Patent Application
20230059511
Reference is made to U.S. Provisional Patent Application No. 63/222,916, filed Jul. 16, 2021, U.S. Provisional Patent Application Ser. No. 63/053,498 filed Jul. 17, 2020, U.S. Provisional Patent Application Ser. No. 63/222,916, filed Jul. 16, 2021, PCT Patent Application Serial No. PCT/US2021/042079 filed Jul. 16, 2021, and to U.S. Provisional Patent Applications Ser. No. 63/345,821, filed May 25, 2022, the contents of which are incorporated herein by reference in their entireties.
Reference is made to GB patent application Serial No. 1900858.0, filed 22 Jan. 2019, U.S. patent application Ser. No. 62/951,770, filed 20 Dec. 2019, International application PCT/GB2020/050120, filed 20 Jan. 2020, and U.S. provisional patent application 63/053,494, filed Jul. 17, 2020.
The foregoing applications, and all documents cited therein or during their prosecution (“appln cited documents”) and all documents cited or referenced in the appln cited documents, and all documents cited or referenced herein (“herein cited documents”), and all documents cited or referenced in herein cited documents, together with any manufacturer's instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the invention. More specifically, all referenced documents are incorporated by reference to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference.
The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled ReplacementSeqListing_INSTB006C2.xml, created on Aug. 25, 2022, which is 267,014 bytes in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety.
The present invention relates to a chimeric molecule useful in adoptive cell therapy (ACT), and cells comprising the same. The chimeric molecule can act as a modulator of cellular activity enhancing responses when an endogenous T-cell receptor (TCR) is engaged with its cognate antigen. The present invention also provides proteins, nucleic acids encoding the chimeric molecule and therapeutic uses thereof.
Adoptive cell therapy (ACT) using autologous T-cells to mediate cancer regression has shown much promise in early clinical trials. Several general approaches have been taken such as the use of naturally occurring tumor reactive or tumor infiltrating lymphocytes (TILs) expanded ex vivo. Additionally, T-cells may be genetically modified to retarget them towards defined tumor antigens. This can be done via the gene transfer of peptide (p)-major histocompatibility complex (MHC) specific T-cell Receptors (TCRs) or synthetic fusions between tumor specific single chain antibody fragment (scFv) and T-cell signaling domains (e.g. CD3), the latter being termed chimeric antigen receptors (CARs).
TIL and TCR transfer has proven particularly good when targeting melanoma (Rosenberg et al. 2011; Morgan 2006), whereas CAR therapy has shown much promise in the treatment of certain B-cell malignancies (Grupp et al. 2013).
Costimulatory signals are useful to achieve robust CAR T cell expansion, function, persistence and antitumor activity. The success of CAR therapy in leukemia has been partly attributed to the incorporation of costimulatory domains (e.g. CD28 or CD137) into the CAR construct, signals from which synergize with the signal provided by CD3ζ to enhance anti-tumor activity. The basis of this observation relates to the classical signal 1/signal 2 paradigm of T-cell activation. Here signal 1, provided by the TCR complex, synergizes with signal 2 provided by costimulatory receptors such as CD28, CD137 or CD134 to permit the cells to undergo clonal expansion, IL2 production and long term survival without the activation induced cell death (AICD) associated with signal 1 alone. Furthermore the involvement of signal 2 enhances the signal generated through signal 1 allowing the cells to respond better to low avidity interactions such as those encountered during anti-tumor responses.
Targeted costimulation will have beneficial effects for non-CAR-based T-cell therapies. For example, incorporating costimulatory domains into a chimeric TCR has been shown to enhance responses of T-cells towards pMHC (Govers 2014). While tumor infiltrating lymphocytes (TILs) utilize their endogenous TCRs to mediate tumor recognition, it has not been possible to engineer the endogenous TCR. Thus TIL are subject to substantial limitations as tumor cells express very few costimulatory ligands. The ability to induce targeted costimulation of TIL, or indeed any other adoptive T-cell therapy product, would be beneficial.
Citation or identification of any document in this application is not an admission that such document is available as prior art to the present invention.
Provided herein are chimeric molecules, in particular chimeric proteins, designed to provide costimulation when the endogenous TCR is engaged with its cognate antigen. Mechanistically, the proposed constructs may be incorporated in the endogenous TCR complex. When the endogenous TCR complex machinery is engaged with their cognate antigen, the TCR receptor complex aggregates, forcing the clustering of these chimeric constructs. This clustering results in the activation of their signaling domains, causing an increase in costimulation. This costimulation manifests itself in a measurable improvement in the effector function of the recipient T cell: increased in activation markers, increase cytokine secretion (IL-2 in particular) and increased proliferation.
Some embodiments herein relate to a chimeric molecule, advantageously a chimeric protein, that provides costimulation to the T cell when the endogenous T cell receptor is engaged. This molecule may comprise a TCR clustering domain and a signaling domain that may contain a CD40 intracellular domain or signaling fragment thereof.
The TCR clustering domain may be one or more of the proteins typically found in the TCR complex, such as but not limited to, CD3D, CD3E, CD3G, CD3Z, CD3-eta and the constant chains of pre-TCR alpha (PTCRA) TCR alpha, TCR beta, TCR gamma or TCR delta.
The signaling domain may also comprise, an additional full length costimulatory domain, including but not limited to CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (OX40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6.
While CD3D, CD3E, CD3G, CD3Z work alone; the constructs containing TCR constant chains (either alpha/beta or gamma/delta) are preferably co-expressed with their respective partner in bicistronic configuration: TCR alpha with TCR beta and TCR gamma with TCR delta. Therefore, TCR alpha containing constructs are advantageously co-expressed with TCR beta and vice versa; and TCR gamma containing constructs should be co-expressed with TCR delta and vice versa. In the context of TILs and any other alpha-beta T cells; the preferred configuration includes TCR gamma-delta; and in gamma-delta T cells, the preferred configuration includes TCR alpha-beta to minimize interference/disruption with the endogenous TCR machinery and the TCR pairing.
For CD3D, CD3E, CD3G and CD3Z, the transmembrane and extracellular portions are advantageously utilized. However, the present invention also contemplates portions or the totality of their intracellular components, which could potentially minimize the disruption of the endogenous TCR complex signaling or help to further amplify the endogenous TCR signaling.
In another aspect, the invention provides a chimeric protein comprising a clustering domain and a signaling domain that may contain a CD40 intracellular domain or signaling fragment thereof. In some embodiments, the clustering domain is capable of oligomerization and/or self assembly. In some embodiments, clustering comprises formation of a homodimer or homotrimer. In some embodiments, clustering comprises oligomerization with a different protein to form a heterodimer or heterotrimer. In some embodiments, the chimeric protein is constitutive as signaling, for example independent of receptor engagement by an extracellular ligand or independent of receptor engagement by an extracellular ligand attached to a different cell. In some embodiments, the clustering domain comprises a transmembrane domain. In some embodiments, the clustering domain comprises a transmembrane domain and further comprises activating mutations that promote dimerization or oligomerization. In some embodiments, the clustering domain comprises an extracellular domain, such as but not limited to an extracellular domain of a receptor. In some embodiments, the clustering domain comprises an extracellular domain of a receptor and further comprises activating mutations in the extracellular domain that promote dimerization or oligomerization. In some embodiments, the clustering domain comprises a leucine zipper. In some embodiments, the leucine zipper comprises or constitutes a transmembrane domain. In some embodiments, the leucine zipper comprises or constitutes a soluble domain. Non-limiting examples of clustering domains include clustering domains of the thrombopoietin receptor (TpoR), erythropoietin receptor (EpoR), growth hormone receptor (GHR), glycophorin A (GPA) transmembrane domain, and activating mutants thereof. In some embodiments, clustering may be modulated by a small molecule. In some embodiments, clustering may be modulated by post-translational modifications.
In another aspect, the invention provides a chimeric protein which comprises an extracellular ligand binding domain linked to an intracellular signaling domain by a transmembrane domain. In some embodiments, the extracellular ligand binding domain is selected or engineered to bind to an extracellular ligand that maintains two or more copies of the chimeric protein in proximity to one another such that the signaling domain is activated. The extracellular ligand binding domain is considered one part of a specific binding pair (sbp) and the extracellular ligand is the second part of the specific binding pair. In some embodiments, one member of the sbp comprises a protein or receptor or extracellular portion thereof and the second sbp comprises a binding protein specific for the first member of the sbp. In some embodiments, the extracellular sbp is bivalent. In some embodiments, the extracellular sbp is trivalent. Nonlimiting examples of extracellular ligands include antibodies and bivalent antigen binding fragments thereof. Non-limiting examples of extracellular ligand binding domains of chimeric proteins of the invention (i.e., sbp members) include, without limitation, NKG2A, CD27, CD137, GITR, PD-1, PD-L1, FasL, OX40, CTLA4, ICOS, CD40, EGFR, HER2 and extracellular portions thereof. Complementary sbp members include, without limitation, pembrolizumab for PD1, trastuzumab for HER2, cetuximab for EGFR, tremelimumab for CTLA4, varlilumab for CD27, and urelumab for CD137. In some embodiments, the intracellular signaling domain comprises a CD40 intracellular domain or signaling fragment thereof.
In some embodiments, the CD40 signaling domain comprises SEQ ID NO:154, SEQ ID NO:155, or SEQ ID NO:156. In some embodiments, the CD40 signaling fragment comprises, consists, or consists essentially of an SH3 motif (KPTNKAPH, PTNKAPHP or PTNKAPH), TRAF2 motif (PKQE, PKQET, PVQE, PVQET, SVQE, SVQET), TRAF6 motif (QEPQEINFP or QEPQEINFP), PKA motif (KKPTNKA, SRISVQE, or a combination thereof, or is a full length CD40 intracellular domain. In some embodiments, one or more of the SH3, TRAF2, TRAF6, or PKA motifs of the CD40 signaling domain is mutated. In some embodiments, one or more of the SH3, TRAF2, TRAF6, or PKA motifs of the CD40 signaling domain is present in multiple copies.
Disclosed in this application is an engineered protein. In some embodiments, the engineered protein has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 166, wherein the sequence is not SEQ ID NO: 123.
In some embodiments, the engineered protein has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 167, wherein the sequence is not SEQ ID NO: 123.
In some embodiments, the engineered protein further comprises a binding domain, CD28 domain, and CD40 domain. In some embodiments, the engineered protein further comprises a signal peptide sequence. In some embodiments, the signal peptide sequence has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 157. In some embodiments, the binding domain comprises a VL sequence, a VH sequence, and an at least one linker. In some embodiments, the at least one linker has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 159 or 161. In some embodiments, the binding domain comprises two linker sequences. In some embodiments, the two linker sequences have at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to amino acid sequences SEQ ID NO: 159 and SEQ ID NO: 161, respectively. In some embodiments, the VL sequence has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 158. In some embodiments, the VH sequence has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 160. In some embodiments, the CD40 domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 165. In some embodiments, the CD28 domain comprises a CD28 transmembrane domain. In some embodiments, the CD28 transmembrane domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 163. In some embodiments, the CD28 domain comprises a CD28 extracellular domain. In some embodiments, the CD28 extracellular domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 162. In some embodiments, the CD28 domain comprises a CD28 intracellular domain. In some embodiments, the CD28 intracellular domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 164. In some embodiments, the protein further comprises 1, 2, 3, 4, 5, or all 6 CDR sequence(s) selected from the group consisting of: QASQSLSNLLA (SEQ ID NO: 168), GASNLES (SEQ ID NO: 169), QGGHYSGL (SEQ ID NO: 170), TNDMN (SEQ ID NO: 171), VIYSDDTPDYATWAKG (SEQ ID NO: 172), and/or GHYDSAVYAYALNI (SEQ ID NO: 173). In some embodiments, the binding domain and CD28 domain are connected by an at least one linker.
