/F92P/K93V/R94L/P109H/I126L/K1691, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/P74L/Y80N/E81V/L85R/K89N/A91T/F92P/K93V/R94L/L97R, S21P/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/P74L/Y80N/E81V/L85R/K89N/D90N/A91T/F92P/K93V/R94L/T 130A/N149S/E162G, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/V68M/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T130A, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/V68M/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T130A/N149S/R190S, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/P74L/Y80N/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T 130A/R190S, C16G/V22A/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/V68M/D76G/E81V/L85R/K89N/A91 T/F92P/K93V/R94L/1118 T/T130A/S140T/N149S/K1691/H178R/N192D, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94F/E117V/1118T/N149S/S168G/H188Q, V22A/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/V68M/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T130A, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/N64S/E81V/L85R/K89N/A91T/F92P/K93V/R94F/1118T/T130A/N149S/K1691, V22A/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/V68M/E81V/L85R/K89N/A91T/F92P/K93V/R94L/D115G/1118T/T130A/G133D/N149S, S129P, A91G/S129P, 169T/L70Q/A91G/T120S, Y31H/S129P, T28A/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/V 104L/T130A/N149S, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/L97R/N149S/H188Q, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/L97R/N149S, H18L/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/V68A/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T130A/N149S/T154I, A12G/R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/V68A/E81V/L85R/K89N/A91T/F92P/K93V/R94L/L97R/T130A/L183H, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118T/T 130A/S140T/N149S/K169S, R29D/Y31L/Q33H/K36G/M381/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118T/T130A/N149S/K1691/Q193L, V22A/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118T/T130A/N149S, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118T/T130A/N149S, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118T/T130A/N149S/K1691, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94F/T130A/N149S/K1691, I118T/C128R, Q27R/R29C/M42T/S129P/E160G, S129P/T154A, S21P/L70Q/D90G/T120S/T130A, L70Q/A91G/N144D, L70Q/A91G/I118A/T120S/T130A/K169E, V4M/L70Q/A91G/I118V/T120S/T130A/K169E, L70Q/A91G/I118V/T120S/T130A/K169E, L70Q/A91G/I118V/T120S/T130A, V20L/L70Q/A91S/I118V/T120S/T130A, L70Q/A91G/E117G/II18V/T120S/T130A, A91G/II18V/T120S/T130A, L70R/A91G/II18V/T120S/T130A/T199S, L70Q/E81A/A91G/1118V/T120S/1127T/T130A, T28S/L70Q/A91G/E95K/I118V/T120S/I126V/T130A/K169E, N63S/L70Q/A91G/S114T/II18V/T120S/T130A, K36E/I67T/L70Q/A91G/1118V/T120S/T130A/N152T, E52G/L70Q/A91G/D107N/I118V/T120S/T130A/K169E, K37E/F59S/L70Q/A91G/1118V/T120S/T130A/K185E, D60V/A91G/I118V/T120S/T130A/K169E, K54M/L70Q/A91G/Y164H/T120S, M38T/L70Q/E77G/A91G/I118V/T120S/T130A/N152T, Y31H/T41G/M43L/L70Q/A91G/I118V/T120S/I126V/T130A, L65H/D90G/T110A/F116L, R29H/E52G/D90N/1118V/T120S/T130A, I67T/L70Q/A91G/I118V/T120S, L70Q/A91G/T110A/II18V/T120S/T130A, M38V/T41D/M431/W50G/D76G/V83A/K89E/1118V/T120S/I126V/T130A, A12V/S15F/Y31H/M38L/T41G/M43L/D90N/T130A/P137L/N149D/N152T, 167F/L70R/E88G/A91G/I118V/T120S/T130A, E24G/L25P/L70Q/A91G/I118V/T120S/N152T, A91G/F92L/F108L/1118V/T120S, E88D/K89R/D90K/A91G/F92Y/K93R/N122S/N177S, K36G/K37Q/M38I/L40M/F59L/E81V/L85R/K89N/A91T/F92P/K93V/R94L/E99G/T130A/N149S, K36G/L40M, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/Il 18V/T120S/1127T/T130A, H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/I 118V/T120S/1127T/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/K169E/M174T, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/N48D/F59L/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/H188D, H18R/R29D/Y31L/Q33H/K36G/K37E/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/E143G/K169E/M174V/H188D, R29D/130V/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/I 118V/T120S/1127T/T130A/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120 S/I127T/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/F108L/1118V/T120S/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/N149D/K169E/H188D, H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/K169E/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/C128Y/T130A/H188D, H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/E99D/T130A, H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/K169E, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/I61N/E81V/L85R/K89N/A91T/F92P/K93V/R94F/V104A/1118V/T120S/I126V/T130A, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94F/1118V/T120S/T130A, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/T62S/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/K169E/T175A, H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/L142S/H188D, Cl6S/H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T110A/II18V/H188D, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/A91G/I118V/T120S/1127T/T130A/H188, R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/L70Q/D76G/A91G/S103L/I118V/T120S/1127T/T130A, Y53C/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/K169E, T62S/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/T130A/K169E, Y53C/L70Q/D90G/T130A/N149D/N152T/H188D, H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/1118V/T120S/1127T/T130A/H188D, and H18L/R29D/Y31L/Q33H/K36G/M38I/T41A/M43R/M47T/E81V/L85R/K89N/A91T/F92P/K93V/R94L/T130A/N149S.
In some embodiments, the ARBM is or an IgD (e.g. IgV) of wild-type CD80 set forth in Table 8 or a vIgD thereof comprising any of the modifications (e.g. substitutions) listed in Table 8. Table 8 also provides exemplary sequences by reference to SEQ ID NO for ARBMs containing an ECD or IgV domain of CD80. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. IgV) also can be included in a sequence of an ARBM, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 8 is not to be construed as limiting. For example, the particular domain, such as the ECD or IgV domain, can be several amino acids longer or shorter, such as 1-10, e.g. 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO.
In some embodiments, the ARBM is or contains a wild-type CD80 ECD set forth in SEQ ID NO: 28 or a variant CD80 ECD sequence set forth in any one of SEQ ID NOS: 932-1004, 2656-2751. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any one of SEQ ID NOS: 932-1004, 2656-2751 and contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD80 ECD, e.g. not present in SEQ ID NO:28. In some embodiments, the ARBM is or contains a specific binding fragment of any of the ECD sequences set forth in any one of SEQ ID NOS: 932-1004, 2656-2751) and contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD80, e.g. not present in SEQ ID NO:28.
In some embodiments, the ARBM is or contains a wild-type CD80 IgV set forth in any one of SEQ ID NOs: 1005, 1079, 2615, 2654, or 3580 or a variant IgV sequence set forth in any one of SEQ ID NOS: 1006-1078, 1080-1152, 2752-2943. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 1006-1078, 1080-1152, 2752-2943 and contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD80, e.g. not present in SEQ ID NO: 1005, 2615, 2654, or 3580. In some embodiments, ARBM is or contains a specific binding fragment of any of the IgV set forth in any one of SEQ ID NOS: 77-149, 151-223, 2105-2296) and that contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD80, e.g. not present in SEQ ID NO: 1005, 2615 or 2654, or 3580.
c. CD86 IgD or vIgD
Provided herein are immunomodulatory proteins containing an ARBM that is or contains one or more IgD, such as a wild-type or unmodified IgD or a vIgD, of CD86. In some embodiments, the ARBM is not the full length sequence of the CD86. In some aspects, the ARBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of CD86. In some embodiments, the ARBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:29 or a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgV sequence set forth in SEQ ID NO: 1195, or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an ARBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified CD86. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO: 29 or 1195 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 29 or 1195. In some embodiments, an ARBM containing a vIgD of CD86 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NO: 29 or 1195.
In some embodiments, the ARBM is or contains a vIgD that is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for CD28 relative to the binding activity of the wild-type or unmodified IgD for CD28. In some embodiments, the increase in binding activity, e.g. binding affinity, for CD28 is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions).
In some embodiments, the equilibrium dissociation constant (Kd) of the ARBM to CD28 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less. In some embodiments, the ARBM binds to CD28 with a Kd of from or from about 100 pm to 5000 pm, 100 pm to 2000 pm, 100 pm to 1500 pm, 100 pm to 1000 pm, 100 pm to 800 pm, 100 pm to 500 pm, 100 pm to 400 pm, 400 pm to 4000 pm, 400 pm to 2000 pm, 400 pm to 1500 pm, 400 pm to 1000 pm, 400 pm to 800 pm, 400 pm to 500 pm, 500 pm to 5000 pm, 500 pm to 2000 pm, 500 pm to 1500 pm, 500 pm to 1000 pm, 500 pm to 800 pm, 800 pm to 5000 pm, 800 pm to 2000 pm, 800 pm to 1500 pm, 800 pm to 1000 pm, 1000 pm to 5000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm, 1500 pm to 5000 pm, 1500 to 2000 pm to 2000 pm to 50000 pm. In some embodiments, the ABRM binds to CD28 with a Kd of less than 200 pM, 300 pM, 400 pM, 500 pM. In some embodiments, the ABRM binds to CD28 with a Kd of greater than or greater than about 500 pm but less than or less than about 2000 pm, such as from or from about 500 pm to 1500 pm, 500 pm to 1250 pm, 500 pm to 1000 pm, 500 pm to 750 pm, 750 pm to 1500 pm, 750 pm to 1250 pm, 750 pm to 1000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm or 1500 pm to 2000 pm.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a CD86 ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:29 or, where applicable, the unmodified IgV sequence set forth in SEQ ID NO: 1195. It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs: 29 or 1195. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the ARBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified CD86. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of CD86 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD86 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of CD80 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CD86 or a specific binding fragment thereof and in an IgC domain or domains of CD86 or a specific binding fragment thereof.
In some embodiments, the ARBM is or contains a vIgD that has one or more amino acid modifications (e.g., substitutions) in an unmodified IgD of CD86 or specific binding fragment thereof corresponding to position(s) 35, 90, and/or 102 with reference to numbering of SEQ ID NO: 29 or 1195. In some embodiments, the ARBM is or contains a vIgD of CD86 that one or more amino acid modifications (e.g., substitutions) from among Q35H, H90L, and/or Q102H or a conservative amino acid substitution thereof. In some embodiments, the one or more amino acid modification(s), e.g. substitution(s), is Q35H/H90L/Q102H.
In some embodiments, the ARBM is or contains an IgD (e.g. IgV) of wild-type CD86 set forth in Table 9 or a vIgD thereof comprising any of the modifications (e.g. substitutions) listed in Table 9. Table 9 also provides exemplary sequences by reference to SEQ ID NO for ARBMs containing an ECD or IgV domain of CD86. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. IgV) also can be included in a sequence of an ARBM, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 9 is not to be construed as limiting. For example, the particular domain, such as the ECD or IgV domain, can be several amino acids longer or shorter, such as 1-10, e.g. 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO.
In some embodiments, the ARBM is or contains a wild-type CD86 ECD set forth in SEQ ID NO: 29 or a variant CD86 ECD set forth in any one of SEQ ID NOS: 1191-1194. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any one of SEQ ID NOS: 1191-1194 and contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD86, e.g. not present in SEQ ID NO:29. In some embodiments, the ARBM is or contains a specific binding fragment of any of the ECD sequences set forth in any one of SEQ ID NOS: 1191-1194 and that contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD86, e.g. not present in SEQ ID NO:29.
In some embodiments, the ARBM is or contains a wild-type CD86 IgV set forth in SEQ ID NO: 1195 or a variant IgV sequence set forth in any one of SEQ ID NOS: 1196-1199. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 1196-1199 and contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD86, e.g. not present in SEQ ID NO:1195. In some embodiments, the ARBM is or contains a specific binding fragment of any of the IgV sequences set forth in any one of SEQ ID NOS: 1196-1199 and that contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CD86, e.g. not present in the sequence set forth in SEQ ID NO:1195.
2. CD2 Binding Molecules
Provided herein are immunomodulatory proteins containing an ARBM that is or contains a binding molecule that binds to CD2, such as to human CD2. In some embodiments, the ARBM of the immunomodulatory protein binds to the ectodomain of CD2. In some embodiments, the ARBM binds to CD2 on the surface of a cell, such as on the surface of a T cell.
In some embodiments, the provided immunomodulatory protein contains an ARBM that is or contains an antibody that binds CD2 or is an antigen-binding antibody fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding fragment binds to CD2, such as to human CD2. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of an anti-CD2 antibody or antigen-binding fragment.
In some embodiments, the ARBM is or contains one or more IgD(s) or a specific binding fragment thereof, such as an unmodified or wild-type IgD or a vIgD or a specific binding fragment thereof, of an IgSF family member that bind CD2. In some embodiments, the CD2 is human CD2. Exemplary IgSF family members that bind to CD2 include LFA-3 (CD58) and CD48.
In some embodiments, the ARBM is or contains one or more IgD that is an IgD, or a vIgD thereof, of an LFA-3 polypeptide, such as a wild-type LFA-3, e.g. a human LFA-3. In some embodiments, the ARBM is not the full length sequence of the LFA-3. In some aspects, the ARBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of LFA-3. In some embodiments, the ARBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:3239 or is a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgD (e.g. IgV or IgC) sequence of LFA-3, such as human LFA-3. In some embodiments, the ARBM is or contains an IgD sequence set forth in SEQ ID NO:2946, or is a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgD sequence set forth in SEQ ID NO:3650, or is a specific binding fragment thereof.
In some aspects, the ARBM contains one or more IgD that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified LFA-3, which, in some aspects, result in increased binding of the ARBM to CD2. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO:3239 or 2946 or 3650 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3239 or 2946 or 3650. In some embodiments, an ARBM containing a vIgD of LFA-3 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 3239 or 2946 or 3650.
In some embodiments, the ARBM is or contains one or more IgD that is an IgD, or a vIgD thereof, of a CD48 polypeptide, such as a wild-type CD48, e.g. a human CD48. In some embodiments, the ARBM is not the full length sequence of the CD48. In some aspects, the ARBM is a soluble polypeptide, is not membrane-expressed and/or lacks the GPI anchor or is mutated in the GPI anchoring moiety (e.g. residue S220) of CD48, e.g. set forth in SEQ ID NO:3493. In some embodiments, the ARBM only contains an IgD or vIgD, or a specific binding fragment thereof, such as only contains an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the ARBM is or contains the sequence set forth in SEQ ID NO:3493 or is a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgD (e.g. IgC) sequence of CD48, such as human CD48. In some embodiments, the ARBM is or contain an IgD (e.g. IgC) sequence set forth as amino acid residues 29-127 of SEQ ID NO:3493, or is a specific binding fragment thereof. In some embodiments, the ARBM is or contain an IgD (e.g. IgC) sequence set forth as amino acid residues 132-212 of SEQ ID NO:3493, or is a specific binding fragment thereof.
In some aspects, the ARBM contains one or more IgD that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified CD48, which, in some aspects, result in increased binding of the ARBM to CD2. In some embodiments, modifications provided herein can be in an ARBM containing the sequence set forth in SEQ ID NO:3493 or in an IgC domain or specific binding fragment thereof, or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3493 or in an IgC domain or specific binding fragment thereof. In some embodiments, an ARBM containing a vIgD of CD48 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 3493 or in an IgC domain or specific binding fragment thereof
3. CD3 Binding Molecules
Provided herein are immunomodulatory proteins containing an ARBM that is or contains a binding molecule that binds to CD3, such as to human CD3. In some embodiments, the ARBM of the immunomodulatory protein binds to the ectodomain of CD3. In some embodiments, the ARBM binds to CD3 on the surface of a cell, such as on the surface of a T cell.
In some embodiments, the provided immunomodulatory polypeptides contain an ARBM that is or contains an antibody that binds CD3 or is an antigen-binding fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding fragment binds to CD3, such as to human CD3. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of an anti-CD3 antibody or antigen-binding fragment. In some aspects, the anti-CD3 antibody is OKT3 or a fragment thereof, or is an antigen binding fragment containing a VH chain region and/or VL chain region of OKT3. In some embodiments, the anti-CD3 antibody has the sequence set forth in SEQ ID NO:2522 or has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the amino acid sequence of SEQ ID NO: 2522.
4. CD4 Binding Molecules
Provided herein are immunomodulatory proteins containing an ARBM that is or contains a binding molecule that binds to CD4, such as to human CD4. In some embodiments, the ARBM of the immunomodulatory protein binds to the ectodomain of CD4. In some embodiments, the ARBM binds to CD4 on the surface of a cell, such as on the surface of a T cell.
In some embodiments, the provided immunomodulatory protein contains an ARBM that is or contains an antibody that binds CD4 or is an antigen-binding antibody fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding fragment binds to CD4, such as to human CD4. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of an anti-CD4 antibody or antigen-binding fragment.
In some embodiments, the ARBM is or contains interleukin-16 (IL-16; Uniprot accession number Q14005) or a portion thereof that binds to CD4. In some embodiments, the IL-16 or portion thereof is mammalian, such as is human. In some embodiments, the IL-16 polypeptide is a mature IL-16 polypeptide and/or has a sequence of a processed pro-IL-16. In some aspects, the ARBM is or contains residues 1212-1332 of a wild-type or unmodified pro-IL-16, e.g. human pro-IL-16. In some embodiments, the ARBM is or contains the sequence set forth in SEQ ID NO: 2521 or has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in SEQ ID NO: 2521.
5. Ligands of Activating Receptor
a. Ligand of CD80 or CD86, e.g. CTLA-4 IgD or vIgD
Provided herein are immunomodulatory proteins containing an ARBM that is or contains a ligand an activating receptor. In some aspects, the activating receptor is CD28, e.g. human CD28, and/or the ligand of the activating receptor is CD80 or CD86, e.g. human CD80 or human CD86. In some embodiments, the ARBM of the immunomodulatory protein binds to the ectodomain of CD80 or CD86. In some embodiments, the ARBM binds to CD80 or CD86 on the surface of a cell, such as on the surface of an APC.
In some embodiments, the ARBM is an antibody that binds CD80 or CD86 or is an antigen-binding antibody fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding antibody fragment binds human CD80 or human CD86. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of an anti-CD80 antibody or antigen-binding fragment or an anti-CD86 antibody or antigen-binding fragment.
In some embodiments, the ARBM is or contains an IgD (e.g. IgV) or a specific binding fragment thereof, such as an unmodified or wild-type IgD or a vIgD or a specific binding fragment thereof, of an IgSF family member that binds CD80 or CD86, such as human CD80 or human CD86. In some embodiments, the ARBM is or contains one or more IgD that is an IgD, or a vIgD thereof, of a CTLA-4 polypeptide, such as a wild-type CTLA-4, e.g. a human CTLA-4. In some aspects, the ARBM contains one or more IgD (e.g. IgV) that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified CTLA-4, which, in some aspects, result in increased binding of the ARBM to CD80 or CD86. Exemplary IgDs or vIgDs of CTLA-4 binding partners for inclusion as an ARBM in the provided immunomodulatory proteins are described. In some embodiments, the ARBM is or contains a vIgD polypeptide that exhibit increased binding activity, such as binding affinity, for CD80 or CD86 compared to a corresponding wild-type or unmodified IgD.
CTLA-4 has been exploited as a therapeutic drug for treating autoimmune disease by attenuating T cell activation through modulation of CD80 and/or CD86 interactions. Specifically, Abatacept and Belatacept are FDA approved therapeutics for use in rheumatoid arthritis and transplant setting, respectively. Abatacept is wild-type CTLA-4 IgSF domain fused to an Fc portion of an antibody. Belatacept is a modified variant of CTLA-4 IgSF domain, containing a substitution of tyrosine for the alanine at position 31 and a glutamic acid for the leucine at position 106 (A31Y/L106E), corresponding to positions 31 and 106 of the wild-type reference CTLA-4 ECD sequence set forth in SEQ ID NO:36, to confer increased affinity toward CD80 and CD86 ligands (Kremer et al., N Engl J Med. 2003; 349(20):1907-1915; Larsen et al, Am J Transplant. 2005; 5(3):443-453).
In some embodiments, the ARBM is not the full length sequence of the CTLA-4. In some aspects, the ARBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of CTLA-4. In some embodiments, the ARBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:36 or 2655 or is a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgD (e.g. IgV) sequence of CTLA-4, such as human CTLA-4. In some embodiments, the ARBM is or contain an IgD (e.g. IgV) sequence set forth in SEQ ID NO:2947, or is a specific binding fragment thereof.
In some embodiments, the immunomodulatory protein contains an ARBM that is or contains a vIgD containing one or more amino acid modifications, e.g. substitutions, in an IgD of a wild-type or unmodified CTLA-4. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO: 36, 2655 or 2947 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 36, 2655 or 2947. In some embodiments, an ARBM containing a vIgD of CTLA-4 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 36, 2655 or 2947.
In some embodiments, the ARBM is or contains a vIgD that is an affinity-modified IgSF domain that has an increased binding activity, such as binding affinity, for CD80 or CD86 relative to the binding activity of the wild-type or unmodified IgD for CD80 or CD86. In some embodiments, the increase in binding activity, e.g. binding affinity, for CD80 or CD86 is increased at least about 5%, such as at least about 10%, 15%, 20%, 25%, 35%, 50%, 75%, 100%, 200% or more. In some embodiments, the increase in binding activity, e.g. binding affinity, is more than 1.2-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold 40-fold, or 50-fold. In such examples, the wild-type or unmodified IgD has the same sequence as the vIgD except that it does not contain the one or more amino acid modifications (e.g. substitutions).
In some embodiments, the equilibrium dissociation constant (Kd) of the ARBM to CD80 or CD86 can be less than 1×10−5M, 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M or 1×10−11M, or 1×10−12 M or less. In some embodiments, the ARBM binds to CD80 or CD86 with a Kd of from or from about 100 pm to 5000 pm, 100 pm to 2000 pm, 100 pm to 1500 pm, 100 pm to 1000 pm, 100 pm to 800 pm, 100 pm to 500 pm, 100 pm to 400 pm, 400 pm to 4000 pm, 400 pm to 2000 pm, 400 pm to 1500 pm, 400 pm to 1000 pm, 400 pm to 800 pm, 400 pm to 500 pm, 500 pm to 5000 pm, 500 pm to 2000 pm, 500 pm to 1500 pm, 500 pm to 1000 pm, 500 pm to 800 pm, 800 pm to 5000 pm, 800 pm to 2000 pm, 800 pm to 1500 pm, 800 pm to 1000 pm, 1000 pm to 5000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm, 1500 pm to 5000 pm, 1500 to 2000 pm to 2000 pm to 50000 pm. In some embodiments, the ABRM binds to CD80 or CD86 with a Kd of less than 200 pM, 300 pM, 400 pM, 500 pM. In some embodiments, the ABRM binds to CD80 or CD86 with a Kd of greater than or greater than about 500 pm but less than or less than about 2000 pm, such as from or from about 500 pm to 1500 pm, 500 pm to 1250 pm, 500 pm to 1000 pm, 500 pm to 750 pm, 750 pm to 1500 pm, 750 pm to 1250 pm, 750 pm to 1000 pm, 1000 pm to 2000 pm, 1000 pm to 1500 pm or 1500 pm to 2000 pm.
Unless stated otherwise, the amino acid modification(s) present in a vIgD of a CTLA-4 ECD or an IgD (e.g. IgV) thereof are designated by amino acid position number corresponding to the numbering of positions of the unmodified ECD sequence set forth in SEQ ID NO:36 or 2655. It is within the level of a skilled artisan to identify the corresponding position of a modification, e.g. amino acid substitution, in an ECD or a portion thereof containing an IgSF domain (e.g. IgV) thereof, such as by alignment of a reference sequence with SEQ ID NOs: 36 or 2655. In the listing of modifications throughout this disclosure, the amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed after the number. If the modification is a deletion of the position a “del” is indicated and if the modification is an insertion at the position an “ins” is indicated. In some cases, an insertion is listed with the amino acid position indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before and after the number and the identified variant amino acid insertion listed after the unmodified (e.g. wild-type) amino acid.
In some embodiments, the ARBM contains a vIgD that has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid modifications, e.g. substitutions. The one or more amino acid modifications, e.g. substitutions, can be in the ectodomain (extracellular domain) of the wild-type or unmodified CTLA-4. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the ECD domain of CTLA-4 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CTLA-4 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in an IgC domain of CTLA-4 or a specific binding fragment thereof. In some embodiments, the one or more amino acid modifications, e.g. substitutions, are in the IgV domain of CTLA-4 or a specific binding fragment thereof and in an IgC domain or domains of CTLA-4 or a specific binding fragment thereof.
In some embodiments, the ARBM is or contains a vIgD that has one or more amino modification, e.g. substitutions, in an unmodified IgD of CTLA-4 or specific binding fragment thereof corresponding to position(s) 6, 10, 12, 14, 15, 16, 18, 19, 20, 22, 24, 26, 27, 28, 29, 30, 31, 33, 35, 37, 38, 41, 42, 43, 45, 46, 47, 48, 53, 54, 55, 56, 58, 59, 61, 63, 64, 65, 67, 69, 71, 72, 73, 75, 76, 82, 85, 86, 87, 89, 91, 93, 95, 96, 97, 98, 99, 105, 106, 108, 110, 113, 115, 116, 117, 118, 119, 120, 121, 122, 124, 125 and/or 126 with reference to positions set forth in SEQ ID NO:36.
In some embodiments, the ARBM contains a vIgD that has one or more amino acid modification, e.g. substitutions, in an unmodified CTLA-4 or specific binding fragment thereof corresponding to position(s) 12, 18, 26, 29, 31, 53, 56, 58, 63, 72, 98, 99, 105, 106, and/or 117 with reference to positions set forth in SEQ ID NO:36 or 2655. In some embodiments, the ARBM is or contains a vIgD of CTLA-4 that has one or more amino acid modifications selected from L12F, L12H, L12P, I18A, I18F, I18N, I18T, I18V, A26D, A26S, A26T, G29R, G29W, A31Y, T53S, M56K, M56L, M56R, M56T, M56V, N58D, N58S, L63H, L63P, S72G, S72T, L98Q, L98R, M99I, M99L, Y105F, Y105L, L106E, L106I, L106R, I117E, I117L, I117M, and/or I117T, or a conservative amino acid substitution thereof.
In some embodiments, the ARBM is or contains a vIgD of CTLA-4 that has one or more amino acid modifications selected from A6T, V10A, L12F, L12H, L12I, L12P, S14N, S15P, R16C, R16G, R16H, I18A, I18F, I18N, I18T, I18V, A19V, S20N, V22A, V22I, E24Q, A26D, A26S, A26T, S27P, P28L, G29R, G29W, K30R, A31Y, E33M, E33V, R35K, T37S, V38I, Q41L, A42S, A42T, A42V, D43N, Q45H, V46E, T47A, E48R, T53S, Y54F, M55R, M55T, M55V, M56K, M56L, M56R, M56T, M56V, N58D, N58S, E59D, E59G, T61A, T61I, T61N, T61R, T61S, L63H, L63P, D64E, D64N, D64V, D65G, I67N, I67T, I67V, T69A, T69I, T69S, T71A, T71I, S72G, S72T, S73R, N75D, Q76R, Q82H, Q82R, R85G, A86T, M87A, M87K, M87T, M87V, T89A, T89M, T89S, L91R, I93L, I93V, K95R, V96I, E97Q, L98Q, L98R, M99I, M99L, Y105F, Y105L, L106E, L106I, L106N, L106R, L106V, I108F, 1108V, N110K, N110S, N110Y, Q113H, Y115H, Y115N, V116A, I117E, I117K, I117L, I117M, I117T, P119H, E120D, P121S, C122P, D124P, D1241, S1251, S125P, D126P, and/or D126T, or a conservative amino acid substitution thereof. In some embodiments, the the ARBM is or contains a vIgD that has one or more amino acid modification from L12F, L12H, L12I, L12P, I18A, I18F, I18N, I18T, I18V, A26D, A26S, A26T, G29R, G29W, E33M, E33V, T53S, M55R, M55T, M55V, M56K, M56L, M56R, M56T, M56V, N58D, N58S, L63H, L63P, S72G, S72T, M87A, M87K, M87T, M87V, L98Q, L98R, M99I, M99L, Y105F, Y105L, L106I, L106N, L106R, L106V, I117E, I117K, I117L, I117M, and/or I117T, or a conservative amino acid substitution thereof. In some embodiments, the ARBM is or contains a vIgD that has one or more amino acid modifications selected from 112F, L12P, I18T, A26T, G29W, T53S, M55T, M56K, M56T, N58S, S72G, M99L, L63P, L98Q, Y105L, L106I, and/or I117L, or a conservative amino acid substitution thereof. In some embodiments, the ARBM is or contains a vIgD has one or more amino acid modifications selected from L12P, I18T, A26T, G29W, A31Y, T53S, M55T, M56K, N58S, S72G, M99L, L63P, L98Q, Y105L, L106E, L106I, and/or I117L, or a conservative amino acid substitution thereof. In some embodiments, the ARBM is or contains a vIgD that has one or more amino acid modifications selected from A26T, G29W, L63P, S72G, L98Q, M99L, Y105L and/or L106I, or a conservative amino acid substitution thereof.
In some embodiments, the ARBM is or contains a vIgD that has two or more amino acid modifications selected from among A6T, V10A, L12F, L12H, L12I, L12P, S14N, S15P, R16C, R16G, R16H, I18A, I18F, I18N, I18T, I18V, A19V, S20N, V22A, V22I, E24Q, A26D, A26S, A26T, S27P, P28L, G29R, G29W, K30R, A31Y, E33M, E33V, R35K, T37S, V38I, Q41L, A42S, A42T, A42V, D43N, Q45H, V46E, T47A, E48R, T53S, Y54F, M55R, M55T, M55V, M56K, M56L, M56R, M56T, M56V, N58D, N58S, E59D, E59G, T61A, T61I, T61N, T61R, T61S, L63H, L63P, D64E, D64N, D64V, D65G, 167N, I67T, 167V, T69A, T69I, T69S, T71A, T71I, S72G, S72T, S73R, N75D, Q76R, Q82H, Q82R, R85G, A86T, M87A, M87K, M87T, M87V, T89A, T89M, T89S, L91R, I93L, 193V, K95R, V96I, E97Q, L98Q, L98R, M99I, M99L, Y105F, Y105L, L106E, L106I, L106N, L106R, L106V, I108F, 1108V, N110K, N110S, N110Y, Q113H, Y115H, Y115N, V116A, I117E, I117K, I117L, I117M, I117T, P119H, E120D, P121S, C122P, D124P, D1241, S1251, S125P, D126P, and/or D126T.
In some embodiments, the ARBM is or contain a vIgD of CTLA-4 that has an amino acid substitution in an unmodified or wild-type CTLA-4 polypeptide or specific binding fragment thereof corresponding to A26T, G29W, T53S, L63P, S72G, L98Q, M99L, Y105L and/or L106I. In some embodiments, the ARBM is or contains a vIgD of CTLA-4 that contains the amino acid substitutions A26T/G29W, A26T/T53S, A26T/L63P, A26T/S72G, A26T/L98Q, A26T/M99L, A26T/Y105L, A26T/L106I, A26T/G29W, G29W/T53S, G29W/L63P, G29W/S72G, G29W/L98Q, G29W/M99L, G29W/Y105L, G29W/L106I, A26T/T53S, G29W/T53S, T53S/L63P, T53S/S72G, T53S/L98Q, T53S/M99L, T53S/Y105L, or T53S/L106I, A26T/L63P, G29W/L63P, T53S/L63P, L63P/S72G, L63P/L98Q, L63P/M99L, L63P/Y105L, or L63P/L106I, A26T/S72G, G29W/S72G, T53S/S72G, L63P/S72G, S72G/L98Q, S72G/M99L, S72G/Y105L or S72G/L106I, A26T/L98Q, G29W/L98Q, T53S/L98Q, L63P/L98Q, S72G/L98Q, L98Q/M99L, L98Q/Y105L or L98Q/L106I, A26T/M99L, G29W/M99L, T53S/M99L, L63P/M99L, S72G/M99L, L98Q/M99L, M99L/Y105L, M99L/L106I, A26T/Y105L, G29W/Y105L, T53S/Y105L, L63P/Y105L, S72G/Y105L, L98Q/Y105L, M99L/Y105L, Y105L/L106I, A26T/L106I, G29W/L106I, T53S/L106IL63P/L106I, S72G/L106I, L98Q/L106I, M99L/L106I, Y105L/L106I. The variant CTLA-4 polypeptide can include further amino acid modifications (e.g. substitutions), such as any described herein, in accord with provided embodiments.
In some embodiments, the amino acid modification(s), e.g. substitutions(s) are A31Y/L106E, A6T/A26T/M55T/M99L/Y105L, V10A/G29W/T53S/M56K/L63P/L98Q/Y105L/P121S, V10A/L63P/D64V/S72G/L98Q/M99L/Y105L, V10A/L63P/L98Q/Y105L, L12F/R16H/G29W/M56T/L98Q/Y105L, L12F/A26T/L63P/L98Q/Y105L/L106R, L12F/K30R/S72G/Q82R/L98Q/M99L/Y105L, L12H/I18V/A42T/M55T/N58D/L98R/Y105L/L106I/P121S, L12H/E33M/L98Q/Y105L, L12H/M55T/E59D/L63P/M99L, L12H/L63P/S72G/L98Q/Y105L, L12I/M55T/M56V/I67T/M99L/L106R/I108F, L12P/R16H/A26T/T61S/L63P/M87V/L98Q/M99L/Y105L/L106I/I117L, L12P/I18T/A26T/M55T/T69S/S72G/M99L/Y105L, L12P/A26T, L12P/A26T/L63P, L12P/A26T/L63P/S72G/T89M/L98Q/M99L/Y105L, L12P/G29W/L63P/S72G/L98Q/Y105L, L12P/G29W/L63P/S72G/L98Q/Y105L/L106I, L12P/A26T/L63P/L98Q/M99L/Y105L, L12P/A26T/L63P/L98Q/Y105L, L12P/A26T/L63P/L98Q/Y105L/L106I, L12P/G29W/D43N/N58S/L63P/L98Q/M99L/Y105L, L12P/M56V/L63P/V96I/L98Q/M99L/Y105L/Y115H, L12P/L63P/S72G/L98Q/M99L/Y105L, L12P/L63P/S72G/L98Q/M99L/Y105L/L106N, L12P/L63P/S72G/L98Q/M99L/Y105L/L106N/I117L, S14N/R16C/I18T/M56K/T61A/L63P/A86T/M99L, S15P/118V/M56T/L98Q/M99L/Y105L, R16C/G29W/E33V/M55T/L63P/L98Q/Y105L, I18A/L63P/S72G/L98Q/Y105L, I18F/L63P/L98Q/M99L/Y105L/P121S, Il8N/A26T/L63H/T89A/L98Q/M99L/Y105L, I18N/L63P/S72T/M87T/L98Q/Y105L/N110S, I18T/A26S/M55T/M56V/L63P/S72G/L98Q/M99L/Y105L/I117K, I18T/A26T/L63P/S72G/L98Q/Y105L, I18T/A26T/L63P/Q82R/L98Q/Y105L, I18T/G29R/L63P/S72G/L98Q/M99L/Y105L, I18T/G29W/L63P/L98Q/Y105L, I18T/E48R/L63P/T69S/L98Q/Y105L/N110Y, I18T/T61R/L63P/S72G/L98Q/M99L/Y105L, I18T/L63P/S72G/M87K/L98Q/M99L/Y105L, I18T/L63P/S72G/L98Q/M99L/Y105L, I18T/L63P/S72G/L98Q/Y105L/I108V, I18V/A26T/L63P/D64E/L98Q/Y105L/L106R/N110K, I18V/G29W/L63P/S72G/L98Q/Y105L, A19V/G29W/R35K/L63P/L98Q/M99L/Y105L, S20N/A26T/L63P/L98Q/M99L/Y105L, V22A/L63P/L98Q/M99L/Y105L/P119H, V22I/L63P/L98Q/Y105L/I117M, E24Q/L63P/S72G/L98Q/M99L/Y105L, A26D/S72G/L98Q/M99L/Y105L, A26T/A42V/Q45H/I67N/M87K/E97Q/M99L, A26T/V46E/L63P/D65G/L98Q, A26T/T47A/M56K/L63P/S72G/Q82R/L98Q/M99L/Y105L, A26T/T53S/M56K/L63P/L98Q/Y105L, A26T/T53S/L63P/L98Q/Y105L/L106I/I117L, A26T/Y54F/M56K/M99L/Y105L, A26T/M55R/L98Q/M99L/Y105L, A26T/M55T/L63P/S72G/L98Q/M99L/Y105L, A26T/M55T/L63P/L98Q/M99L/Y105L, A26T/L63P/D65G/L98Q/M99L/Y105L, A26T/L63P/M87V/N110K/I117E, A26T/L63P/S72G/L98Q/M99L/Y105L, A26T/L63P/S72G/L98Q/Y105L/L106I/I117L, A26T/L63P/L98Q/M99L/Y105L, A26T/167N/S72G/L98Q/M99L/Y105L, S27P/M56K/L63P/S72G/S73R/T89A/M99L/Y105L/I117M, P28L/E33V/L63P/S72G/L98Q/M99L/Y105L, P28L/E33V/L63P/S72G/L98R/M99L/Y105L, G29W/T53S/M56K/N58S/L63P/M87V/L98Q/Y105L, G29W/T53S/M56K/N58S/L63P/M87V/L98Q/Y105L/I108V, G29W/T53S/M56K/N58S/L63P/M87V/L98Q/Y105L/P121S, G29W/T53S/M56K/T61N/L63P/L98Q/Y105L, G29W/T53S/M56K/L63P/Q82H/L98Q/M99I/Y105L, G29W/T53S/M56K/L63P/L98Q/Y105L, G29W/T53S/L63P/S72G/L98Q/Y105L, G29W/M55V/E59G/L63P/L98Q/Y105L, G29W/M56T/L63P/L98Q/Y105L/L106I/I117L, G29W/N58D/167V/L98Q/M99L/Y105L, G29W/N58S/L63P/D64N/L98Q/M99L/Y105L, G29W/N58S/L63P/T69I/L98Q/M99L/Y105L, G29W/N58S/L63P/S72G/L98Q/Y105L, G29W/N58S/L63P/S72G/L98Q/Y105L/L106I, G29W/N58S/L63P/S72G/L98Q/Y105L/L106V, G29W/N58S/L63P/S72G/M87V/L98Q/Y105L, G29W/N58S/L63P/Q82R/L98Q/Y105L, G29W/N58S/L63P/M87T/L98Q/M99L/Y105L, G29W/N58S/L63P/L98Q/Y105L, G29W/E59G/L63P/L98Q/Y105L, G29W/T61I/L63P/S72G/L98Q/M99L/Y105L, G29W/L63P/D65G/S72G/L98Q/Y105L, G29W/L63P/167V/S72G/L98Q/Y105L, G29W/L63P/S72G/L98Q/Y105L/L106I, G29W/L63P/S72G/L98Q/Y105L/L106I/I117L, G29W/L63P/S72G/L98Q/Y105L/I117L, G29W/L63P/S72G/L98Q/Y105L/P121S, G29W/L63P/L98Q/M99L/Y105L, G29W/S72G/Q76R/L98Q/Y105L/L106I/Q113H, G29W/M87K/T89S/L98Q/M99L/Y105L/I108V/I117L, G29W/M87K/I93V/L98Q/M99L/Y105L, G29W/L98Q/M99L/Y105L, E33M/A42T/L98Q/Y105L, E33M/L63P/S72G/L98Q/Y105L, E33M/L63P/S72G/L98Q/Y105L/I108F, E33M/L63P/S72G/L98Q/Y105L/I117L, E33M/Q82H/L98Q/M99L/Y105L, E33V/A42S/M55T/L98Q/M99L/Y105L, T37S/M56V/L98Q/Y105L, V38I/L63P/S72G/L98Q/M99L/Y105L, Q41L/Y54F/M56K/M99L/I108F, T53S/M56V/L98Q/Y105L, M55T/L63P/T71I/M99L/Y105L, M55T/S72G/L98Q/M99L/Y105L, M55T/E97Q/M99L/Y105F, M56K/L63P/N75D/V96I/M99L/Y105L/L106I, M56L/L63P/L98Q/Y105L/L106I/I117L, M56R/L63P/L98Q/M99L/Y105L, M56T/L91R/L98Q/Y105L, M56V/E59G/L63P/S72G/M87K/I93V/L98Q/M99L/Y105L/I117E, T61A/L63P/S72G/L98Q/M99L/Y105L, L63P/T69A/L98Q/M99L/Y105L/L106R/V116A, L63P/S72G/M87A/L98Q/Y105L, L63P/S72G/I93L/L98Q/M99L/Y105L, L63P/S72G/L98Q/M99L/Y105L, L63P/S72G/L98Q/M99L/Y105L/L106I/I117L, L63P/S72G/L98Q/Y105L, L63P/S72G/L98Q/Y105L/L106I/I117L, L63P/S72G/Y105L, L63P/M87K/M99L/L106R, L63P/Q82H/L98Q/M99L/Y105L, L63P/K95R, L63P/L98Q, L63P/L98Q/M99L/Y105L, L63P/L98Q/M99L/Y105L/L106I, L63P/L98Q/M99L/Y105L/I108V, L63P/L98Q/M99L/Y105L/I117M, L63P/L98Q/Y105L, L63P/L98Q/V116A, L63P/L98R/N110K, L63P/M99L/Y105L/I108F, I67V/S72G/Q82H/T89A/L98Q/M99L/Y105L, 872G/R85G/L98Q/M99L/Y105L/L106I, S72G/L98Q/M99L/Y105L/I117T, L98Q/M99L/Y105L, L98Q/M99L/Y105L/L106I/I117T, L98Q/M99L/Y105L/L106I/Y115N, L98Q/Y105L, and L98R/N110K.
In some embodiments, the ARBM is or contains a vIgD of CTLA-4 that additionally includes the amino acid modifications C122S with reference to positions set forth in SEQ ID NO:36 or 2655.
In some embodiments, the ARBM is or contains an IgD (e.g. IgV) of wild-type CTLA-4 set forth in Table 10 or a vIgD thereof comprising any of the modifications (e.g. substitutions) listed in Table 10. Table 10 also provides exemplary sequences by reference to SEQ ID NO for the extracellular domain (ECD) or IgV domain of CTLA-4. As indicated, the exact locus or residues corresponding to a given domain can vary, such as depending on the methods used to identify or classify the domain. Also, in some cases, adjacent N- and/or C-terminal amino acids of a given domain (e.g. IgV) also can be included in a sequence of an ARBM, such as to ensure proper folding of the domain when expressed. Thus, it is understood that the exemplification of the SEQ ID NOS in Table 10 is not to be construed as limiting. For example, the particular domain, such as the IgV domain, of a variant CTLA-4 polypeptide can be several amino acids longer or shorter, such as 1-10, e.g. 1, 2, 3, 4, 5, 6 or 7 amino acids longer or shorter, than the sequence of amino acids set forth in the respective SEQ ID NO.
In some embodiments, the ARBM is or contains a wild-type CTLA-4 ECD set forth in SEQ ID NO: 36 or SEQ ID NO:2655 or a variant CTLA-4 ECD set forth in any one of SEQ ID NOS: 2519, 2520, 2948-3041, 3043-3048, 3050-3099, 3230, 3231, 3582-3614 or 3648. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any one of SEQ ID NOS: 2519, 2520, 2948-3041, 3043-3048, 3050-3099, 3230, 3231, 3582-3614 or 3684 and contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified CTLA-4, e.g. not present in SEQ ID NO:36 or 2655. In some embodiments, the ARBM is or contains a specific binding fragment of any of the ECD sequences set forth in any one of SEQ ID NOS: 2519, 2520, 2948-3041, 3043-3048, 3050-3099, 3230, 3231, 3582-3614 or 3648 and that contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified CTLA-4, e.g. not present in SEQ ID NO:36 or 2655.
In some embodiments, the ARBM is or contains a wild-type CTLA-4 IgV set forth in SEQ ID NO: 2947 or a variant IgV sequence set forth in any one of SEQ ID NOS: 3100-3229, 3232, 3615-3647 or 3649. In some embodiments, the ARBM is or contains a sequence that exhibits at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, such as at least 96% identity, 97% identity, 98% identity, or 99% identity to any of the IgV sequences set forth in any one of SEQ ID NOS: 3100-3229, 3232, 3615-3647 or 3649 and contains the amino acid modification(s), e.g., substitution(s), not present in the wild-type or unmodified CTLA-4, e.g. not present in SEQ ID NO:2947. In some embodiments, the ARBM is a specific binding fragment of any of the IgV sequences set forth in any one of SEQ ID NOS: 3100-3229, 3232, 3615-3647 or 3649 and that contains the amino acid modification(s), e.g. substitution(s) not present in the wild-type or unmodified CTLA-4, e.g. set forth in SEQ ID NO:2947.
b. MHC Binding Molecules
Provided herein are immunomodulatory proteins containing an ARBM that is or contains a binding molecule that binds an major histocompatibility complex (MHC), e.g. MHC class I or MHC class II. In some embodiments, the MHC is human, e.g. human MHC class I or human MHC class II. In some embodiments, the ARBM binds to an MCH on the surface of a cell, such as on the surface of an APC.
In some embodiments, the provided immunomodulatory proteins contain an ARBM is or contains an antibody that binds an MHC or is an antigen-binding fragment thereof (e.g. Fab or scFv). In some embodiments, the antibody or antigen-binding antibody fragment thereof binds human MHC, such as human MHC class I and/or human MHC class II. In some embodiments, the antibody is a pan-MHC antibody. In some embodiments, the antibody is a single chain variable fragment (e.g. scFv) containing a VH and VL of an anti-MHC antibody or antigen-binding fragment, such as is a pan-MHC scFv antibody.
In some embodiments, the ARBM is or contains one or more IgD(s) or a specific binding fragment thereof, such as an unmodified or wild-type IgD or a vIgD or a specific binding fragment thereof, of an IgSF family member that bind an MHC, such as an MHC class I or an MHC class II. In some embodiments, the MHC is human MHC, such as a human MHC class I or human MHC class II. In some embodiments, the ARBM is or contains one or more IgD that is an IgD, or a vIgD thereof, of a TCR, CD4, CD8, or LAG3 polypeptide, such as a wild-type TCR, CD4, CD8 or LAG3, e.g. a human TCR, a human CD4, human CD8 or human LAG3. In some embodiments, the ARBM is not the full length sequence of the TCR, CD4, CD8 or LAG3. In some aspects, the ARBM is a soluble polypeptide, is not membrane-expressed and/or lacks the transmembrane and/or cytoplasmic domain of a TCR, CD4, CD8 or LAG3. In some embodiments, the ARBM only contains an extracellular domain (ECD) or a specific binding fragment thereof containing a IgD or vIgD, such as only contains an IgV domain or an IgC domain or specific binding fragment thereof, or combinations thereof.
In some embodiments, the ARBM is or contains an IgD of a wild-type or unmodified CD4 or a vIgD thereof. In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:40 or is a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgD sequence of CD4, such as humanCD4. In some embodiments, the ARBM is or contain an IgD sequence set forth in SEQ ID NO:3490, or is a specific binding fragment thereof.
In some aspects, the ARBM contains one or more IgD that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified CD4, which, in some aspects, result in increased binding of the ARBM to an MHC molecule. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO:40 or 3490 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 40 or 3490. In some embodiments, an ARBM containing a vIgD of CD4 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 40 or 3490.
In some embodiments, the ARBM is or contains an IgD of a wild-type or unmodified CD8, such as a CD8alpha (CD8a) and/or CD8beta (CD8b), or a vIgD thereof. In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:41 or 42 or is a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgD sequence of CD8a or CD8b, such as human CD8a or CD8b. In some embodiments, the ARBM is or contain an IgD sequence set forth in SEQ ID NO:3491 or 3233, or is a specific binding fragment thereof.
In some aspects, the ARBM contains one or more IgD that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified CD4, which, in some aspects, result in increased binding of the ARBM to an MHC molecule. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO:41, 32, 3491 or 3233 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 41, 32, 3491 or 3233. In some embodiments, an ARBM containing a vIgD of CD8 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 41, 32, 3491 or 3233.
In some embodiments, the ARBM is or contains an IgD of a wild-type or unmodified LAG3 or a vIgD thereof. In some embodiments, the ARBM is or contains the ECD sequence set forth in SEQ ID NO:43 or is a specific binding fragment thereof. In some embodiments, the ARBM is or contains an IgD sequence of LAG3, such as human LAG3. In some embodiments, the ARBM is or contain an IgD sequence set forth in SEQ ID NO:3492, or is a specific binding fragment thereof.
In some aspects, the ARBM contains one or more IgD that is an vIgD containing one or more amino acid modifications (e.g., substitutions, deletions or additions) compared to an IgD of a wild-type or unmodified LAG3, which, in some aspects, result in increased binding of the ARBM to an MHC molecule. In some embodiments, modifications provided herein can be in an ARBM containing an unmodified IgD set forth in SEQ ID NO:43 or 3492 or in a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 43 or 3492. In some embodiments, an ARBM containing a vIgD of LAG3 has at least about 85%, 86%, 86%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity with the sequence set forth in any of SEQ ID NOs: 43 or 3492.
Provided herein are single-domain immunomodulatory proteins that contain one or more inhibitory receptor binding molecule (IRBM) that binds to an inhibitory receptor or one or more activating receptor binding molecule (ARBM) that binds to an activating receptor or a ligand of an activating receptor. In some embodiments, the IRBM can be any binding molecule that binds to an inhibitory receptor, such as those described in Section I. A. In some embodiments, the ARBM can be any binding molecule that binds to an activating receptor or a ligand thereof, such as any described in Section I. B. In some embodiments, the single-domain immunomodulatory protein contains one or more IRBM or ARBM that includes an antibody or an antigen-binding antibody fragment. In some aspects, the single-domain immunomodulatory protein contains an IRBM or ARBM that is a human antibody and/or an antibody that binds a human protein.
In some embodiments, the single-domain immunomodulatory protein contains an IRBM or ARBM that is not an antibody or antigen-binding fragment. In some embodiments, the IRBM or ARBM is or contains a non-antibody immunoglobulin superfamily (IgSF) domain (IgD) of an IgSF member, or is a specific binding fragment of such an IgSF domain. In some embodiments, the at least one of the IRBM or ARBM can be a variant IgD in which is contained one or more amino acid modifications (e.g. substitutions) in an IgD, such as any of the exemplary variant IgD provided in Section I.
In some embodiments, the ARBM can bind to an activating receptor with at least a certain binding activity as described in Section I, such as binding affinity, as measured by any of a number of known methods. In some embodiments, the IRBM can bind to an inhibitory receptor with at least a certain binding activity as described in Section I, such as binding affinity, as measured by any of a number of known methods.
In some embodiments, the single-domain immunomodulatory proteins provided herein are soluble proteins and/or do not contain a portion that includes a transmembrane domain. Those of skill will appreciate that cell surface proteins, including proteins of the IgSF, typically have an intracellular domain, a transmembrane domain, and extracellular domain (ECD), and that a soluble form of such proteins can be made using the extracellular domain or an immunologically active subsequence thereof. Thus, in some embodiments, the ARBM or IRBM lacks a transmembrane domain or a portion of the transmembrane domain of an IgSF member. In some embodiments, the ARBM or IRBM lacks the intracellular (cytoplasmic) domain or a portion of the intracellular domain of an IgSF member. In some embodiments, the ARBM or IRBM only contains the ECD domain or a portion thereof containing an IgSF domain, such an IgV domain, or specific binding fragments thereof. In some cases, the ARBM and IRBM independently can include the extracellular domain of an IgSF family member or an IgSF domain or specific binding fragment thereof of an IgSF family member. In some aspects, the IgSF domain is an IgV domain or an IgC domain. In some aspects, the IgSF domain is an IgV domain or an IgC domain. In some aspects, the IRBM and/or ARBM is an IgSF domain of a IgSF family member that is a human protein and/or binds a human protein.
In some embodiments, the provided single-domain immunomodulatory proteins can include the ARBM or IRBM in various configurations or formats, including formats with one or more further moieties. The one or more ARBM or the one or more IRBM can be linked directly or indirectly, via a linker. In some embodiments, the single-domain immunomodulatory proteins can be formatted as multimeric molecules via fusion with a multimerization domain, such as an Fc protein. In some embodiments, the single-domain immunomodulatory proteins are formatted as a monomeric molecules containing single polypeptide fusions of the one or more ARBM or the one or more IRBM. In some embodiments, the single-domain immunomodulatory proteins can be formatted as multimeric molecules, e.g., dimeric, trimer, tetrameric, or pentameric molecules.
Exemplary ARBM or IRBM containing single-domain immunomodulatory proteins are described, as are exemplary formats for such single-domain immunomodulatory proteins.
1. Multi-Domain Immunomodulatory Protein Formats
The multi-domain immunomodulatory proteins containing one or more IRBM and one or more ARBM provided herein can be formatted in a variety of ways, including as a single chain polypeptide fusion or as a multimeric (e.g. dimeric, trimeric, tetrameric, or pentameric) molecules. In some cases, the immunomodulatory proteins can be formatted for secretion from a cell, such as for expression by an engineered cell or infectious agent as described elsewhere herein. The particular format is chosen such that the ARBM of the immunomodulatory protein specifically binds to the activating receptor or a ligand of the activating receptor and the IRBM specifically binds to the IRBM. In some aspects, the particular format is chosen to effect attenuation of an activity of the activating receptor, such as to reduce or decrease an immune response. In further aspects, the particular format is chosen to result in proximalization of the inhibitory receptor and activating receptor on an immune cell, e.g. T cell. In additional aspects, the particular format is chosen to recruit one or more phosphatase, e.g. SHP-1 or SHP-2, to the activating receptor and/or to result in phosphatase dependent dephosphorylation of the activating receptor.
In some embodiments, the format of the multi-domain immunomodulatory protein is chosen to avoid crosslinking or engagement of the activating receptor. Thus, in some aspects, the provided immunomodulatory proteins do not exhibit multivalent binding to the activating receptor. In some aspects, for the immunomodulatory proteins generated in a cis binding strategy (e.g. containing an IRBM that binds to an inhibitory receptor and an ARBM that binds to an activating receptor on the same cell, such as same T cell) a relatively smaller molecular weight, monomeric and/or single chain polypeptide fusion of the immunomodulatory protein is contemplated. In some embodiments, for the immunomodulatory proteins generated in a trans binding strategy (e.g. containing an IRBM that binds to an inhibitory receptor on a T cell and an ARBM that binds to a ligand of an activating receptor on an APC), it may not be necessary for the immunomodulatory protein to be formatted to minimize or avoid multivalent binding and/or to be of a smaller size. Hence, in some aspects, multi-domain immunomodulatory proteins that act in a trans binding strategy are formatted as dimeric proteins.
In some embodiments, the provided multi-domain immunomodulatory proteins can include one or more ARBM and one or more IRBM. In some embodiments, an immunomodulatory protein can include one or more ARBM described herein and any one or more IRBM described herein. In some embodiments, the immunomodulatory protein comprises exactly 1, 2, 3, 4, 5 ARBMs, which, in some aspects, are the same or are of identical sequence when a plurality are included. In some embodiments, each of a plurality of ARBM, e.g. 2, 3, 4, or 5, are linked directly or indirectly via a linker to another ARBM. In some aspects, at least one of the plurality of ARBM molecules are linked directly or indirectly via a linker to an IRBM.
In some embodiments, the immunomodulatory proteins comprises exactly 1, 2, 3, 4, 5 IRBMs, which, in some aspects, are the same or are of identical sequence when a plurality are included. In some embodiments, each of a plurality of IRBM, e.g. 2, 3, 4, or 5, are linked directly or indirectly via a linker to another IRBM. In some aspects, at least one of the plurality of IRBM molecules are linked directly or indirectly via a linker to an ARBM. In some embodiments, the modular format of the provided immunomodulatory proteins provides flexibility for engineering or generating immunomodulatory proteins for modulating activity at an immune synapse involving modulating interactions between and activating receptor and inhibitory receptor and their ligands.
In some embodiments, the multi-domain immunomodulatory protein contains a polypeptide that includes at least one ARBM and at least one IRBM. In some embodiments, the immunomodulatory protein includes a polypeptide containing an ARBM linked directly or indirectly via a linker to an IRBM, in either order. In some embodiments, at least one IRBM is amino terminal to at least one ARBM in the polypeptide. In some embodiments, at least one IRBM is carboxy terminal to at least one ARBM in the polypeptide.
In addition to single polypeptide chain embodiments, in some embodiments two, three, four, or more of a polypeptides containing one or more IRBM and/or one or more ARBM can be covalently or non-covalently attached to each other. In some embodiments, at least one polypeptide chain contains one or more IRBM and at least one polypeptide chain contains one or more ARBM. In some embodiments, each of at least two polypeptide chain contains at least one IRBM and at least one ARBM. Thus, monomeric, dimeric, and higher order (e.g., 3, 4, 5, or more) multimeric proteins are provided herein. For example, in some embodiments exactly two polypeptides, each containing one or more IRBM and/or one or more ARBM, can be covalently or non-covalently attached to each other to form a dimer. In some embodiments, the two polypeptides can be attached via a multimerization domain, in which, in some aspects, one or both of the IRBM and ARBM are linked directly or indirectly via a linker to the multimerization domain. In such embodiments, the multimerization domain can be the same or different. In some embodiments, the multimerization domain, such as an Fc region, facilitates attachment of two polypeptide chains via interchain cysteine disulfide bond. Compositions comprising two or more polypeptides can be of an identical sequence or substantially identical sequence of polypeptide (e.g., a homodimer) or of a non-identical sequence of polypeptides (e.g., a heterodimer).
In some embodiments, the multi-domain immunomodulatory protein can further include a tag or moiety.
Non-limiting examples of components for inclusion in provided formats are further described in section III.3.
2. Single-Domain Immunomodulatory Protein Formats
The single-domain immunomodulatory proteins containing one or more IRBM or one or more ARBM can be formatted in a variety of ways, including as a single chain polypeptide fusion or as a multimeric (e.g. dimeric, trimeric, tetrameric, or pentameric) molecules. In some cases, the immunomodulatory proteins can be formatted for secretion from a cell, such as for expression by an engineered cell or infectious agent as described elsewhere herein. In some aspects, the particular format is chosen to effect attenuation of an activity of the activating receptor, such as to reduce or decrease an immune response.
In some embodiments, the single-domain immunomodulatory protein includes a plurality of IRBM polypeptides, such as 2, 3, 4 or 5 IRBMs. In some embodiments, each of the IRBM is the same or has the same sequence. In some embodiments, each of a plurality of IRBM, e.g. 2, 3, 4, or 5, are linked directly or indirectly via a linker to another IRBM. In some aspects, at least one of the plurality of IRBM molecules are linked directly or indirectly via a linker to an ARBM.
In some embodiments, the single-domain immunomodulatory protein includes a plurality of ARBM polypeptides, such as 2, 3, 4 or 5 ARBM. In some embodiments, each of the ARBM is the same or has the same sequence. In some embodiments, each of a plurality of ARBM, e.g. 2, 3, 4, or 5, are linked directly or indirectly via a linker to another ARBM. In some aspects, at least one of the plurality of ARBM molecules are linked directly or indirectly via a linker to an IRBM.
In addition to single polypeptide chain embodiments, in some embodiments two, three, four, or more of a polypeptides containing one or more IRBM or one or more ARBM can be covalently or non-covalently attached to each other. In some embodiments, at least one polypeptide chain contains one or more IRBM. In some embodiments, at least one polypeptide chain contains one or more ARBM. Thus, monomeric, dimeric, and higher order (e.g., 3, 4, 5, or more) multimeric proteins are provided herein. For example, in some embodiments exactly two polypeptides, each containing one or more IRBM or one or more ARBM, can be covalently or non-covalently attached to each other to form a dimer. In some embodiments, the two polypeptides can be attached via a multimerization domain, in which, in some aspects, the IRBM or ARBM are linked directly or indirectly via a linker to the multimerization domain. In such embodiments, the multimerization domain can be the same or different. In some embodiments, the multimerization domain, such as an Fc region, facilitates attachment of two polypeptide chains via interchain cysteine disulfide bond. Compositions comprising two or more polypeptides can be of an identical sequence or substantially identical sequence of polypeptide (e.g., a homodimer) or of a non-identical sequence of polypeptides (e.g., a heterodimer).
In some embodiments, the single-domain immunomodulatory protein can further include a tag or moiety.
Non-limiting examples of components for inclusion in provided formats are further described in Section 111.3.
3. Components
a. Linkers
For the multi-domain and single-domain immunomodulatory proteins provided herein, linkers, or spacers, can be used to connect components of a polypeptide, such as any ARBM and/or IRBM provided herein. In some cases, a linker is a peptide or polypeptide sequence {e.g. a synthetic peptide or polypeptide sequence), or is a non-peptide linker able to connect two moieties. In some aspects, a linker is used or chosen to maintain the structural flexibility and other conformational characteristics of the individual residues or at the secondary, tertiary, or quaternary structural levels of domains of the polypeptide fusion protein, such as in order to maintain functional properties of the immunomodulatory protein. Linkers can also provide additional beneficial properties to the protein, such as increased protein expression in mammalian expression systems, improved biophysical properties such as stability and solubility, improved protein purification and detection and/or increased enzymatic activity. In some examples, two or more linkers can be linked in tandem.
In some aspects, the linkers can be peptide linker. In other aspects, the linker includes chemical linking agents and heterobifunctional linking agents. In some cases, the linker is not cleavable. In other cases, a linker can contain one or more protease-cleavable sites, which can be located within the sequence of the linker or flanking the linker at either end of the linker sequence.
When multiple linkers are present in the immunomodulatory protein between ARBM, IRBM or other moieties, each of the linkers can be the same or different. Generally, linkers or multiple linkers provide flexibility to the polypeptide molecule.
In some embodiments, one or more “peptide linkers” link the ARBM, IRBM, or other moieties of the immunomodulatory protein. In some embodiments, a peptide linker can be a single amino acid residue or greater in length. In some embodiments, the peptide linker has at least one amino acid residue but is no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid residues in length. In some embodiments, the linker is a flexible linker. Linking moieties are described, for example, in Huston et al. (1988) PNAS 85:5879-5883, Whitlow et al. (1993) Protein Engineering 6:989-995, and Newton et al, (1996) Biochemistry 35:545-553. Other suitable peptide linkers include any of those described in U.S. Pat. Nos. 4,751,180 or 4,935,233.
In some examples, a peptide linker includes peptides (or polypeptides) {e.g., natural, or non-naturally occurring peptides) which includes an amino acid sequence that links or genetically fuses a first linear sequence of amino acids to a second linear sequence of amino acids to which it is not naturally linked or genetically fused in nature. For example, the peptide linker can include non-naturally occurring polypeptides which are modified forms of naturally occurring polypeptides (e.g., that includes a mutation such as an addition, substitution or deletion). In another example, the peptide linker can include non-naturally occurring amino acids. In another example, the peptide linker can include naturally occurring amino acids occurring in a linear sequence that does not occur in nature. In still another example, the peptide linker can include a naturally occurring polypeptide sequence. Linking moieties can also include derivatives and analogs of the naturally occurring amino acids, as well as various non-naturally occurring amino acids (D- or L-), hydrophobic or non-hydrophobic, known in the art.
Exemplary peptide linkers are linkers with the formula Ser(Gly4Ser)n (or (Gly-Ser)n residues with some Glu or Lys residues dispersed throughout to increase solubility, where n can be an integer from 1 to 20, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20. Other exemplary linkers include peptide linkers with the formula [(Gly)x-Sery]z where x is from 1 to 4, y is 0 or 1, and z is from 1 to 50. In other examples, the peptide linker includes the sequence Gn, where n can be an integer from 1 to 100. In another example, the sequence of the peptide linker can be (GA)n or (GGS)n.