In some embodiments, an engineered protein is provided. It can comprise an amino acid sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO: 166 or 167, wherein the amino acid sequence does not include at least one of:
In some embodiments, a CoStAR is provided. It can comprise: a) an optional signal peptide; b) a binding domain, wherein the binding domain binds to an anti-pembrolizumab antibody or binding fragment thereof; c) a CD28 domain; and d) a CD40 domain. Wherein a) is optionally linked to b), wherein b) is linked to c), wherein c) is linked to d), and wherein the CoStAR comprises an amino acid sequence that: i) lacks at least one of:
ii) has an amino acid sequence that is greater than 95% identical to SEQ ID NO: 166 or 167; iii) has an amino acid sequence that is greater than 80% identical to SEQ ID NO: 166 or 167 and is not SEQ ID NO: 123; or iv) any combination of i-iv.
In some embodiments, a fusion protein is provided. The fusion protein comprises a) a means for binding to an antibody that binds to pembrolizumab; b) a CD28 domain; and c) CD40 domain. Wherein a) is linked to b), wherein b) is linked to c), and wherein the fusion protein comprises an amino acid sequence that: i) lacks at least one of:
ii) has an amino acid sequence that is greater than 95% identical to SEQ ID NO: 166 or 167; iii) has an amino acid sequence that is greater than 80% identical to SEQ ID NO: 166 or 167 and is not SEQ ID NO: 123; or iv) any combination of i-iv.
In some embodiments, a fusion protein is provided that comprises the amino acid sequence of SEQ ID NO: 166.
In some embodiments, a fusion protein is provided that comprises the amino acid sequence of SEQ ID NO: 167.
In some embodiments, a nucleic acid which encodes the protein of any one of the preceding claims.
Also disclosed herein is a nucleic acid which encodes a protein of any one of the embodiments of the present application.
Also disclosed herein is a vector which comprises a nucleic acid of any one of the embodiments of the present application.
Also disclosed herein is a cell which expresses a protein of any one of the embodiments of the present application.
Also disclosed herein is a cell which expresses at least two proteins of any one of the embodiments of the present application.
Also disclosed herein is a method of making the cell of any one of the embodiments of the present application which comprises the step of transducing or transfecting a cell with a vector of any one of the embodiments of the present application.
Also disclosed herein is a method for preparing a population of cells that express a protein of any one of the embodiments of the present application, comprising detecting expression of the protein on the surface of cells transfected or transduced with a vector according to any one of the embodiments of the present application and selecting cells which are identified as expressing the protein.
Also disclosed herein is a cell population produced by the method of any one of the methods disclosed in the present application.
Also disclosed herein is a cell population which is enriched for cell expression a protein of any one of the embodiments of the present application.
Also disclosed herein is a method for treating a disease in a subject in need thereof, which comprises the step of administering the cell of any one of the embodiments of the present application, or the cell population of any one of the embodiments of the present application, to the subject.
Accordingly, it is an object of the invention not to encompass within the invention any previously known product, process of making the product, or method of using the product such that Applicants reserve the right and hereby disclose a disclaimer of any previously known product, process, or method. It is further noted that the invention does not intend to encompass within the scope of the invention any product, process, or making of the product or method of using the product, which does not meet the written description and enablement requirements of the USPTO (35 U.S.C. § 112, first paragraph) or the EPO (Article 83 of the EPC), such that Applicants reserve the right and hereby disclose a disclaimer of any previously described product, process of making the product, or method of using the product. It may be advantageous in the practice of the invention to be in compliance with Art. 53(c) EPC and Rule 28(b) and (c) EPC. All rights to explicitly disclaim any embodiments that are the subject of any granted patent(s) of applicant in the lineage of this application or in any other lineage or in any prior filed application of any third party is explicitly reserved. Nothing herein is to be construed as a promise.
It is noted that in this disclosure and particularly in the claims and/or paragraphs, terms such as “comprises”, “comprised”, “comprising” and the like can have the meaning attributed to it in U.S. Patent law; e.g., they can mean “includes”, “included”, “including”, and the like; and that terms such as “consisting essentially of” and “consists essentially of” have the meaning ascribed to them in U.S. Patent law, e.g., they allow for elements not explicitly recited, but exclude elements that are found in the prior art or that affect a basic or novel characteristic of the invention.
These and other embodiments are disclosed or are obvious from and encompassed by, the following Detailed Description.
The following detailed description, given by way of example, but not intended to limit the invention solely to the specific embodiments described, may best be understood in conjunction with the accompanying drawings.
Disclosed herein are a variety of engineered proteins. In some embodiments, the engineered protein that has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 166, and wherein the sequence is not SEQ ID NO: 123. In some embodiments, the engineered protein has at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 70 and 100%, identity to SEQ ID NO: 166. In some embodiments, the engineered protein has an at least 80% identity to SEQ ID NO:166. In some embodiments, the engineered protein has an at least 90% identity to SEQ ID NO:166. In some embodiments, the engineered protein is SEQ ID NO:166 (
In some embodiments, the engineered protein that has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 167, and wherein the sequence is not SEQ ID NO: 123. In some embodiments, the engineered protein that has at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 70 and 100%, identity to SEQ ID NO: 167. In some embodiments, the engineered protein has an at least 80% identity to SEQ ID NO:167. In some embodiments, the engineered protein has an at least 90% identity to SEQ ID NO:167. In some embodiments, the engineered protein is SEQ ID NO:167 (
In some embodiments, an engineered protein is provided that has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 166, and wherein the sequence is not SEQ ID NO: 123.
In some embodiments, an engineered protein is provided that has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 167, and wherein the sequence is not SEQ ID NO: 123.
In some embodiments, the engineered protein, CoStAR or fusion protein has a general structure as depicted in
In some embodiments, the engineered protein CoStAR or fusion protein has a general structure as depicted in
In some embodiments, the engineered protein CoStAR or fusion protein comprises at least one sequence depicted in
In some embodiments, the arrangement in
In some embodiments, the engineered protein, CoStAR or fusion protein is as depicted in
In some embodiments, the engineered protein comprises a binding domain. In some embodiments, the engineered protein comprises a CD28 domain. In some embodiments, the engineered protein comprises a CD40 domain. In some embodiments, the engineered protein comprises 1, 2, or all 3 of a binding domain, a CD28 domain, and/or a CD40 domain.
In some embodiments, the engineered protein comprises a signal peptide sequence. The term “signal peptide” is given its usual scientific meaning, and thus refers a short peptide that functions in translocating the rest of the attached protein. “Signal peptide” thus may also be called a signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide. It will be understood that the signal peptide may be any peptide with the function of signaling for the attached peptide to be translocated to the plasma membrane of a cell. In some embodiments, the signal peptide sequence has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 157.
In some embodiments, the binding domain comprises 1, 2, or all 3 of a VL sequence, a VH sequence, and/or an at least one linker. In some embodiments, the at least one linker has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 159 or 161. In some embodiments, the binding domain comprises two linker sequences. In some embodiments, the two linker sequences have at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to amino acid sequences SEQ ID NO: 159 and SEQ ID NO: 161, respectively.
In some embodiments, the VL sequence has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 158. In some embodiments, the VH sequence has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 160. In some embodiments, all 3 of the heavy chain CDRs and/or all three of the light chain CDRs within the VH and VL are identical to the heavy and/or light chain CDRs contained within SEQ ID NOs: 158 and 160. In some embodiments, 1, 2, 3, 4, 5 or 6 of the CDRs have 1, 2, 3, 4 or more point mutations. In some embodiments, 1, 2, 3, 4, 5, or 6 CDRs are 70, 80, 85, 90, 95, 96, 97, 98, 99 or 100% identical to the corresponding CDRs within SEQ ID NOs: 158 and/or 160.
In some embodiments, the protein comprises 1, 2, 3, 4, 5, or all 6 CDR sequence(s) selected from the group consisting of: QASQSLSNLLA (SEQ ID NO: 168), GASNLES (SEQ ID NO: 169), QGGHYSGL (SEQ ID NO: 170), TNDMN (SEQ ID NO: 171), VIYSDDTPDYATWAKG (SEQ ID NO: 172), and/or GHYDSAVYAYALNI (SEQ ID NO: 173). In some embodiments, the binding domain and CD28 domain are connected by an at least one linker. In some embodiments, 1, 2, 3, 4, 5 or 6 of the CDRs have 1, 2, 3, 4, or more point mutations. In some embodiments, 1, 2, 3, 4, 5, or 6 CDRs are 70, 80, 85, 90, 95, 96, 97, 98, 99 or 100% identical to the CDRs.
Also disclosed herein is an engineered protein comprising an amino acid sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to the amino acid sequence of SEQ ID NO: 166 or 167.
In some embodiments, an engineered protein is provided that comprises an amino acid sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO: 166 or 167, wherein the amino acid sequence does not include at least one of: QKLISEEDLE (SEQ ID NO: 174) or LVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQV YSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKI (SEQ ID NO: 175).
In some embodiments, the CD40 domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to the amino acid sequence of SEQ ID NO: 165. In some embodiments, the CD28 domain comprises a CD28 transmembrane domain. In some embodiments, the CD28 transmembrane domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 163. In some embodiments, the CD28 domain comprises a CD28 extracellular domain. In some embodiments, the CD28 extracellular domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 162. In some embodiments, the CD28 domain comprises a CD28 intracellular domain. In some embodiments, the CD28 intracellular domain has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identity to SEQ ID NO: 164.
In some embodiments, the amino acid sequence and/or fusion protein and/or engineered protein does not include at least one of: QKLISEEDLE (SEQ ID NO: 174) or LVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQV YSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKI (SEQ ID NO: 175). In some embodiments, the engineered protein lacks both of QKLISEEDLE (SEQ ID NO: 174) and
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 157.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 158.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 159.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 160.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 161.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 162.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 163.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 164.
In some embodiments, the engineered protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 165.
In some embodiments, the engineered protein comprises 1, 2, 3, 4, 5, 6, 7, 8, and/or 9 sequence(s) that have at least 80% identity to SEQ ID NOS: 157-165, respectively. In some embodiments, the engineered protein comprises 1, 2, 3, 4, 5, 6, 7, 8, and/or 9 sequence(s) that have at least 90% identity to SEQ ID NOS: 157-165, respectively. In some embodiments, the engineered protein comprises 1, 2, 3, 4, 5, 6, 7, 8, and/or 9 sequence(s) that have at least 95% identity to SEQ ID NOS: 157-165, respectively. In some embodiments, the engineered protein comprises 1, 2, 3, 4, 5, 6, 7, 8, and/or 9 sequence(s) that have at least 98% identity to SEQ ID NOS: 157-165, respectively. In some embodiments, the engineered protein comprises 1, 2, 3, 4, 5, 6, 7, 8, and/or 9 sequence(s) selected from the group consisting of: SEQ ID NOS: 157-165.
Also disclosed herein is a CoStAR. In some embodiments, the CoStAR comprises an optional signal peptide, a binding domain, wherein the binding domain binds to an anti-pembrolizumab antibody or binding fragment thereof, a CD28 domain, and a CD40 domain, wherein the signal peptide is optionally linked to the binding domain, wherein the binding domain is linked to the CD28 domain, wherein the CD28 domain is linked to the CD40 domain, and wherein the CoStAR comprises an amino acid sequence that: i) lacks at least one of: QKLISEEDLE (SEQ ID NO: 174) or
LVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYS Q QLQVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKI (SEQ ID NO: 175); ii) has an amino acid sequence that is greater than 95% identical to SEQ ID NO: 166 or 167; iii) has an amino acid sequence that is greater than 80% identical to SEQ ID NO: 166 or 167 and is not SEQ ID NO: 123; or iv) any combination of i-iv.