In some embodiments, the linker is (in one-letter amino acid code): GGGGS (“4GS”; SEQ ID NO: 1942) or multimers of the 4GS linker, such as repeats of 2, 3, 4, or 5 4GS linkers. In some embodiments, the peptide linker is the peptide linker is (GGGGS)2 or (GGGGS)3 as set forth in SEQ ID NOs: 240 and 239, respectively. In some embodiments, the linker also can include a series of alanine residues alone or in addition to another peptide linker (such as a 4GS linker or multimer thereof). In some embodiments, the number of alanine residues in each series is: 2, 3, 4, 5, or 6 alanines. In some embodiments, the linker is a rigid linker. For example, the linker is an α-helical linker. In some embodiments, the linker is (in one-letter amino acid code): EAAAK or multimers of the EAAAK linker, such as repeats of 2, 3, 4, or 5 EAAAK linkers, such as set forth in SEQ ID NO: 3240 (1×EAAAK), SEQ ID NO: 3241 (3×EAAAK) or SEQ ID NO: 3242 (5×EAAAK). In some embodiments, the linker can further include amino acids introduced by cloning and/or from a restriction site, for example the linker can include the amino acids GS (in one-letter amino acid code) as introduced by use of the restriction site BAMHI. In some embodiments, the linker (in one-letter amino acid code) is GSGGGGS (SEQ ID NO: 1941) or GGGGSSA (SEQ ID NO: 2524). In some examples, the linker is a 2×GGGGS followed by three alanines (GGGGSGGGGSAAA; SEQ ID NO:241).
In some embodiments, a polynucleotide encoding a desired peptide linker can be inserted between, and in the same reading frame as a polynucleotide encoding any ARBM, IRBM or other moiety in the provided immunomodulatory protein and between another moiety, using any suitable conventional technique.
b. Multimerization Domain
In some embodiments, the immunomodulatory protein containing one or more ARBM(s) and/or IRBM(s) is multimeric, such as dimeric, trimeric, tetrameric, or pentameric. For the dimeric format, the immunomodulatory protein comprises a first polypeptide and a second polypeptide. In some embodiments, the first and/or second polypeptide is or contains an ARBM, IRBM, or both. In aspects, the ARBM and/or IRBM is linked, directly or indirectly via a linker, to a multimerization domain. In some aspects, the mutlimerization domain increase half-life of the molecule.
In one example, the immunomodulatory protein provided herein is a dimer. In some cases, the immunomodulatory protein is a homodimer that contains a first and second polypeptide subunit that are the same, i.e. each has the same amino acid sequence containing the identical IRBM(s) and ARBM(s). The homodimer can be formed by transforming a nucleic acid molecule encoding the variant polypeptide into a cell, which, upon secretion, results in covalent or non-covalent interaction between residues of polypeptide subunits to mediate formation of the dimer.
In another example, the immunomodulatory protein is a heterodimer that contains a first and second polypeptide subunit that are different. In such an example, one or both of the first or second polypeptide subunit contains a sequence of amino acids of an ARBM and IRBM. In some cases, both the first and second polypeptide subunit can contain a sequence of amino acids of an ARBM and a sequence of amino acids of an IRBM. The heterodimer can be formed by transforming into a cell both a first nucleic acid molecule encoding a first polypeptide subunit and a second nucleic acid molecule encoding a second different polypeptide subunit. In some aspects, the heterodimer is produced upon expression and secretion from a cell as a result of covalent or non-covalent interaction between residues of the two polypeptide subunits to mediate formation of the dimer. In such processes, generally a mixture of dimeric molecules is formed, including homodimers and heterodimers. For the generation of heterodimers, additional steps for purification can be necessary. For example, the first and second polypeptide can be engineered to include a tag with metal chelates or other epitope, where the tags are different. The tagged domains can be used for rapid purification by metal-chelate chromatography, and/or by antibodies, to allow for detection by western blots, immunoprecipitation, or activity depletion/blocking in bioassays.
Interaction of two or more polypeptides of the immunomodulatory proteins can be facilitated by their linkage, either directly or indirectly, to any moiety or other polypeptide that are themselves able to interact to form a stable structure. For example, separate encoded polypeptide chains can be joined by multimerization, whereby multimerization of the polypeptides is mediated by a multimerization domain. Typically, the multimerization domain provides for the formation of a stable protein-protein interaction between a first polypeptide and a second polypeptide.
In some embodiments, the two or more individual polypeptides of the immunomodulatory proteins can be joined by multimerization, such as joined as dimeric, trimeric, tetrameric, or pentameric molecules. In some cases, the individual polypeptides are the same. For example, a trimeric molecule can be formed from three copies of the same individual polypeptide. In other examples, a tetrameric molecule is generated from four copies of the same individual polypeptides. In further examples, a pentameric molecule is generated from five copies of the same individual polypeptides. In some embodiments of the configurations, the individual polypeptides of an immunomodulatory proteins containing an ARBM and/or IRBM are fused to a multimerization domain. In some cases, the individual polypeptides of a multi-domain immunomodulatory protein containing an ARBM and IRBM are fused to a multimerization domain. In some examples, the individual polypeptides of a single-domain immunomodulatory proteins containing an ARBM or IRBM are fused to a multimerization domain, such as a multimerization domain that promotes trimerization, tetramerization, or pentamerization of the proteins.
In some embodiments, a multimerization domain includes any capable of forming a stable protein-protein interaction. The multimerization domains can interact via an immunoglobulin sequence (e.g. Fc domain; see e.g., International Patent Pub. Nos. WO 93/10151 and WO 2005/063816 US; U.S. Pub. No. 2006/0024298; U.S. Pat. No. 5,457,035); leucine zipper (e.g. from nuclear transforming proteins fos and jun or the proto-oncogene c-myc or from General Control of Nitrogen (GCN4)) (ee e.g., Busch and Sassone-Corsi (1990) Trends Genetics, 6:36-40; Gentz et al., (1989) Science, 243:1695-1699); a hydrophobic region; a hydrophilic region; or a free thiol which forms an intermolecular disulfide bond between the chimeric molecules of a homo- or heteromultimer. In addition, a multimerization domain can include an amino acid sequence comprising a protuberance complementary to an amino acid sequence comprising a hole, such as is described, for example, in U.S. Pat. No. 5,731,168; International Patent Pub. Nos. WO 98/50431 and WO 2005/063816; Ridgway et al. (1996) Protein Engineering, 9:617-621. Such a multimerization region can be engineered such that steric interactions not only promote stable interaction, but further promote the formation of heterodimers over homodimers from a mixture of chimeric monomers. Generally, protuberances are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains (e.g., tyrosine or tryptophan). Compensatory cavities of identical or similar size to the protuberances are optionally created on the interface of the second polypeptide by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine). Exemplary multimerization domains are described below.
The ARBM and/or IRBM can be joined anywhere, but typically via its N- or C-terminus, to the N- or C-terminus of a multimerization domain to form a chimeric polypeptide. The linkage can be direct or indirect via a linker. Also, the chimeric polypeptide can be a fusion protein or can be formed by chemical linkage, such as through covalent or non-covalent interactions. For example, when preparing a chimeric polypeptide containing a multimerization domain, nucleic acid encoding all or part of an ARBM and/or IRBM can be operably linked to nucleic acid encoding the multimerization domain sequence, directly or indirectly or optionally via a linker domain. In some cases, the construct encodes a chimeric protein where the C-terminus of the ARBM and/or IRBM is joined to the N-terminus of the multimerization domain. In some instances, a construct can encode a chimeric protein where the N-terminus of the ARBM and/or IRBM is joined to the N- or C-terminus of the multimerization domain.
A polypeptide multimer contains two chimeric proteins created by linking, directly or indirectly, two of the same or different ARBM and/or IRBM directly or indirectly to a multimerization domain. In some examples, where the multimerization domain is a polypeptide, a gene fusion encoding the ARBM and/or IRBM and multimerization domain is inserted into an appropriate expression vector. The resulting chimeric or fusion protein can be expressed in host cells transformed with the recombinant expression vector, and allowed to assemble into multimers, where the multimerization domains interact to form multivalent polypeptides. Chemical linkage of multimerization domains to the ARBM and/or IRBM can be effected using heterobifunctional linkers.
The resulting chimeric polypeptides, such as fusion proteins, and multimers formed therefrom, can be purified by any suitable method such as, for example, by affinity chromatography over Protein A or Protein G columns. Where two nucleic acid molecules encoding different polypeptides are transformed into cells, formation of homo- and heterodimers will occur. Conditions for expression can be adjusted so that heterodimer formation is favored over homodimer formation.
In some embodiments, the immunomodulatory protein comprises an ARBM and/or IRBM attached to an immunoglobulin Fc (yielding an “immunomodulatory Fc fusion.”) In some embodiments, the attachment of the ARBM and/or IRBM is at the N-terminus of the Fc. In some embodiments, the attachment of the ARBM and/or IRBM is at the C-terminus of the Fc. In some embodiments, two or more ARBM and/or IRBM (the same or different) are independently attached at the N-terminus and at the C-terminus. Thus, homo- or heteromultimeric polypeptides can be generated from co-expression of separate ARMB and/or IRBM containing polypeptides. The first and second polypeptides can be the same or different. In some embodiments, the first and/or second polypeptide each contains two or more ARBM and/or IRBM linked to the Fc sequence. In some embodiments, the first and/or second polypeptide each contains three IRBMs and one ARBM linked to the Fc sequence.
In some embodiments, the Fc is murine or human Fc. In some embodiments, the Fc is a mammalian or human IgG1, lgG2, lgG3, or lgG4 Fc regions. In some embodiments, the Fc is derived from IgG1, such as human IgG1. In some embodiments, the Fc comprises the amino acid sequence set forth in SEQ ID NO: 187 or a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 187.
In some embodiments, the Fc region contains one more modifications to alter (e.g. reduce) one or more of its normal functions. In general, the Fc region is responsible for effector functions, such as complement-dependent cytotoxicity (CDC) and antibody-dependent cell cytotoxicity (ADCC), in addition to the antigen-binding capacity, which is the main function of immunoglobulins. Additionally, the FcRn sequence present in the Fc region plays the role of regulating the IgG level in serum by increasing the in vivo half-life by conjugation to an in vivo FcRn receptor. In some embodiments, such functions can be reduced or altered in an Fc for use with the provided Fc fusion proteins.
In some embodiments, one or more amino acid modifications may be introduced into the Fc region, thereby generating an Fc region variant. In some embodiments, the Fc region variant has decreased effector function. There are many examples of changes or mutations to Fc sequences that can alter effector function. For example, WO 00/42072, WO2006019447, WO2012125850, WO2015/107026, US2016/0017041 and Shields et al. J Biol. Chem. 9(2): 6591-6604 (2001) describe exemplary Fc variants with improved or diminished binding to FcRs. The contents of those publications are specifically incorporated herein by reference.
In some embodiments, the provided immunomodulatory proteins comprise an Fc region that exhibits reduced effector functions, which makes it a desirable candidate for applications in which the half-life of the immunomodulatory protein in vivo is important yet certain effector functions (such as CDC and ADCC) are unnecessary or deleterious. In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/depletion of CDC and/or ADCC activities. For example, Fc receptor (FcR) binding assays can be conducted to ensure that the immunomodulatory protein lacks FcγR binding (hence likely lacking ADCC activity), but retains FcRn binding ability. The primary cells for mediating ADCC, NK cells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII and FcγRIII FcR expression on hematopoietic cells is summarized in Table 2 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991). Non-limiting examples of in vitro assays to assess ADCC activity of a molecule of interest is described in U.S. Pat. No. 5,500,362 (see, e.g. Hellstrom, I. et al. Proc. Nat'l Acad. Sci. USA 83:7059-7063 (1986)) and Hellstrom, I et al., Proc. Nat'l Acad. Sci. USA 82:1499-1502 (1985); U.S. Pat. No. 5,821,337 (see Bruggemann, M. et al., J. Exp. Med. 166:1351-1361 (1987)). Alternatively, non-radioactive assay methods may be employed (see, for example, ACTI™ non-radioactive cytotoxicity assay for flow cytometry (CellTechnology, Inc. Mountain View, Calif.; and CytoTox 96™ non-radioactive cytotoxicity assay (Promega, Madison, Wis.). Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in an animal model such as that disclosed in Clynes et al. Proc. Nat'l Acad. Sci. USA 95:652-656 (1998). C1q binding assays may also be carried out to confirm that the immunomodulatory protein n is unable to bind C1q and hence lacks CDC activity. See, e.g., C1q and C3c binding ELISA in WO 2006/029879 and WO 2005/100402. To assess complement activation, a CDC assay may be performed (see, for example, Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996); Cragg, M. S. et al., Blood 101:1045-1052 (2003); and Cragg, M. S. and M. J. Glennie, Blood 103:2738-2743 (2004)). FcRn binding and in vivo clearance/half life determinations can also be performed using methods known in the art (see, e.g., Petkova, S. B. et al., Int'l. Immunol. 18(12):1759-1769 (2006)).
Immunomodulatory protein with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 by EU numbering (U.S. Pat. No. 6,737,056). Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327 by EU numbering, including the so-called “DANA” Fc mutant with substitution of residues 265 and 297 to alanine (U.S. Pat. No. 7,332,581).
In some embodiments, the Fc region of immunomodulatory proteins has an Fc region in which any one or more of amino acids at positions 234, 235, 236, 237, 238, 239, 270, 297, 298, 325, and 329 (indicated by EU numbering) are substituted with different amino acids compared to the native Fc region. Such alterations of Fc region are not limited to the above-described alterations, and include, for example, alterations such as deglycosylated chains (N297A and N297Q), IgG1-N297G, IgG1-L234A/L235A, IgG1-L234A/L235E/G237A, IgG1-A325A/A330S/P331S, IgG1-C226S/C229S, IgG1-C226S/C229S/E233P/L234V/L235A, IgG1-E233P/L234V/L235A/G236del/S267K, IgG1-L234F/L235E/P331S, IgG1-S267E/L328F, IgG2-V234A/G237A, IgG2-H268Q/V309L/A330S/A331S, IgG4-L235A/G237A/E318A, and IgG4-L236E described in Current Opinion in Biotechnology (2009) 20 (6), 685-691; alterations such as G236R/L328R, L235G/G236R, N325A/L328R, and N325LL328R described in WO 2008/092117; amino acid insertions at positions 233, 234, 235, and 237 (indicated by EU numbering); and alterations at the sites described in WO 2000/042072.
Certain Fc variants with improved or diminished binding to FcRs are described. (See, e.g., U.S. Pat. No. 6,737,056; WO 2004/056312, WO2006019447 and Shields et al., J. Biol. Chem. 9(2): 6591-6604 (2001).)
In some embodiments, there is provided an immunomodulatory protein comprising a variant Fc region comprising one or more amino acid substitutions which increase half-life and/or improve binding to the neonatal Fc receptor (FcRn). Antibodies with increased half-lives and improved binding to FcRn are described in US2005/0014934A1 (Hinton et al.) or WO2015107026. Those antibodies comprise an Fc region with one or more substitutions therein which improve binding of the Fc region to FcRn. Such Fc variants include those with substitutions at one or more of Fc region residues: 238, 256, 265, 272, 286, 303, 305, 307, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424 or 434 by EU numbering, e.g., substitution of Fc region residue 434 (U.S. Pat. No. 7,371,826).
In some embodiments, the Fc region of the immunomodulatory protein comprises one or more amino acid substitution E356D and M358L by EU numbering. In some embodiments, the Fc region of the immunomodulatory protein comprises one or more amino acid substitutions C220S, C226S and/or C229S by EU numbering. In some embodiments, the Fc region of the immunomodulatory protein comprises one or more amino acid substitutions R292C and V302C. See also Duncan & Winter, Nature 322:738-40 (1988); U.S. Pat. Nos. 5,648,260; 5,624,821; and WO 94/29351 concerning other examples of Fc region variants.
In some embodiments, alterations are made in the Fc region that result in diminished C1q binding and/or Complement Dependent Cytotoxicity (CDC), e.g., as described in U.S. Pat. No. 6,194,551, WO 99/51642, and Idusogie et al., J. Immunol. 164: 4178-4184 (2000).
In some embodiments, there is provided an immunomodulatory protein comprising a variant Fc region comprising one or more amino acid modifications, wherein the variant Fc region is derived from IgG1, such as human IgG1. In some embodiments, the variant Fc region is derived from the amino acid sequence set forth in SEQ ID NO: 187. In some embodiments, the Fc contains at least one amino acid substitution that is N82G by numbering of SEQ ID NO: 187 (corresponding to N297G by EU numbering). In some embodiments, the Fc further contains at least one amino acid substitution that is R77C or V87C by numbering of SEQ ID NO: 187 (corresponding to R292C or V302C by EU numbering). In some embodiments, the variant Fc region further comprises a C5S amino acid modification by numbering of SEQ ID NO: 187 (corresponding to C220S by EU numbering). For example, in some embodiments, the variant Fc region comprises the following amino acid modifications: V297G and one or more of the following amino acid modifications C220S, R292C or V302C by EU numbering (corresponding to N82G and one or more of the following amino acid modifications C5S, R77C or V87C with reference to SEQ ID NO:187), e.g., the Fc region comprises the sequence set forth in SEQ ID NO:1157. In some embodiments, the variant Fc region comprises one or more of the amino acid modifications C220S, L234A, L235E or G237A, e.g. the Fc region comprises the sequence set forth in SEQ ID NO:1158. In some embodiments, the variant Fc region comprises one or more of the amino acid modifications C220S, L235P, L234V, L235A, G236del or S267K, e.g. the Fc region comprises the sequence set forth in SEQ ID NO:1159. In some embodiments, the variant Fc comprises one or more of the amino acid modifications C220S, L234A, L235E, G237A, E356D or M358L, e.g. the Fc region comprises the sequence set forth in SEQ ID NO:1155.
In some embodiments, the Fc region lacks the C-terminal lysine corresponding to position 232 of the wild-type or unmodified Fc set forth in SEQ ID NO: 187 (corresponding to K447del by EU numbering). In some aspects, such an Fc region can additionally include one or more additional modifications, e.g. amino acid substitutions, such as any as described. Exemplary of such an Fc region is set forth in SEQ ID NO: 1938, 1939, 1940, or 1715.
In some embodiments, there is provided an immunomodulatory protein comprising a variant Fc region in which the variant Fc comprises the sequence of amino acids set forth in any of SEQ ID NOS:1155, 1157, 1158, 1159, 1715, 1938, 1939, or 1940 or a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of SEQ ID NOS: 1155, 1157, 1158, 1159, 1715, 1938, 1939, or 1940.
In some embodiments, the Fc is derived from IgG2, such as human IgG2. In some embodiments, the Fc comprises the amino acid sequence set forth in SEQ ID NO: 188 or a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 188.
In some embodiments, the Fc comprises the amino acid sequence set forth in SEQ ID NO: 1200 or a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 1200. In some embodiments, the IgG4 Fc is a stabilized Fc in which the CH3 domain of human IgG4 is substituted with the CH3 domain of human IgG1 and which exhibits inhibited aggregate formation, an antibody in which the CH3 and CH2 domains of human IgG4 are substituted with the CH3 and CH2 domains of human IgG1, respectively, or an antibody in which arginine at position 409 indicated in the EU index proposed by Kabat et al. of human IgG4 is substituted with lysine and which exhibits inhibited aggregate formation (see e.g. U.S. Pat. No. 8,911,726. In some embodiments, the Fc is an IgG4 containing the S228P mutation, which has been shown to prevent recombination between a therapeutic antibody and an endogenous IgG4 by Fab-arm exchange (see e.g. Labrijin et al. (2009) Nat. Biotechnol., 27(8): 767-71.) In some embodiments, the Fc comprises the amino acid sequence set forth in SEQ ID NO: 1201 or a sequence of amino acids that exhibits at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 1201.
In some embodiments, the immunomodulatory protein is a homodimer that contains a first immunomodulatory Fc fusion polypeptide and a second immunomodulatory Fc fusion polypeptide in which the first and second polypeptide are the same. In some embodiments, a first Fc polypeptide fusion contains an Fc region and one or more ARBM and/or IRBM and a second polypeptide fusion contains an Fc region and one or more ARBM and/or IRBM. In such embodiments, the Fc region can be any as described above.
In some embodiments, the immunomodulatory protein contains a first immunomodulatory Fc fusion polypeptide and a second immunomodulatory Fc fusion polypeptide in which the first and second polypeptide are different. In some embodiments, a first Fc polypeptide fusion contains an Fc region and one or more ARBM and/or IRBM and a second polypeptide fusion contains an Fc region and one or more ARBM and/or IRBM. In such embodiments, the Fc region can be a region that promotes or facilitates formation of heterodimers.
In some embodiments, a sequence of amino acids is added preceding the Fc sequence for constructs in which the Fc sequence is the N-terminal portion of the sequence. In some cases, the sequence of amino acids HMSSVSAQ (SEQ ID NO:1156) is added immediately preceding the Fc sequence for constructs in which the Fc sequence is N-terminal portion of the sequence.
In some embodiments, the Fc domain of one or both of the first and second immunomodulatory Fc fusion polypeptides comprise a modification (e.g. substitution) such that the interface of the Fc molecule is modified to facilitate and/or promote heterodimerization. Methods to promote heterodimerization of Fc chains include mutagenesis of the Fc region, such as by including a set of “knob-into-hole” mutations or including mutations to effect electrostatic steering of the Fc to favor attractive interactions among different polypeptide chains.
In some embodiments, modifications include introduction of a protuberance (knob) into a first Fc polypeptide and a cavity (hole) into a second Fc polypeptide such that the protuberance is positionable in the cavity to promote complexing of the first and second Fc-containing polypeptides. Amino acids targeted for replacement and/or modification to create protuberances or cavities in a polypeptide are typically interface amino acids that interact or contact with one or more amino acids in the interface of a second polypeptide.
In some embodiments, a first polypeptide that is modified to contain protuberance (hole) amino acids include replacement of a native or original amino acid with an amino acid that has at least one side chain which projects from the interface of the first polypeptide and is therefore positionable in a compensatory cavity (hole) in an adjacent interface of a second polypeptide. Most often, the replacement amino acid is one which has a larger side chain volume than the original amino acid residue. One of skill in the art knows how to determine and/or assess the properties of amino acid residues to identify those that are ideal replacement amino acids to create a protuberance. In some embodiments, the replacement residues for the formation of a protuberance are naturally occurring amino acid residues and include, for example, arginine (R), phenylalanine (F), tyrosine (Y), or tryptophan (W). In some examples, the original residue identified for replacement is an amino acid residue that has a small side chain such as, for example, alanine, asparagine, aspartic acid, glycine, serine, threonine, or valine.
In some embodiments, a second polypeptide that is modified to contain a cavity (hole) is one that includes replacement of a native or original amino acid with an amino acid that has at least one side chain that is recessed from the interface of the second polypeptide and thus is able to accommodate a corresponding protuberance from the interface of a first polypeptide. Most often, the replacement amino acid is one which has a smaller side chain volume than the original amino acid residue. One of skill in the art knows how to determine and/or assess the properties of amino acid residues to identify those that are ideal replacement residues for the formation of a cavity. Generally, the replacement residues for the formation of a cavity are naturally occurring amino acids and include, for example, alanine (A), serine (S), threonine (T) and valine (V). In some examples, the original amino acid identified for replacement is an amino acid that has a large side chain such as, for example, tyrosine, arginine, phenylalanine, or tryptophan.
The CH3 interface of human IgG1, for example, involves sixteen residues on each domain located on four anti-parallel β-strands which buries 1090 A2 from each surface (see e.g., Deisenhofer et al. (1981) Biochemistry, 20:2361-2370; Miller et al., (1990) J Mol. Biol., 216, 965-973; Ridgway et al., (1996) Prot. Engin., 9: 617-621; U.S. Pat. No. 5,731,168). Modifications of a CH3 domain to create protuberances or cavities are described, for example, in U.S. Pat. No. 5,731,168; International Patent Applications WO98/50431 and WO 2005/063816; and Ridgway et al., (1996) Prot. Engin., 9: 617-621. In some examples, modifications of a CH3 domain to create protuberances or cavities are typically targeted to residues located on the two central anti-parallel β-strands. The aim is to minimize the risk that the protuberances which are created can be accommodated by protruding into the surrounding solvent rather than being accommodated by a compensatory cavity in the partner CH3 domain.
In some embodiments, the heterodimeric molecule contains a T366W mutation in the CH3 domain of the “knobs chain” and T366S, L368A, Y407V mutations in the CH3 domain of the “hole chain”. In some cases, an additional interchain disulfide bridge between the CH3 domains can also be used (Merchant, A. M., et al., Nature Biotech. 16 (1998) 677-681) e.g. by introducing a Y349C mutation into the CH3 domain of the “knobs” or “hole” chain and a E356C mutation or a S354C mutation into the CH3 domain of the other chain. In some embodiments, the heterodimeric molecule contains S354C, T366W mutations in one of the two CH3 domains and Y349C, T366S, L368A, Y407V mutations in the other of the two CH3 domains. In some embodiments, the heterodimeric molecule comprises E356C, T366W mutations in one of the two CH3 domains and Y349C, T366S, L368A, Y407V mutations in the other of the two CH3 domains. In some embodiments, the heterodimeric molecule comprises Y349C, T366W mutations in one of the two CH3 domains and E356C, T366S, L368A, Y407V mutations in the other of the two CH3 domains. In some embodiments, the heterodimeric molecule comprises Y349C, T366W mutations in one of the two CH3 domains and S354C, T366S, L368A, Y407V mutations in the other of the two CH3 domains. Examples of other knobs-in-holes technologies are known in the art, e.g. as described by EP 1 870 459 A1.
In some embodiments, an Fc variant containing CH3 protuberance (knob) or cavity (hole) modifications can be joined to a multi-domain immunomodulatory polypeptide anywhere, but typically via its N- or C-terminus, to the N- or C-terminus of the one or more ARBM or IRBM, such as to form a fusion polypeptide. The linkage can be direct or indirect via a linker. Typically, a knob and hole molecule is generated by co-expression of a first stacked immunomodulatory polypeptide linked to an Fc variant containing CH3 protuberance modification(s) with a second stacked immunomodulatory polypeptide linked to an Fc variant containing CH3 cavity modification(s). In some embodiments, the knob or hold Fc region lacks the C-terminal lysine corresponding to position 232 of the wild-type or unmodified Fc set forth in SEQ ID NO: 187 (corresponding to K447del by EU numbering). Exemplary sequences for knob and hole Fc polypeptides are set forth in SEQ ID NOs: 1153, 1154, 2558, and 2559. In some embodiments, a heterodimeric stack molecule contains a first Fc polypeptide fusion containing an Fc region (knob) and a first variant polypeptide and/or second IgSF domain (e.g. second variant IgSF domain) and a second Fc polypeptide fusion containing an Fc region (hole) contains a stuffer sequence HMSSVSAQ (SEQ ID NO:1156) immediately preceding both Fc regions of the first and second Fc polypeptide fusion.
In some embodiments, the Fc region of each polypeptide of a heterodimer includes a mutation to altered charge polarity across the Fc dimer interface such that coexpression of electrostatically matched Fc chains support favorable attractive interactions thereby promoting desired Fc heterodimer formation, whereas unfavorable repulsive charge interactions suppress unwanted Fc homodimer formation (Guneskaran et al. (2010) JBC, 285: 19637-19646). In some embodiments, at least one polypeptide containing an ARBM and/or IRBM is linked directly or indirectly to an Fc containing mutations to positively charged residues (e.g. E356K, E357K and/or D399K by EU numbering; designated K chain set forth), such as set forth in SEQ ID NO:2544. In such embodiments, the other polypeptide of the heterodimer containing an ARBM and/or IRBM is linked directly or indirectly to an Fc containing mutations to negatively charged residues (e.g. K370D, K392D and K409D by EU numbering; designated D chain), such as set forth in SEQ ID NO:2545. When co-expressed in a cell, association between the K and D chains is possible but the chains do not substantially self-associate due to charge repulsion.
In some embodiments, any of the above mutations in an Fc backbone can be made in an allotype containing residues Glu (E) and Met (M) at positions 356 and 358.
In some embodiments, the Fc region of the heterodimeric molecule additionally can contain one or more other Fc mutation, such as any described above. In some embodiments, the heterodimer molecule contains an Fc region with a mutation that reduces effector function. In some embodiments, such Fc regions contain mutations C220S, L234A, L235E and/or G237A by EU numbering.
In some embodiments, the wild-type IgG1 Fc can be the Fc set forth in SEQ ID NO: 187 having an allotype containing residues Glu (E) and Met (M) at positions 356 and 358 by EU numbering. In other embodiments, the wild-type IgG1 Fc contains amino acids of the human G1m1 allotype, such as residues containing Asp (D) and Leu (L) at positions 356 and 358, e.g. as set forth in SEQ ID NO:3538. Thus, in some cases, an Fc provided herein can contain amino acid substitutions E356D and M358L to reconstitute residues of allotype G1 ml. In some aspects, a wild-type Fc is modified by one or more amino acid substitutions to reduce effector activity or to render the Fc inert for Fc effector function. Exemplary effectorless or inert mutations include those described herein. Among effectorless mutations that can be included in an Fc of constructs provided herein are L234A, L235E and G237A by EU numbering. In some embodiments, a wild-type Fc is further modified by the removal of one or more cysteine residue, such as by replacement of the cysteine residues to a serine residue at position 220 (C220S) by EU numbering. Exemplary inert Fc regions having reduced effector function are set forth in SEQ ID NO: 1158 and SEQ ID NO:3579, which are based on allotypes set forth in SEQ ID NO:187 or SEQ ID NO: 3538, respectively. In some embodiments, an Fc region used in a construct provided herein can further lack a C-terminal lysine residue.
In some configurations, a first and second polypeptide of a heterodimeric Fc fusion protein can be linked to a moiety for detection and/or purification. In some aspects, the first and second polypeptide are linked to different tags or moieties. In some aspects, the tag or moiety of the first and second polypeptide is independently selected from a poly-histidine tag (HHHHHH; SEQ ID NO: 2011), a flag-tag (DYKDDDDK; SEQ ID NO: 2010), a Myc-tag, or fluorescent protein-tags (e.g., EGFP, set forth in SEQ ID NOs: 3042, 3049, or 3243). In some examples, the first polypeptide containing an ARBM and the second polypeptide containing an IRBM each further contain a moiety for detection and/or purification, such as a poly-histidine tag (HHHHHH; SEQ ID NO: 2011) and/or a flag-tag (DYKDDDDK; SEQ ID NO: 2010).
In some embodiments, the ARBM and/or IRBM is directly linked to the Fc sequence. In some embodiments, the ARBM and/or IRBM is indirectly linked to the Fc sequence, such as via a linker. In some embodiments, one or more “peptide linkers” link the ARBM and/or IRBM and the Fc domain. In some embodiments, a peptide linker can be a single amino acid residue or greater in length. In some embodiments, the peptide linker has at least one amino acid residue but is no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid residues in length. Exemplary linkers are set forth in subsection “Linker.”
In some embodiments, the immunomodulatory protein forms a multimer, e.g., a dimer. In some embodiments, the dimer is a homodimer in which the two polypeptides of the immunomodoulatory protein are the same. In some embodiments, the dimer is a heterodimer in which the two polypeptides of the immunomodoulatory protein are different.
In some embodiment, individual polypeptide of a multi-domain polypeptide or individual polypeptides of a single-domain polypeptide are linked to a multimerization domain that forms an immimmunomodulatory protein is a trimer, tetramer or pentamer. In some embodiments, the individual polypeptides of such a molecule are the same. In some embodiments, such a multimerization domain is a cartilage oligomeric matrix protein (COMP) assembly domain, a vasodilator-stimulated phosphoprotein (VASP) tetramerization domain or a ZymoZipper (ZZ) 12.6 domain.
In some embodiments, the multimerization domain is a portion of the cartilage oligomeric matrix protein (COMP) assembly domain (Voulgaraki et al., Immunology (2005) 115(3):337-346. In some examples, the COMP is or contains an amino acid sequence as set forth in SEQ ID NO: 3503 (e.g. amino acids 29-72 of the full length COMP, Uniprot accession number P49747) or a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3503.
In some embodiments, the multimerization domain is a vasodilator-stimulated phosphoprotein (VASP) tetramerization domain (Bachmann et al., J Biol Chem (1999) 274(33):23549-23557). In some embodiments, the VASP is or contains an amino acid sequence as set forth in SEQ ID NO: 3504 (e.g. amino acids 343-375 of the full length VASP; Uniprot accession number P50552) or a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3504.