Also disclosed herein is a fusion protein. In some embodiments, the fusion protein comprises a means for binding to an antibody that binds to pembrolizumab, a CD28 domain, and a CD40 domain, wherein the means for binding to an antibody is linked to a CD28 domain, wherein the CD28 domain is linked to the CD40 domain, and wherein the fusion protein comprises an amino acid sequence that: i) lacks at least one of: QKLISEEDLE (SEQ ID NO: 174) or LVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQV YSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKI (SEQ ID NO: 175); ii) has an amino acid sequence that is greater than 95% identical to SEQ ID NO: 166 or 167; iii) has an amino acid sequence that is greater than 80% identical to SEQ ID NO: 166 or 167 and is not SEQ ID NO: 123; or iv) any combination of i-iv. In some embodiments, the means for binding to pembrolizumab is an anti-pembrolizumab antibody. In some embodiments, the anti-pembrolizumab antibody is
In some embodiments, the binding domain or the means for binding to an antibody that binds to pembrolizumab comprises: 1, 2, 3, 4, 5, or all 6 CDR sequence(s) selected from the group consisting of: QASQSLSNLLA (SEQ ID NO: 168), GASNLES (SEQ ID NO: 169), QGGHYSGL (SEQ ID NO: 170), TNDMN (SEQ ID NO: 171), VIYSDDTPDYATWAKG (SEQ ID NO: 172), and/or GHYDSAVYAYALNI (SEQ ID NO: 173). In some embodiments, 1, 2, 3, 4, 5 or 6 of the CDRs have 1, 2, 3, 4, or more point mutations. In some embodiments, 1, 2, 3, 4, 5, or 6 CDRs are 70, 80, 85, 90, 95, 96, 97, 98, 99 or 100% identical to the CDRs.
In some embodiments, the CD28 domain comprises: SEQ ID Nos: 162, 163, and 164, or a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical thereto. In some embodiments, the CD40 domain comprises: SEQ ID No: 165, or a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical thereto.
Also disclosed herein is a fusion protein comprising the amino acid sequence of SEQ ID NO: 166. In some embodiments, the fusion protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 166. Also disclosed herein is a fusion protein comprising the amino acid sequence of SEQ ID NO: 167. In some embodiments, the fusion protein comprises a sequence that is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%, or any integer that is between 80 and 100%, identical to SEQ ID NO: 167.
Also disclosed herein is a nucleic acid which encodes a protein of any one of the embodiments of the present application.
Also disclosed herein is a vector which comprises a nucleic acid of any one of the embodiments of the present application.
Also disclosed herein is a cell which expresses a protein of any one of the embodiments of the present application.
Also disclosed herein is a cell which expresses at least two proteins of any one of the embodiments of the present application.
Also disclosed herein is a method of making the cell of any one of the embodiments of the present application which comprises the step of transducing or transfecting a cell with a vector of any one of the embodiments of the present application.
Also disclosed herein is a method for preparing a population of cells that express a protein of any one of the embodiments of the present application, comprising detecting expression of the protein on the surface of cells transfected or transduced with a vector according to any one of the embodiments of the present application and selecting cells which are identified as expressing the protein.
Also disclosed herein is a cell population produced by the method of any one of the methods disclosed in the present application.
Also disclosed herein is a cell population which is enriched for cell expression a protein of any one of the embodiments of the present application.
Also disclosed herein is a method for treating a disease in a subject in need thereof, which comprises the step of administering the cell of any one of the embodiments of the present application, or the cell population of any one of the embodiments of the present application, to the subject.
As used herein, “full length protein” or “full length receptor” refers to a receptor protein, such as, for example, a CD40 receptor protein. The term “full length” encompasses receptor proteins lacking up to about 5 or up to 10 amino acids, for example 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids, at the N-terminal of the mature receptor protein once its signal peptide has been cleaved. For instance, while a specific cleavage site of a receptors N-terminal signal peptide may be defined, variability in exact point of cleavage has been observed. The term “full length” does not imply presence or absence of amino acids of the receptors N-terminal signal peptide. In one embodiment, the term “full length” (e.g. a full length CD28 or a full length CD40 intracellular domain, according to certain aspects of the invention) encompasses mature receptor proteins (e.g. CD28 according to certain aspects of the invention) lacking the N terminal signal peptide lacking up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N-terminal of the mature receptor protein once its signal peptide has been cleaved. As mentioned above, a “full length” CD28 receptor or other receptor or TCR clustering domain according to the various aspects of the invention does not include the signal peptide and may lack up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N-terminal of the mature receptor protein (e.g. N terminal residues N, K, I, L and/or V). This is shown in the exemplary fusions, e.g. SEQ ID Nos. 4-12 (note that these may lack up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N-terminal of the mature receptor protein as shown in the boxed region).
The chimeric protein of the present invention may comprise a TCR clustering domain as well as a signaling domain that advantageously may comprise a CD40 intracellular domain.
The term “T cell receptor,” or “TCR,” refers to a heterodimeric receptor composed of αβ or γδ chains that pair on the surface of a T cell. Each α, β, γ, and δ chain is composed of two Ig-like domains: a variable domain (V) that confers antigen recognition through the complementarity determining regions (CDR), followed by a constant domain I that is anchored to cell membrane by a connecting peptide and a Transmembral™) region. The TM region associates with the invariant subunits of the CD3 signaling apparatus. Each of the V domains has three CDRs. These CDRs interact with a complex between an antigenic peptide bound to a protein encoded by the major histocompatibility complex (pMHC) (Davis and Bjorkman (1988) Nature, 334, 395-402; Davis et al. (1998) Annu Rev Immunol, 16, 523-544; Murphy (2012), xix, 868 p.).
Costimulatory receptor proteins useful in the chimeric proteins of the invention include, without limitation, CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (OX40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6, which in their natural form comprise extracellular ligand binding domains and intracellular signal transducing domains. For example, CD2 is characterized as a cell adhesion molecule found on the surface of T cells and is capable of initiating intracellular signals necessary for T cell activation. CD27 is characterized as a type II transmembrane glycoprotein belonging to the TNFR superfamily (TNFRSF) whose expression on B cells is induced by antigen-receptor activation in B cells. CD28 is one of the proteins on T cells and is the receptor for CD80 (B7.1) and CD86 (B7.2) ligands on antigen-presenting cells. CD137 (4-1BB) ligand is found on most leukocytes and on some non-immune cells. OX40 ligand is expressed on many antigen-presenting cells such as DC2s (dendritic cells), macrophages, and B lymphocytes. In one embodiment, the costimulatory receptor protein is full length CD28 as defined herein.
CD40 is a member of the tumor necrosis factor receptor (TNFR) superfamily and several isoforms are generated by alternative splicing. Its ligand, CD154 (also called CD40L) is a protein that is primarily expressed on activated T cells. For reference, the human CD40 isoform 1 protein sequence is set forth in GenBank accession No. NP_001241.1, including signal peptide (amino acids 1-20), transmembrane domain (amino acids 194-215), and cytoplasmic domain (amino acids 216-277)(SEQ ID NO:22). CD40 receptor signaling involves adaptor proteins including but not limited to TNF receptor-associated factors (TRAF), and the cytoplasmic domain comprises signaling components, including but not limited to an SH3 motif (KPTNKAPH), TRAF2 motif (PKQE, PVQE, SVQE), TRAF6 motif (QEPQEINFP) and PKA motif (KKPTNKA, SRISVQE). Further motifs for binding to TRAF1, TRAF2, TRAF3, and TRAF5 comprise the major consensus sequence (P/S/A/T)X(Q/E)E or minor consensus sequence PXQXXD and can be identified in or obtained from, without limitation, TNFR family members such as CD30, Ox40, 4-1BB, and the EBV oncoprotein LMP1. (See, e.g., Ye, H et al., The Structural Basis for the Recognition of Diverse Receptor Sequences by TRAF2. Molecular Cell, 1999; 4(3):321-30. doi: 10.1016/S1097-2765(00)80334-2; Park H H, Structure of TRAF Family: Current Understanding of Receptor Recognition. Front. Immunol. 2018; 9:1999. doi: 10.3389/fimmu.2018.01999).
Examples disclosed herein demonstrate operation of CD40 as a signaling domain and further that cytokine and chemokine expression profiles are altered by signaling domain selection. In this regard, the CD40 signaling domains of the invention provide distinct and overlapping responses induced by the different factor binding sites. (See, e.g., Ahonen, C L et al., The CD40-TRAF6 axis controls affinity maturation and the generation of long-lived plasma cells. Nat Immunol. 2002; 3: 451-456; Mackey M F et al., Distinct contributions of different CD40 TRAF binding sites to CD154-induced dendritic cell maturation and IL-12 secretion. Eur J Immunol. 2003; 33: 779-789; Mukundan L et al., TNF receptor-associated factor 6 is an essential mediator of CD40-activated proinflammatory pathways in monocytes and macrophages. J Immunol. 2005; 174: 1081-1090.
In some embodiments, a chimeric protein of the invention comprises substantially all of a CD40 costimulatory domain. In some embodiments, a chimeric protein of the invention comprises two or more CD40 costimulatory domains. In some embodiments, a chimeric protein of the invention comprises a CD40 costimulatory domain signaling component or motif, including but not limited to an SH3 motif (KPTNKAPH), TRAF2 motif (PKQE, PVQE, SVQE), TRAF3 motif, TRAF6 motif (QEPQEINFP) or PKA motif (KKPTNKA, SRISVQE) as well as two or more, or three or more, or four or more such components of motifs, which can be in multiple copies and arranged in any order. In some embodiments, a chimeric protein of the invention comprises a CD40 costimulatory domain and a CD40 costimulatory domain signaling component or motif.
In some embodiments, selection of one or more costimulatory domain signaling component or motif is guided by the cell in which the chimeric protein is to be expressed and/or a desired costimulatory activity more closely identified with a signaling component or motif, or avoidance of a costimulatory activity more closely identified with a signaling component or motif.
In some embodiments, a chimeric protein signaling domain comprises, in addition to a CD40 costimulatory domain or signaling component or motif thereof, or two or more such domains or components or motifs or combinations thereof, an additional full length costimulatory domain or signaling component thereof from, without limitation, CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (OX40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6.
For reference, the human CD28 protein sequence is set forth in GenBank accession No. NP_006130.1, including signal peptide (amino acids 1-18), extracellular domain (amino acids 19-152), transmembrane domain (amino acids 153-179) and cytoplasmic domain (amino acids 180-200). The extracellular domain includes an immunoglobulin type domain (amino acids 21-136) which contains amino acids with compose the antigen binding site and amino acids that form the homodimer interface. The extracellular domain includes several asparagine residues which may be glycosylated, and the intracellular domain comprises serine and tyrosine residues, which may be phosphorylated.
For reference, the human CD8 alpha chain protein sequence is set forth by GenBank accession No. NP_001139345.1, including signal peptide (amino acids 1-21), extracellular domain (amino acids 22-182), transmembrane domain (amino acids 183-203), and cytoplasmic domain (amino acids 204-235). The extracellular domain includes an immunoglobulin type domain (amino acids 28-128) which contains amino acids with compose the antigen binding site and amino acids that form the homodimer interface. The extracellular domain includes several asparagine residues which may be glycosylated, and the intracellular domain comprises serine and tyrosine residues, which may be phosphorylated.
For reference, the human IgG4 constant region sequence is set forth in UniProtKB/Swiss-Prot: accession No. P01861.1, including CH1 (amino acids 1-98), hinge (amino acids 99-110), CH2 (amino acids 111-220), CH3 (amino acids 221-327). The CH2 region includes asparagine at amino acid 177, which is the glycosylated and associated with Fc receptor and antibody-dependent cell-mediated cytotoxicity (ADCC).
For reference, the protein sequence of human CD137 (41BB), another TNFR superfamily member, is set forth by GenBank accession No. NP_001552.2, including signal peptide (amino acids 1-23), extracellular domain (amino acids 24-186), transmembrane domain (amino acids 187-213), and cytoplasmic domain (amino acids 214-255).
For reference, the human CD134 (OX40) protein sequence is set forth by GenBank accession No. NP_003318.1, including signal peptide (amino acids 1-28), extracellular domain (amino acids 29-214), transmembrane domain (amino acids 215-235), and cytoplasmic domain (amino acids 236-277). This receptor has been shown to activate NF-kappaB through its interaction with adaptor proteins TRAF2 and TRAF5 and studies suggest that this receptor promotes expression of apoptosis inhibitors BCL2 and BCL21L1/BCL2-XL.
The human T-cell surface antigen CD2 has at least two isoforms. For reference, the human CD2 isoform1 protein sequence is set forth by NP_001315538.1, including signal peptide (amino acids 1-24), extracellular domain (amino acids 25-235), transmembrane domain (amino acids 236-261), and cytoplasmic domain (amino acids 262-377). The human CD2 isoform2 protein sequence is set forth by NP_001758.2
For reference, the human CD357 (GITR) isoform-1 protein sequence is set forth by GenBank accession No. NP_004186.1, including signal peptide (amino acids 1-25), extracellular domain (amino acids 26-162), transmembrane domain (amino acids 163-183), and cytoplasmic domain (amino acids 184-241).
For reference, the human CD29 (beta1 integrin) protein sequence is set forth by GenBank accession No. NP_596867, including signal peptide (amino acids 1-20), extracellular domain (amino acids 21-728), transmembrane domain (amino acids 729-751), and cytoplasmic domain (amino acids 752-798).
The human CD150 (SLAM) protein sequence has at several isoforms. In addition to the transmembrane form of CD150 (mCD150), cells of hematopoietic lineage express mRNA encoding the secreted form of CD150 (sCD150), which lacks the entire transmembrane region of 30 amino acids. For reference, human SLAM isoform b is set forth by GenBank accession No. NP_003028.1, including signal peptide (amino acids 1-20), extracellular domain (amino acids 21-237), transmembrane domain (amino acids 238-258), and cytoplasmic domain (amino acids 259-335). Human SLAM isoform a is set forth by GenBank accession No. NP_001317683.1.
In embodiments of the invention, a chimeric protein may be expressed alone under the control of a promoter in a therapeutic population of cells that have therapeutic activity, for example, Tumor Infiltrating Lymphocytes (TILs). Alternatively, the chimeric protein may be expressed along with a therapeutic transgene such as a chimeric antigen receptor (CAR) and/or T-cell Receptor (TCR). Suitable TCRs and CARs are well known in the literature, for example HLA-A*02-NYESO-1 specific TCRs (Rapoport et al. Nat Med 2015) or anti-CD19scFv.CD3ζ fusion CARs (Kochenderfer et al. J Clin Oncol 2015) which have been successfully used to treat Myeloma or B-cell malignancies respectively. The chimeric proteins described herein may be expressed with any known CAR or TCR thus providing the cell with a regulatable growth switch to allow cell expansion in-vitro or in-vivo, and a conventional activation mechanism in the form of the TCR or CAR for anti-cancer activity. Thus the invention provides a cell for use in adoptive cell therapy comprising a chimeric protein as described herein and a TCR and/or CAR that specifically binds to a tumor associated antigen. An exemplary chimeric protein comprising CD28 includes an extracellular antigen binding domain and an extracellular, transmembrane and intracellular signaling domain.
A chimeric protein of the invention optionally comprises a spacer region between the TCR clustering domain and the costimulatory receptor. As used herein, the term “spacer” refers to the extracellular structural region of a chimeric protein that separates the TCR clustering domain from the signaling domain of the chimeric protein. In some embodiments long spacers are employed, for example to target membrane-proximal epitopes or glycosylated antigens (see Guest R. D. et al. The role of extracellular spacer regions in the optimal design of chimeric immune receptors: evaluation of four different scFvs and antigens. J. Immunother. 2005; 28:203-211; Wilkie S. et al., Retargeting of human T cells to tumor-associated MUC1: the evolution of a chimeric antigen receptor. J. Immunol. 2008; 180:4901-4909). In other embodiments, chimeric proteins bear short spacers, for example to target membrane distal epitopes (see Hudecek M. et al., Receptor affinity and extracellular domain modifications affect tumor recognition by ROR1-specific chimeric antigen receptor T cells. Clin. Cancer Res. 2013; 19:3153-3164; Hudecek M. et a127acarbazine27nalling extracellular spacer domain of chimeric antigen receptors is decisive for in vivo antitumor activity. Cancer Immunol. Res. 2015; 3:125-135). In some embodiments, the spacer comprises all or part of or is derived from an IgG hinge, including but not limited to IgG1, IgG2, or IgG4. By “derived from an Ig hinge” is meant a spacer comprising insertions, deletions, or mutations in an IgG hinge. In some embodiments, a spacer can comprise all or part of one or more antibody constant domains, such as but not limited to CH2 and/or CH3 domains. In some embodiments, in a spacer comprising all or part of a CH2 domain, the CH2 domain is modified so as not to bind to an Fc receptor. For example, Fc receptor binding in myeloid cells has been found to impair CAR T cell functionality. In some embodiments, the spacer comprises all or part of an Ig-like hinge from CD28, CD8, or other protein comprising a hinge region. In some embodiments of the invention that comprise a spacer, the spacer is from 1 and 50 amino acids in length.
In some embodiments, the chimeric protein extracellular domain comprises a linker. Linkers comprise short runs of amino acids used to connect domains, for example a binding domain with a spacer or transmembrane domain. In order for there to be flexibility to bind ligand, a ligand binding domain will usually be connected to a spacer or a transmembrane domain by flexible linker comprising from about 5 to 25 amino acids, such as, for example, AAAGSGGSG or GGGGSGGGGSGGGGS. In some embodiments, a chimeric protein comprises a TCR clustering domain joined directly to a signaling domain by a linker, and without a spacer. In some embodiments, a chimeric protein comprises a binding domain joined directly to a transmembrane by a spacer and without a linker.
As discussed above, in some embodiments, a chimeric protein comprises a full length primary costimulatory receptor which can comprise an extracellular ligand binding and intracellular signaling portion of, without limitation, CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (OX40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6. In other embodiments, the chimeric protein, for instance may comprise an extracellular ligand binding domain of one of the aforementioned proteins and an intracellular signaling domain of another of the aforementioned proteins. In some embodiments, the signaling portion of the chimeric protein comprises a single signaling domain. In other embodiments, the signaling portion of the chimeric protein comprises a second intracellular signaling domain such as but not limited to: CD2, CD27, CD28, CD40, CD134 (OX40), CD137 (4-1BB), CD150 (SLAM). In some embodiments, the first and second intracellular signaling domains are the same. In other embodiments, the first and second intracellular signaling domains are different. In some embodiments, the costimulatory receptor is capable of dimerization. Without being bound by theory, it is thought that chimeric proteins dimerize or associate with other accessory molecules for signal initiation. In some embodiments, chimeric proteins dimerize or associate with accessory molecules through transmembrane domain interactions. In some embodiments, dimerization or association with accessory molecules is assisted by costimulatory receptor interactions in the intracellular portion, and/or the extracellular portion of the costimulatory receptor.
Although the main function of the transmembrane is to anchor the chimeric protein in the T cell membrane, in some embodiments, the transmembrane domain influences chimeric protein function. In some embodiments, the transmembrane domain is comprised by the full length primary costimulatory receptor domain. In embodiments of the invention wherein the chimeric protein construct comprises an extracellular domain of one receptor and an intracellular signaling domain of a second receptor, the transmembrane domain can be that of the extracellular domain or the intracellular domain. In some embodiments, the transmembrane domain is from CD4, CD8α, CD28, or ICOS. Gueden et al. associated use of the ICOS transmembrane domain with increased CART cell persistence and overall anti-tumor efficacy (Guedan S. et al., Enhancing CART cell persistence through ICOS and 4-1BB costimulation. JCI Insight. 2018; 3:96976). In an embodiment, the transmembrane domain comprises a hydrophobic α helix that spans the cell membrane.
In some embodiments, amino acid sequence variants of the TCR clustering domain or other moieties provided herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of the moiety. Amino acid sequence variants of an antibody moiety may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the clustering moiety, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the antibody moiety. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics.
In some embodiments, TCR clustering domain moieties comprising one or more amino acid substitutions, deletions, or insertions are provided. Amino acid substitutions may be introduced into a binding domain of interest and the products screened for a desired activity, e.g., retained/improved clustering or decreased immunogenicity. In some embodiments, amino acid substitutions may be introduced into one or more of the primary co-stimulatory receptor domain (extracellular or intracellular), secondary costimulatory receptor domain, or extracellular co-receptor domain. Accordingly, the invention encompasses chimeric proteins and component parts particularly disclosed herein as well as variants thereof, i.e. chimeric proteins and component parts having at least 75%, at least 80%, at least 85%, at least 87%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% sequence identity to the amino acid sequences particularly disclosed herein. The terms “percent similarity,” “percent identity,” and “percent homology” when referring to a particular sequence are used as set forth in the University of Wisconsin GCG software program BestFit. Other algorithms may be used, e.g. BLAST, psiBLAST or TBLASTN (which use the method of Altschul et al. (1990) J. Mol. Biol. 215: 405-410), FASTA (which uses the method of Pearson and Lipman (1988) PNAS USA 85: 2444-2448).
Particular amino acid sequence variants may differ from a reference sequence by insertion, addition, substitution or deletion of 1 amino acid, 2, 3, 4, 5-10, 10-20 or 20-30 amino acids. In some embodiments, a variant sequence may comprise the reference sequence with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more residues inserted, deleted or substituted. For example, 5, 10, 15, up to 20, up to 30 or up to 40 residues may be inserted, deleted or substituted.
In some preferred embodiments, a variant may differ from a reference sequence by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more conservative substitutions. Conservative substitutions involve the replacement of an amino acid with a different amino acid having similar properties. For example, an aliphatic residue may be replaced by another aliphatic residue, a non-polar residue may be replaced by another non-polar residue, an acidic residue may be replaced by another acidic residue, a basic residue may be replaced by another basic residue, a polar residue may be replaced by another polar residue or an aromatic residue may be replaced by another aromatic residue. Conservative substitutions may, for example, be between amino acids within the following groups:
Conservative substitutions are shown in Table 1 below.
Amino acids may be grouped into different classes according to common side-chain properties: a. hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile; b. neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; c. acidic: Asp, Glu; d. basic: His, Lys, Arg; e. residues that influence chain orientation: Gly, Pro; aromatic: Trp, Tyr, Phe. Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
The cells used in the present invention may be any lymphocyte that is useful in adoptive cell therapy, such as a T-cell or a natural killer (NK) cell, an NKT cell, a gamma/delta T-cell or T regulatory cell. The cells may be allogeneic or autologous to the patient.
T cells or T lymphocytes are a type of lymphocyte that have a central role in cell-mediated immunity. They can be distinguished from other lymphocytes, such as B cells and natural killer cells (NK cells), by the presence of a T-cell receptor (TCR) on the cell surface. There are various types of T cell, as summarized below. Cytotoxic T cells (TC cells, or CTLs) destroy virally infected cells and tumor cells, and are also implicated in transplant rejection. CTLs express the CD8 molecule at their surface.