In some embodiments, the multimerization domain is a ZymoZipper (ZZ) 12.6 domain. In some embodiments, the ZZ domain is or contains an amino acid sequence as set forth in SEQ ID NO: 3505 (See U.S. Pat. No. 7,655,439) or a sequence that has 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to SEQ ID NO: 3505.
Also provided are nucleic acid molecules encoding the immunomodulatory protein. In some embodiments, for production of immunomodulatory protein, a nucleic acid molecule encoding the immunomodulatory protein is inserted into an appropriate expression vector. The resulting immunomodulatory protein can be expressed in host cells transformed with the expression where assembly between Fc domains occurs by interchain disulfide bonds formed between the Fc moieties to yield dimeric, such as divalent, immunomodulatory proteins.
The resulting immunomodulatory protein containing an ARBM, IRBM, and Fc, can be easily purified by affinity chromatography over Protein A or Protein G columns. For the generation of heterodimers, additional steps for purification can be necessary. For example, where two nucleic acids encoding different immunomodulatory proteins are transformed into cells, the formation of heterodimers must be biochemically achieved since immunomodulatory protein carrying the Fc-domain will be expressed as disulfide-linked homodimers as well. Thus, homodimers can be reduced under conditions that favor the disruption of interchain disulfides, but do no effect intra-chain disulfides. In some cases, different immunomodulatory protein monomers are mixed in equimolar amounts and oxidized to form a mixture of homo- and heterodimers. The components of this mixture are separated by chromatographic techniques. Alternatively, the formation of this type of heterodimer can be biased by genetically engineering and expressing immunomodulatory proteins containing Fc fusion molecules that contain one or more ARBM and/or IRBM using knob-into-hole methods described below.
c. Tags or Moieties
In some embodiments, the one or more polypeptides containing an ARBM and/or IRBM in the provided immunomodulatory proteins can further include a tag or moiety. In some embodiments, the further moiety is a protein, peptide, small molecule or nucleic acid. In some cases, the immunomodulatory protein is linked, directly or indirectly to more than one further moiety, such as 2, 3, 4, 5, or 6, further moieties.
In some embodiments, the moiety is a half-life extending molecule. Exemplary of such half-life extending molecules include, but are not limited to, albumin, an albumin-binding polypeptide, Pro/Ala/Ser (PAS), a C-terminal peptide (CTP) of the beta subunit of human chorionic gonadotropin, polyethylene glycol (PEG), long unstructured hydrophilic sequences of amino acids (XTEN), hydroxyethyl starch (HES), an albumin-binding small molecule, or a combination thereof.
In some embodiments, the immunomodulatory polypeptide comprising an ARBM and/or IRBM can include conformationally disordered polypeptide sequences composed of the amino acids Pro, Ala, and Ser (See e.g., WO2008/155134, SEQ ID NO: 904). In some cases, the amino acid repeat is at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more amino acid residues, wherein each repeat comprises (an) Ala, Ser, and Pro residue(s). Thus, provided herein is an immunomodulatory protein is a PASylated protein wherein the ARBM and/or IRBM are linked, directly or indirectly via a linker, to Pro/Ala/Ser (PAS). In some embodiments, one or more additional linker structures may be used.
In some embodiments, the moiety facilitates detection or purification of the immunomodulatory protein. In some cases, the immunomodulatory protein, such as at least one of or each polypeptide of a multimer (e.g. dimer, trimer, tetramer, or pentamer) thereof, comprises a tag or moiety, e.g. affinity or purification tag, linked. In some aspects, such a tag or moiety can be linked directly or indirectly via a linker to the N- and/or c-terminus of the polypeptide. Various suitable polypeptide tags and/or fusion domains are known, and include but are not limited to, a poly-histidine (His) tag, a FLAG-tag (SEQ ID NO: 2010), a Myc-tag, and fluorescent protein-tags (e.g., EGFP, set forth in SEQ ID NOs:3042, 3049, or 3243). In some cases, the tag is a His tag containing at least six histidine residues (set forth in SEQ ID NO: 2011).
In some cases, the immunomodulatory protein comprising an ARBM and IRBM further comprises various combinations of moieties. For example, the immunomodulatory protein comprising an ARBM or IRBM further comprises one or more polyhistidine-tag and FLAG tag. In some cases, the combination of moieties, such as two or more moieties, can be included on the same polypeptide. In some cases, the combination of moieties, such as two or more moieties, can be included on different polypeptide, such as in connection with embodiments relating to heterodimeric immunomodulatory polypeptides.
Provided herein are isolated or recombinant nucleic acids collectively referred to as “nucleic acids” which encode any of the immunomodulatory proteins provided herein. In some embodiments, nucleic acids provided herein, including all described below, are useful in recombinant production (e.g., expression) of immunomodulatory proteins provided herein. In some embodiments, nucleic acids provided herein, including all described below, are useful in expression of multi-domain immunomodulatory proteins provided herein in cells, such as in engineered cells, e.g. immune cells, or infectious agent cells. The nucleic acids provided herein can be in the form of RNA or in the form of DNA, and include mRNA, cRNA, recombinant or synthetic RNA and DNA, and cDNA. The nucleic acids provided herein are typically DNA molecules, and usually double-stranded DNA molecules. However, single-stranded DNA, single-stranded RNA, double-stranded RNA, and hybrid DNA/RNA nucleic acids or combinations thereof comprising any of the nucleotide sequences of the invention also are provided.
Also provided herein are recombinant expression vectors and recombinant host cells useful in producing the multi-domain immunomodulatory proteins provided herein.
Also provided herein are engineered cells, such as engineered immune cells, containing any of the provided nucleic acids or encoded multi-domain immunomodulatory proteins, such as any of the transmembrane immunomodulatory polypeptides or secretable immunomodulatory polypeptides.
Also provided herein are infectious agents, such as bacterial or viral cells, containing any of the provided nucleic acids or encoded multi-domain immunomodulatory proteins, such as any of the secretable immunomodulatory polypeptides.
In any of the above provided embodiments, the nucleic acids encoding the immunomodulatory polypeptides provided herein can be introduced into cells using recombinant DNA and cloning techniques. To do so, a recombinant DNA molecule encoding an immunomodulatory polypeptide is prepared. Methods of preparing such DNA molecules are well known in the art. For instance, sequences coding for the peptides could be excised from DNA using suitable restriction enzymes. Alternatively, the DNA molecule could be synthesized using chemical synthesis techniques, such as the phosphoramidite method. Also, a combination of these techniques could be used. In some instances, a recombinant or synthetic nucleic acid may be generated through polymerase chain reaction (PCR). In some embodiments, a DNA insert can be generated encoding one or more multi-domain immunomodulatory proteins containing at least one affinity-modified IgSF domain and, in some embodiments, a signal peptide, a transmembrane domain and/or an endodomain in accord with the provided description. This DNA insert can be cloned into an appropriate transduction/transfection vector as is known to those of skill in the art. Also provided are expression vectors containing the nucleic acid molecules.
In some embodiments, the expression vectors are capable of expressing the immunomodulatory proteins in an appropriate cell under conditions suited to expression of the protein. In some aspects, nucleic acid molecule or an expression vector comprises the DNA molecule that encodes the immunomodulatory protein operatively linked to appropriate expression control sequences. Methods of effecting this operative linking, either before or after the DNA molecule is inserted into the vector, are well known. Expression control sequences include promoters, activators, enhancers, operators, ribosomal binding sites, start signals, stop signals, cap signals, polyadenylation signals, and other signals involved with the control of transcription or translation.
In some embodiments, expression of the immunomodulatory protein is controlled by a promoter or enhancer to control or regulate expression. The promoter is operably linked to the portion of the nucleic acid molecule encoding the variant polypeptide or immunomodulatory protein. In some embodiments, the promotor is a constitutively active promotor (such as a tissue-specific constitutively active promotor or other constitutive promotor). In some embodiments, the promoter is a tissue- or cell-specific promoter to restrict expression to specific cell types (e.g., T cells) or tissues. In some embodiments the nucleic acid molecule includes tissue-specific promoters and enhancers. Exemplary tissue-specific promoters, target tissues and autoimmune diseases associated with the specified target tissue(s) are set forth in Table 11.
In some embodiments, the promotor is an inducible promotor, which may be responsive to an inducing agent (such as a T cell activation signal) or a condition of a targeted environment, such as hypoxia.
In some embodiments the nucleic acid molecule includes a condition-dependent promoter. In such embodiments a promoter is selected to regulate gene expression in a disease-related manner. Exemplary condition-dependent promoters include hypoxic gene regulatory systems that utilize one or more hypoxic response elements (HRE) and transcription mediated by the transcription factor HIF-1, which is assembled under hypoxic conditions, such as during inflammation, e.g., in inflamed joints. In some embodiments, glucose or insulin-responsive promoters or elements, such as glucose response elements (GRE) and/or insulin-like growth factor binding protein-1 basal promoter, can be included in the provided nucleic acid molecules, for use or administration, for example, to patients with a glucose-related disorder, such as diabetes.
In some embodiments, a constitutive promoter is operatively linked to the nucleic acid molecule encoding the variant polypeptide or immunomodulatory protein. Exemplary constitutive promoters include the Simian vacuolating virus 40 (SV40) promoter, the cytomegalovirus (CMV) promoter, the ubiquitin C (UbC) promoter, and the EF-1 alpha (EF1a) promoter. In some embodiments, the constitutive promoter is tissue specific. For example, in some embodiments, the promoter allows for constitutive expression of the immunomodulatory protein in specific tissues, such as immune cells, lymphocytes, or T cells. Exemplary tissue-specific promoters are described in U.S. Pat. No. 5,998,205, including, for example, a fetoprotein, DF3, tyrosinase, CEA, surfactant protein, and ErbB2 promoters.
In some embodiments, an inducible promoter is operatively linked to the nucleic acid molecule encoding the variant polypeptide or immunomodulatory protein such that expression of the nucleic acid is controllable by controlling the presence or absence of the appropriate inducer of transcription. For example, the promoter can be a regulated promoter and transcription factor expression system, such as the published tetracycline-regulated systems or other regulatable systems (see, e.g. published International PCT Appl. No. WO 01/30843), to allow regulated expression of the encoded polypeptide. An exemplary regulatable promoter system is the Tet-On (and Tet-Off) system available, for example, from Clontech (Palo Alto, Calif.). This promoter system allows the regulated expression of the transgene controlled by tetracycline or tetracycline derivatives, such as doxycycline. Other regulatable promoter systems are known (see e.g., published U.S. Application No. 2002-0168714, entitled “Regulation of Gene Expression Using Single-Chain, Monomeric, Ligand Dependent Polypeptide Switches,” which describes gene switches that contain ligand binding domains and transcriptional regulating domains, such as those from hormone receptors). Other exemplary inducible promoters of the tetracycline systems include repressor (tetR), rapamycin, ecdysone, mifepristone, and streptogramin systems.
In some embodiments, the promotor is responsive to an element responsive to T-cell activation signaling. Solely by way of example, in some embodiments, an engineered T cell comprises an expression vector encoding the immunomodulatory protein and a promotor operatively linked to control expression of the immunomodulatory protein. The engineered T cell can be activated, for example by signaling through an engineered T cell receptor (TCR) or a chimeric antigen rector (CAR), and thereby triggering expression and secretion of the immunomodulatory protein through the responsive promotor.
In some embodiments, an inducible promoter is operatively linked to the nucleic acid molecule encoding the immunomodulatory protein such that the immunomodulatory protein is expressed in response to a nuclear factor of activated T-cells (NFAT) or nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB). For example, in some embodiments, the inducible promoter comprises a binding site for NFAT or NF-κB. For example, in some embodiments, the promoter is an NFAT or NF-κB promoter or a functional variant thereof. Thus, in some embodiments, the nucleic acids make it possible to control the expression of immunomodulatory protein while also reducing or eliminating the toxicity of the immunomodulatory protein. In particular, engineered immune cells comprising the nucleic acids of the invention express and secrete the immunomodulatory protein only when the cell (e.g., a T-cell receptor (TCR) or a chimeric antigen receptor (CAR) expressed by the cell) is specifically stimulated by an antigen and/or the cell (e.g., the calcium signaling pathway of the cell) is non-specifically stimulated by, e.g., phorbol myristate acetate (PMA)/Ionomycin. Accordingly, the expression and, in some cases, secretion, of immunomodulatory protein can be controlled to occur only when and where it is needed (e.g., in the presence of an infectious disease-causing agent, cancer, or at a tumor site), which can decrease or avoid undesired immunomodulatory protein interactions.
In some embodiments, the nucleic acid encoding an immunomodulatory protein described herein comprises a suitable nucleotide sequence that encodes a NFAT promoter, NF-κB promoter, or a functional variant thereof. “NFAT promoter” as used herein means one or more NFAT responsive elements linked to a minimal promoter. “NF-κB promoter” refers to one or more NF-κB responsive elements linked to a minimal promoter. In some embodiments, the minimal promoter of a gene is a minimal human IL-2 promoter or a CMV promoter. The NFAT responsive elements may comprise, e.g., NFAT1, NFAT2, NFAT3, and/or NFAT4 responsive elements. The NFAT promoter, NF-κB promoter, or a functional variant thereof may comprise any number of binding motifs, e.g., at least two, at least three, at least four, at least five, or at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, or up to twelve binding motifs.
The resulting recombinant expression vector having the DNA molecule thereon is used to transform an appropriate host. This transformation can be performed using methods well known in the art. In some embodiments, a nucleic acid provided herein further comprises nucleotide sequence that encodes a secretory or signal peptide operably linked to the nucleic acid encoding an immunomodulatory polypeptide such that a resultant soluble immunomodulatory polypeptide is recovered from the culture medium, host cell, or host cell periplasm. In other embodiments, the appropriate expression control signals are chosen to allow for membrane expression of an immunomodulatory polypeptide. Furthermore, commercially available kits as well as contract manufacturing companies can also be utilized to make engineered cells or recombinant host cells provided herein.
In some embodiments, the resulting expression vector having the DNA molecule thereon is used to transform, such as transduce, an appropriate cell. The introduction can be performed using methods well known in the art. Exemplary methods include those for transfer of nucleic acids encoding the receptors, including via viral, e.g., retroviral or lentiviral, transduction, transposons, and electroporation. In some embodiments, the expression vector is a viral vector. In some embodiments, the nucleic acid is transferred into cells by lentiviral or retroviral transduction methods.
Any of a large number of publicly available and well-known mammalian host cells, including mammalian T-cells or APCs, can be used in the preparing the polypeptides or engineered cells. The selection of a cell is dependent upon a number of factors recognized by the art. These include, for example, compatibility with the chosen expression vector, toxicity of the peptides encoded by the DNA molecule, rate of transformation, ease of recovery of the peptides, expression characteristics, bio-safety and costs. A balance of these factors must be struck with the understanding that not all cells can be equally effective for the expression of a particular DNA sequence.
In some embodiments, the host cells can be a variety of eukaryotic cells, such as in yeast cells, or with mammalian cells such as Chinese hamster ovary (CHO) or HEK293 cells. In some embodiments, the host cell is a suspension cell and the polypeptide is engineered or produced in cultured suspension, such as in cultured suspension CHO cells, e.g. CHO-S cells. In some examples, the cell line is a CHO cell line that is deficient in DHFR (DHFR-), such as DG44 and DUXB11. In some embodiments, the cell is deficient in glutamine synthase (GS), e.g. CHO-S cells, CHOK1 SV cells, and CHOZN((R)) GS−/− cells. In some embodiments, the CHO cells, such as suspension CHO cells, may be CHO-S-2H2 cells, CHO-S-clone 14 cells, or ExpiCHO-S cells.
In some embodiments, host cells can also be prokaryotic cells, such as with E. coli. The transformed recombinant host is cultured under polypeptide expressing conditions, and then purified to obtain a soluble protein. Recombinant host cells can be cultured under conventional fermentation conditions so that the desired polypeptides are expressed. Such fermentation conditions are well known in the art. Finally, the polypeptides provided herein can be recovered and purified from recombinant cell cultures by any of a number of methods well known in the art, including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, and affinity chromatography. Protein refolding steps can be used, as desired, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed in the final purification steps.
In some embodiments, the cell is an immune cell, such as any described above in connection with preparing engineered cells. In some embodiments, such engineered cells are primary cells. In some embodiments, the engineered cells are autologous to the subject. In some embodiment, the engineered cells are allogeneic to the subject. In some embodiments, the engineered cells are obtained from a subject, such as by leukapheresis, and transformed ex vivo for expression of the immunomodulatory polypeptide, e.g. transmembrane immunomodulatory polypeptide or secretable immunomodulatory polypeptide.
Also provided are nucleic acids encoding any of the variant immunomodulatory polypeptides contained in infectious agents described herein. In some embodiments, the infectious agents deliver the nucleic acids to a cell in the subject, and/or permit expression of the encoded variant polypeptides in the cell. Also provided are nucleic acids that are used to generate, produce or modify such infectious agents. For example, in some embodiments, provided are vectors and/or plasmids that contain nucleic acids encoding the variant immunomodulatory polypeptides, for generation of the infectious agents, delivery to the cells in a subject and/or expression of the variant immunomodulatory polypeptides in the cells in the subject.
In some embodiments, the provided nucleic acids are recombinant viral or bacterial vectors containing nucleic acid sequences encoding the variant immunomodulatory polypeptides. In some embodiments, the recombinant vectors can be used to produce an infectious agent that contains nucleic acid sequences encoding the variant immunomodulatory polypeptides and/or to be delivered to a target cell in the subject for expression by the target cell. In some embodiments, the recombinant vector is an expression vector. In some embodiments, the recombinant vector includes appropriate sequences necessary for generation and/or production of the infectious agent and expression in the target cell.
In some embodiments, the recombinant vector is a plasmid or cosmid. Plasmid or cosmid containing nucleic acid sequences encoding the variant immunomodulatory polypeptides, as described herein, is readily constructed using standard techniques well known in the art. For generation of the infectious agent, the vector or genome can be constructed in a plasmid form that can then be transfected into a packaging or producer cell line or a host bacterium. The recombinant vectors can be generated using any of the recombinant techniques known in the art. In some embodiments, the vectors can include a prokaryotic origin of replication and/or a gene whose expression confers a detectable or selectable marker such as a drug resistance for propagation and/or selection in prokaryotic systems.
In some embodiments, the recombinant vector is a viral vector. Exemplary recombinant viral vectors include a lentiviral vector genome, poxvirus vector genome, vaccinia virus vector genome, adenovirus vector genome, adenovirus-associated virus vector genome, herpes virus vector genome, and alpha virus vector genome. Viral vectors can be live, attenuated, replication conditional or replication deficient, non-pathogenic (defective), replication competent viral vector, and/or is modified to express a heterologous gene product, e.g., the variant immunomodulatory polypeptides provided herein. Vectors for generation of viruses also can be modified to alter attenuation of the virus, which includes any method of increasing or decreasing the transcriptional or translational load.
Exemplary viral vectors that can be used include modified vaccinia virus vectors (see, e.g., Guerra et al., J. Virol. 80:985-98 (2006); Tartaglia et al., AIDS Research and Human Retroviruses 8: 1445-47 (1992); Gheradi et al., J. Gen. Virol. 86:2925-36 (2005); Mayr et al., Infection 3:6-14 (1975); Hu et al., J. Virol. 75: 10300-308 (2001); U.S. Pat. Nos. 5,698,530, 6,998,252, 5,443,964, 7,247,615 and 7,368,116); adenovirus vector or adenovirus-associated virus vectors (see, e.g., Molin et al., J. Virol. 72:8358-61 (1998); Narumi et al., Am J. Respir. Cell Mol. Biol. 19:936-41 (1998); Mercier et al., Proc. Natl. Acad. Sci. USA 101:6188-93 (2004); U.S. Pat. Nos. 6,143,290; 6,596,535; 6,855,317; 6,936,257; 7,125,717; 7,378,087; 7,550,296); retroviral vectors including those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), ecotropic retroviruses, simian immunodeficiency virus (SIV), human immunodeficiency virus (HIV), and combinations (see, e.g., Buchscher et al., J. Virol. 66:2731-39 (1992); Johann et al., J. Virol. 66: 1635-40 (1992); Sommerfelt et al., Virology 176:58-59 (1990); Wilson et al., J. Virol. 63:2374-78 (1989); Miller et al., J. Virol. 65:2220-24 (1991); Miller et al., Mol. Cell Biol. 10:4239 (1990); Kolberg, NIH Res. 4:43 1992; Cornetta et al., Hum. Gene Ther. 2:215 (1991)); lentiviral vectors including those based upon Human Immunodeficiency Virus (HIV-1), HIV-2, feline immunodeficiency virus (FIV), equine infectious anemia virus, Simian Immunodeficiency Virus (SIV), and maedi/visna virus (see, e.g., Pfeifer et al., Annu. Rev. Genomics Hum. Genet. 2: 177-211 (2001); Zufferey et al., J. Virol. 72: 9873, 1998; Miyoshi et al., J. Virol. 72:8150, 1998; Philpott and Thrasher, Human Gene Therapy 18:483, 2007; Engelman et al., J. Virol. 69: 2729, 1995; Nightingale et al., Mol. Therapy, 13: 1121, 2006; Brown et al., J. Virol. 73:9011 (1999); WO 2009/076524; WO 2012/141984; WO 2016/011083; McWilliams et al., J. Virol. 77: 11150, 2003; Powell et al., J. Virol. 70:5288, 1996) or any, variants thereof, and/or vectors that can be used to generate any of the viruses described above. In some embodiments, the recombinant vector can include regulatory sequences, such as promoter or enhancer sequences, that can regulate the expression of the viral genome, such as in the case for RNA viruses, in the packaging cell line (see, e.g., U.S. Pat. Nos. 5,385,839 and 5,168,062).
In some embodiments, the recombinant vector is an expression vector, e.g., an expression vector that permits expression of the encoded gene product when delivered into the target cell, e.g., a cell in the subject, e.g., a tumor cell, an immune cell and/or an APC. In some embodiments, the recombinant expression vectors contained in the infectious agent are capable of expressing the immunomodulatory proteins in the target cell in the subject, under conditions suited to expression of the protein.
In some aspects, nucleic acids or an expression vector comprises a nucleic acid sequence that encodes the immunomodulatory protein operatively linked to appropriate expression control sequences. Methods of affecting this operative linking, either before or after the nucleic acid sequence encoding the immunomodulatory protein is inserted into the vector, are well known. Expression control sequences include promoters, activators, enhancers, operators, ribosomal binding sites, start signals, stop signals, cap signals, polyadenylation signals, and other signals involved with the control of transcription or translation. The promoter can be operably linked to the portion of the nucleic acid sequence encoding the immunomodulatory protein. In some embodiments, the promotor is a constitutively active promotor in the target cell (such as a tissue-specific constitutively active promotor or other constitutive promotor). For example, the recombinant expression vector may also include, lymphoid tissue-specific transcriptional regulatory elements (TRE) such as a B lymphocyte, T lymphocyte, or dendritic cell specific TRE. Lymphoid tissue specific TRE are known in the art (see, e.g., Thompson et al., Mol. Cell. Biol. 12:1043-53 (1992); Todd et al., J. Exp. Med. 177:1663-74 (1993); Penix et al., J. Exp. Med. 178:1483-96 (1993)). In some embodiments, the promotor is an inducible promotor, which may be responsive to an inducing agent (such as a T cell activation signal). In some embodiments, nucleic acids delivered to the target cell in the subject, e.g., immune cell, cell localized to an inflammatory environment, and/or APC, can be operably linked to any of the regulatory elements described above.
In some embodiments, the vector is a bacterial vector, e.g., a bacterial plasmid or cosmid. In some embodiments, the bacterial vector is delivered to the target cell, e.g., immune cells, cells localized to an inflammatory environment, and/or APCs, via bacterial-mediated transfer of plasmid DNA to mammalian cells (also referred to as “bactofection”). In some embodiments, the delivered bacterial vector also contains appropriate expression control sequences for expression in the target cells, such as a promoter sequence and/or enhancer sequences, or any regulatory or control sequences described above. In some embodiments, the bacterial vector contains appropriate expression control sequences for expression and/or secretion of the encoded variant polypeptides in the infectious agent, e.g., the bacterium.
In some embodiments, polypeptides provided herein can also be made by synthetic methods. Solid phase synthesis is the preferred technique of making individual peptides since it is the most cost-effective method of making small peptides. For example, well known solid phase synthesis techniques include the use of protecting groups, linkers, and solid phase supports, as well as specific protection and deprotection reaction conditions, linker cleavage conditions, use of scavengers, and other aspects of solid phase peptide synthesis. Peptides can then be assembled into the polypeptides as provided herein.
Provided herein are engineered cells and infectious agents that express the provided multi-domain immunomodulatory proteins. In some embodiments, provided are engineered cells that contain nucleic acid(s) encoding any of the multi-domain immunomodulatory proteins provided herein. Also provided are infectious agents that contain nucleic acids encoding any of the multi-domain immunomodulatory proteins. In some embodiments, such infectious agents can deliver the nucleic acids encoding the multi-domain immunomodulatory proteins described herein to a target cell in a subject, e.g., immune cell and/or antigen-presenting cell (APC) or tumor cell in a subject. In some embodiments, the expressed immunomodulatory protein is a secretable protein that is expressed and secreted from the cell or infectious agent. Also provided are nucleic acids contained in such engineered cells and infectious agents, and/or nucleic acids for generation or modification of such engineered cells or infectious agents, such as vectors and/or plasmids, and compositions containing such engineered cells or infectious agents.
A. Secreted Immunomodulatory Proteins
In some embodiments, the multi-domain immunomodulatory protein is secretable, such as when expressed from a cell or when expressed by a cell infected by an infectious agent. In some embodiments, such a secretable immunomodulatory protein does not comprise a transmembrane domain or a cytoplasmic signaling domain. In some embodiments, the immunomodulatory protein is not conjugated to a half-life extending moiety (such as an Fc domain or a multimerization domain). In some embodiments, the immunomodulatory protein comprises a signal peptide, such as an antibody signal peptide or other efficient signal sequence to get domains outside of cell. When the immunomodulatory protein comprises a signal peptide and is expressed by an engineered cell or a cell infected by an infectious agent, the signal peptide causes the immunomodulatory protein to be secreted by the cell. Generally, the signal peptide, or a portion of the signal peptide, is cleaved from the immunomodulatory protein with secretion. The immunomodulatory protein can be encoded by a nucleic acid (which can be part of an expression vector). In some embodiments, the immunomodulatory protein is expressed and secreted by a cell (such as an immune cell, for example a primary immune cell).
Thus, in some embodiments, there are provided multi-domain immunomodulatory proteins that further comprise a signal peptide. In some embodiments, provided herein is a nucleic acid molecule encoding the multi-domain immunomodulatory protein operably connected to a secretion sequence encoding the signal peptide. In some embodiments, the encoded immunomodulatory protein is secreted when expressed from a cell.
A signal peptide is a sequence on the N-terminus of an immunomodulatory protein that signals secretion of the immunomodulatory protein from a cell. In some embodiments, the signal peptide is about 5 to about 40 amino acids in length (such as about 5 to about 7, about 7 to about 10, about 10 to about 15, about 15 to about 20, about 20 to about 25, or about 25 to about 30, about 30 to about 35, or about 35 to about 40 amino acids in length).
In some embodiments, the signal peptide is a native signal peptide from one of the corresponding native IgSF family members of the multi-domain immunomodulatory protein (see Table 1, Table 6A or Table 6B). In some embodiments, the signal peptide is a non-native signal peptide. In some embodiments, the non-native signal peptide is a signal peptide or mutant thereof of a family member from the same IgSF family as the wild-type IgSF family member. In some embodiments, the non-native signal peptide is a signal peptide or mutant thereof from an IgSF family member from a different IgSF family that the wild-type IgSF family member. In some embodiments, the signal peptide is a signal peptide or mutant thereof from a non-IgSF protein family, such as a signal peptide from an immunoglobulin (such as IgG heavy chain or IgG-kappa light chain), a cytokine (such as interleukin-2 (IL-2), or CD33), a serum albumin protein (e.g. HSA or albumin), a human azurocidin preprotein signal sequence, a luciferase, a trypsinogen (e.g. chymotrypsinogen or trypsinogen) or other signal peptide able to efficiently secrete a protein from a cell. Exemplary signal peptides include any described in Table 12.
In some embodiments of a secretable immunomodulatory protein, the immunomodulatory protein comprises a signal peptide when expressed, and the signal peptide (or a portion thereof) is cleaved from the immunomodulatory protein upon secretion from a cell.
B. Cells and Engineering Cells
Provided herein are engineered cells expressing any of the provided immunomodulatory polypeptides. In some embodiments, the engineered cells express and are capable of or are able to secrete the immunomodulatory protein from the cells under conditions suitable for secretion of the protein. In some embodiments, the engineered cells can be administered to the subject, such as for treating a disease or condition, including any as described herein.
In some embodiments, the immunomodulatory protein is expressed on or in a lymphocyte such as a tumor infiltrating lymphocyte (TIL), T-cell or NK cell, or on a myeloid cell. In some embodiments, the engineered cells are antigen presenting cells (APCs). In some embodiments, the engineered cells are engineered mammalian T-cells or engineered mammalian antigen presenting cells (APCs). In some embodiments, the engineered T-cells or APCs are human or murine cells.
In some embodiments, engineered T-cells include, but are not limited to, regulatory T cells, T helper cells, cytotoxic T-cells (alternatively, cytotoxic T lymphocytes or CTLs), natural killer T-cells, memory T-cells, or gamma delta T-cells. In some embodiments, the engineered T cells are CD4+ or CD8+. In some aspects the engineered T cells can be activated T cells. In some embodiments, the engineered T cells are regulatory T cells (Treg).
In some embodiments, the engineered cell, e.g. T cell, can further express a chimeric antigen receptor (CAR) or engineered T cell receptor (TCR). In some aspects, the CAR or TCR are specific for an antigen expressed by a cell or tissue associated with a disease or condition, such as an inflammatory tissue or cell. In some cases, binding of a CAR or TCR to the antigen can guide the engineered cell to the cell or tissue specific antigen and locally deliver the provided immunomodulatory protein, e.g. secretable immunomodulatory protein.
In some embodiments, the immunomodulatory polypeptides, such as secretable immunomodulatory proteins, can be incorporated into engineered cells, such as engineered T cells or engineered APCs, by a variety of strategies such as those employed for recombinant host cells. A variety of methods to introduce a DNA construct into primary T cells are known in the art. In some embodiments, viral transduction or plasmid electroporation are employed. In some embodiments, a nucleic acid encoding the immunomodulatory protein is sub-cloned into a viral vector, such as a retroviral vector, which allows expression in the host mammalian cell. The expression vector can be introduced into a mammalian host cell and, under host cell culture conditions, the immunomodulatory protein is expressed, such as is secreted, from the cell.
In an exemplary example, primary T-cells can be purified ex vivo (CD4 cells or CD8 cells or both) and stimulated with an activation protocol consisting of various TCR/CD28 agonists, such as anti-CD3/anti-CD28 coated beads. After a 2 or 3 day activation process, a recombinant expression vector containing an immunomodulatory polypeptide can be stably introduced into the primary T cells through art standard lentiviral or retroviral transduction protocols or plasmid electroporation strategies. Cells can be monitored for immunomodulatory polypeptide expression by, for example, flow cytometry using anti-epitope tag or antibodies that cross-react with native parental molecule. T-cells that express the immunomodulatory polypeptide can be enriched through sorting with anti-epitope tag antibodies or enriched for high or low expression depending on the application. A composition containing the engineered cell can be assessed or monitored for secretion of the immunomodulatory protein, such as by detection in the media or supernatant usinng an anti-eptitope tag.
C. Infectious Agent
Provided herein are infectious agents, e.g., virus or bacteria, containing nucleic acid sequences that encode any of the multi-domain immunomodulatory proteins, including secretable proteins described herein, and by virtue of contact and/or infection of a cell, the cell expresses, and, in some cases secretes, the multi-domain immunomodulatory proteins. In some embodiments, the infectious agent can be administered to the subject, such as for treating a disease or condition, including any as described herein. In some embodiments, the infectious agent can be contacted with cells from the subject ex vivo.
In some embodiments, the infectious agent is a microorganism or a microbe. In some embodiments, the infectious agent is a virus or a bacterium. In some embodiments, the infectious agent is a virus. In some embodiments, the infectious agent is a bacterium. In some embodiments, such infectious agents can deliver nucleic acid sequences encoding any of the multi-domain immunomodulatory proteins, including secretable proteins described herein. Thus, in some embodiments, the cell in a subject that is infected or contacted by the infectious agents can be rendered to express on the cell surface or secrete, the variant immunomodulatory polypeptides. In some embodiments, the infectious agent can also deliver one or more other therapeutics or nucleic acids encoding other therapeutics to the cell and/or to an environment within the subject. In some embodiments, other therapeutics that can be delivered by the infectious agents include cytokines or other immunomodulatory molecules.
In some embodiments, the cells in the subject that are targeted by the infectious agent include an immune cell and/or an antigen-presenting cell (APC). In some embodiments, the infectious agent delivers the nucleic acids encoding the variant polypeptides, such as multi-domain immunomodulatory proteins, including secretable immunomodulatory proteins, to an appropriate cell (for example, a T cell that recognizes peptide/MHC on an APC such as a Treg cell) or tissue (e.g., lymphoid tissue) that modulates an immune response and/or a specific cell-medicated immune response. In some embodiments, the infectious agent targets a T cell, such as a regulatory T cell (Treg). In some embodiments, the nucleic acid molecule delivered by the infectious agents described herein include appropriate nucleic acid sequences necessary for the expression of the operably linked coding sequences encoding the variant immunomodulatory polypeptides, in a particular target cell, e.g., regulatory elements such as promoters.
In some embodiments, the infectious agent that contains nucleic acid sequences encoding the immunomodulatory polypeptides can also contain nucleic acid sequences that encode one or more additional gene products, e.g., cytokines, prodrug converting enzymes, cytotoxins and/or detectable gene products. In some embodiments, the additional gene product can be a therapeutic gene product that can result in death of the target cell (e.g., immune cell) or gene products that can inhibit or suppress or regulate an immune response (e.g., cytokine). Exemplary gene products also include an immunomodulatory molecule, an immune checkpoint activator, an antibody, a cytokine, a growth factor, an antigen, a cytotoxic gene product, a pro-apoptotic gene product, an anti-apoptotic gene product, a cell matrix degradative gene, and other genes described herein or known to one of skill in the art.
1. Viruses
In some embodiments, the infectious agent is a virus. In some embodiments, the infectious agent is a virus that targets particular cells, e.g., immune cells. In some embodiments, the infectious agent targets an immune cell or a T cell.
In some embodiments, the virus is an adenovirus (Ad); adeno-associated virus (AAV); herpes simplex virus (HSV); retroviral vector, such as Moloney murine leukemia virus (MMLV); hybrid retrovirus (e.g., containing various retroviral LTRs on their 5′ end, optimal for production of high-titer viral stocks, and spleen focus-forming virus (SFFV) LTR on 3′ end); lentiviral vector, such as human immunodeficiency virus (HIV-1), HIV-2, bovine lentivirus, feline lentivirus, or simian lentivirus; self-inactivating vector (SIV).
In some embodiments, the infectious agent is a modified herpes simplex virus. In some embodiments, the infectious agent is a modified version of Talimogene laherparepvec (also known as T-Vec, Imlygic or OncoVex GM-CSF), that is modified to contain nucleic acids encoding any of the variant immunomodulatory polypeptides described herein, such as multi-domain immunomodulatory proteins described herein. In some embodiments, the infectious agent is a modified herpes simplex virus that is described, e.g., in WO 2007/052029, WO 1999/038955, US 2004/0063094, US 2014/0154216, or, variants thereof.
In some embodiments, wherein the infectious agent is a virus, the tropism of viral particles is modified so that only cells expressing particular surface markers are transduced.
2. Bacteria
In some embodiments, the infectious agent is a bacterium. For example, in some embodiments, the bacteria can deliver nucleic acids encoding any of the multi-domain immunomodulatory proteins described herein to a target cell in the subject, such as an immune cell. In some embodiments, the bacterium can be preferentially targeted to a specific environment within a subject, such as an inflammatory environment, for expression and/or secretion of the variant immunomodulatory polypeptides and/or to target specific cells in the environment for expression of the variant immunomodulatory polypeptides.
In some embodiments, the bacterium delivers the nucleic acids to the cells via bacterial-mediated transfer of plasmid DNA to mammalian cells (also referred to as “bactofection”). For example, in some embodiments, delivery of genetic material is achieved through entry of the entire bacterium into target cells. In some embodiments, spontaneous or induced bacterial lysis can lead to the release of plasmid for subsequent eukaryotic cell expression. In some embodiments, the bacterium can deliver nucleic acids to non-phagocytic mammalian cells (e.g., certain immune cells or tissue types). In some embodiments, the nucleic acids delivered by the bacterium can be transferred to the nucleus of the cell in the subject for expression. In some embodiments, the nucleic acids also include appropriate nucleic acid sequences necessary for the expression of the operably linked sequences encoding the variant immunomodulatory polypeptides in a particular host cell, e.g., regulatory elements such as promoters or enhancers. In some embodiments, the infectious agent that is a bacterium can deliver nucleic acids encoding the immunomodulatory proteins in the form of an RNA, such as a pre-made translation-competent RNA delivered to the cytoplasm of the target cell for translation by the target cell's machinery.
In some embodiments, the bacterium can replicate and lyse the target cells, e.g., immune cells. In some embodiments, the bacterium can contain and/or release nucleic acid sequences and/or gene products in the cytoplasm of the target cells, thereby killing the target cell, e.g., immune cell. In some embodiments, the infectious agent is bacterium that can replicate specifically in a particular environment in the subject, e.g., inflammatory environment. For example, in some embodiments, the bacterium can replicate specifically in anaerobic or hypoxic microenvironments. In some embodiments, conditions or factors present in particular environments, e.g., aspartate, serine, citrate, ribose or galactose produced by cells in the inflammatory environment, can act as chemoattractants to attract the bacterium to the environment. In some embodiments, the bacterium can express and/or secrete the immunomodulatory proteins described herein in the environment, e.g., inflammatory environment.
In some embodiments, the infectious agent is a bacterium that is a Listeria sp., a Bifidobacterium sp., an Escherichia sp., a Clostridium sp., a Salmonella sp., a Shigella sp., a Vibrio sp. or a Yersinia sp. In some embodiments, the bacterium is selected from among one or more of Listeria monocytogenes, Salmonella typhimurium, Salmonella choleraesuis, Escherichia coli, Vibrio cholera, Clostridium perfringens, Clostridium butyricum, Clostridium novyi, Clostridium acetobutylicum, Bifidobacterium infantis, Bifidobacterium longum and Bifidobacterium adolescentis. In some embodiments, the bacterium is an engineered bacterium. In some embodiments, the bacterium is an engineered bacterium such as those described in, e.g., Seow and Wood (2009) Molecular Therapy 17(5):767-777; Baban et al. (2010) Bioengineered Bugs 1:6, 385-394; Patyar et al. (2010) J Biomed Sci 17:21; Tangney et al. (2010) Bioengineered Bugs 1:4, 284-287; van Pijkeren et al. (2010) Hum Gene Ther. 21(4):405-416; WO 2012/149364; WO 2014/198002; U.S. Pat. Nos. 9,103,831; 9,453,227; US 2014/0186401; US 2004/0146488; US 2011/0293705; US 2015/0359909 and EP 3020816. The bacterium can be modified to deliver nucleic acid sequences encoding any of the variant immunomodulatory polypeptides, conjugates and/or fusions provided herein, and/or to express such variant immunomodulatory polypeptides in the subject.
Provided herein are compositions containing any of the provided immunomodulatory proteins, engineered cells or infectious agents described herein. The pharmaceutical composition can further comprise a pharmaceutically acceptable excipient. For example, the pharmaceutical composition can contain one or more excipients for modifying, maintaining or preserving, for example, the pH, osmolarity, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsorption, or penetration of the composition. In some aspects, a skilled artisan understands that a pharmaceutical composition containing cells may differ from a pharmaceutical composition containing a protein.
In some embodiments, the pharmaceutical composition is a solid, such as a powder, capsule, or tablet. For example, the components of the pharmaceutical composition can be lyophilized. In some embodiments, the solid pharmaceutical composition is reconstituted or dissolved in a liquid prior to administration.
In some embodiments, the pharmaceutical composition is a liquid, for example multi-domain immunomodulatory proteins dissolved in an aqueous solution (such as physiological saline or Ringer's solution). In some embodiments, the pH of the pharmaceutical composition is between about 4.0 and about 8.5 (such as between about 4.0 and about 5.0, between about 4.5 and about 5.5, between about 5.0 and about 6.0, between about 5.5 and about 6.5, between about 6.0 and about 7.0, between about 6.5 and about 7.5, between about 7.0 and about 8.0, or between about 7.5 and about 8.5).
In some embodiments, the pharmaceutical composition comprises a pharmaceutically-acceptable excipient, for example a filler, binder, coating, preservative, lubricant, flavoring agent, sweetening agent, coloring agent, a solvent, a buffering agent, a chelating agent, or stabilizer. Examples of pharmaceutically-acceptable fillers include cellulose, dibasic calcium phosphate, calcium carbonate, microcrystalline cellulose, sucrose, lactose, glucose, mannitol, sorbitol, maltol, pregelatinized starch, corn starch, or potato starch. Examples of pharmaceutically-acceptable binders include polyvinylpyrrolidone, starch, lactose, xylitol, sorbitol, maltitol, gelatin, sucrose, polyethylene glycol, methyl cellulose, or cellulose. Examples of pharmaceutically-acceptable coatings include hydroxypropyl methylcellulose (HPMC), shellac, corn protein zein, or gelatin. Examples of pharmaceutically-acceptable disintegrants include polyvinylpyrrolidone, carboxymethyl cellulose, or sodium starch glycolate. Examples of pharmaceutically-acceptable lubricants include polyethylene glycol, magnesium stearate, or stearic acid. Examples of pharmaceutically-acceptable preservatives include methyl parabens, ethyl parabens, propyl paraben, benzoic acid, or sorbic acid. Examples of pharmaceutically-acceptable sweetening agents include sucrose, saccharine, aspartame, or sorbitol. Examples of pharmaceutically-acceptable buffering agents include carbonates, citrates, gluconates, acetates, phosphates, or tartrates.
In some embodiments, the pharmaceutical composition further comprises an agent for the controlled or sustained release of the product, such as injectable microspheres, bio-erodible particles, polymeric compounds (polylactic acid, polyglycolic acid), beads, or liposomes.
In some embodiments, the pharmaceutical composition is sterile. Sterilization may be accomplished by filtration through sterile filtration membranes or radiation. Where the composition is lyophilized, sterilization using this method may be conducted either prior to or following lyophilization and reconstitution. The composition for parenteral administration may be stored in lyophilized form or in solution. In addition, parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
In some embodiments, provided are pharmaceutical compositions containing the transmembrane immunomodulatory proteins, including engineered cells expressing such transmembrane immunomodulatory proteins. In some embodiments, the pharmaceutical compositions and formulations include one or more optional pharmaceutically acceptable carrier or excipient. Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives. Compositions of the present invention are preferably formulated for intravenous administration.
In some embodiments, the pharmaceutical composition contains infectious agents containing nucleic acid sequences encoding the immunomodulatory variant polypeptides. In some embodiments, the pharmaceutical composition contains a dose of infectious agents suitable for administration to a subject that is suitable for treatment. In some embodiments, the pharmaceutical composition contains an infectious agent that is a virus, at a single or multiple dosage amount, of between about between or between about 1×105 and about 1×1012 plaque-forming units (pfu), 1×106 and 1×1010 pfu, or 1×107 and 1×1010 pfu, each inclusive, such as at least or at least about or at about 1×106, 1×107, 1×108, 1×109, 2×109, 3×109, 4×109, 5×109 pfu or about 1×1010 pfu. In some embodiments, the pharmaceutical composition can contain a virus concentration of from or from about 105 to about 1010 pfu/mL, for example, 5×106 to 5×109 or 1×107 to 1×109 pfu/mL, such as at least or at least about or at about 106 pfu/mL, 107 pfu/mL, 108 pfu/mL or 109 pfu/mL. In some embodiments, the pharmaceutical composition contains an infectious agent that is a bacterium, at a single or multiple dosage amount, of between about between or between about 1×103 and about 1×109 colony-forming units (cfu), 1×104 and 1×109 cfu, or 1×105 and 1×107 cfu, each inclusive, such as at least or at least about or at about 1×104, 1×105, 1×106, 1×10, 1×108 or 1×109 cfu. In some embodiments, the pharmaceutical composition can contain a bacterial concentration of from or from about 103 to about 108 cfu/mL, for example, 5×105 to 5×107 or 1×106 to 1×107 cfu/mL, such as at least or at least about or at about 105 cfu/mL, 106 cfu/mL, 107 cfu/mL or 108 cfu/mL
Such a formulation may, for example, be in a form suitable for intravenous infusion. A pharmaceutically acceptable carrier may be a pharmaceutically acceptable material, composition, or vehicle that is involved in carrying or transporting cells of interest from one tissue, organ, or portion of the body to another tissue, organ, or portion of the body. For example, the carrier may be a liquid or solid filler, diluent, excipient, solvent, or encapsulating material, or some combination thereof. Each component of the carrier must be “pharmaceutically acceptable” in that it must be compatible with the other ingredients of the formulation. It also must be suitable for contact with any tissue, organ, or portion of the body that it may encounter, meaning that it must not carry a risk of toxicity, irritation, allergic response, immunogenicity, or any other complication that excessively outweighs its therapeutic benefits.
In some embodiments, the pharmaceutical composition is administered to a subject. Generally, dosages and routes of administration of the pharmaceutical composition are determined according to the size and condition of the subject, according to standard pharmaceutical practice. For example, the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models such as mice, rats, rabbits, dogs, pigs, or monkeys. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. The exact dosage will be determined in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active compound or to maintain the desired effect. Factors that may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy.
Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation. The frequency of dosing will depend upon the pharmacokinetic parameters of the molecule in the formulation used. Typically, a composition is administered until a dosage is reached that achieves the desired effect. The composition may therefore be administered as a single dose, or as multiple doses (at the same or different concentrations/dosages) over time, or as a continuous infusion. Further refinement of the appropriate dosage is routinely made. Appropriate dosages may be ascertained through use of appropriate dose-response data. A number of biomarkers or physiological markers for therapeutic effect can be monitored including T cell activation or proliferation, cytokine synthesis or production (e.g., production of TNF-α, IFN-γ, IL-2), induction of various activation markers (e.g., CD25, IL-2 receptor), inflammation, joint swelling or tenderness, serum level of C-reactive protein, anti-collagen antibody production, and/or T cell-dependent antibody response(s).
In some embodiments, the pharmaceutical composition is administered to a subject through any route, including orally, transdermally, by inhalation, intravenously, intra-arterially, intramuscularly, direct application to a wound site, application to a surgical site, intraperitoneally, by suppository, subcutaneously, intradermally, transcutaneously, by nebulization, intrapleurally, intraventricularly, intra-articularly, intraocularly, or intraspinally.
In some embodiments, the dosage of the pharmaceutical composition is a single dose or a repeated dose. In some embodiments, the doses are given to a subject once per day, twice per day, three times per day, or four or more times per day. In some embodiments, about 1 or more (such as about 2 or more, about 3 or more, about 4 or more, about 5 or more, about 6 or more, or about 7 or more) doses are given in a week. In some embodiments, multiple doses are given over the course of days, weeks, months, or years. In some embodiments, a course of treatment is about 1 or more doses (such as about 2 or more does, about 3 or more doses, about 4 or more doses, about 5 or more doses, about 7 or more doses, about 10 or more doses, about 15 or more doses, about 25 or more doses, about 40 or more doses, about 50 or more doses, or about 100 or more doses).
In some embodiments, an administered dose of the pharmaceutical composition is about 1 μg of protein per kg subject body mass or more (such as about 2 μg of protein per kg subject body mass or more, about 5 μg of protein per kg subject body mass or more, about 10 μg of protein per kg subject body mass or more, about 25 μg of protein per kg subject body mass or more, about 50 μg of protein per kg subject body mass or more, about 100 μg of protein per kg subject body mass or more, about 250 μg of protein per kg subject body mass or more, about 500 μg of protein per kg subject body mass or more, about 1 mg of protein per kg subject body mass or more, about 2 mg of protein per kg subject body mass or more, or about 5 mg of protein per kg subject body mass or more).
In some embodiments, a therapeutic amount of a cell composition is administered. Typically, precise amount of the compositions of the present invention to be administered can be determined by a physician with consideration of individual differences in age, weight, tumor size, extent of infection or metastasis, and condition of the patient (subject). It can generally be stated that a pharmaceutical composition comprising engineered cells, e.g. T cells, as described herein may be administered at a dosage of 104 to 109 cells/kg body weight, such as 105 to 106 cells/kg body weight, including all integer values within those ranges. Engineered cell compositions, such as T cell compositions, may also be administered multiple times at these dosages. The cells can be administered by using infusion techniques that are commonly known in immunotherapy (see, e.g., Rosenberg et al, New Eng. J. of Med. 319: 1676, 1988). The optimal dosage and treatment regime for a particular patient can readily be determined by one skilled in the art of medicine by monitoring the patient for signs of disease and adjusting the treatment accordingly.
A variety of means are known for determining if administration of a therapeutic composition of the invention sufficiently modulates immunological activity by eliminating, sequestering, or inactivating immune cells mediating or capable of mediating an undesired immune response; inducing, generating, or turning on immune cells that mediate or are capable of mediating a protective immune response; changing the physical or functional properties of immune cells; or a combination of these effects. Examples of measurements of the modulation of immunological activity include, but are not limited to, examination of the presence or absence of immune cell populations (using flow cytometry, immunohistochemistry, histology, electron microscopy, polymerase chain reaction (PCR)); measurement of the functional capacity of immune cells including ability or resistance to proliferate or divide in response to a signal (such as using T-cell proliferation assays and pepscan analysis based on 3H-thymidine incorporation following stimulation with anti-CD3 antibody, anti-T-cell receptor antibody, anti-CD28 antibody, calcium ionophores, PMA (phorbol 12-myristate 13-acetate) antigen presenting cells loaded with a peptide or protein antigen; B cell proliferation assays); measurement of the ability to kill or lyse other cells (such as cytotoxic T cell assays); measurements of the cytokines, chemokines, cell surface molecules, antibodies and other products of the cells (e.g., by flow cytometry, enzyme-linked immunosorbent assays, Western blot analysis, protein microarray analysis, immunoprecipitation analysis); measurement of biochemical markers of activation of immune cells or signaling pathways within immune cells (e.g., Western blot and immunoprecipitation analysis of tyrosine, serine or threonine phosphorylation, polypeptide cleavage, and formation or dissociation of protein complexes; protein array analysis; DNA transcriptional, profiling using DNA arrays or subtractive hybridization); measurements of cell death by apoptosis, necrosis, or other mechanisms (e.g., annexin V staining, TUNEL assays, gel electrophoresis to measure DNA laddering, histology; fluorogenic caspase assays, Western blot analysis of caspase substrates); measurement of the genes, proteins, and other molecules produced by immune cells (e.g., Northern blot analysis, polymerase chain reaction, DNA microarrays, protein microarrays, 2-dimensional gel electrophoresis, Western blot analysis, enzyme linked immunosorbent assays, flow cytometry); and measurement of clinical symptoms or outcomes such as improvement of autoimmune, neurodegenerative, and other diseases involving self-proteins or self-polypeptides (clinical scores, requirements for use of additional therapies, functional status, imaging studies) for example, by measuring relapse rate or disease severity (using clinical scores known to the ordinarily skilled artisan) in the case of multiple sclerosis, measuring blood glucose in the case of type I diabetes, or joint inflammation in the case of rheumatoid arthritis.
In some embodiments, the multi-domain immunomodulatory proteins provided herein exhibit immunomodulatory activity to modulate T cell activation or response. In some embodiments, T cell activation or response is reduced, decreased or attenuated. Among T cell responses that can be modulated by provided immunomodulatory proteins include one or more of cell cycle inhibition, reduced cell survival, reduced cell proliferation, reduced cytokine production (e.g. IFN-gamma or IL-2), or reduced T-cell cytotoxicity. In some embodiments, the reduced activity is observed in vitro in a primary T cell activation assays, such as in a Jurkat reporter assay, SEB assay or mixed lymphocyte reaction (MLR) assay. In some embodiments, the reduced or decreased activity is observed in vivo upon administration to a subject, such as a human or mammalian subject.
In some embodiments, the activity is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% compared to the activity in the same assay in the absence of the immunomodulatory protein. In some embodiments, the activity is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% compared to the activity in the same assay presence of a control in which the control is a protein that is known or suspected not to modulate T cell activity, e.g. an Fc only control. In some embodiments, the activity is reduced to a level that is greater than the reduction observed by a reference immunomodulatory protein containing only the ARBM or containing only the IRBM, such as is reduced by greater than or greater than about 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 2.0-fold, 3.0-fold, 4.0-fold 5.0-fold or more compared to the reference immunomodulatory protein.
In some embodiments, multi-domain immunomodulatory proteins modulate IFN-gamma expression or production or IL-2 expression of production in a T cell assay relative to a control protein or reference immunomodulatory protein (e.g. containing only an ARBM or only an IRBM or containing a wild-type or unmodified IgSF domain).
In some ses, modulation of IFN-gamma or IL-2 expression or production is a decrease in IFN-gamma or IL-2 expression or production relative to the control or reference protein.
In some aspects, assays typically employed in connection with assaying modulation of immune activity of the provided immunomodulatory proteins include assays involving co-culture of T cells and antigen presenting cells. Such assays are well-known in the art and include, for example, the MLR (mixed lymphocyte reaction) assays measuring interferon-gamma or IL-2 cytokine levels in culture supernatants (Wang et al., Cancer Immunol Res. 2014 September: 2(9):846-56). In such assays, immunomodulatory proteins can in some embodiments decrease IFN-gamma (interferon-gamma) or IL-2 expression or production in a primary T-cell assay relative to a control or reference protein.
In some embodiments, in assaying for the ability of a provided immunomodulatory protein to modulate, e.g. decrease, IFN-gamma or IL-2 expression or production a T cell reporter assay can be used. In some embodiments, the T cell is a Jurkat T cell line or is derived from Jurkat T cell lines. In reporter assays, the reporter cell line (e.g. Jurkat reporter cell) also is generated to overexpress an activating receptor, such as a costimulatory receptor, that is the binding partner of the immunomodulatory protein. In some embodiments, the reporter cell line is generated to overexpress an inhibitory receptor that is the binding partner of the immunomodulatory protein. For example, in the case of an immunomodulatory protein, the reporter cell line (e.g. Jurkat reporter cell) can be generated to overexpress PD-1. In some embodiments, the reporter T cells also contains a reporter construct containing an inducible promoter responsive to T cell activation operably linked to a reporter. In some embodiments, the reporter is a fluorescent or luminescent reporter. In some embodiments, the reporter is luciferase. In some embodiments, the promoter is responsive to CD3 signaling. In some embodiments, the promoter is an NFAT promoter. In some embodiments, the promoter is responsive to costimulatory signaling, e.g. CD28 costimulatory signaling. In some embodiments, the promoter is an IL-2 promoter.
In aspects of a reporter assay, a reporter cell line is stimulated, such as by co-incubation with antigen presenting cells (APCs), including APCs expressing one or more ligands of an activating receptor, e.g. costimulatory receptor, e.g. ICOSL, CD80, CD86, PD-L1, PD-L2, CD155 or CD112. In some embodiments, the APCs are artificial APCs. Artificial APCs are well known to a skilled artisan. In some embodiments, artificial APCs are derived from one or more mammalian cell line, such as K562, CHO or 293 cells. In some embodiments, the aAPCs can also express an anti-CD3 antibody (e.g. OKT3).
In some embodiments, the Jurkat reporter cells are co-incubated with artificial APCs in the presence of the immunomodulatory protein. In some embodiments, reporter expression is monitored, such as by determining the luminescence or fluorescence of the cells. In some embodiments, normal interactions between Jurkat cells and APCs, e.g. via activating receptor and their ligand, result in an enhancement of or increase in the reporter signal, such as compared to control, e.g. reporter expression by co-incubation of control T cells and APCs in which the activating receptor and ligand interaction is not present. In some embodiments, a provided immunomodulatory protein provided herein attenuates or decreases the reporter signal, thereby resulting in a decrease in the reporter signal compared to the absence of the immunomodulatory protein.
Use of proper controls is known to those of skill in the art, however, in the aforementioned embodiments, a control typically involves use of a reference protein containing one of the proteins of the immunomodulatory protein. In some embodiments, the control is of the same form or corresponding form as the immunomodulatory protein. For example, if the immunomodulatory protein is a soluble form containing one or more ARBM and IRBM fused to an Fc protein, than the control is a soluble form containing the ARBM or IRBM fused to the Fc protein. Irrespective of whether the binding affinity and/or selectivity to the inhibitory or activating receptor is increased or decreased, an immunomodulatory protein in some embodiments will decrease a T cell response, e.g. IFN-gamma or IL-2 expression or production, in a T-cell assay relative to a control or reference protein. In some embodiments, a provided immunomodulatory protein decreases a T cell response, e.g. IFN-gamma or IL-2 expression or production (i.e., protein expression), relative to a control or reference protein by at least: 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or higher.
In some cases, activity of a multi-domain immunomodulatory protein as provided can be assessed using an appropriate animal model. In some embodiments, the animal model is a model of autoimmune disease. Animal models of autoimmune activities include spontaneous animal models, such as spontaneous mouse models for autoimmune diseases, generated through the crossing of animal (e.g., mouse) strains that have genetic susceptibility genes or loci followed by careful monitoring of the animals for the development of disease phenotype. Exemplary spontaneous animal models include the nonobese diabetic (NOD) mouse model, which spontaneously develops type 1 diabetes mellitus (T1D)-like phenotypes, and the NZB/W F1 mouse model, which spontaneously develops systemic lupus erythematosus (SLE)-like phenotypes. Another exemplary animal model of autoimmune disease includes the experimental autoimmune encephalomyelitis (EAE) mouse model, generated by autoantigen injection for the study of multiple sclerosis (MS). Exemplary rheumatoid arthritis (RA) models include human T-cell leukemia virus type I (HTLV-I) transgenic mouse models and IL-1 receptor antagonist (IL-1Ra) deficient (KO) mouse models. Concanavalin A (Con A)-induced hepatitis in the mouse is an exemplary model for autoimmune hepatitis (Tiegs et al., 1992, JCI, Mizuhara H., JEM, 1994, Toyabe S, JI, 1997). Other exemplary animal models include graft versus host-disease (GVHD) mouse model, syngeneic transplant mouse models, and bone marrow transplant models. Animal models are widely used to study pathology and treatment of autoimmune disease and can be used to assess the use, dosage, and efficacy of the multi-domain immunomodulatory proteins provided herein.
Provided herein are compositions and methods relating to the provided immunomodulatory proteins, engineered cells and infectious agents described herein for use in modulating immunological activity of a mammalian cell. The compositions can be used in associated methods to, for example, modulate immunological activity in an immunotherapy approach to the treatment of a disease. For example, in some embodiments the pharmaceutical composition is used to treat inflammatory or autoimmune disorders, cancer, organ transplantation, viral infections, and/or bacterial infections in a mammal. The pharmaceutical composition can modulate (e.g. increase or decrease) an immune response to treat the disease. In particular embodiments, the provided multi-domain immunomodulatory proteins and pharmaceutical compositions thereof can be used for the treatment of inflammatory or autoimmune disorders.
In some embodiments, the method comprises contacting a multi-domain immunomodulatory protein (which may be secreted by an engineered cell) provided herein with a mammalian cell under conditions that are permissive to specific binding of the protein and modulation of the immunological activity of the mammalian cell. The methods can be employed ex vivo or in vivo.
Such methods and uses include therapeutic methods and uses, for example, involving administration of the molecules or engineered cells, or compositions containing the same, to a subject having a disease, condition, or disorder. In some cases, such as for multi-domain immunomodulatory proteins that reduce or decrease an immune response or T cell response, the disease or disorder is an autoimmune or inflammatory disease or disorder. In some cases, such as for multi-domain immunomodulatory proteins that increase an immune response or T cell response, the disease or disorder is a tumor or cancer. In some embodiments, the multi-domain immunomodulatory protein or pharmaceutical composition thereof is administered in an effective amount to effect treatment of the disease or disorder. Uses include uses of multi-domain immunomodulatory proteins or pharmaceutical compositions thereof in such methods and treatments, and in the preparation of a medicament in order to carry out such therapeutic methods. In some embodiments, the methods are carried out by administering a multi-domain immunomodulatory protein or compositions comprising the same, to the subject having or suspected of having the disease or condition. In some embodiments, the methods thereby treat the disease or condition or disorder in the subject.
In some embodiments, the method of modulating immunological activity is achieved by administering an immunomodulatory protein to a subject. In other cases, modulating an immunological activity is achieved by administering an engineered cell expressing the immunomodulatory protein, including expression and secretion of an immunomodulatory protein of the present invention by an immune cell, such as a lymphocyte (e.g., a T-cell or TIL) or NK cell engineered to express and secrete the immunomodulatory protein. In such embodiments, the method can conducted by adoptive cell transfer of engineered cells expressing and secreting the immunomodulatory protein (e.g., a T-cell) are infused back into the patient. In some embodiments, modulating an immunological activity is achieved by administering an infectious agent capable of infecting a cell in a subject, such as to express and secrete the immunomodulatory protein in the subject.
The pharmaceutical compositions described herein can be used in a variety of therapeutic applications, such as the treatment of a disease. For example, in some embodiments the pharmaceutical composition is used to treat inflammatory or autoimmune disorders, organ transplantation, viral infections, and/or bacterial infections in a mammal. The pharmaceutical composition can modulate an immune response to treat the disease. In some embodiments, the pharmaceutical composition suppresses an immune response, which can be useful in the treatment of inflammatory or autoimmune disorders, or organ transplantation.
The provided methods are believed to have utility in a variety of applications, including, but not limited to, e.g., in prophylactic or therapeutic methods for treating a variety of immune system diseases or conditions in a mammal in which modulation or regulation of the immune system and immune system responses is beneficial. For example, suppressing an immune response can be beneficial in prophylactic and/or therapeutic methods for inhibiting rejection of a tissue, cell, or organ transplant from a donor by a recipient. In a therapeutic context, the mammalian subject is typically one with an immune system disease or condition, and administration is conducted to prevent further progression of the disease or condition.
In some embodiments, the provided compositions can attenuate an immune response, such as, for example, where the immunomodulatory protein comprises an affinity modified IgSF domain of an inhibitory ligand. In some embodiments, the compositions can be used to treat an autoimmune disease. In some embodiments, the administration of a therapeutic composition of the invention to a subject suffering from an immune system disease (e.g., autoimmune disease) can result in suppression or inhibition of such immune system attack or biological responses associated therewith. By suppressing this immune system attack on healthy body tissues, the resulting physical symptoms (e.g., pain, joint inflammation, joint swelling or tenderness) resulting from or associated with such attack on healthy tissues can be decreased or alleviated, and the biological and physical damage resulting from or associated with the immune system attack can be decreased, retarded, or stopped. In a prophylactic context, the subject may be one with, susceptible to, or believed to present an immune system disease, disorder or condition, and administration is typically conducted to prevent progression of the disease, disorder or condition, inhibit or alleviate symptoms, signs, or biological responses associated therewith, prevent bodily damage potentially resulting therefrom, and/or maintain or improve the subject's physical functioning.
In some embodiments, the inflammatory or autoimmune disorder is antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis, a vasculitis, an autoimmune skin disease, transplantation, a Rheumatic disease, an inflammatory gastrointestinal disease, an inflammatory eye disease, an inflammatory neurological disease, an inflammatory pulmonary disease, an inflammatory endocrine disease, or an autoimmune hematological disease.