These cells recognize their targets by binding to antigen associated with MHC class I, which is present on the surface of all nucleated cells. Through IL-10, adenosine and other molecules secreted by regulatory T cells, the CD8+ cells can be inactivated to an anergic state, which prevent autoimmune diseases such as experimental autoimmune encephalomyelitis.
Memory T cells are a subset of antigen-specific T cells that persist long-term after an infection has resolved. They quickly expand to large numbers of effector T cells upon re-exposure to their cognate antigen, thus providing the immune system with “memory” against past infections. Memory T cells comprise three subtypes: central memory T cells (TCM cells) and two types of effector memory T cells (TEM cells and TEMRA cells). Memory cells may be either CD4+ or CD8+. Memory T cells typically express the cell surface protein CD45RO. Regulatory T cells (Treg cells), formerly known as suppressor T cells, are crucial for the maintenance of immunological tolerance. Their major role is to shut down T cell-mediated immunity toward the end of an immune reaction and to suppress auto-reactive T cells that escaped the process of negative selection in the thymus.
Two major classes of CD4+ Treg cells have been described—naturally occurring Treg cells and adaptive Treg cells. Naturally occurring Treg cells (also known as CD4+CD25+FoxP3+ Treg cells) arise in the thymus and have been linked to interactions between developing T cells with both myeloid (CD11c+) and plasmacytoid (CD123+) dendritic cells that have been activated with TSLP. Naturally occurring Treg cells can be distinguished from other T cells by the presence of an intracellular molecule called FoxP3. Adaptive Treg cells (also known as Tr1 cells or Th3 cells) may originate during a normal immune response.
Natural Killer Cells (or NK cells) are a type of cytolytic cell which form part of the innate immune system. NK cells provide rapid responses to innate signals from virally infected cells in an MHC independent manner. NK cells (belonging to the group of innate lymphoid cells) are defined as large granular lymphocytes (LGL) and constitute the third kind of cells differentiated from the common lymphoid progenitor generating B and T lymphocytes.
In some embodiments, therapeutic cells of the invention comprise autologous cells engineered to express a chimeric protein. In some embodiments, therapeutic cells of the invention comprise allogeneic cells engineered to express a chimeric protein. Autologous cells expressing chimeric proteins may be advantageous in avoiding graft-versus-host disease (GVHD) due to TCR-mediated recognition of recipient alloantigens.
An aspect of the invention provides a nucleic acid sequence of the invention, encoding any of the chimeric proteins, polypeptides, or proteins described herein (including functional portions and functional variants thereof). As used herein, the terms “polynucleotide”, “nucleotide”, and “nucleic acid” are intended to be synonymous with each other. It will be understood by a skilled person that numerous different polynucleotides and nucleic acids can encode the same polypeptide as a result of the degeneracy of the genetic code. In addition, it is to be understood that skilled persons may, using routine techniques, make nucleotide substitutions that do not affect the polypeptide sequence encoded by the polynucleotides described here to reflect the codon usage of any particular host organism in which the polypeptides are to be expressed, e.g. codon optimization. Nucleic acids according to the invention may comprise DNA or RNA. They may be single stranded or double-stranded. They may also be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to oligonucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones, addition of acridine or polylysine‘chains at’ the 3′ and/or 5′ ends of the molecule. For the purposes of the present invention, it is to be understood that the polynucleotides may be modified by any method available in the art. Such modifications may be carried out in order to enhance the in vivo activity or life span of polynucleotides of interest.
The terms “variant”, “homologue” or “derivative” in relation to a nucleotide sequence include any substitution of, variation of, modification of, replacement of, deletion of or addition of one (or more) nucleic acid from or to the sequence.
The nucleic acid sequence may encode the protein sequence shown as SEQ ID NO:2 or a variant thereof. The nucleotide sequence may comprise a codon optimized nucleic acid sequence shown engineered for expression in human cells.
The invention also provides a nucleic acid sequence which comprises a nucleic acid sequence encoding a chimeric protein and a further nucleic acid sequence encoding a T-cell receptor (TCR) and/or chimeric antigen receptor (CAR).
The nucleic acid sequences may be joined by a sequence allowing co-expression of the two or more nucleic acid sequences. For example, the construct may comprise an internal promoter, an internal ribosome entry sequence (IRES) sequence or a sequence encoding a cleavage site. The cleavage site may be self-cleaving, such that when the polypeptide is produced, it is immediately cleaved into the discrete proteins without the need for any external cleavage activity. Various self-cleaving sites are known, including the Foot- and Mouth disease virus (FMDV) and the 2A self-cleaving peptide. The co-expressing sequence may be an internal ribosome entry sequence (IRES). The co-expressing sequence may be an internal promoter.
In an aspect, the present invention provides a vector which comprises a nucleic acid sequence or nucleic acid construct of the invention.
Such a vector may be used to introduce the nucleic acid sequence(s) or nucleic acid construct(s) into a host cell so that it expresses one or more chimeric protein(s) according to the first aspect of the invention and, optionally, one or more other proteins of interest (POI), for example a TCR or a CAR. The vector may, for example, be a plasmid or a viral vector, such as a retroviral vector or a lentiviral vector, or a transposon-based vector or synthetic mRNA.
The nucleic acids of the present invention may also be used for nucleic acid immunization and gene therapy, using standard gene delivery protocols. Methods for gene delivery are known in the art. See, e.g., U.S. Pat. Nos. 5,399,346, 5,580,859, 5,589,466, incorporated by reference herein in their entireties.
Vectors derived from retroviruses, such as the lentivirus, are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene or transgenes and its propagation in daughter cells. The vector may be capable of transfecting or transducing a lymphocyte including a T cell or an NK cell. The present invention also provides vectors in which a nucleic acid of the present invention is inserted. The expression of natural or synthetic nucleic acids encoding a chimeric protein, and optionally a TCR or CAR is typically achieved by operably linking a nucleic acid encoding the chimeric protein and TCR/CAR polypeptide or portions thereof to one or more promoters, and incorporating the construct into an expression vector.
Additional promoter elements, e.g., enhancers, regulate the frequency of transcriptional initiation. Typically, these are located in the region 30-110 bp upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well. The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the thymidine kinase (tk) promoter, the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline.
One example of a suitable promoter is the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto. Another example of a suitable promoter is Elongation Growth Factor-1α (EF-1α). However, other constitutive promoter sequences may also be used, including, but not limited to the simian virus 40 (SV40) early promoter, mouse mammary tumor virus (MMTV), human immunodeficiency virus (HIV) long terminal repeat (LTR) promoter, MoMuLV promoter, MSCV promoter, MND promoter, an avian leukemia virus promoter, an Epstein-Barr virus immediate early promoter, a Rous sarcoma virus promoter, as well as human gene promoters such as, but not limited to, the actin promoter, the myosin promoter, the hemoglobin promoter, and the creatine kinase promoter.
The vectors can be suitable for replication and integration in eukaryotic cells. Typical cloning vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence. Viral vector technology is well known in the art and is described, for example, in Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York), and in other virology and molecular biology manuals, see also, WO 01/96584; WO 01/29058; and U.S. Pat. No. 6,326,193). In some embodiments, the constructs expressed are as shown in SEQ ID NOS:32-65 and 67-79. In some embodiments the nucleic acids are multi-cistronic constructs that permit the expression of multiple transgenes (e.g., chimeric protein and a TCR and/or CAR etc.) under the control of a single promoter. In some embodiments, the transgenes (e.g., chimeric protein and a TCR and/or CAR etc.) are separated by a self-cleaving 2A peptide. Examples of 2A peptides useful in the nucleic acid constructs of the invention include F2A, P2A, T2A and E2A. In other embodiments of the invention, the nucleic acid construct of the invention is a multi-cistronic construct comprising two promoters; one promoter driving the expression of chimeric protein and the other promoter driving the expression of the TCR or CAR. In some embodiments, the dual promoter constructs of the invention are uni-directional. In other embodiments, the dual promoter constructs of the invention are bi-directional. In order to assess the expression of the chimeric protein polypeptide or portions thereof, the expression vector to be introduced into a cell can also contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of expressing cells from the population of cells sought to be transfected or transduced through viral vectors.
Prior to expansion and genetic modification, a source of cells (e.g., immune effector cells, e.g., T cells or NK cells) is obtained from a subject. The term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals). Examples of subjects include humans, dogs, cats, mice, rats, and transgenic species thereof. T cells can be obtained from a number of sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
In one aspect, T cells are isolated from peripheral blood lymphocytes by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLL™ gradient or by counterflow centrifugal elutriation.
In another aspect, Tumor infiltrating cells (TILs) are isolated and/or expanded from a tumor, for example by a fragmented, dissected, or enzyme digested tumor biopsy or mass.
A specific subpopulation of T cells, such as CD3+, CD28+, CD4+, CD8+, CD45RA+, and CD45RO+T cells, can be further isolated by positive or negative selection techniques. For example, in one aspect, T cells are isolated by incubation with anti-CD3/anti-CD28-conjugated beads, such as DYNABEADS® M-450 CD3/CD28 T, for a time period sufficient for positive selection of the desired T cells. In one aspect, the time period is about 30 minutes. In a further aspect, the time period ranges from 30 minutes to 36 hours or longer and all integer values there between. In a further aspect, the time period is at least 1, 2, 3, 4, 5, or 6 hours. In yet another preferred aspect, the time period is 10 to 24 hours. In one aspect, the incubation time period is 24 hours. Longer incubation times may be used to isolate T cells in any situation where there are few T cells as compared to other cell types, such in isolating tumor infiltrating lymphocytes (TIL) from tumor tissue or from immunocompromised individuals. Further, use of longer incubation times can increase the efficiency of capture of CD8+ T cells. Thus, by simply shortening or lengthening the time T cells are allowed to bind to the CD3/CD28 beads and/or by increasing or decreasing the ratio of beads to T cells (as described further herein), subpopulations of T cells can be preferentially selected for or against at culture initiation or at other time points during the process. Additionally, by increasing or decreasing the ratio of anti-CD3 and/or anti-CD28 antibodies on the beads or other surface, subpopulations of T cells can be preferentially selected for or against at culture initiation or at other desired time points. The skilled artisan would recognize that multiple rounds of selection can also be used in the context of this invention. In certain aspects, it may be desirable to perform the selection procedure and use“the “unselected” cells in the activation and expansion procwss. “Unselected” cells can also be subjected to further rounds of selection.
Enrichment of a T cell population by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells. One method is cell sorting and/or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected. For example, to enrich for CD4+ cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CD16, HLA-DR, and CD8. In certain aspects, it may be desirable to enrich for or positively select for regulatory T cells which typically express CD4+, CD25+, CD62Lhi, GITR+, CD137, PD1, TIM3, LAG-3, CD150 and FoxP3+. Alternatively, in certain aspects, T regulatory cells are depleted by anti-CD25 conjugated beads or other similar method of selection.
The methods described herein can include, e.g., selection of a specific subpopulation of immune effector cells, e.g., T cells, that are a T regulatory cell-depleted population, CD25+ depleted cells, using, e.g., a negative selection technique, e.g., described herein. Preferably, the population of T regulatory depleted cells contains less than 30%, 25%, 20%, 15%, 10%, 5%, 4%, 3%, 2%, 1% of CD25+ cells.
A specific subpopulation of chimeric protein effector cells that specifically bind to a target antigen can be enriched for by positive selection techniques. For example, in some embodiments, effector cells are enriched for by incubation with target antigen-conjugated beads for a time period sufficient for positive selection of the desired abTCR effector cells. In some embodiments, the time period is about 30 minutes. In some embodiments, the time period ranges from 30 minutes to 36 hours or longer (including all ranges between these values). In some embodiments, the time period is at least one, 2, 3, 4, 5, or 6 hours. In some embodiments, the time period is 10 to 24 hours. In some embodiments, the incubation time period is 24 hours. For isolation of effector cells present at low levels in the heterogeneous cell population, use of longer incubation times, such as 24 hours, can increase cell yield. Longer incubation times may be used to isolate effector cells in any situation where there are few effector cells as compared to other cell types. The skilled artisan would recognize that multiple rounds of selection can also be used in the context of this invention.
T cells for stimulation can also be frozen after a washing step. After the washing step that removes plasma and platelets, the cells may be suspended in a freezing solution. While many freezing solutions and parameters are known in the art and will be useful in this context, one method involves using PBS containing 20% DMSO and 8% human serum albumin, or culture media containing 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin and 7.5% DMSO, or 31.25% Plasmalyte-A, 31.25% Dextrose 5%, 0.45% NaCl, 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin, and 7.5% DMSO or other suitable cell freezing media containing for example, Hespan and PlasmaLyte A, the cells then are frozen to −80° C. at a rate of 1° per minute and stored in the vapor phase of a liquid nitrogen storage tank. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at −20° C. or in liquid nitrogen.
In embodiments described herein, the immune effector cell can be an allogeneic immune effector cell, e.g., T cell or NK cell.
A T cell described herein can be, e.g., engineered such that it does not express a functional HLA on its surface. For example, a T cell described herein, can be engineered such that cell surface expression HLA, e.g., HLA class 1 and/or HLA class II, is downregulated. In some aspects, downregulation of HLA may be accomplished by reducing or eliminating expression of beta-2 microglobulin (B2M).
In some embodiments, the T cell can lack a functional TCR and a functional HLA, e.g., HLA class I and/or HLA class II. Modified T cells that lack expression of a functional TCR and/or HLA can be obtained by any suitable means, including a knock out or knock down of one or more subunit of TCR or HLA. For example, the T cell can include a knock down of TCR and/or HLA using siRNA, shRNA, clustered regularly interspaced short palindromic repeats (CRISPR) transcription-activator like effector nuclease (TALEN), or zinc finger endonuclease (ZFN).
In some embodiments, the allogeneic cell can be a cell which does not expresses or expresses at low levels an inhibitory molecule, e.g. a cell engineered by any method described herein. For example, the cell can be a cell that does not express or expresses at low levels an inhibitory molecule, e.g., that can decrease the ability of a chimeric protein-expressing cell to mount an immune effector response. Examples of inhibitory molecules include PD1, PD-L1, PD-L2, CTLA4, TIM3, CEACAM (e.g., CEACAM-1, CEACAM-3 and/or CEACAM-5), LAGS, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4, CD80, CD86, B7-H3 (CD276), B7-H4 (VTCN1), HVEM (TNFRSF14 or CD270), KIR, A2aR, MHC class I, MHC class II, Ga19, adenosine, and TGFR beta. Inhibition of an inhibitory molecule, e.g., by inhibition at the DNA, RNA or protein level, can optimize a CAR-expressing cell performance. In embodiments, an inhibitory nucleic acid, e.g., an inhibitory nucleic acid, e.g., a dsRNA, e.g., an siRNA or shRNA, a clustered regularly interspaced short palindromic repeats (CRISPR), a transcription-activator like effector nuclease (TALEN), or a zinc finger endonuclease (ZFN), e.g., as described herein, can be used.
T cells may be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and U.S. Patent Application Publication No. 20060121005.
Generally, the T cells of the invention may be expanded by contact with a surface having attached thereto an agent that stimulates a CD3/TCR complex associated signal and a ligand that stimulates a costimulatory molecule on the surface of the T cells. In particular, T cell populations may be stimulated as described herein, such as by contact with an anti-CD3 antibody, or antigen-binding fragment thereof, or an anti-CD2 antibody immobilized on a surface, or by contact with a protein kinase C activator (e.g., bryostatin) in conjunction with a calcium ionophore. For co-stimulation of an accessory molecule on the surface of the T cells, a ligand that binds the accessory molecule is used. For example, a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells. To stimulate proliferation of either CD4+ T cells or CD8+ T cells, an anti-CD3 antibody and an anti-CD28 antibody can be used. Examples of an anti-CD28 antibody include 9.3, B-T3, XR-CD28 (Diaclone, Besancon, France) can be used as can other methods commonly known in the art (Berg et al., Transplant Proc. 30(8):3975-3977, 1998; Haanen et al., J. Exp. Med. 190(9):13191328, 1999; Garland et al., J. Immunol Meth. 227(1-2):53-63, 1999).
In some embodiments, expansion can be performed using flasks or containers, or gas-permeable containers known by those of skill in the art and can proceed for 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days, about 7 days to about 14 days, about 8 days to about 14 days, about 9 days to about 14 days, about 10 days to about 14 days, about 11 days to about 14 days, about 12 days to about 14 days, or about 13 days to about 14 days. In some embodiments, the second TIL expansion can proceed for about 14 days.
In some embodiments, the expansion can be performed using non-specific T-cell receptor stimulation in the presence of interleukin-2 (IL-2) or interleukin-15 (IL-15). The non-specific T-cell receptor stimulus can include, for example, an anti-CD3 antibody, such as about 30 ng/ml of OKT3, a mouse monoclonal anti-CD3 antibody (commercially available from Ortho-McNeil, Raritan, N.J. or Miltenyi Biotech, Auburn, Calif.) or UHCT-1 (commercially available from BioLegend, San Diego, Calif., USA). Chimeric protein cells can be expanded in vitro by including one or more antigens, including antigenic portions thereof, such as epitope(s), of a cancer, which can be optionally expressed from a vector, such as a human leukocyte antigen A2 (HLA-A2) binding peptide, e.g., 0.3.mu.M MART-1:26-35 (27L) or gp100:209-217 (210M), optionally in the presence of a T-cell growth factor, such as 300 IU/mL IL-2 or IL-15. Other suitable antigens may include, e.g., NY-ESO-1, TRP-1, TRP-2, tyrosinase cancer antigen, MAGE-A3, SSX-2, and VEGFR2, or antigenic portions thereof. Chimeric protein cells may also be rapidly expanded by re-stimulation with the same antigen(s) of the cancer pulsed onto HLA-A2-expressing antigen-presenting cells. Alternatively, the chimeric protein cells can be further stimulated with, e.g., example, irradiated, autologous lymphocytes or with irradiated HLA-A2+ allogeneic lymphocytes and IL-2. In some embodiments, the stimulation occurs as part of the expansion. In some embodiments, the expansion occurs in the presence of irradiated, autologous lymphocytes or with irradiated HLA-A2+ allogeneic lymphocytes and IL-2.
In some embodiments, the cell culture medium comprises IL-2. In some embodiments, the cell culture medium comprises about 1000 IU/mL, about 1500 IU/mL, about 2000 IU/mL, about 2500 IU/mL, about 3000 IU/mL, about 3500 IU/mL, about 4000 IU/mL, about 4500 IU/mL, about 5000 IU/mL, about 5500 IU/mL, about 6000 IU/mL, about 6500 IU/mL, about 7000 IU/mL, about 7500 IU/mL, or about 8000 IU/mL, or between 1000 and 2000 IU/mL, between 2000 and 3000 IU/mL, between 3000 and 4000 IU/mL, between 4000 and 5000 IU/mL, between 5000 and 6000 IU/mL, between 6000 and 7000 IU/mL, between 7000 and 8000 IU/mL, or between 8000 IU/mL of IL-2.
In some embodiments, the cell culture medium comprises OKT3 antibody. In some embodiments, the cell culture medium comprises about 0.1 ng/mL, about 0.5 ng/mL, about 1 ng/mL, about 2.5 ng/mL, about 5 ng/mL, about 7.5 ng/mL, about 10 ng/mL, about 15 ng/mL, about 20 ng/mL, about 25 ng/mL, about 30 ng/mL, about 35 ng/mL, about 40 ng/mL, about 50 ng/mL, about 60 ng/mL, about 70 ng/mL, about 80 ng/mL, about 90 ng/mL, about 100 ng/mL, about 200 ng/mL, about 500 ng/mL, about 1 μg/mL or between 0.1 ng/mL and 1 ng/mL, between 1 ng/mL and 5 ng/mL, between 5 ng/mL and 10 ng/mL, between 10 ng/mL and 20 ng/mL, between 20 ng/mL and 30 ng/mL, between 30 ng/mL and 40 ng/mL, between 40 ng/mL and 50 ng/mL, or between 50 ng/mL and 100 ng/mL of OKT3 antibody.
In some embodiments, a combination of IL-2, IL-7, IL-15, and/or IL-21 are employed as a combination during the expansion. In some embodiments, IL-2, IL-7, IL-15, and/or IL-21 as well as any combinations thereof can be included during the expansion. In some embodiments, a combination of IL-2, IL-15, and IL-21 are employed as a combination during the expansion. In some embodiments, IL-2, IL-15, and IL-21 as well as any combinations thereof can be included.
In some embodiments, the expansion can be conducted in a supplemented cell culture medium comprising IL-2, OKT-3, and antigen-presenting feeder cells.
In some embodiments, the expansion culture media comprises about 500 IU/mL of IL-15, about 400 IU/mL of IL-15, about 300 IU/mL of IL-15, about 200 IU/mL of IL-15, about 180 IU/mL of IL-15, about 160 IU/mL of IL-15, about 140 IU/mL of IL-15, about 120 IU/mL of IL-15, or about 100 IU/mL of IL-15, or about 500 IU/mL of IL-15 to about 100 IU/mL of IL-15, or about 400 IU/mL of IL-15 to about 100 IU/mL of IL-15 or about 300 IU/mL of IL-15 to about 100 IU/mL of IL-15 or about 200 IU/mL of IL-15, or about 180 IU/mL of IL-15.
In some embodiments, the expansion culture media comprises about 20 IU/mL of IL-21, about 15 IU/mL of IL-21, about 12 IU/mL of IL-21, about 10 IU/mL of IL-21, about 5 IU/mL of IL-21, about 4 IU/mL of IL-21, about 3 IU/mL of IL-21, about 2 IU/mL of IL-21, about 1 IU/mL of IL-21, or about 0.5 IU/mL of IL-21, or about 20 IU/mL of IL-21 to about 0.5 IU/mL of IL-21, or about 15 IU/mL of IL-21 to about 0.5 IU/mL of IL-21, or about 12 IU/mL of IL-21 to about 0.5 IU/mL of IL-21, or about 10 IU/mL of IL-21 to about 0.5 IU/mL of IL-21, or about 5 IU/mL of IL-21 to about 1 IU/mL of IL-21, or about 2 IU/mL of IL-21. In some embodiments, the cell culture medium comprises about 1 IU/mL of IL-21, or about 0.5 IU/mL of IL-21.
In some embodiments the antigen-presenting feeder cells (APCs) are PBMCs. In an embodiment, the ratio of chimeric protein cells to PBMCs and/or antigen-presenting cells in the expansion is about 1 to 25, about 1 to 50, about 1 to 100, about 1 to 125, about 1 to 150, about 1 to 175, about 1 to 200, about 1 to 225, about 1 to 250, about 1 to 275, about 1 to 300, about 1 to 325, about 1 to 350, about 1 to 375, about 1 to 400, or about 1 to 500, or between 1 to 50 and 1 to 300, or between 1 to 100 and 1 to 200.