The immune system disease or disorder of the patient may be or involve, e.g., but is not limited to, Addison's Disease, Allergy, Alopecia Areata, Alzheimer's, Antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis, Ankylosing Spondylitis, Antiphospholipid Syndrome (Hughes Syndrome), arthritis, Asthma, Atherosclerosis, Atherosclerotic plaque, autoimmune disease (e.g., lupus, RA, MS, Graves' disease, etc.), Autoimmune Hemolytic Anemia, Autoimmune Hepatitis, Autoimmune inner ear disease, Autoimmune Lymphoproliferative syndrome, Autoimmune Myocarditis, Autoimmune Oophoritis, Autoimmune Orchitis, Azoospermia, Behcet's Disease, Berger's Disease, Bullous Pemphigoid, Cardiomyopathy, Cardiovascular disease, Celiac Sprue/Coeliac disease, Chronic Fatigue Immune Dysfunction Syndrome (CFIDS), Chronic idiopathic polyneuritis, Chronic Inflammatory Demyelinating, Polyradicalneuropathy (CIPD), Chronic relapsing polyneuropathy (Guillain-Barré syndrome), Churg-Strauss Syndrome (CSS), Cicatricial Pemphigoid, Cold Agglutinin Disease (CAD), COPD, CREST syndrome, Crohn's disease, Dermatitis, Herpetiformus, Dermatomyositis, diabetes, Discoid Lupus, Eczema, Epidermolysis bullosa acquisita, Essential Mixed Cryoglobulinemia, Evan's Syndrome, Exopthalmos, Fibromyalgia, Goodpasture's Syndrome, graft-related disease or disorder, Graves' Disease, GVHD, Hashimoto's Thyroiditis, Idiopathic Pulmonary Fibrosis, Idiopathic Thrombocytopenia Purpura (ITP), IgA Nephropathy, immunoproliferative disease or disorder (e.g., psoriasis), Inflammatory bowel disease (IBD), Insulin Dependent Diabetes Mellitus (IDDM), Interstitial lung disease, juvenile diabetes, Juvenile Arthritis, juvenile idiopathic arthritis (JIA), Kawasaki's Disease, Lambert-Eaton Myasthenic Syndrome, Lichen Planus, lupus, Lupus Nephritis, Lymphoscytic Lypophisitis, Ménière's Disease, Miller Fish Syndrome/acute disseminated encephalomyeloradiculopathy, Mixed Connective Tissue Disease, Multiple Sclerosis (MS), muscular rheumatism, Myalgic encephalomyelitis (ME), Myasthenia Gravis, Ocular Inflammation, Pemphigus Foliaceus, Pemphigus Vulgaris, Pernicious Anaemia, Polyarteritis Nodosa, Polychondritis, Polyglandular Syndromes (Whitaker's syndrome), Polymyalgia Rheumatica, Polymyositis, Primary Agammaglobulinemia, Primary Biliary Cirrhosis/Autoimmune cholangiopathy, Psoriasis, Psoriatic arthritis, Raynaud's Phenomenon, Reiter's Syndrome/Reactive arthritis, Restenosis, Rheumatic Fever, rheumatic disease, Rheumatoid Arthritis, Sarcoidosis, Schmidt's syndrome, Scleroderma, Sjörgen's Syndrome, Solid-organ transplant rejection (kidney, heart, liver, lung, etc.), Stiff-Man Syndrome, Systemic Lupus Erythematosus (SLE), systemic scleroderma, Takayasu Arteritis, Temporal Arteritis/Giant Cell Arteritis, Thyroiditis, Type 1 diabetes, Type 2 diabetes, Ulcerative colitis, Uveitis, Vasculitis, Vitiligo, Wegener's Granulomatosis, and preventing or suppressing an immune response associated with rejection of a donor tissue, cell, graft, or organ transplant by a recipient subject. Graft-related diseases or disorders include graft versus host disease (GVDH), such as associated with bone marrow transplantation, and immune disorders resulting from or associated with rejection of organ, tissue, or cell graft transplantation (e.g., tissue or cell allografts or xenografts), including, e.g., grafts of skin, muscle, neurons, islets, organs, parenchymal cells of the liver, etc. With regard to a donor tissue, cell, graft or solid organ transplant in a recipient subject, it is believed that a therapeutic composition of the invention disclosed herein may be effective in preventing acute rejection of such transplant in the recipient and/or for long-term maintenance therapy to prevent rejection of such transplant in the recipient (e.g., inhibiting rejection of insulin-producing islet cell transplant from a donor in the subject recipient suffering from diabetes).
The inflammatory and autoimmune disorders that can be treated by the pharmaceutical compositions and the treatment methods described herein include, but are not limited to, Addison's Disease, allergies, alopecia areata, Alzheimer's, antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis, ankylosing spondylitis, antiphospholipid syndrome (Hughes Syndrome), asthma, atherosclerosis, rheumatoid arthritis, autoimmune hemolytic anemia, autoimmune hepatitis, autoimmune inner ear disease, autoimmune lymphoproliferative syndrome, autoimmune myocarditis, autoimmune oophoritis, autoimmune orchitis, azoospermia, Behcet's Disease, Berger's Disease, bullous pemphigoid, cardiomyopathy, cardiovascular disease, celiac Sprue/coeliac disease, chronic fatigue immune dysfunction syndrome (CFIDS), chronic idiopathic polyneuritis, chronic inflammatory demyelinating, polyradicalneuropathy (CIDP), chronic relapsing polyneuropathy (Guillain-Barre syndrome), Churg-Strauss Syndrome (CSS), cicatricial pemphigoid, cold agglutinin disease (CAD), COPD (chronic obstructive pulmonary disease), CREST syndrome, Crohn's disease, dermatitis, herpetiformus, dermatomyositis, diabetes, discoid lupus, eczema, epidermolysis bullosa acquisita, essential mixed cryoglobulinemia, Evan's Syndrome, exopthalmos, fibromyalgia, Goodpasture's Syndrome, Graves' Disease, Hashimoto's thyroiditis, idiopathic pulmonary fibrosis, idiopathic thrombocytopenia purpura (ITP), IgA nephropathy, immunoproliferative disease or disorder, inflammatory bowel disease (IBD), interstitial lung disease, juvenile arthritis, juvenile idiopathic arthritis (JIA), Kawasaki's Disease, Lambert-Eaton Myasthenic Syndrome, lichen planus, lupus nephritis, lymphocytic hypophysitis, Ménière's Disease, Miller Fish Syndrome/acute disseminated encephalomyeloradiculopathy, mixed connective tissue disease, multiple sclerosis (MS), muscular rheumatism, myalgic encephalomyelitis (ME), myasthenia gravis, ocular inflammation, pemphigus foliaceus, pemphigus vulgaris, pernicious anaemia, polyarteritis nodosa, polychondritis, polyglandular syndromes (Whitaker's syndrome), polymyalgia rheumatica, polymyositis, primary agammaglobulinemia, primary biliary cirrhosis/autoimmune cholangiopathy, psoriasis, psoriatic arthritis, Raynaud's Phenomenon, Reiter's Syndrome/reactive arthritis, restenosis, rheumatic fever, rheumatic disease, sarcoidosis, Schmidt's syndrome, scleroderma, Sjörgen's Syndrome, stiff-man syndrome, systemic lupus erythematosus (SLE), systemic scleroderma, Takayasu arteritis, temporal arteritis/giant cell arteritis, thyroiditis, Type 1 diabetes, ulcerative colitis, uveitis, vasculitis, vitiligo, interstitial bowel disease or Wegener's Granulomatosis. In some embodiments, the inflammatory or autoimmune disorder is selected from interstitial bowel disease, transplant, Crohn's disease, ulcerative colitis, multiple sclerosis, asthma, rheumatoid arthritis, and psoriasis.
In some embodiments, the disease or condition is one that is a result of PDL1 dysregulation. In some embodiments, the disease or condition is a vasculitis that is a giant cell arteritis (GCA).
In some embodiments, the pharmaceutical composition is administered to modulate an autoimmune condition. For example, suppressing an immune response can be beneficial in methods for inhibiting rejection of a tissue, cell, or organ transplant from a donor by a recipient. Accordingly, in some embodiments, the pharmaceutical compositions described herein are used to limit or prevent graft-related or transplant related diseases or disorders, such as graft versus host disease (GVHD). In some embodiments, the pharmaceutical compositions are used to suppress autoimmune rejection of transplanted or grafted bone marrow, organs, skin, muscle, neurons, islets, or parenchymal cells.
In some embodiments, a therapeutic amount of the pharmaceutical composition is administered. Typically, precise amount of the compositions of the present invention to be administered can be determined by a physician with consideration of individual differences in age, weight, extent of infection, and condition of the patient (subject). The optimal dosage and treatment regime for a particular patient can readily be determined by one skilled in the art of medicine by monitoring the patient for signs of disease and adjusting the treatment accordingly.
The administration of the subject compositions may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The compositions described herein may be administered to a patient subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous (i.v.) injection, or intraperitoneally. In one embodiment, the therapeutic composition is administered to a patient by intradermal or subcutaneous injection. In another embodiment, the therapeutic composition is administered by i.v. injection.
Cell compositions engineered to express and secrete immunomodulatory proteins of the present invention and associated methods can be used in immunotherapy applications. In some embodiments, cells isolated from a mammal, such as a mouse or human, can be engineered to express and secrete an immunomodulatory protein. In some embodiments, the mammalian cell serving as a host cell for expression and secretion or surface expression of an immunomodulatory protein is a lymphocyte such as a tumor infiltrating lymphocyte (TIL), a natural killer (NK) cell, or a T-cell such as a CD8+ cytotoxic T lymphocyte or a CD4+ helper T lymphocyte. In aspects of the provided method, the engineered cells are contacted, generally under physiological conditions, with a mammalian cell in which modulation of immunological activity is desired. For example, the mammalian cell can be a murine or human cell such as with immune cells, such as antigen presenting cell and/or T cell. In some embodiments, the engineered cells are autologous cells. In other embodiments, the cells are allogeneic. Cells can be contacted in vivo or ex vivo. In some embodiments, the engineered cells are administered to the subject, such as by infusion. Thus, composition and methods can be used in adoptive cell transfer immunotherapy. In some embodiments, the cells are autologous cells.
It can generally be stated that a pharmaceutical composition comprising engineered cells, e.g. T cells, as described herein may be administered at a dosage of 104 to 109 cells/kg body weight, such as 105 to 106 cells/kg body weight, including all integer values within those ranges. Engineered cell compositions, such as T cell compositions, may be administered multiple times at these dosages. The cells can be administered by using infusion techniques that are commonly known in immunotherapy (see, e.g., Rosenberg et al, New Eng. J. of Med. 319: 1676, 1988). In some cases, the cell compositions may be injected directly into a site of infection.
In some embodiments, the method is conducted by administration of a pharmaceutical compositions containing infectious agent containing a nucleic acid molecule encoding the immunomodulatory protein as a secretable immunomodulatory protein. In some embodiments, the pharmaceutical composition contains a dose of infectious agents suitable for administration to a subject that is suitable for treatment. In some embodiments, the pharmaceutical composition contains an infectious agent that is a virus, at a single or multiple dosage amount, of between about between or between about 1×105 and about 1×1012 plaque-forming units (pfu), 1×106 and 1×1010 pfu, or 1×107 and 1×1010 pfu, each inclusive, such as at least or at least about or at about 1×106, 1×107, 1×108, 1×109, 2×109, 3×109, 4×109, 5×109 pfu or about 1×1010 pfu. In some embodiments, the pharmaceutical composition can contain a virus concentration of from or from about 105 to about 1010 pfu/mL, for example, 5×106 to 5×109 or 1×107 to 1×109 pfu/mL, such as at least or at least about or at about 106 pfu/mL, 107 pfu/mL, 108 pfu/mL or 109 pfu/mL. In some embodiments, the pharmaceutical composition contains an infectious agent that is a bacterium, at a single or multiple dosage amount, of between about between or between about 1×103 and about 1×109 colony-forming units (cfu), 1×104 and 1×109 cfu, or 1×105 and 1×107 cfu, each inclusive, such as at least or at least about or at about 1×104, 1×105, 1×106, 1×107, 1×108 or 1×109 cfu. In some embodiments, the pharmaceutical composition can contain a bacterial concentration of from or from about 103 to about 108 cfu/mL, for example, 5×105 to 5×107 or 1×106 to 1×107 cfu/mL, such as at least or at least about or at about 105 cfu/mL, 106 cfu/mL, 107 cfu/mL or 108 cfu/mL.
In some embodiments, the pharmaceutical composition is administered as a monotherapy (i.e., as a single agent) or as a combination therapy (i.e., in combination with one or more additional immunosuppressant agents). In some embodiments, the additional agent is a glucocorticoid (e.g., prednisone, dexamethasone, and hydrocortisone), cytostatic agent, such as a cytostatic agent that affect proliferation of T cells and/or B cells (e.g., purine analogs, alkylating agents, or antimetabolites), an antibody (e.g., anti-CD20, anti-CD25 or anti-CD3 monoclonal antibodies), cyclosporine, tacrolimus, sirolimus, everolimus, an interferon, an opiod, a TNF binding protein, mycophenolate, small biological agent, such as fingolimod or myriocin, cytokine, such as interferon beta-1a, an integrin agonist, or an integrin antagonist.
Also provided herein are articles of manufacture that comprise the pharmaceutical compositions described herein in suitable packaging. Suitable packaging for compositions (such as ophthalmic compositions) described herein are known in the art, and include, for example, vials (such as sealed vials), vessels, ampules, bottles, jars, flexible packaging (e.g., sealed Mylar or plastic bags), and the like. These articles of manufacture may further be sterilized and/or sealed.
Further provided are kits comprising the pharmaceutical compositions (or articles of manufacture) described herein, which may further comprise instruction(s) on methods of using the composition, such as uses described herein. The kits described herein may also include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for performing any methods described herein.
The following examples are included for illustrative purposes only and are not intended to limit the scope of the invention.
Multi-domain immunomodulatory proteins were generated containing (1) at least one inhibitory receptor binding molecule (IRBM) that binds to an immune cell inhibitory receptor or inhibitory receptor complex (e.g. PD-1) and (2) at least one activating receptor binding molecule (ARBM) that binds to an immune cell activating receptor or activating receptor complex (e.g. CD28, CD3, CD4). Among binding molecules that were included as individual IRBM and ARBM in the multi-domain immunomodulatory proteins were non-antibody immunoglobulin superfamily (IgSF) domains, such as an extracellular domain (ECD) or immunoglobulin-like V-type (IgV) domain, or a variant IgSF domain (vIgD) that was affinity-modified and selected for increased binding affinity to the target binding partner compared to the unmodified or wild-type IgSF domain. Examples 8-13 below describe exemplary variant IgSF domains for inclusion as an IRBM or ARBM.
Exemplary IRBMs and ARBMs used in the immunomodulatory proteins are listed in Tables E1.A and E1.B, respectively.
Various multi-domain immunomodulatory proteins using the molecules listed above were generated in various configurations as summarized below. In some aspects, the configurations were chosen to affect spatial proximalization of ITIM bearing inhibitory receptors with activating receptors on T cells to make possible attenuation of T cell activation and/or tolerance induction (
In some cases, multi-domain immunomodulatory proteins were generated in a cis binding strategy to target the inhibitory receptor (e.g. PD-1 or TIGIT) and activating receptor (e.g. CD2, CD3, CD4 or CD28) on T cells, which, in some cases, proximalize or cluster the inhibitory receptor and the activating receptor on the surface of the same T cell (
In other cases, multi-domain immunomodulatory proteins were generated in a trans binding strategy to target the inhibitory receptor (e.g. PD-1 or TIGIT) on the T cell and a ligand of the activating receptor (e.g. CD80 or CD86) on an antigen-presenting cell (APC) (
The immunomodulatory proteins, in either a cis-binding strategy or trans-binding strategy configuration, were generated as either multimeric molecules via fusion with an Fc protein or as monomeric molecules.
A. Multimeric Configurations
In some configurations, the generated multi-domain immunomodulatory proteins were generated as multimeric proteins by fusion with an Fc molecule. The ARBM or IRBM of the multi-domain immunomodulatory protein were variously linked to the N- or C-terminus of a human IgG1 Fc region via a peptide linker, such as a GSGGS (SEQ ID NO: 2523), GGGGS (G4S; SEQ ID NO: 1942), GSGGGGS (SEQ ID NO: 1941), GGGGSGGGGS (2×GGGGS; SEQ ID NO: 240), GGGGSGGGGSGGGGS (3×GGGGS; SEQ ID NO: 239), GGGGSSA (SEQ ID NO: 2524) peptide linker, or combinations thereof.
For generating homodimeric Fc fusions, an exemplary IgG1 Fc region used in generated constructs had the sequence set forth in SEQ ID NO:1155 and contained the mutation C220S by EU numbering and the mutations L234A, L235E, and G237A, by EU numbering, to reduce effector function (the mutations corresponded to C5S, L19A, L20E, G22A, with reference to wild-type human IgG1 Fc set forth in SEQ ID NO:187). In some cases, the Fc used in the constructs had the sequence set forth in SEQ ID NO:1715, which further contained removal of the C-terminal lysine, K447del by EU numbering (corresponding to deletion of position 232, with reference to wild-type or unmodified Fc set forth in SEQ ID NO: 187).
In some cases, an exemplary IgG1 Fc region used in generated constructs had the sequence set forth in SEQ ID NO:3538 and contained the mutation C220S by EU numbering and contained amino acid substitutions E356D and M358L to reconstitute residues of allotype G1 m1, by EU numbering (the mutations corresponded to C5S, E141D, and M143L). In some embodiments, the wild-type IgG1 Fc can be the Fc set forth in SEQ ID NO: 187 having an allotype containing residues Glu (E) and Met (M) at positions 356 and 358 by EU numbering. In some embodiments, the Fc region further contained removal of the C-terminal lysine, K447del by EU numbering (corresponding to deletion of position 232) with reference to wild-type human IgG1 Fc set forth in SEQ ID NO:187).
In some aspects, a wild-type Fc was used that was modified by one or more amino acid substitutions to reduce effector activity or to render the Fc inert for Fc effector function such as effectorless mutations L234A, L235E and G237A by EU numbering or R292C, N297G and V302C by EU numbering. In some embodiments, a wild-type Fc was further modified by the removal of one or more cysteine residue, such as by replacement of the cysteine residues to a serine residue at position 220 (C220S) by EU numbering. Exemplary inert Fc regions having reduced effector function used in exemplary constructs are set forth in SEQ ID NO: 1158 and SEQ ID NO:3579, which are based on allotypes set forth in SEQ ID NO:187 or SEQ ID NO: 3538, respectively. In some embodiments, an Fc region used in a construct provided herein can further lack a C-terminal lysine residue, such as set forth in SEQ ID NO:1715. Another exemplary inert Fc region having reduced effector function used in exemplary constructs is set forth in SEQ ID NO:1157.
Table E2 describes exemplary generated multi-domain homodimeric immunomodulatory Fc fusion proteins.
In some configurations, the generated multi-domain immunomodulatory Fc fusion proteins further contained a moiety for detection and/or purification, such as a poly-histidine tag (HHHHHH; SEQ ID NO: 2011) or a flag-tag (DYKDDDDK; SEQ ID NO: 2010). In such examples, the resulting immunomodulatory Fc fusion protein was generated as a heterodimer in which the ARBM or IRBM were each tagged with a different moiety and each fused to either an Fc K chain or an Fc D chain as part of the K/D chain system. In exemplary generated molecules, the exemplary K chain set forth in SEQ ID NO:2544 contained mutations to positively charged residues (E356K, E357K and D399K by EU numbering) and the exemplary D chain set forth in SEQ ID NO: 2545 contained mutations to negatively charged residues (K370D, K392D and K409D by EU numbering), such that, when co-expressed in a cell, association between the K and D chains was possible but the chains did not substantially self-associate due to charge repulsion. In addition, the above mutations were made in an Fc backbone having an allotype containing residues Glu (E) and Met (M) at positions 356 and 358, and also contained mutations C220S, L234A, L235E and G237A by EU numbering.
Table E3A describe exemplary generated multi-domain immunomodulatory Fc fusion proteins.
In another strategy, multimeric multi-domain immunomodulatory proteins were generated as heterodimeric molecules by “knobs-into-hole” engineering. In such an example, the heterodimer was generated by co-expressing an ARBM and an IRBM that each were fused to either (1) a first “knob” Fc subunit (set forth in SEQ ID NO:1153 or 2558 containing the mutations S354C and T366W by EU numbering, corresponding to S139C and T151W with reference to wild-type human IgG1 Fc set forth in SEQ ID NO:187); and (2) a second “hole” Fc subunit (set forth in SEQ ID NO:1154 and 2559, containing the mutations Y349C, T366S, L368A and Y407V by EU numbering, corresponding to Y134C, T151S, L153A and Y192V with reference to wild-type human IgG1 Fc set forth in SEQ ID NO:187) for expression of a heterodimeric molecule. In addition, both the knob and hole Fc also contained mutations L19A, L20E, G22A to reduce effector function and contained replacement of the cysteine residue to a serine residue at position 5 (C5S), each compared to the wild-type or unmodified Fc set forth in SEQ ID NO: 187 (corresponding to C220S, L234A, L235E and G237A by EU numbering, respectively). Each chain of the heterodimer also further contained a moiety for detection and/or purification, such as a poly-histidine tag (HHHHHH; SEQ ID NO: 2011) or a flag-tag (DYKDDDDK; SEQ ID NO: 2010).
Table E3B describe exemplary generated multi-domain immunomodulatory Fc fusion proteins.
In some cases, the multimeric multi-domain immunomodulatory proteins were generated as trimeric, tetrameric, or pentameric molecules. In such configurations, the immunomodulatory proteins containing an ARBM and IRBM were generated as fusions with: a portion of the cartilage oligomeric matrix protein (COMP) assembly domain as set forth in SEQ ID NO: 3503 (e.g. amino acids 29-72 of the full length COMP, Uniprot accession number P49747) for promoting pentamerization of the proteins; a vasodilator-stimulated phosphoprotein (VASP) tetramerization domain as set forth in SEQ ID NO: 3504 (e.g. amino acids 343-375 of the full length VASP; Uniprot accession number P50552) for promoting tetramerization of the proteins; or a ZymoZipper (ZZ) 12.6 domain as set forth in SEQ ID NO: 3505 (See U.S. Pat. No. 7,655,439) for promoting trimerization of the proteins. The multi-domain immunomodulatory proteins also further contained a moiety for detection and/or purification, such as a poly-histidine tag (HHHHHH; SEQ ID NO: 2011), flag-tag (DYKDDDDK; SEQ ID NO: 2010), or both.
Table E4 describe exemplary generated multimeric multi-domain immunomodulatory Fc fusion proteins.
Nucleic acid molecule encoding the immunomodulatory proteins also contained residues encoding the exemplary signal peptide MGSTAILALLLAVLQGVSA (set forth in SEQ ID NO: 186). Expression constructs encoding Fc fusion proteins of interest were transiently expressed in Expi293 HEK293 cells (e.g. Invitrogen) with Expifectamine™ reagents and media following the manufacture'r instructions. Supernatants were harvested and protein was captured and eluted from a Protein A column using an AKTA protein purification system. The eluted material was then separated by an additional preparative SEC step to generate non-aggregated (monomeric), highly purified material. This material was buffer exchanged into 10 mM Acetate, 9% Sucrose, pH 5.0. (A5Su) The protein was vialed in a sterile biosafety cabinet and frozen at −80 C. A vial was thawed and assessed by analytical SEC to demonstrate the material was stable and predominantly non-aggregated (monomeric) after thaw.
B. Monomeric Configurations
In some configurations, the generated multi-domain immunomodulatory proteins were generated as monomeric molecules containing an ARBM and an IRBM linked together with a peptide linker. Exemplary linkers used in the generated proteins included GSGGS (SEQ ID NO: 2523), GGGGS (G4S; SEQ ID NO: 1942), GSGGGGS (SEQ ID NO: 1941), GGGGSGGGGS (2×GGGGS; SEQ ID NO: 240), GGGGSGGGGSGGGGS (3×GGGGS; SEQ ID NO: 239), GGGGSSA (SEQ ID NO: 2524), or any combinations thereof. In some cases, the monomeric immunomodulatory proteins also contained an N- or C-terminal moiety for detection and/or purification, such as a poly-histidine tag (HHHHHH; SEQ ID NO:2011) and/or a flag-tag (DYKDDDDK; SEQ ID NO: 2010). Nucleic acid molecules encoding the monomeric immunomodulatory proteins also contained residues encoding the exemplary signal peptide MGSTAILALLLAVLQGVSA (set forth in SEQ ID NO: 186).
Table E5 describes exemplary generated multi-domain immunomodulatory monomeric proteins.
This Example describes binding studies of purified proteins generated as described in Example 1 to assess specificity and affinity of various multi-domain immunomodulatory proteins for two different binding partners. Binding studies were carried out on cells transfected with relevant binding partners of the IRBM or ARBM of the multi-domain molecules.
For staining by flow cytometry, 100,000 cells expressing the various cell-expressed binding partners were plated in 96-well round-bottom plates. Cells were spun down and resuspended in staining buffer (PBS (phosphate buffered saline), 1% BSA (bovine serum albumin), 1 mM EDTA, and 0.1% sodium azide) for 20 minutes to block non-specific binding. Afterwards, cells were centrifuged again and resuspended in 50 μL staining buffer containing 100 nM of molecules containing exemplary multi-domain immunomodulatory proteins. As a control, binding was assessed on 100 nM of respective individual ARBM and IRBM molecules.
Primary staining was performed on ice for 45 minutes, before washing cells twice in 200 μL staining buffer. PE-conjugated anti-human Fc (Jackson ImmunoResearch, USA) or PE-conjugated anti-FLAG (BioLegend, USA) was diluted 1:150 in 50 μL staining buffer and added to cells and incubated another 30 minutes on ice. Secondary antibody was washed out twice, cells were fixed in 4% formaldehyde/PBS, and samples were analyzed on Intellicyt flow cytometer (Intellicyt Corp., USA). Mean Fluorescence Intensity (MFI) was calculated with FlowJo Version 10 software (FlowJo LLC, USA).
Binding studies were carried out on 100,000 CHO cells stably transduced with PD-1 (CHO/PD-1 cells) or K562 cells stably transduced with CD80 (K562/CD80) or were carried out using Jurkat cells (human acute T cell lymphoma cells, Promega Corp., USA) which endogenously express CD4, CD28 and T cell receptor. The following control immunomodulatory proteins were assessed: (1) variant PD-L1 IgV-Fc (D43G/N45D/L56Q/V58A/G101G-ins (G101GG) (SEQ ID NO:303), (2) variant PD-L2 IgV-Fc (H15Q/T47A/K65R/S67L/Q82R/V89D) (SEQ ID NO:1417); (3) variant CTLA-4-Fc (A31Y/L106E) (SEQ ID NO:2519 or 2520), (4) anti-PD-1 antibody Nivolumab, or (5) Fc only control.
Table E6 and E7 set forth the binding activity as measured by the Mean Fluorescence Intensity (MFI) value for binding of 100 nM of each immunomodulatory protein tested to cells expressing the various cell-expressed counter structures. As shown in Table E6 and E7, several immunomodulatory proteins bound multiple binding partners including PD-1 and CD28, CD4, and/or CD80.
The binding of additional immunomodulatory proteins containing PD-L1 IgV/PD-L2 IgV and CTLA-4 to targets was assessed substantially as described above. In addition to the control molecules described above, a variant PD-L1 IgV-Flag-His (D43G/N45D/L56Q/V58A/G101G-ins (G101GG) (SEQ ID NO:303)) was also assessed. Exemplary multi-domain immunomodulatory proteins from Table E2 were assessed including those as set forth in SEQ ID NOs: 3518, 3519, 3521, 3522, and 3523. Binding results in
CHO cells were transduced to stably express human PD-1 (CHO/PD-1 cells) or human CTLA-4 (CHO/CTLA-4). Jurkat cells were used to measure binding to endogenously expressed human T cell receptor (TCR) (Jurkat/TCR cells) and CD28 (Jurkat/CD28). To measure binding to ICOS, transiently transfected HEK293 cells were used. Proteins bound to the cell surface were detected using an anti-Flag tag PE secondary reagent.
As shown in Table E8A-E8B, a number of immunomodulatory proteins were observed to bind multiple binding partners including PD-1 and CD28, CD4, and/or CD80. Among the results shown, immunomodulatory proteins with PD-L1 IgV or PD-L2 IgV molecules at the N-terminus and ICOSL molecules at the C-terminus (PD-L1 IgV/PD-L2 IgV-ICOSL IgV) showed greater binding to PD-1 as compared to molecules generated with molecules in the reverse order (ICOSL IgV-PD-L1 IgV/PD-L2 IgV). All values reported are PE MFI at the test concentration of 100 nM. For Tables E8A-E8B, an anti-Flag-PE detection reagent was used for detecting the tested molecules.
CHO cells were transduced to stably express human PD-1 (CHO/PD-1 cells) or human CTLA-4 (CHO/CTLA-4). Jurkat cells were used to measure binding to endogenously expressed human CD28 (Jurkat/CD28). To measure binding to ICOS, transiently transfected HEK293 cells were used. Proteins bound to the cell surface were detected using an anti-Flag tag PE secondary reagent. Binding results shown in Table E9A are MFI at 100 nM test concentration.
Additional multi-domain immunomodulatory proteins described in Example 1 were assessed for binding to cognate binding partners substantially as described above. Jurkat IL-2 reporter cells (described in Example 3 below) were transfected to express human PD-1 (Jurkat/IL-2/PD-1 cells) or human TIGIT (Jurkat/IL-2/TIGIT). CHO cells were transfected to express CD2 (CHO-CD2) or CD80 (CHO-CD80). Expi293 cells were transfected to express CD28 (Expi-CD28). Proteins bound to the cell surface were detected using an anti-Flag tag PE secondary reagent or an Anti-hFc-PE MFI, depending on the construct. Mean fluorescence intensity (MFI) was determined. The half maximal binding concentration (EC50; nM) was determined by nonlinear regression by fitting the data to a sigmoidal dose-response (variable slope; Hill slope=1). Results are shown in Table E9B. As shown, a number of immunomodulatory proteins were observed to bind multiple binding partners.
This Example describes a Jurkat/IL2 and Jurkat/IL2/PD-1 reporter assay to assess inhibitory activity of exemplary multi-domain immunomodulatory proteins generated as described in Example 1. In this assay, activity was tested on multi-domain proteins containing an ARBM able to bind CD28 (e.g. CD80, CD86, CTLA-4 or ICOSL) and an IRBM able to bind to PD-1 (PD-L1 or PD-L1). To distinguish between inhibitory activity due to blockade of CD28 signaling versus inhibitory activity via activity of the PD-1-binding IRBM, two reporter cell assays were used. In the first assay, Jurkat reporter cells expressing an IL-2-luciferase reporter were incubated with artificial antigen presenting cells (aAPC) displaying cell surface anti-CD3 single chain Fv (OKT3) and CD80 (K562/OKT3/CD80 aAPC) (
For both assays, Jurkat cells were suspended at 2×106 cells/mL in RPMI1640+5% FBS and were then plated at 50 μL/well for a total of 100,000 cells per well. To each well, indicated test immunomodulatory proteins were added to the Jurkat cells at concentrations ranging from approximately 0.4 nM to 50 nM, or, in some cases, 0.4 nM to 100 nM. As a control, activity of respective individual ARBM and IRBM molecules also was assessed. The Jurkat cells with test or control proteins were incubated for 15 minutes at room temperature. K562/OKT3/CD80 aAPC were brought to 0.8×106 cells/mL and 25 μL of cells was added to each well bringing the final volume of each well to 100 μL. Jurkat cells and K562 aAPCs were incubated for 5-6 hours at 37 degrees Celsius in a humidified 5% CO2 incubation chamber. Plates were then removed from the incubator and acclimated to room temperature for 15 minutes. 100 μL of a cell lysis and luciferase substrate solution (BioGlo®, Promega Corp, USA) was added to each well and the plates were placed on an orbital shaker for 10 minutes at room temperature. Luminescence was measured with a 1 second per well integration time using a BioTek Cytation luminometer (BioTek Corp., USA). An average relative luminescence value was determined for each test immunomodulatory protein or control protein.