In certain aspects, the primary stimulatory signal and the costimulatory signal for the T cell may be provided by different protocols. For example, the agents providing each signal may be in solution or coupled to a surface. When coupled to a surface, the agents may be coupled to the same surface (i.e., in “cis” formation) or to separate surfaces “i.e., in “trans” formation). Alternatively, one agent may be coupled to a surface and the other agent in solution. In one aspect, the agent providing the costimulatory signal is bound to a cell surface and the agent providing the primary activation signal is in solution or coupled to a surface. In certain aspects, both agents can be in solution. In one aspect, the agents may be in soluble form, and then cross-linked to a surface, such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents. In this regard, see for example, U.S. Patent Application Publication Nos. 20040101519 and 20060034810 for artificial antigen presenting cells (aAPCs) that are contemplated for use in activating and expanding T cells in the present invention.
In one aspect, the two agents are immobilized on beads, either on the same bead, i.e., “cis,” or to separate beads, i.e., “trans.” By way of example, the agent providing the primary activation signal is an anti-CD3 antibody or an antigen-binding fragment thereof and the agent providing the costimulatory signal is an anti-CD28 antibody or antigen-binding fragment thereof; and both agents are co-immobilized to the same bead in equivalent molecular amounts. In one aspect, a 1:1 ratio of each antibody bound to the beads for CD4+ T cell expansion and T cell growth is used. In certain aspects of the present invention, a ratio of anti CD3:CD28 antibodies bound to the beads is used such that an increase in T cell expansion is observed as compared to the expansion observed using a ratio of 1:1. In one particular aspect an increase of from about 1 to about 3 fold is observed as compared to the expansion observed using a ratio of 1:1. In one aspect, the ratio of CD3:CD28 antibody bound to the beads ranges from 100:1 to 1:100 and all integer values there between. In one aspect of the present invention, more anti-CD28 antibody is bound to the particles than anti-CD3 antibody, i.e., the ratio of CD3:CD28 is less than one. In certain aspects of the invention, the ratio of anti CD28 antibody to anti CD3 antibody bound to the beads is greater than 2:1. In one particular aspect, a 1:100 CD3:CD28 ratio of antibody bound to beads is used. In one aspect, a 1:75 CD3:CD28 ratio of antibody bound to beads is used. In a further aspect, a 1:50 CD3:CD28 ratio of antibody bound to beads is used. In one aspect, a 1:30 CD3:CD28 ratio of antibody bound to beads is used. In one preferred aspect, a 1:10 CD3:CD28 ratio of antibody bound to beads is used. In one aspect, a 1:3 CD3:CD28 ratio of antibody bound to the beads is used. In yet one aspect, a 3:1 CD3:CD28 ratio of antibody bound to the beads is used.
Ratios of particles to cells from 1:500 to 500:1 and any integer values in between may be used to stimulate T cells or other target cells. As those of ordinary skill in the art can readily appreciate, the ratio of particles to cells may depend on particle size relative to the target cell. For example, small sized beads could only bind a few cells, while larger beads could bind many. In certain aspects the ratio of cells to particles ranges from 1:100 to 100:1 and any integer values in-between and in further aspects the ratio comprises 1:9 to 9:1 and any integer values in between, can also be used to stimulate T cells. The ratio of anti-CD3- and anti-CD28-coupled particles to T cells that result in T cell stimulation can vary as noted above, however certain preferred values include 1:100, 1:50, 1:40, 1:30, 1:20, 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, and 15:1 with one preferred ratio being at least 1:1 particles per T cell. In one aspect, a ratio of particles to cells of 1:1 or less is used. In one particular aspect, a preferred particle: cell ratio is 1:5. In further aspects, the ratio of particles to cells can be varied depending on the day of stimulation. For example, in one aspect, the ratio of particles to cells is from 1:1 to 10:1 on the first day and additional particles are added to the cells every day or every other day thereafter for up to 10 days, at final ratios of from 1:1 to 1:10 (based on cell counts on the day of addition). In one particular aspect, the ratio of particles to cells is 1:1 on the first day of stimulation and adjusted to 1:5 on the third and fifth days of stimulation. In one aspect, particles are added on a daily or every other day basis to a final ratio of 1:1 on the first day, and 1:5 on the third and fifth days of stimulation. In one aspect, the ratio of particles to cells is 2:1 on the first day of stimulation and adjusted to 1:10 on the third and fifth days of stimulation. In one aspect, particles are added on a daily or every other day basis to a final ratio of 1:1 on the first day, and 1:10 on the third and fifth days of stimulation. One of skill in the art will appreciate that a variety of other ratios may be suitable for use in the present invention. In particular, ratios will vary depending on particle size and on cell size and type. In one aspect, the most typical ratios for use are in the neighborhood of 1:1, 2:1 and 3:1 on the first day.
In further aspects of the present invention, the cells, such as T cells, are combined with agent-coated beads, the beads and the cells are subsequently separated, and then the cells are cultured. In an alternative aspect, prior to culture, the agent-coated beads and cells are not separated but are cultured together. In a further aspect, the beads and cells are first concentrated by application of a force, such as a magnetic force, resulting in increased ligation of cell surface markers, thereby inducing cell stimulation.
Viral- and non-viral-based genetic engineering tools can be used to generate chimeric protein cells, including without limitation T cells, NK cells resulting in permanent or transient expression of therapeutic genes. Retrovirus-based gene delivery is a mature, well-characterized technology, which has been used to permanently integrate CARs into the host cell genome (Scholler J., e.g. Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci. Transl. Med. 2012; 4:132ra53; Rosenberg S. A. et al., Gene transfer into humans—immunotherapy of patients with advanced melanoma, using tumor-infiltrating lymphocytes modified by retroviral gene transduction. N. Engl. J. Med. 1990; 323:570-578)
Non-viral DNA transfection methods can also be used. For example, Singh et al describes use of the Sleeping Beauty (SB) transposon system developed to engineer CAR T cells (Singh H., et al., Redirecting specificity of T-cell populations for CD19 using the Sleeping Beauty system. Cancer Res. 2008; 68:2961-2971) and is being used in clinical trials (see e.g., ClinicalTrials.gov: NCT00968760 and NCT01653717). The same technology is applicable to engineer chimeric protein cells.
Multiple SB enzymes have been used to deliver transgenes. Mates describes a hyperactive transposase (SB100X) with approximately 100-fold enhancement in efficiency when compared to the first-generation transposase. SB100X supported 35-50% stable gene transfer in human CD34(+) cells enriched in hematopoietic stem or progenitor cells. (Mates L. et al., Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates. Nat. Genet. 2009; 41:753-761) and multiple transgenes can be delivered from multicistronic single plasmids (e.g., Thokala R. et al., Redirecting specificity of T cells using the Sleeping Beauty system to express chimeric antigen receptors by mix-and-matching of VL and VH domains targeting cD123+ tumors. PLoS ONE. 2016; 11:e0159477) or multiple plasmids (e.g., Hurton L. V. et al., Tethered IL-15 augments antitumor activity and promotes a stem-cell memory subset in tumor-specific T cells. Proc. Natl. Acad. Sci. USA. 2016; 113:E7788-E7797). Such systems are used with chimeric proteins of the invention.
Morita et al, describes the piggyBac transposon system to integrate larger transgenes (Morita D. et al., Enhanced expression of anti-CD19 chimeric antigen receptor in piggyBac transposon-engineered T cells. Mol. Ther. Methods Clin. Dev. 2017; 8:131-140) Nakazawa et al. describes use of the system to generate EBV-specific cytotoxic T-cells expressing HER2-specific chimeric antigen receptor (Nakazawa Y et al, PiggyBac-mediated cancer immunotherapy using EBV-specific cytotoxic T-cells expressing HER2-specific chimeric antigen receptor. Mol. Ther. 2011; 19:2133-2143). Manuri et al used the system to generate CD-19 specific T cells (Manuri P. V. R. et al., piggyBac transposon/transposase system to generate CD19-specific T cells for the treatment of B-lineage malignancies. Hum. Gene Ther. 2010; 21:427-437).
Transposon technology is easy and economical. One potential drawback is the longer expansion protocols currently employed may result in T cell differentiation, impaired activity and poor persistence of the infused cells. Monjezi et al describe development minicircle vectors that minimize these difficulties through higher efficiency integrations (Monjezi R. et al., Enhanced CAR T-cell engineering using non-viral Sleeping Beauty transposition from minicircle vectors. Leukemia. 2017; 31:186-194). These transposon technologies can be used for chimeric proteins of the invention.
The present invention also relates to a pharmaceutical composition containing a vector or a chimeric protein expressing cell of the invention together with a pharmaceutically acceptable carrier, diluent or excipient, and optionally one or more further pharmaceutically active polypeptides and/or compounds.
In some embodiments, a pharmaceutical composition is provided comprising a chimeric protein described above and a pharmaceutically acceptable carrier. In some embodiments, a pharmaceutical composition is provided comprising a nucleic acid encoding a chimeric protein according to any of the embodiments described above and a pharmaceutically acceptable carrier. In some embodiments, a pharmaceutical composition is provided comprising an effector cell expressing a chimeric protein described above and a pharmaceutically acceptable carrier. Such a formulation may, for example, be in a form suitable for intravenous infusion.
As used herein, by “pharmaceutically acceptable” or “pharmacologically compatible” is meant a material that is not biologically or otherwise undesirable, e.g., the material may be incorporated into a pharmaceutical composition administered to a patient without causing any significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the composition in which it is contained. Pharmaceutically acceptable carriers or excipients have preferably met the required standards of toxicological and manufacturing testing and/or are included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug administration.
An aspect of the invention provides a population of modified T cells expressing a recombinant chimeric protein. A suitable population may be produced by a method described above.
The population of modified T cells may be for use as a medicament. For example, a population of modified T cells as described herein may be used in cancer immunotherapy therapy, for example adoptive T cell therapy.
Other aspects of the invention provide the use of a population of modified T cells as described herein for the manufacture of a medicament for the treatment of cancer, a population of modified T cells as described herein for the treatment of cancer, and a method of treatment of cancer may comprise administering a population of modified T cells as described herein to an individual in need thereof.
The population of modified T cells may be autologous i.e. the modified T cells were originally obtained from the same individual to whom they are subsequently administered (i.e. the donor and recipient individual are the same). A suitable population of modified T cells for administration to the individual may be produced by a method comprising providing an initial population of T cells obtained from the individual, modifying the T cells to express a cAMP PDE or fragment thereof and an antigen receptor which binds specifically to cancer cells in the individual, and culturing the modified T cells.
The population of modified T cells may be allogeneic i.e. the modified T cells were originally obtained from a different individual to the individual to whom they are subsequently administered (i.e. the donor and recipient individual are different). The donor and recipient individuals may be HLA matched to avoid GVHD and other undesirable immune effects. A suitable population of modified T cells for administration to a recipient individual may be produced by a method comprising providing an initial population of T cells obtained from a donor individual, modifying the T cells to express a chimeric protein which binds specifically to cancer cells in the recipient individual, and culturing the modified T cells.
Following administration of the modified T cells, the recipient individual may exhibit a T cell mediated immune response against cancer cells in the recipient individual. This may have a beneficial effect on the cancer condition in the individual.
Cancer conditions may be characterized by the abnormal proliferation of malignant cancer cells and may include leukaemias, such as AML, CML, ALL and CLL, lymphomas, such as Hodgkin lymphoma, non-Hodgkin lymphoma and multiple myeloma, and solid cancers such as sarcomas, skin cancer, melanoma, bladder cancer, brain cancer, breast cancer, uterus cancer, ovary cancer, prostate cancer, lung cancer, colorectal cancer, cervical cancer, liver cancer, head and neck cancer, oesophageal cancer, pancreas cancer, renal cancer, adrenal cancer, stomach cancer, testicular cancer, cancer of the gall bladder and biliary tracts, thyroid cancer, thymus cancer, cancer of bone, and cerebral cancer, as well as cancer of unknown primary (CUP).