The assays described above were carried out on multi-domain immunomodulatory proteins, containing PD-L1/PD-L2 IgV and CTLA-4 ECD, generated as Fc fusion proteins or as monomeric proteins. Specifically, the following exemplary multi-domain immunomodulatory proteins were assessed: PD-L1 303-Fc-CTLA-4 2520 (SEQ ID NO: 2541), PD-L2 1417-Fc-CTLA-4 2520 (SEQ ID NO:2543) and PD-L1 303-CTLA-4 2520 (SEQ ID NO:2651). As a control, individual ARBM and IRBM molecules, in either a monomeric or Fc fusion protein format, also were assessed, including the individual PD-L1 IgV (SEQ ID NO:303; PD-L1 303), PD-L2 IgV (SEQ ID NO:1417, PD-L2 1417) or CTLA-4 ECD (SEQ ID NO: 36; CTLA-4 36), each containing a flag/his tag; the individual PD-L1 IgV (SEQ ID NO:303) fused to an Fc set forth in SEQ ID NO: 1715) (PD-L1 303-Fc); the individual PD-L2 IgV (SEQ ID NO:1417) fused to an Fc set forth in SEQ ID NO: 1715 (PD-L2 1417-Fc); or the individual CTLA-4 ECD (SEQ ID NO:2519) fused to an Fc set forth in SEQ ID NO: 1715 (CTLA-4 2519-Fc).
Luciferase activity of Jurkat effector cells expressing IL-2-luciferase reporter co-cultured with K562 aAPCs in the presence of immunomodulatory molecules, as determined using Assay #1, is shown in
Luciferase activity of Jurkat effector cells expressing PD-1 and IL-2-luciferase reporter co-cultured with K562 aAPCs in the presence of immunomodulatory molecules, as determined using Assay #2, are shown in
Additional tested molecules containing a PD-L1 IgV or a PD-L2 IgV and CTLA-4 ECD generated as multimeric homodimer immunomodulatory proteins tested in Assay #1 and Assay #2 are shown in
Similar to Assay #2, the exemplary multi-domain immunomodulatory proteins were further assessed by measuring luciferase activity of Jurkat effector cells expressing PD-1 and IL-2-luciferase reporter co-cultured with K562 aAPCs in the presence of immunomodulatory molecules except with the addition of either a human IgG or an anti-PD-1 antibody (nivolumab). As shown in
The assays described above were carried out on multi-domain immunomodulatory proteins, containing a PD-L1 IgV or a PD-L2 IgV and ICOSL IgV, generated as monomeric proteins. For PD-L1 IgV molecules, the following exemplary multi-domain immunomodulatory proteins were assessed: PD-L1 303-ICOSL 2247 (SEQ ID NO:2595), ICOSL 2247-PD-L1 303 (SEQ ID NO:2597), PD-L1 303-ICOSL 2266 (SEQ ID NO:2599), ICOSL 2266-PD-L1 303 (SEQ ID NO:2601), PD-L1 303-ICOSL 2264 (SEQ ID NO:2603), ICOSL 2264-PD-L1 303 (SEQ ID NO:2605), PD-L1 303-ICOSL 2244 (SEQ ID NO: 2607), and ICOSL 2244-PD-L1-303 (SEQ ID NO:2609). For PD-L2 IgV molecules, the following exemplary multi-domain immunomodulatory proteins were assessed: PD-L2 1417-ICOSL 2247 (SEQ ID NO:2579), ICOSL 2247-PD-L2 1417 (SEQ ID NO:2581), PD-L2 1417-ICOSL 2266 (SEQ ID NO:2583), ICOSL 2266-PD-L2 1417 (SEQ ID NO:2585), PD-L2 1417-ICOSL 2264 (SEQ ID NO:2587), ICOSL 2264-PD-L2 1417 (SEQ ID NO:2589), PD-L2 1417-ICOSL 2244 (SEQ ID NO: 2591), and ICOSL 2244-PD-L2 1417 (SEQ ID NO:2593). As a control, individual ARBM and IRBM molecules, in a monomeric protein format, also were assessed, including PD-L1 IgV (SEQ ID NO:303; PD-L1 303), PD-L2 IgV (SEQ ID NO:1417, PD-L2 1417) or ICOSL IgV (SEQ ID NO:2264; ICOSL 2264). The ICOSL 2264 alone control exhibited comparable activity to the CTLA-4 ECD Fc containing A31Y/L106E (SEQ ID NO: 2519) described in
For PD-L1 IgV-containing immunomodulatory proteins, luciferase activity of Jurkat effector cells co-cultured with K562 aAPCs in the presence of immunomodulatory molecules as determined using Assay #1 or Assay #2 are shown in
For PD-L2 IgV-containing immunomodulatory proteins, luciferase activity of Jurkat effector cells co-cultured with K562 aAPCs in the presence of immunomodulatory molecules as determined using Assay #1 or Assay #2 are shown in
Combined with the results in assay #1 above, these results are consistent with an observation that inhibitory activities of the exemplary PD-L1 303-ICOSL 2266 (SEQ ID NO:2599), PD-L1 303-ICOSL 2264 (SEQ ID NO:2603) and PD-L2 1417-ICOSL 2264 (SEQ ID NO:2587) multi-domain immunomodulatory protein were due to binding to PD-1 and CD28. The results also indicate that affinity maturation of individual IgSF domains also can improve the observed activity, since, in this experiment, inhibitory activity was not observed in either assay #1 or assay #2 with the exemplary immunomodulatory protein containing a wild-type ICOSL IgV domain (e.g. containing ICOSL 2244) or containing a ICOSL variant with lower improved affinity for cognate binding partners (e.g. containing ICOSL 2266).
Additional tested molecules containing a PD-L1 IgV or a PD-L2 IgV and ICOSL IgV generated as multimeric homodimer immunomodulatory proteins tested in Assay #1 and Assay #2 are shown in
To assess dependence of the inhibitory activity of exemplary multi-domain immunomodulatory proteins on binding of PD-1, the Jurkat/IL2/PD-1 reporter assay described in Example 3 (Assay #2) was carried out in the presence of a blocking antibody. Specifically, in this example, the following exemplary multi-domain immunomodulatory proteins were assessed: PD-L1 303-Fc-CTLA-4 2520 (SEQ ID NO: 2541), PD-L2 1417-Fc-CTLA-4 2520 (SEQ ID NO:2543) and PD-L1 303-CTLA-4 2520 (SEQ ID NO:2651). As a control, monomeric variant CTLA-4 ECD (CTLA-4-2520) containing a flag/his tag, or a variant CTLA-4-Fc fusion (containing CTLA-4 ECD set forth in SEQ ID NO:2519 fused to an Fc set forth in SEQ ID NO: 1715; CTLA-4 2519-Fc) were assessed. Activity in the presence of an Fc only control also was assessed. Assay #2 was performed essentially as described above. All test proteins were added at 11 nM and where indicated, anti-PD-1 antibody was added at 10 nM. For each condition, an average relative luminescence value was determined for each test immunomodulatory protein or control protein.
As shown in
The Jurkat/IL2/PD-1 reporter assay (Assay #2) described in Example 3 was carried out in the presence of exemplary PD-L1 IgV/PD-L2 IgV-CD80/CD86 IgV. The assay was carried out substantially as described in Example 3 by incubating Jurkat/IL2/PD-1 reporter cells with exemplary immunomodulatory proteins (at concentrations ranging from 0.4 nM to 50 nM) for approximately 15 minutes prior to adding K562/OKT3/CD80 aAPC. Specifically, the assessed multi-domain immunomodulatory proteins included monomeric proteins containing a variant PD-L1 IgV (e.g. PD-L1 303) or a variant PD-L2 IgV (e.g. PD-L2 1417) linked in various configurations to either wildtype CD80 IgV (SEQ ID NO: 2615), a variant CD80 IgV (SEQ ID NO: 2616) or wild-type CD86 (SEQ ID NO: 2610), as shown in
As a control, individual IRBM or ARBM molecules also were assessed as follows: PD-L1 IgV (SEQ ID NO:303; PD-L1 303), PD-L2 IgV (SEQ ID NO:1417, PD-L2 1417) or ICOSL IgV (SEQ ID NO: 2264; ICOSL-2264), each containing a flag/his tag. An Fc only control also was assessed.
Results with multi-domain immunomodulatory proteins containing PD-L1 IgV-CD80 IgV are shown in
This Example describes a PD-1/CD28 proximalization assay to assess effects of exemplary multi-domain immunomodulatory protein upon binding to its targets. The assay was a proximity dimerization assay using a beta-Galactosidase (beta-Gal) Enzyme Fragment Complementation assay system. The assay utilizes a first surface expressed protein fused with an enzyme donor tag (ProLink™ (PK)) and a second surface expressed protein fused with an enzyme acceptor protein (EA). When in close proximity, complementation of the two enzyme fragments occurs, forming a functional beta-Gal enzyme that hydrolyzes a substrate to generate a chemiluminescent signal.
To assess proximalization of the inhibitory receptor (PD-1) and activating receptor (CD28), mammalian expression vectors were designed to express the extracellular and transmembrane domains of full-length CD28 (CD28 FL) or truncated CD28 (residues 1-188, SEQ ID NO:2944; tCD28)) fused to the PK- and EA-tag at the C-terminus. The CD28 constructs were then transfected via retroviral infection into a human U2OS parental cell line (DiscoverX, USA; cat. #93-1130C3) that expressed human PD-1 (amino acids 1-199) fused to either EA (PD1-EA; U2OS PD1(1-199)-EA cell line) or PK (PD1-PK; U2OS PD1(1-199)-PK cell line). Four cells lines were generated as follows: U2OS CD28(FL)-PK/PD-1(1-199)-EA, U2OS PD-1(1-199)-PK/CD28(FL)-EA, U2OS CD28(1-188)-PK/PD-1(1-199)-EA and U2OS PD-1(1-199) PK/CD28(1-188)-EA. The resulting cells were selected with the appropriate selective agents to generate stable cell lines.
The PD-1-CD28 cells lines were assessed for expression of the PK-fusion protein and EA-fusion protein using in vitro complementation assays, where the cells were evaluated for enzyme activity in the absence and presence of exogenous complementing fragment. Stable U2OS cell lines co-expressing either PD-1(1-199)-PK or -EA fusion proteins with full-length or truncated CD28(1-188)-EA or —PK were lysed in the presence of beta-Gal enzyme substrate only or in the presence of beta-Gal enzyme substrate with complementary EA or PK enzyme fragment added. After 1 hour of incubation, luciferase activity was measured. The luciferase values found in the four PD1-CD28 cell lines were elevated after adding complementary EA or PK enzyme fragments as compared to the basal enzyme activity observed in cell lines in the absence of added EA or PK enzyme fragments, indicating complementation of the fusion proteins. The addition of complementary enzyme fragments for the PD1 fusion proteins in each lysed cell line resulted in greater increases in luciferase activity than conditions containing complementary enzyme fragments for the CD28 fusion protein, consistent with a higher expression of PD-1 in the cell lines. Immunostaining for PD-1 and CD28 in the cell lines by flow cytometry confirmed higher expression of PD-1 than CD28 in the cell lines.
To assess the effect of multi-domain immunomodulatory proteins in the assay, the U2OS PD1-CD28 cell lines (U2OS CD28(FL)-PK/PD-1(1-199)-EA, U2OS CD28(1-188)-PK/PD-1(1-199)-EA or U2OS PD-1(1-199) PK/CD28(1-188)-EA) were plated at 5000 cells/well in quadruplicate in wells of a 384 well plates and cells were allowed to adhere to the plates for about 4 hours at 37° C./5% CO2. Multi-domain immunomodulatory proteins were added to the cells in a series of 1:3 dilutions. Specifically, exemplary monomeric multi-domain immunomodulatory proteins were assessed as follows: PD-L1 303-ICOSL 2264 (SEQ ID NO:2603) and PD-L2 1417-ICOSL 2264 (SEQ ID NO:2587). As a control, the individual variant PD-L2 IgV set forth in SEQ ID NO:1417 also was assessed. The plates were incubated overnight (16 hours) at 37° C./5% CO2. The substrate for beta-Gal was added to the cells, incubated for 1 hour in the dark at room temperature, and luciferase levels were measured.
As shown in
This Example describes a Jurkat PD-1 SHP2 Signaling Assay to assess the effect of the multi-domain immunomodulatory proteins to recruit the cytoplasmic protein tyrosine phosphatase, SHP-1 or SHP-2, to PD-1. In an exemplary assay, a Jurkat cell line containing a ProLink™ (PK) tagged PD-1 receptor and an Enzyme Acceptor (EA) tagged SHP-2 domain were used (e.g. DiscoverX, USA; cat. #93-1106C19). In the assay, SHP-2 recruitment to PD-1 results in the EA and PK being in close proximity to allow complementation of the two enzyme fragments forming a functional beta-Gal enzyme that hydrolyzes a substrate to generate a chemiluminescent signal.
Jurkat PD-1-PK/SHP2-EA cells were plated in quadruplicate in wells of a 384 well plate at a density of about 5000 cells/well. The exemplary multi-domain immunomodulatory protein PD-L1 303-ICOSL 2264 (SEQ ID NO:2603) was added to the cells in a series of 1:3 dilutions. As a control, wild-type PD-L1 as an Fc fusion (PD-L1-Fc; R&D Systems, Cat. No. 156-B7) or the individual variant PD-L2 IgV set forth in SEQ ID NO:1417 as a monomeric protein were assessed. Cells were incubated for 3 hours at room temperature. The substrate for beta-Gal was added to the wells, incubated for 1 hour at room temperature in the dark, and the luciferase was measured. As shown in
The Jurkat PD-1 SHP2 signaling assay was also used to assess additional exemplary monomeric or multimeric heterodimer PD-L1-ICOSL multi-domain immunomodulatory proteins. Jurkat/PD-1 cells were co-cultured with K562/OKT3 or K562/OKT3/CD80 aAPC and the tested immunomodulatory proteins. Exemplary multi-domain immunomodulatory proteins from Tables E3B, E4 and E5 were assessed including those as set forth in SEQ ID NO: 3500, 3501, 3502, 3507, 3513+3514, and 3515+3514. Individual ARBM or IRBM containing molecules were also assessed, including those with PD-L1 (SEQ ID NO: 303, 3506, 3525, 3533+3534), with ICOSL (SEQ ID NO: 3527, 3528), and with PD-L2 (SEQ ID NO:1417, 3533+3512). An Fc only control was also used. As shown in
The Jurkat PD-1 SHP2 signaling assay was also used to assess exemplary multi-domain immunomodulatory proteins from Table E2 including those set forth in SEQ ID NO:3518, 3519, 3521, 3522, and 3523. Jurkat/PD-1 cells were co-cultured with K562/OKT3/CD80 aAPC and the tested immunomodulatory proteins. In addition, control molecules including (1) variant PD-L1 IgV-Fc (SEQ ID NO:303), (2) variant PD-L2 IgV-Fc (SEQ ID NO:1417); (3) Fc only control, (4) variant CTLA-4 ECD-Fc: (SEQ ID NO: 3037), or (5) a wildtype human PD-L1-Fc were also tested. As shown in
Example 1 describes the generation of mutant DNA constructs of human CD155, CD112, PD-L1, PD-L2, CD86 (B7-2), CD80 (B7-1), ICOSL, and CTLA-4 IgSF domains for translation and expression on the surface of yeast as yeast display libraries.
A. Degenerate Libraries
Constructs were generated based on a wildtype human sequence set forth below:
For libraries that target specific residues for complete or partial randomization with degenerate codons, the DNA encoding the IgSF domains were ordered from Integrated DNA Technologies (Coralville, Iowa) as a set of overlapping oligonucleotides of up to 80 base pairs (bp) in length. To generate a library of diverse variants of the IgSF domains, the oligonucleotides contained desired degenerate codons, such as specific mixed base sets to code for various amino acid substitutions, were generated using an algorithm at the URL: rosettadesign.med.unc.edu/SwiftLib/.
In general, positions to mutate and degenerate codons were chosen from crystal structure information or homology models built from this structure containing the target-ligand pairs of interest to identify ligand contact residues, such as target side chain residues that interact with the ligand, as well as residues that are at the protein interaction interface. This analysis was performed using a structure viewer available at the URL: spdbv.vital-it.ch. For CD80, there are no CD80 structures available with ligands CD28 and PD-L1, so the same library was also used to select for binders of CD28 (binds the same region on CD80 as CTLA-4) and PD-L1 (not known if PD-L1 binds the same site as CTLA-4).
The next step in library design was the alignment of human, mouse, rat, and monkey sequences to identify which of the residues chosen for mutagenesis were conserved residues. Based on this analysis, conserved target residues were mutated with degenerate codons that only specified conservative amino acid changes plus the wild-type residue. Residues that were not conserved were mutated more aggressively, but also included the wild-type residue. Degenerate codons that also encoded the wild-type residue were deployed to avoid excessive mutagenesis of target protein. For the same reason, only up to 20 positions were targeted for mutagenesis for each library. Mutational analysis was focused on contact and non-contact interfacial residues that were within 6 Å of the binding surface with their side chains directed toward the ligand/counter structure.
To generate DNA encoding the targeted library, overlapping oligos of up to 80 nucleotides in length and containing degenerate codons at the residue positions targeted for mutagenesis, were ordered from Integrated DNA Technologies (Coralville, USA). The oligonucleotides were dissolved in sterile water, mixed in equimolar ratios, heated to 95° C. for five minutes and slowly cooled to room temperature for annealing. ECD or IgV domain-specific oligonucleotide primers that anneal to the start and end of the domain gene sequence were then used to generate PCR product. IgV domain-specific oligonucleotides which overlap by 40 bp with pBYDS03 cloning vector (Life Technologies, USA), beyond and including the BamHI and KpnI cloning sites, were then used to amplify 100 ng of PCR product from the prior step to generate a total of at least 12 μg of DNA for every electroporation. ECD-specific oligonucleotides which overlap by 40-50 bp with a modified version of pBYDS03 cloning vector (Life Technologies USA), beyond and including the BamH1 and KpnI cloning sites, were then used to amplify 100 ng of PCR product from the prior step to generate a total of at least 5 μg of DNA. Both polymerase chain reactions (PCRs) used OneTaq 2×PCR master mix (New England Biolabs, USA). The products from the second PCR were purified using a PCR purification kit (Qiagen, Germany) and resuspended in sterile deionized water. Alternatively, Ultramers® (Integrated DNA Technologies) of up to 200 bp in length were used in conjunction with megaprimer PCR (URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC146891/pdf/253371.pdf) to generate larger stretches of degenerate codons that could not be as easily incorporated using multiple small overlapping primers. Following the generation of full length product using megaprimer PCR, the mutant IgV domain library was PCR amplified again using DNA primers containing 40 bp overlap region with pBYDS03 cloning variant for homologous recombination into yeast.
To prepare for library insertion, pBYDS03 vector was digested with BamHI and KpnI restriction enzymes (New England Biolabs, USA) and the large vector fragment was gel-purified and dissolved in sterile, deionized water. Electroporation-ready DNA for the next step was generated by mixing 12 μg of library DNA insert with 4 μg of linearized vector in a total volume of 50 μL deionized and sterile water.
An alternative method to generate targeted libraries is to carry out site-directed mutagenesis (Multisite kit, Agilent, USA) of the target IgV domain with oligonucleotides containing degenerate codons. This approach is used to generate sublibraries that only target a few specific stretches of DNA for mutagenesis. In these cases, sublibraries are mixed before proceeding to the selection steps. In general, library sizes were in the range of 10E7 to 10E8 clones, except that sublibraries were only in the range of 10E4 to 10E5.
B. Random Libraries
Random libraries were also constructed to identify variants of the various IgSF domains. DNA encoding the wild-type IgSF domain was cloned between the BamHI and KpnI sites of yeast display vector pBYDS03 and then released using the same restriction enzymes. The DNA was then mutagenized with the Genemorph II Kit (Agilent Genomics, USA) to generate an average of three to five amino acid changes per library variant. Mutagenized DNA was then amplified by the two-step PCR and further processed as described above for targeted libraries.
For some IgSF domains, after completing several rounds of selection using beads and iterative FACS, a pool of clones were further mutated via error prone PCR. Thus, a second generation mutant library was created for some domains following the steps outlined as above though using selection output DNA as template rather than wildtype IgV plasmid sequence as template.
To introduce degenerate and random library DNA into yeast, electroporation-competent cells of yeast strain BJ5464 (ATCC.org; ATCC number 208288) were prepared and electroporated on a Gene Pulser II (Biorad, USA) with the electroporation-ready DNA from the steps above essentially as described (Colby, D. W. et al. 2004 Methods Enzymology 388, 348-358). The only exception was that transformed cells were grown in non-inducing minimal selective SCD-Leu medium to accommodate the LEU2 selective marker carried by modified plasmid pBYDS03. One liter of SCD-Leu media consists of 14.7 grams of sodium citrate, 4.29 grams of citric acid monohydrate, 20 grams of dextrose, 6.7 grams of yeast nitrogen base, and 1.6 grams yeast synthetic drop-out media supplement without leucine. The medium was filter sterilized before use, using a 0.22 μm vacuum filter device.
Library size was determined by plating dilutions of freshly recovered cells on SCD-Leu agar plates and then extrapolating library size from the number of single colonies from plating that generated at least 50 colonies per plate. The remainder of the electroporated culture was grown to saturation and cells from this culture were subcultured (e.g., 1/100) into the same medium once more and grown to saturation to minimize the fraction of untransformed cells and to allow for segregation of plasmid from cells that may contain two or more library variants. To maintain library diversity, this subculturing step was carried out using an inoculum that contained at least 10× more cells than the calculated library size. Cells from the second saturated culture were resuspended in fresh medium containing sterile 25% (weight/volume) glycerol to a density of 10E10/mL and frozen and stored at −80° C. (frozen library stock).
Example 10 describes the selection of yeast cells expressing affinity-modified variants of CD155, CD112, PD-L1, PD-L2, CD80, CD86, ICOSL, and CTLA-4. Cells were processed to reduce non-binders and to enrich for CD155, CD112, PD-L1, PD-L2, CD80, CD86, ICOSL, and CTLA-4 variants with the ability to bind their exogenous recombinant counter-structure proteins.
A number of cells equal to at least 10 times the estimated library size were thawed from individual library stocks, suspended to 1.0×10E6 cells/mL in non-inducing SCD-Leu medium, and grown overnight. The next day, a number of cells equal to 10 times the library size were centrifuged at 2000 RPM for two minutes and resuspended to 0.5×10E6 cells/mL in inducing SCDG-Leu media. One liter of SCDG-Leu induction media consists of 5.4 grams Na2HPO4, 8.56 grams NaH2PO4H2O, 20 grams galactose, 2.0 grams dextrose, 6.7 grams yeast nitrogen base, and 1.6 grams yeast synthetic drop out media supplement without leucine dissolved in water and sterilized through a 0.22 μm membrane filter device. The culture was grown in induction medium for 1 day at room temperature to induce expression of library proteins on the yeast cell surface.
Cells were sorted two to three times using Protein A magnetic beads (New England Biolabs, USA) loaded with cognate ligand to reduce non-binders and enrich for all variants with the ability to bind their exogenous recombinant counter-structure proteins. This was then followed by multiple rounds of fluorescence activated cell sorting (FACS) using exogenous counter-structure protein staining to enrich the fraction of yeast cells that displays improved binding (R&D Systems, USA). In some cases, these positive selections were alternated with negative FACS selections to remove clones that bound to other counter structure proteins. Magnetic bead enrichment and selections by flow cytometry were carried out essentially as described in Miller K. D., et al., Current Protocols in Cytometry 4.7.1-4.7.30, July 2008.
For CD155 variants provided in Table E10A, CD155 libraries were selected against each of TIGIT, CD96, and CD226, separately. For CD155 variants provided in Table E10B-E10F, selection involved two positive selections with the desired counter structures TIGIT and CD96 followed by one negative selection with the counter structure CD226 to select away from CD226 and improve binding specificity of the variant CD155. For selection, concentrations of the counter structures (TIGIT/CD96) and selection stringency of the positive sorts were varied to optimize lead identification. The concentration of CD226 for the negative selection was kept at 100 nM.
For CD112 variants provided in Table E11A, CD112 libraries were selected against each of TIGIT, CD112R, and CD226, separately. Target ligand proteins human rTIGIT.Fc (i.e., recombinant TIGIT-Fc fusion protein) and rCD226.Fc were purchased from R&D Systems (USA) and human rCD112R.Fc was made. Magnetic Protein A beads were obtained from New England Biolabs, USA. The EZ-Link™ Micro NHS-PEG4-Biotinylation Kit was used for biotinylation of counter-structure protein, (Life Technologies, USA). For additional CD112 variants provided in Table E11B-E11C, selection involved two positive selections with the desired counter structures TIGIT and CD112R followed by one negative selection with the counter structure CD226 to select away from CD226 and improve binding specificity of the variant CD112. Selection was performed essentially as described above except the concentrations of the counter structures (TIGIT/CD112R) and selection stringency of the positive sorts were varied to optimize lead identification. The concentration of CD226 for the negative selection was kept at 100 nM.
For PD-L1 and PD-L2 shown in Tables E12A-E12C or Tables E13A and E13B, respectively, yeast display targeted or random PD-L1 or PD-L2 libraries were selected against PD-1. With PD-L1 libraries, target ligand proteins were human rPD-1.Fc (i.e., recombinant PD-1-Fc fusion protein from R&D Systems, USA). With PD-L2 libraries, target ligand proteins was rhPD-1.Fc (i.e., recombinant human PD-1-Fc fusion protein from R&D Systems, USA). This was then followed by two to three rounds of flow cytometry sorting using exogenous counter-structure protein staining to enrich the fraction of yeast cells that displays improved binders. Ligand binding of Fc fusion protein to rPD-1.Fc, was detected with PE conjugated human Ig specific goat Fab (Jackson ImmunoResearch, USA). Alternatively, for PD-L1, selections were performed with human rCD80.Fc (i.e., human recombinant CD80 Fc fusion protein from R&D Systems, USA). Selections were carried out largely as described for PD-1 above. Magnetic bead enrichment and selections by flow cytometry are essentially as described in Miller, K. D., et al., Current Protocols in Cytometry 4.7.1-4.7.30, July 2008. PD-L1 variants in Table 22A-B were assessed for binding to cell-expressed counter structures. Additional PD-L1 variants identified in the screen as described above are set forth in Table 22C.
With CD80 and CD86 libraries, target ligand proteins were employed as follows: internally produced human rCTLA4-Fc, human rCD28-Fc, human rPD-L1 (R&D Systems, Minneapolis, USA), and rB7H6.Fc. Magnetic Protein A or streptavidin beads were obtained from New England Biolabs, USA. For biotinylation of counter-structure protein, biotinylation kit cat #21955, Life Technologies, USA, was used. For two-color, flow cytometric sorting, a Bio-Rad S3e sorter was used. CD80 display levels were monitored with an anti-hemagglutinin (HA) antibody labeled with Alexafluor 488 (Life Technologies, USA). Ligand binding of Fc fusion proteins, rCTLA4Fc, rPD-L1 or rCD28Fc, were detected with PE conjugated human Ig specific goat Fab (Jackson ImmunoResearch, USA). For CD80, the second FACS outputs (F2) were compared to parental CD80 yeast for binding rCTLA4Fc rPD-L1, or rCD28Fc by double staining each population with anti-HA (hemagglutinin) tag expression and the anti-human Fc secondary to detect ligand binding. CD80 variants are shown in Tables E14A-E14F.
For ICOSL shown in Tables E15A-E15F, yeast display targeted or random ICOSL libraries were selected against CTLA-4, CD28 and ICOS. Target ligand proteins were sourced from R&D Systems (USA) as follows: human rCD28.Fc (i.e., recombinant CD28-Fc fusion protein), rCTLA4.Fc and rICOS.Fc. The second sort outputs (F2) were compared to parental ICOSL yeast for binding of each rICOS.Fc, rCD28.Fc, and rCTLA4.Fc by double staining each population with anti-HA (hemagglutinin) tag expression and the anti-human Fc secondary to detect ligand binding. Importantly, the MFIs of all F2 outputs described above when measured with the anti-HA tag antibody on FL1 did not increase and sometimes went down compared to wild-type strains, indicating that increased binding was not a function of increased expression of the selected variants on the surface of yeast, and validated gating strategies of only selecting mid to low expressors with high ligand binding.
For CTLA-4 shown in Tables E16A-E16C, yeast display targeted or random libraries were selected against ICOSL and/or CD86. This selection process utilized the following reagents and instruments: human rICOSL.Fc (i.e., recombinant ICOSL-Fc fusion protein) and human rCD86.Fc target ligand proteins were purchased from R & D Systems, USA. The induced yeast library underwent 4 cycles of bead sorts using magnetic beads loaded alternately with ICOSL or CD86 to reduce non-binders and enrich for variant CTLA-4 molecules with the ability to bind ICOSL or CD86. After each cycle of selection, yeast retained through binding to magnetic beads were amplified through growth in SCD media followed by overnight induction in SCDG media. The preliminary selection was followed by two rounds of fluorescence activated cell sorting (FACS) using ICOSL-Fc in round 1 and CD86-Fc in round 2 to enrich the fraction of yeast cells that displays improved binders.
Doublet yeast were gated out using forward scatter (FSC)/side scatter (SSC) parameters, and sort gates were based upon higher ligand binding detected in FL2 that possessed more limited tag expression binding in FL1. For PD-L2, the second round FACS outputs (F2) were compared to parental for binding rPD-1.Fc by double staining each population with anti-HA (hemagglutinin) tag expression and the anti-human Fc-PE secondary to detect ligand binding.
Yeast outputs from the flow cytometric sorts were assayed for higher specific binding affinity. Sort output yeast were expanded and re-induced to express the particular IgSF affinity modified domain variants they encode. This population then can be compared to the parental, wild-type yeast strain, or any other selected outputs, such as the bead output yeast population, by flow cytometry.
Selected variant IgSF domains were further formatted as fusion proteins and tested for binding and functional activity as described below.
Example 11 describes reformatting of selection outputs identified in Example 10 as immunomodulatory proteins containing an affinity modified (variant) IgSF domain fused to an Fc molecule (variant IgV domain-Fc or ECD-Fc fusion molecules).
Output cell pools from final flow cytometric sorts were grown to terminal density in SCD-Leu medium. Plasmid DNA from each output was isolated using a yeast plasmid DNA isolation kit (ZymoResearch, USA). For PD-L2, the plasmid DNA was from at least 10× the number of cells of each sort output. For Fc fusions, PCR primers with added restriction sites suitable for cloning into the Fc fusion vector of choice were used to batch-amplify from the plasmid DNA preps the coding DNA for the mutant target IgV or ECD domains. After restriction digestion, the PCR products were ligated into Fc fusion vector followed by heat shock transformation into E. coli strain XL1 Blue (Agilent, USA) or NEB5alpha (New England Biolabs) as directed by supplier. Alternatively, the outputs were PCR amplified with primers containing 40 bp overlap regions on either end with Fc fusion vector to carry out in vitro recombination using Gibson Assembly Mastermix (New England Biolabs), which was subsequently used in heat shock transformation into E. coli strain NEB5alpha. Exemplary of an Fc fusion vector is pFUSE-hIgG1-Fc2 (InvivoGen, USA).
Dilutions of transformation reactions were plated on LB-agar containing 100 μg/mL carbenicillin (Teknova, USA) to isolate single colonies for selection. Up to 96 colonies from each transformation were then grown in 96 well plates to saturation overnight at 37° C. in LB-carbenicillin broth (Teknova cat #L8112) and a small aliquot from each well was submitted for DNA sequencing of the IgV domain insert in order to identify the mutation(s) in all clones. Sample preparation for DNA sequencing was carried out using protocols provided by the service provider (Genewiz; South Plainfield, N.J.). After removal of sample for DNA sequencing, glycerol was then added to the remaining cultures for a final glycerol content of 25% and plates were stored at −20° C. for future use as master plates (see below). Alternatively, samples for DNA sequencing were generated by replica plating from grown liquid cultures onto solid agar plates using a disposable 96 well replicator (VWR, USA). These plates were incubated overnight to generate growth patches and the plates were submitted to Genewiz as specified by Genewiz. In some instances, resequencing was performed to verify mutations.
After analysis of the Genewiz-generated DNA sequencing data, clones of interest were recovered from master plates and individually grown to density in liquid LB-broth containing 100 μg/mL carbenicillin (Teknova, USA) and cultures were then used for preparation of plasmid DNA of each clone using a standard kit such as the PureYield Plasmid Miniprep System (Promega) or the MidiPlus kit (Qiagen). Identification of clones of interest from Genewiz sequencing data generally involved the following steps. First, DNA sequence data files were downloaded from the Genewiz website. All sequences were then manually curated so that they start at the beginning of the ECD or IgV domain coding region. The curated sequences were then batch-translated using a suitable program available at the URL: www.ebi.ac.uk/Tools/st/emboss_transeq/. The translated sequences were then aligned using a suitable program available at the URL: multalin.toulouse.inra.fr/multalin/multalin.html. Alternatively, Genewiz sequences were processed to generate alignments using Ugene software (http://ugene.net).
Clones of interest were then identified from alignments using the following criteria: 1) identical clone occurs at least two times in the alignment and 2) a mutation occurs at least two times in the alignment and preferably in distinct clones. Clones that meet at least one of these criteria were assumed to be clones that have been enriched by the sorting process due to improved binding.
To generate recombinant immunomodulatory proteins that are Fc fusion proteins containing an IgV domain or ECD of the various IgSF proteins with at least one affinity-modified domain, the DNA encoding the variant was generated to encode a protein as follows: variant (mutant) ECD or IgV domain followed by a linker of three alanines (AAA) followed by an inert Fc lacking effector function, set forth in SEQ ID NO: 1938, containing the mutations C220S, R292C, N297G and V302C by EU numbering (corresponding to C5S, R77C, N82G and V87C with reference to wild-type human IgG1 Fc set forth in SEQ ID NO: 187); or 1939, containing the mutations C220S, L234A, L235E and G237A by EU numbering. In some cases, the encoding DNA was generated to encode a protein as follows: variant (mutant) IgV domain followed by a linker of three alanines (AAA) followed by a human IgG1 Fc set forth in SEQ ID NO: 1157 containing the mutations R292C, N297G and V302C by EU numbering (corresponding to R77C, N82G and V87C with reference to wild-type human IgG1 Fc set forth in SEQ ID NO: 187).
Alternatively, ECD or IgV domains were fused in a similar manner but with a linker containing the amino acids (GSGGGGS; SEQ ID NO: 1941) followed by an inert Fc lacking effector function, set forth in SEQ ID NO: 1939. In some cases, the NotI cloning site which contributes to the AAA linker sequence was deleted to generate a direct fusion of the ICOSL ECD and the beginning of the Fc. In some cases, ECD or IgV domains were fused in a similar manner but with a human IgG1 Fc capable of effector activity (effector). Since the construct does not include an antibody, light chains that can form a covalent bond with a cysteine, such an exemplary human IgG1 Fc (set forth in SEQ ID NO: 1202) contained a replacement of the cysteine residue to a serine residue at position 220 (C220S) by EU numbering (corresponding to position 5 (C5S) with reference to the wild-type or unmodified Fc set forth in SEQ ID NO: 187).
Example 12 describes the high throughput expression and purification of Fc-fusion proteins containing variant ECD or IgV domains as described in the above Examples.
Recombinant variant Fc fusion proteins were produced from suspension-adapted human embryonic kidney (HEK) 293 cells using the Expi293 expression system (Invitrogen, USA). 4 μg of each plasmid DNA from the previous step was added to 200 μL Opti-MEM (Invitrogen, USA) at the same time as 10.8 μL ExpiFectamine was separately added to another 200 μL Opti-MEM. After 5 minutes, the 200 μL of plasmid DNA was mixed with the 200 μL of ExpiFectamine and was further incubated for an additional 20 minutes before adding this mixture to cells. Ten million Expi293 cells were dispensed into separate wells of a sterile 10 mL, conical bottom, deep 24-well growth plate (Thomson Instrument Company, USA) in a volume of 4 mL Expi293 media (Invitrogen, USA). Plates were shaken for 5 days at 120 RPM in a mammalian cell culture incubator set to 95% humidity and 8% CO2. Following a 5-day incubation, cells were pelleted and culture supernatants were retained.
In general, proteins were purified from supernatants using a high throughput 96-well Filter Plate (Thomson Catalog number 931919), each well loaded with 60 μL of Mab SelectSure settled bead (GE Healthcare cat. no. 17543801). Protein was eluted with four consecutive 200 μl fractions of 50 mM Acetate pH 3.3. Each fraction's pH was adjusted to above pH 5.0 with 4 μL 2 M Tris pH 8.0. Fractions were pooled and quantitated using 280 nm absorbance measured by Nanodrop instrument (Thermo Fisher Scientific, USA), and protein purity was assessed by loading 5 μg of non-reduced protein on Mini-Protean TGX Stain-Free gels. Proteins were then visualized on a Bio Rad Chemi Doc XRS gel imager.
In some cases, proteins were purified from supernatants using a high throughput 96 well Protein A purification kit using the manufacturer's protocol (Catalog number 45202, Life Technologies, USA). Resulting elution fractions were buffer exchanged into PBS using Zeba 96 well spin desalting plate (Catalog number 89807, Life Technologies, USA) using the manufacturer's protocol. Purified protein was quantitated using 280 nm absorbance measured by Nanodrop instrument (Thermo Fisher Scientific, USA), and protein purity was assessed by loading 5 μg of protein on NUPAGE pre-cast, polyacrylamide gels (Life Technologies, USA) under denaturing and reducing conditions and subsequent gel electrophoresis. Proteins were visualized in gel using standard Coomassie staining.
This Example describes Fc-fusion binding studies of purified affinity modified CD155, CD112, PD-L1, PD-L2, CD86 (B7-2), CD80 (B7-1), ICOSL, and CTLA-4 proteins, which are other components of the immune synapse (IS) that have a demonstrated dual role in both immune activation and inhibition. The binding of the proteins to cell-expressed counter structures was tested to assess the specificity and affinity of IgSF domain variant immunomodulatory proteins. These examples demonstrate that affinity modification of IgSF domains yields proteins that can act to both increase and decrease immunological activity. Various combinations of those domains as the ARBM or IRBM in the multi-domain immunomodulatory protein can be used to achieve immunomodulatory activity.
A. Binding to Cell-Expressed Counter Structures
To produce cells expressing cognate binding partners, full-length mammalian surface expression constructs for the binding partners were designed in pcDNA3.1 expression vector (Life Technologies) and sourced from Genscript, USA. Binding studies were carried out on transfected HEK293 cells generated to express the full-length mammalian surface ligands using the using the Expi293F transient transfection system (Life Technologies, USA). As a control, binding to mock (non-transfected) cells also was assessed. The number of cells needed for the experiment was determined, and the appropriate 30 mL scale of transfection was performed using the manufacturer's suggested protocol. For each binding partner protein or mock 30 mL transfection, 75 million Expi293F cells were incubated with 30 μg expression construct DNA and 1.5 mL diluted ExpiFectamine 293 reagent for 48 hours, at which point cells were harvested for staining.
For staining and analysis by flow cytometry, 100,000-200,000 cells of appropriate transient transfection or negative control (mock) were plated in 96-well round bottom plates. Cells were spun down and resuspended in staining buffer (PBS (phosphate buffered saline), 1% BSA (bovine serum albumin), and 0.1% sodium azide) for 20 minutes to block non-specific binding. Afterwards, cells were centrifuged and resuspended in staining buffer containing 200 nM to 91 pM of each candidate variant protein, depending on the experiment of each candidate variant Fc protein in 50 μl. As controls, the binding activities of wild-type Fc fusion proteins and/or human IgG (Sigma) were also assessed. Primary staining was performed on ice for 45 minutes, before washing cells in staining buffer twice. PE-conjugated anti-human Fc (Jackson ImmunoResearch, USA) was diluted 1:150 in 50 μL staining buffer and added to cells and incubated another 30 minutes on ice. Secondary antibody was washed out twice, cells were fixed in 4% formaldehyde/PBS, and samples were analyzed on Intellicyt flow cytometer (Intellicyt Corp, USA) or FACScan flow cytometer (Becton Dickinson, USA). Mean Fluorescence Intensity (MFI) was calculated for each transfectant and mock transfected HEK293 with FlowJo Version 10 software (FlowJo LLC, USA).
Mean Fluorescence Intensity (MFI) was calculated for each transfectant and negative parental line with Cell Quest Pro software (Becton Dickinson, USA). A ratio of the MFI value of the tested variant compared to the parental (WT) MFI value was also calculated.
For each Table, the exemplary amino acid substitutions are designated by amino acid position number corresponding to the respective reference unmodified ECD sequence. The amino acid position is indicated in the middle, with the corresponding unmodified (e.g. wild-type) amino acid listed before the number and the identified variant amino acid substitution listed (or inserted designated by a) after the number.
Also shown is the binding activity as measured by the Mean Fluorescence Intensity (MFI) value for binding of each variant Fc-fusion molecule to cells engineered to express the cognate counter structure ligand and the ratio of the MFI compared to the binding of the corresponding unmodified Fc fusion molecule not containing the amino acid substitution(s) to the same cell-expressed counter structure ligand.
B. Anti-CD3 Coimmobilization Assay
Costimulatory bioactivity for some of the fusion variants was determined in anti-CD3 coimmobilization assays. 1 nM or 4 nM mouse anti-human CD3 (OKT3, Biolegends, USA) was diluted in PBS with 1 nM to 80 nM of the variant proteins. This mixture was added to tissue culture treated flat bottom 96 well plates (Corning, USA) overnight to facilitate adherence of the stimulatory proteins to the wells of the plate. The next day, unbound protein was washed off the plates and 100,000 purified human pan T cells (BenTech Bio, US) or human T cell clone BC3 (Astarte Biologics, USA) were added to each well in a final volume of 200 μL of Ex-Vivo 15 media (Lonza, Switzerland). Cells were cultured 3 days before harvesting culture supernatants and measuring human IFN-gamma levels with Duoset ELISA kit (R&D Systems, USA) as mentioned above.
C. Bioactivity Characterization
Bioactivity was also tested in a human Mixed Lymphocyte Reaction (MLR) for some molecules. Human primary dendritic cells (DC) are generated by culturing monocytes isolated from PBMC (BenTech Bio, USA) in vitro for 7 days with 500U/mL rIL-4 (R&D Systems, USA) and 250 U/mL rGM-CSF (R&D Systems, USA) in Ex-Vivo 15 media (Lonza, Switzerland). 10,000 matured DC and 100,000 purified allogeneic CD4+ T cells (BenTech Bio, USA) are co-cultured with variant Fc fusion proteins and controls in 96 well round bottom plates in 200 μL final volume of Ex-Vivo 15 media. On day 5, IFN-gamma secretion in culture supernatants is analyzed using the Human IFN-gamma Duoset ELISA kit (R&D Systems, USA). Optical density is measured by VMax ELISA Microplate Reader (Molecular Devices, USA) and quantitated against titrated rIFN-gamma standard included in the IFN-gamma Duo-set kit (R&D Systems, USA).
The functional activity of the some variant Fc-fusion molecules to modulate the activity of T cells also is shown based on the calculated levels of IFN-gamma in culture supernatants (pg/mL) generated with the indicated variant Fc fusion molecule in an MLR assay. Tables E10A, E11A, E13B, E14E-F, E15A-F, E16A-C also depict the ratio of IFN-gamma produced by each variant IgV-Fc compared to the corresponding unmodified IgV-Fc in an MLR assay.
D. Binding and Bioactivity Data
As shown, the selections resulted in the identification of a number of CD155, CD112, PD-L1, PD-L2, CD86 (B7-2), CD80 (B7-1), ICOSL, and CTLA-4 IgSF domain variants that were affinity-modified to exhibit increased binding for at least one, and in some cases more than one, cognate counter structure ligand. In addition, the results showed that affinity modification of the variant molecules also exhibited improved activities to both increase and decrease immunological activity.
1. CD155 Binding and Bioactivity Data
Purified variant IgV Fc fusion proteins were tested to assess specificity and affinity of CD155 domain variant immunomodulatory proteins for cognate binding partners as described above using HEK293 cells expressing the full-length mammalian surface expression constructs for human TIGIT, CD226 or CD96. For some molecules, soluble rCD155.Fc bioactivity was also tested in a human Mixed Lymphocyte Reaction (MLR).
2. CD112 Binding and Bioactivity Data
Purified variant IgV Fc fusion proteins were tested to assess specificity and affinity of CD155 domain variant immunomodulatory proteins for cognate binding partners as described above using HEK293 cells expressing the full-length mammalian surface expression constructs for human TIGIT, CD112R, CD226 or CD96. For some molecules, soluble rCD112.Fc bioactivity was also tested in a human Mixed Lymphocyte Reaction (MLR).
3. PD-L1 Binding and Bioactivity Data
For PD-L1, binding studies were carried out using Jurkat/IL-2 reporter cells (purchased from Promega Corp. USA) that were then transduced to stably express human PD-1 (Jurkat/PD-1 cells). For staining by flow cytometry, 100,000 Jurkat/PD-1 cells or negative control (Jurkat only) were plated in 96 well round bottom plates. Cells were spun down and resuspended in staining buffer (PBS (phosphate buffered saline), 1% BSA (bovine serum albumin), and 0.1% sodium azide) for 20 minutes to block non-specific binding. Afterwards, cells were centrifuged again and resuspended in 50 μl staining buffer containing 100 nM to 46 pM of each candidate PD-L1 variant Fc fusion protein. As controls, a full extracellular domain of wild-type PD-L1 (composed of one IgV and one IgC domain) fused to Fc (“Full length ECD of PD-L1”) and a IgV domain of wild-type PD-L1 (“wild type PD-L1 IgV”) were tested. Primary staining was performed on ice for 45 minutes, before washing cells twice in 150 ul staining buffer. PE-conjugated anti-human Fc (Jackson ImmunoResearch, USA) was diluted 1:150 in 50 μl staining buffer and added to cells and incubated another 30 minutes on ice. Secondary antibody was washed out twice, cells were fixed in 4% formaldehyde/PBS, and samples were analyzed on Intellicyt flow cytometer (Intellicyt Corp, USA).
4. PD-L2 Binding and Bioactivity Data
Binding studies were carried out using Jurkat/IL-2 reporter cells (purchased from Promega Corp. USA) that were then transduced to stably express PD-1 (Jurkat/PD-1) generally as described above for studies with PD-L1. In addition, protein-protein interactions between PD-1 and PD-L2 domain variant immunomodulatory proteins were further assessed using Fortebio binding assays. PD-1 was loaded individually onto anti-human capture sensors (ForteBio Octet AHC) and Fc fusions of full length wildtype (unmodified) PD-L2 IgV, full length ECD of PD-L2, full length ECD of PD-L1, or variant PD-L2 Fc-fusion molecules were bound to the PD-1 receptor at a single concentration of 100 nM. As a positive control, anti-PD-1 monoclonal antibody (nivolumab) was also assessed. Loading response of anti-human capture sensors of each binding protein being tested with the variant IgV-Fc fusion molecule was determined.
5. CD80 Binding and Bioactivity Data
Binding studies were carried out on cells that express the full-length mammalian surface ligands to assess binding of purified CD80 proteins to cell-expressed CTLA4, PD-L1, and CD28 counter structures. In some cases, second and third generations (Gen) of random mutagenesis and selection were run using procedures substantially described in Examples 8-10. Briefly, yeast plasmid DNA was isolated from outgrown yeast post FACS selection and used as template for mutagenic PCR. To maximize diversity, both characterized individual variants and a pool of FACS selected variants were used as template. The resulting library was subjected to iterative rounds of FACS selection and outgrowth. To increase PDL1 affinity while maintaining CD28 affinity, multiple FASC sort progression paths were taken. The second-generation mutagenic library underwent four FACS selections alternating between CD28- and CTLA4+ selections generating outputs that, when titrated against counter structures, were chosen to be reformatted into Fc vectors. The third-generation mutagenic library used the following FACS selection paths to yield yeast outputs that, when titrated against counter structures, were chosen to be reformatted into Fc vectors: 1. 50 nM PDL1+, 2a. 1 nM CTLA4+, 2b. 20 nM CTLA4−, 2a3. 10 nM PDL1+, 2b3. 10 nM PDL1+, 2b34. 25 nM CD28+. Following selection of yeast expressing affinity modified variants of CD80, the selected variants were reformatted as Fc fusion for the generation of additional Fc-fusion proteins containing IgV CD80 variants. After sequence analysis, individual variants were chosen for protein production, binding and functional assay.
For assessment of binding of selected immunomodulatory fusion proteins to cognate binding partners, cells expressing the CD80 cognate binding partners CTLA4 and PD-L1, full-length mammalian surface expression constructs were generated, incorporated into lentivirus and transduced into CHO cells. Cells were sorted in a Bio-Rad S3 Cell Sorter (Bio-Rad Corp., USA) to >98% purity. Jurkat/IL2 reporter cells, which endogenously express CD28, were used to detect binding to CD28. Staining and analysis by flow cytometry was performed essentially as described in section A.
6. ICOSL Binding and Bioactivity Data
Binding was assessed to cells expressed full-length cognate binding partners CD28, ICOS and CTLA-4 substantially as described above in section A. Bioactivity of the ECD ICOSL variants also was assessed in an anti-CD3 coimmobilization assay or human Mixed Lymphocyte Reaction (MLR) substantially as described above, except that for the coimmobilization assay, costimulatory activity was determined by culture of human T cells with a mixture of 10 nM plate-bound anti-CD3 and 40 nM ICOSL Fc variant proteins.
7 CTLA-1 Binding and Bioactivity Data
Fc-fusion binding studies were performed to assess specificity and affinity of CTLA-4 ECD variant immunomodulatory proteins for binding partners CD80, CD86, and ICOSL. The Fc-fusion variant proteins were further characterized for bioactivity in human primary T cells in vitro assays. Soluble CTLA-4-Fc bioactivity was tested in a human Mixed Lymphocyte Reaction (MLR). Human primary dendritic cells (DC) generated by culturing monocytes isolated from PBMC (BenTech Bio, USA) in vitro for 7 days with 50 ng/mL rIL-4 (R&D Systems, USA) and 80 ng/mL rGM-CSF (R&D Systems, USA) in Ex-Vivo 15 media (Lonza, Switzerland). On days 3 and 5, half of the media was removed and replaced with fresh media containing 50 ng/mL rIL-4 and 80 ng/mL rGM-CSF. To fully induce DC maturation, lipopolysaccharide (LPS) (InvivoGen Corp., USA) was added at 100 ng/mL to the DC cultures on day 6 and cells were incubated for an additional 24 hours. Approximately, 10,000 matured DC and 100,000 purified allogeneic CD3+ T cells (BenTech Bio, USA) were co-cultured with CTLA-4 variant Fc fusion proteins and controls in 96 well round bottom plates in 200 μl final volume of Ex-Vivo 15 media.
a. CTLA-4 Consensus Variants
Additional variants of CTLA-4 ECD were designed by identifying consensus residues identified in the screen described in Examples 8-12 and this Example above that were commonly associated with CTLA-4 that variants that exhibited improved CD80, CD86, and/or ICOSL binding and/or demonstrated suppression of interferon-gamma secretion in the MLR assay. The selected consensus mutations included I18T, A26T, E33V, T53S, M55T, M56K, N58S, L63P, M87V, L98Q, M99L, and Y105L. The consensus mutants were used to generate variant CTLA-4 ECDs by site-directed mutagenesis with reference to the wild-type sequence set forth in SEQ ID NO: 36, which was then formatted as an Fc fusion protein as described in Example 11. The variant CTLA-4 ECD-Fc fusions were tested for binding and bioactivity as described below.
1. Binding and Bioactivity
To produce cells expressing cognate binding partners, full-length mammalian surface expression constructs for each of human CD80, CD86, and ICOSL were designed in pcDNA3.1 expression vector (Life Technologies) and sourced from Genscript, USA. Binding studies were carried out using the Expi293F transient transfection system (Life Technologies, USA) described above. The number of cells needed for the experiment was determined, and the appropriate 30 mL scale of transfection was performed using the manufacturer's suggested protocol. For each counter structure or mock 30 mL transfection, 75 million Expi293F cells were incubated with 30 μg expression construct DNA and 1.5 mL diluted ExpiFectamine™ 293 reagent for 48 hours, at which point cells were harvested for staining.
In some instances, cells with stable expression of cognate binding partners were used. Chinese hamster ovarian cells (CHO) were stably transduced by lentivirus for surface expression of full-length human CD80, CD86, or ICOSL.
For flow cytometric analysis, 200,000 cells of a given transient transfection, stable cell line, or appropriate negative control were plated in 96 well round bottom plates. Cells were spun down and suspended in staining buffer (PBS (phosphate buffered saline), 1% BSA (bovine serum albumin), and 0.1% sodium azide) for 20 minutes to block non-specific binding. Afterwards, cells were centrifuged again and suspended in staining buffer containing 100 nM to 100 pM CTLA-4 variant Fc fusion protein or control in 50 μL. Primary staining was performed for 45 minutes, before washing cells in staining buffer twice. Bound CTLA-4 was detected with PE-conjugated anti-human IgG (Jackson ImmunoResearch, USA) diluted 1:150 in 50 μL staining buffer and incubated for 30 minutes. Alternatively, bound CTLA-4 was detected with anti-CTLA-4 antibody (Biolegend, USA) diluted 1:130 in 50 μL staining buffer for 30 minutes, before washing cells in staining buffer twice. Anti-CTLA-4 antibody was then detected with PE-conjugated anti-mouse IgG (Jackson ImmunoResearch, USA) diluted 1:150 in 50 μL staining buffer and incubated for 30 minutes.
After final incubation, cells were washed twice to remove unbound conjugated antibodies, fixed in 2% formaldehyde/PBS, and analyzed on a Hypercyt (Intellicyte, USA) or LSRII (Becton Dickinson, USA) flow cytometer.
Mean Fluorescence Intensity (MFI) was calculated for each sample with Cell Quest Pro software (Becton Dickinson, USA), FlowJo software (FlowJo, USA), or Forcyte software (Intellicyt, USA).
2. CD86 Blockade Bioassay
Select CTLA-4 variant Fc fusion proteins were assayed for capacity to block CD86-CD28 mediated costimulation as determined by a CD86 blockade bioassay. Artificial antigen presenting cells (APCs) were generated by transducing K562 cells with lentivirus to express cell surface anti-human CD3 single chain Fv (OKT3) and human CD86, yielding K562/OKT3/CD86. Effector cells were generated by transducing Jurkat cells expressing an IL-2-luciferace reporter (Promega) with lentivirus to express a chimeric receptor composed of the extracellular domain of human ICOS and the intracellular domain of human CD28, yielding Jurkat/IL-2/ICOS-CD28. APCs were plated in 33 μL/well of assay buffer (RPMI1640 with 5% FBS) at 2×104 cells/well with CTLA-4-Fc or control proteins in 33 μL/well at 300 nM. APCs and proteins were incubated for 20 minutes at room temperature before the addition of effector cells at 2×105 cell/well in 33 μL/well. The plates were transferred to a 37 degrees Celsius, humidified with 5% CO2 in an incubation chamber for 5 hours, then removed and allowed to acclimate to room temperature for 15 minutes. 100 μL/well of cell lysis and luciferase substrate solution (BioGlo™ luciferase reagent, Promega) was added to each plate and incubated on an orbital shaker for 10 minutes. Relative luminescence values (RLU) were determined for each test sample by measuring luminescence with a 1 second per well integration time using a Cytation 3 imaging reader (BioTek instruments). The percent inhibition mediated by CD86 blockade was determined using the following formula: [(Avg. Control RLU−Experimental RLU)/(Avg. Control RLU)]×100.
The results are summarized below in Table E16D. The values for binding CD80, CD86, and ICOSL (MFI) and percent inhibition CD28 costimulation are provided in addition to the relative ratio, as compared to the corresponding binding and CD86 blockade of the unmodified CTLA-4 polypeptide (ΔWT) for each experiment. As indicated, certain mutations and combinations of mutations were associated with a substantial increase in binding of CTLA-4 ECD to ICOSL, independent of the change in binding to either CD80 or CD86. In some cases, increases in binding to one or both of CD80 or CD86 also were observed.
b. Select CTLA-4 Variants
A further panel of CTLA-4 ECD variants was designed with mutations from a variant CTLA-4 identified in the screen described in Examples 8-12 and this Example above, specifically the variant set forth in SEQ ID NO: 3060 containing mutations L12F/R16H/G29W/M56T/L98Q/Y105L, which was associated with enhanced binding to CD80, CD86, and ICOSL and suppression of interferon-gamma. In some cases, S72G was included because it had been identified as a hot spot that had occurred in greater than 35% of the other top 50 hits that were identified as having suppressive activity. For some generated variants, the strategy included removal of some mutations (reversion mutations), for example, to reduce the number of mutations in the variant. Variant CTLA-4 ECDs were generated by site-directed mutagenesis with reference to the wild-type sequence set forth in SEQ ID NO: 36, which was then formatted as an Fc fusion protein as described in Example 11. The variant CTLA-4 ECD-Fc fusions were tested for binding and bioactivity as described above in this Example.
Table E16E provides the values for binding CD80, CD86, and ICOSL (MFI) and percent inhibition CD28 costimulation in addition to the relative ratio, as compared to the corresponding binding and CD86 blockade of the unmodified CTLA-4 polypeptide (AWT) for each experiment.
This Example describes studies to demonstrate the ability of exemplary multi-domain immunomodulatory proteins to colocalize CD28 and PD-1 using PathHunter® U2OS CD28/PD-1 cells (DiscoverX, USA).
U2OS CD28/PD-1 cells contain two inactive fragments of β-galactosidase (β-gal), an enzyme donor (ED) and enzyme acceptor (EA) attached to CD28 and PD-1. Colocalization of CD28 and PD-1 drives complementation between ED and EA protein fragments, creating an active β-gal enzyme that cleaves a substrate to generate chemiluminescent signal.
For the assay, adherent U2OS CD28/PD-1 cells were harvested from the flask, washed and pelleted. Cells were suspended and plated at 20,000 cells in 50 μl/well of a white, flat-bottomed 96 well plate. The cells were allowed to adhere for 4 hours in a 37 degree Celsius, 5% CO2 incubator. Exemplary multi-domain immunomodulatory proteins or control proteins were titrated and added to the adherent cells in 50 μl/well for a final concentration of 10,000-0.01 pM. The plates were returned the incubator for 18 hours. PathHunter Flash Detection (DiscoverX, Catalog 93-0247) was added at 55 μl/well and incubated for 1 hour in the dark. Relative luminescence values (RLU) were determined for each test sample by measuring luminescence with a one second per well integration time.
As shown in
This Example describes bioactivity of exemplary multi-domain immunomodulatory proteins in human primary T cells to promote the generation of induced regulatory T-cells (iTregs).
Artificial antigen presenting cells (APC) were generated through lentiviral transduction of K562 cells to express cell surface anti-human CD3 single chain Fv (OKT3) and human CD80. Primary human naïve CD4+ T cells were isolated from peripheral blood mononuclear cells and labeled with 0.25 uM carboxyfluorescein succinimidyl ester (CFSE).
APCs were pulsed with 50 μg/ml mitomycin C for 30 minutes at 37 degree Celsius. Cells were washed 3 times prior to use. 20,000 APCs and 50,000 naïve CD4+ T cells were added to wells of a 96 well round-bottom plate with 2 ng/mL recombinant TGF-β1 and the multi-domain immunomodulatory proteins or control proteins at a final concentration of 100, 33, or 11 nM. Cultures were placed in a 37 degree Celsius, 5% CO2 incubator for one week.
iTreg generation was determined by flow cytometric analysis of the percentage and total number of accumulated CD25+FoxP3+ cells after 7 days. For staining, the cells were washed with 170 μL/well DPBS, pelleted and suspended in 100 μL/well Live Dead Near IR stain (Invitrogen, USA) diluted 1:500 in DPBS. Cells were pelleted and stained with 50 μL/well of 1 ug/mL anti-human CD4-BV711 (clone RPA-T4) and CD25-BV421 (clone BC96) (BioLegend, USA) diluted in FACS buffer (PBS 0.5% BSA 0.5 mM EDTA 0.005% NaN3). After a 45 minute incubation, cells were washed twice and fixed overnight at 4 degree Celsius with fixative. Cells were pelleted, fixative removed, and cells were permeabilized with 150 μL/well True-Nuclear permeabilization buffer for 1 hour at 25 degree Celsius. Cells were pelleted and suspended in 50 μL/well of 1 ug/ml FOXP3-AF647 (clone 206D) diluted in permeablization buffer for 1 hour. Cells were washed twice with permeabilization buffer and once with FACS buffer. Cells were analyzed on a LSRII (Becton Dickinson, USA) flow cytometer and mean fluorescence intensity (MFI) determined using FlowJo software (FlowJo, USA, v10.2).
As shown in Table E17, the tested multi-domain immunomodulatory proteins were observed to promote the generation of induced regulatory T-cells (iTregs)
This Example further describes bioactivity of exemplary multi-domain immunomodulatory proteins in human primary T cells.
The multi-domain immunomodulatory proteins were tested in a Staphylococcal enterotoxin B (SEB) assay. Peripheral blood mononuclear cells (PBMC) were labeled with 0.25 uM carboxyfluorescein succinimidyl ester. 200,000 PBMC/well were incubated with 50 ng/mL SEB and titrated multi-domain immunomodulatory proteins or control proteins were added at a final concentration of 100,000-1 pM. Cultures were placed in a 37 degree Celsius, 5% CO2 incubator for four days. Supernatants were collected and the level of secreted IL-2 or IFN-gamma was quantitated by ELISA analysis (BD Biosciences, USA).
As shown in
In another experiment, additional exemplary multi-domain immunomodulatory proteins described in Example 1 were assessed in the SEB assay. Exemplary results are shown in Table E18. As shown, a number of the tested multi-domain immunomodulatory proteins exhibited antagonistic activity in the SEB assay compared to Fc only control.
This Example describes a Jurkat/IL2, Jurkat/IL2/PD-1, and Jurkat/IL2/TIGIT reporter assay to assess inhibitory activity of exemplary multi-domain immunomodulatory proteins generated and described in Example 1. Jurkat reporter cells expressing an IL-2-luciferase reporter (Jurkat/IL2) or the reporter cells that also were transduced to stably express PD1 (Jurkat/IL2/PD1), or or TIGIT (Jurkat/IL2/TIGIT) were added to a microwell plate at a total of 100,000 cells per well. To each well, exemplary multi-domain proteins were added to the wells at 100,000 pM to 32 pM, 1:5 serial dilution of protein to cell and incubated for 15 minutes at room temperature. Approximately 20,000 K562/OKT3/CD80 aAPC described in Example 3 were added to the wells. Plate was spun for 10 seconds at 1200 rpm and then incubated for 5 hours at 37 degrees Celsius in a humidified 5% CO2 incubation chamber. Luminescence was measured as described in Example 3.
Results for exemplary PD-L1-CTLA-4 and PD-L1-ICOSL multidomain immunomodulatory proteins are shown in
Adjusted inhibition was determined to assess if differential inhibition was observed in the Jurkat/IL2/PD-1 or TIGIT reporter cells versus Jurkat/IL-2 cells as a measure of contribution of the inhibitory structure and ligand. Adjusted inhibition was calculated as the percent of inhibition with an exemplary protein−percent inhibition without an exemplary protein. More specifically, PD-L1=(% Inhibition Jurkat/IL-2/PD-1)−(% Inhibition Jurkat/IL-2) and CD155=(% Inhibition Jurkat/IL-2/TIGIT)−(% Inhibition Jurkat/IL-2). Results for adjusted inhibition for exemplary assessed multidomain proteins and controls are shown in
The present invention is not intended to be limited in scope to the particular disclosed embodiments, which are provided, for example, to illustrate various aspects of the invention. Various modifications to the compositions and methods described will become apparent from the description and teachings herein. Such variations may be practiced without departing from the true scope and spirit of the disclosure and are intended to fall within the scope of the present disclosure.
This application claims priority from U.S. provisional patent application No. 62/613,378, filed Jan. 3, 2018, entitled “Multi-domain Immunomodulatory Proteins and Methods of Use Thereof,” and to U.S. provisional application No. 67/733,622, filed Sep. 19, 2018, entitled “Multi-domain Immunomodulatory Proteins and Methods of Use Thereof,” the contents of each of which are incorporated by reference in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US19/12222 | 1/3/2019 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 62613378 | Jan 2018 | US | |
| 62733622 | Sep 2018 | US |