Cancer cells within an individual may be immunologically distinct from normal somatic cells in the individual (i.e. the cancerous tumor may be immunogenic). For example, the cancer cells may be capable of eliciting a systemic immune response in the individual against one or more antigens expressed by the cancer cells. The tumor antigens that elicit the immune response may be specific to cancer cells or may be shared by one or more normal cells in the individual.
An individual suitable for treatment as described above may be a mammal, such as a rodent (e.g. a guinea pig, a hamster, a rat, a mouse), murine (e.g. a mouse), canine (e.g. a dog), feline (e.g. a cat), equine (e.g. a horse), a primate, simian (e.g. a monkey or ape), a monkey (e.g. marmoset, baboon), an ape (e.g. gorilla, chimpanzee, orangutan, gibbon), or a human.
In preferred embodiments, the individual is a human. In other preferred embodiments, non-human mammals, especially mammals that are conventionally used as models for demonstrating therapeutic efficacy in humans (e.g. murine, primate, porcine, canine, or rabbit animals) may be employed.
The term “therapeutically effective amount” refers to an amount of a chimeric protein or composition comprising a chimeric protein as disclosed herein, effective to “treat” a disease or disorder in an individual. In the case of cancer, the therapeutically effective amount of a chimeric protein or composition comprising a chimeric protein as disclosed herein can reduce the number of cancer cells; reduce the tumor size or weight; inhibit (i.e., slow to some extent and preferably stop) cancer cell infiltration into peripheral organs; inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the cancer. To the extent a chimeric protein or composition comprising a chimeric protein as disclosed herein can prevent growth and/or kill existing cancer cells, it can be cytostatic and/or cytotoxic. In some embodiments, the therapeutically effective amount is a growth inhibitory amount. In some embodiments, the therapeutically effective amount is an amount that improves progression free survival of a patient. In the case of infectious disease, such as viral infection, the therapeutically effective amount of a chimeric protein or composition comprising a chimeric protein as disclosed herein can reduce the number of cells infected by the pathogen; reduce the production or release of pathogen-derived antigens; inhibit (i.e., slow to some extent and preferably stop) spread of the pathogen to uninfected cells; and/or relieve to some extent one or more symptoms associated with the infection. In some embodiments, the therapeutically effective amount is an amount that extends the survival of a patient.
Cells, including T and NK cells, expressing chimeric proteins for use in the methods of the present may either be created ex vivo either from a patient's own peripheral blood (autologous), or in the setting of a haematopoietic stem cell transplant from donor peripheral blood (allogenic), or peripheral blood from an unconnected donor (allogenic). Alternatively, T-cells or NK cells may be derived from ex-vivo differentiation of inducible progenitor cells or embryonic progenitor cells to T-cells or NK cells. In these instances, T-cells expressing a chimeric protein and, optionally, a CAR and/or TCR, are generated by introducing DNA or RNA coding for the chimeric protein and, optionally, a CAR and/or TCR, by one of many means including transduction with a viral vector, transfection with DNA or RNA.
T or NK cells expressing a chimeric protein of the present invention and, optionally, expressing a TCR and/or CAR may be used for the treatment of haematological cancers or solid tumors.
A method for the treatment of disease relates to the therapeutic use of a vector or cell, including a T or NK cell, of the invention. In this respect, the vector, or T or NK cell may be administered to a subject having an existing disease or condition in order to lessen, reduce or improve at least one symptom associated with the disease and/or to slow down, reduce or block the progression of the disease. The method of the invention may cause or promote T-cell mediated killing of cancer cells. The vector, or T or NK cell according to the present invention may be administered to a patient with one or more additional therapeutic agents. The one or more additional therapeutic agents can be co-administered to the patient. By “co-administering” is meant administering one or more additional therapeutic agents and the vector, or T or NK cell of the present invention sufficiently close in time such that the vector, or T or NK cell can enhance the effect of one or more additional therapeutic agents, or vice versa. In this regard, the vectors or cells can be administered first and the one or more additional therapeutic agents can be administered second, or vice versa. Alternatively, the vectors or cells and the one or more additional therapeutic agents can be administered simultaneously. One co-administered therapeutic agent that may be useful is IL-2, as this is currently used in existing cell therapies to boost the activity of administered cells. However, IL-2 treatment is associated with toxicity and tolerability issues.
In some embodiments, the addition of the engineered protein to a subject induces cytokine secretion. In some embodiments, the addition of CoStAR to a subject induces cytokine secretion. In some embodiments, the cytokine secretion lowers cytokine levels in the subject, including but not limited to IL-2. In some embodiments, the cytokine secretion following CoStAR exposure results in no detectable IL-2 in the subject. In some embodiments, the addition of the engineered protein to a subject reduces or eliminates the need for administration of exogenous IL-2. In some embodiments, the addition of the CoStAR to a subject reduces or eliminates the need for administration of exogenous IL-2.
In some embodiments, other mechanisms of action are involved in the killing of tumor cells apart from the direct effect of CoStAR. In some embodiments, secretion of cytokines and/or proliferation are evaluated. In some embodiments, tumor cell killing potency is characterized by flow cytometry to enumerate T cells and target cells and plate-based fluorescence or luminescence to measure percent killing. In some embodiments, cytokine secretion potency is characterized at the single cell level by flow cytometry and ELISA/MSD to characterize the population. In some embodiments, proliferation potency is determined by flow cytometry to characterize the population. In some embodiments, TIL potency may be determined by additional analytes, memory phenotype, cytotoxicity using cell lines, cytotoxicity using a patient specific tumor, a cytokine panel, cell proliferation and/or cellular composition.
As mentioned, for administration to a patient, the chimeric protein effector cells can be allogeneic or autologous to the patient. In some embodiments, allogeneic cells are further genetically modified, for example by gene editing, so as to minimize or prevent GVHD and/or a patient's immune response against the chimeric protein cells.
The chimeric protein effector cells are used to treat cancers and neoplastic diseases associated with a target antigen. Cancers and neoplastic diseases that may be treated using any of the methods described herein include tumors that are not vascularized, or not yet substantially vascularized, as well as vascularized tumors. The cancers may comprise non-solid tumors (such as hematological tumors, for example, leukemias and lymphomas) or may comprise solid tumors. Types of cancers to be treated with the chimeric protein effector cells of the invention include, but are not limited to, carcinoma, blastoma, and sarcoma, and certain leukemia or lymphoid malignancies, benign and malignant tumors, and malignancies e.g., sarcomas, carcinomas, and melanomas. Adult tumors/cancers and pediatric tumors/cancers are also included.
Hematologic cancers are cancers of the blood or bone marrow. Examples of hematological (or hematogenous) cancers include leukemias, including acute leukemias (such as acute lymphocytic leukemia, acute myelocytic leukemia, acute myelogenous leukemia and myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia), chronic leukemias (such as chronic myelocytic (granulocytic) leukemia, chronic myelogenous leukemia, and chronic lymphocytic leukemia), polycythemia vera, lymphoma, Hodgkin's disease, non-Hodgkin's lymphoma (indolent and high grade forms), multiple myeloma, plasmacytoma, Waldenstrom's macroglobulinemia, heavy chain disease, myelodysplastic syndrome, hairy cell leukemia and myelodysplasia.
Solid tumors are abnormal masses of tissue that usually do not contain cysts or liquid areas. Solid tumors can be benign or malignant. Different types of solid tumors are named for the type of cells that form them (such as sarcomas, carcinomas, and lymphomas). Examples of solid tumors, such as sarcomas and carcinomas, include adrenocortical carcinoma, cholangiocarcinoma, fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteosarcoma, and other sarcomas, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, stomach cancer, lymphoid malignancy, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer, hepatocellular carcinoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, thyroid cancer (e.g., medullary thyroid carcinoma and papillary thyroid carcinoma), pheochromocytomas sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, Wilms' tumor, cervical cancer (e.g., cervical carcinoma and pre-invasive cervical dysplasia), colorectal cancer, cancer of the anus, anal canal, or anorectum, vaginal cancer, cancer of the vulva (e.g., squamous cell carcinoma, intraepithelial carcinoma, adenocarcinoma, and fibrosarcoma), penile cancer, oropharyngeal cancer, esophageal cancer, head cancers (e.g., squamous cell carcinoma), neck cancers (e.g., squamous cell carcinoma), testicular cancer (e.g., seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, Leydig cell tumor, fibroma, fibroadenoma, adenomatoid tumors, and lipoma), bladder carcinoma, kidney cancer, melanoma, cancer of the uterus (e.g., endometrial carcinoma), urothelial cancers (e.g., squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma, ureter cancer, and urinary bladder cancer), and CNS tumors (such as a glioma (such as brainstem glioma and mixed gliomas), glioblastoma (also known as glioblastoma multiforme) astrocytoma, CNS lymphoma, germinoma, medulloblastoma, Schwannoma craniopharyogioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, neuroblastoma, retinoblastoma and brain metastases).
When “an immunologically effective amount,” “an anti-tumor effective amount,” “a tumor-inhibiting effective amount,” or “therapeutic amount” is indicated, the 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 the T cells described herein may be administered at a dosage of 104 to 109 cells/kg body weight, in some instances 105 to 106 cells/kg body weight, including all integer values within those ranges. 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).
A chimeric protein-expressing cell described herein may be used in combination with other known agents and therapie“. Administered” “in combination”, as used herein, means that two (or more) different treatments are delivered to the subject during the course of the subject's affliction with the disorder, e.g., the two or more treatments are delivered after the subject has been diagnosed with the disorder and before the disorder has been cured or eliminated or treatment has ceased for other reasons. In some embodiments, the delivery of one treatment is still occurring when the delivery of the second begins, so that there is overlap in terms of administration. This is sometimes referred to herein is “simultaneous” or “concurrent delivery”. In other embodiments, the delivery of one treatment ends before the delivery of the other treatment begins. In some embodiments of either case, the treatment is more effective because of combined administration. For example, the second treatment is more effective, e.g., an equivalent effect is seen with less of the second treatment, or the second treatment reduces symptoms to a greater extent, than would be seen if the second treatment were administered in the absence of the first treatment, or the analogous situation is seen with the first treatment. In some embodiments, delivery is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one treatment delivered in the absence of the other. The effect of the two treatments can be partially additive, wholly additive, or greater than additive. The delivery can be such that an effect of the first treatment delivered is still detectable when the second is delivered.
A chimeric protein-expressing cell described herein and the at least one additional therapeutic agent can be administered simultaneously, in the same or in separate compositions, or sequentially. For sequential administration, the CAR-expressing cell described herein can be administered first, and the additional agent can be administered second, or the order of administration can be reversed.
The chimeric protein therapy and/or other therapeutic agents, procedures or modalities can be administered during periods of active disorder, or during a period of remission or less active disease. The chimeric protein therapy can be administered before the other treatment, concurrently with the treatment, post-treatment, or during remission of the disorder.
When administered in combination, the therapy and the additional agent (e.g., second or third agent), or all, can be administered in an amount or dose that is higher, lower or the same than the amount or dosage of each agent used individually, e.g., as a monotherapy. In some embodiments, the administered amount or dosage of the chimeric protein therapy, the additional agent (e.g., second or third agent), or all, is lower (e.g., at least 20%, at least 30%, at least 40%, or at least 50%) than the amount or dosage of each agent used individually, e.g., as a monotherapy. In other embodiments, the amount or dosage of the chimeric protein therapy, the additional agent (e.g., second or third agent), or all, that results in a desired effect (e.g., treatment of cancer) is lower (e.g., at least 20%, at least 30%, at least 40%, or at least 50% lower) than the amount or dosage of each agent used individually, e.g., as a monotherapy, required to achieve the same therapeutic effect.
In further aspects, a chimeric protein-expressing cell described herein may be used in a treatment regimen in combination with surgery, chemotherapy, radiation, immunosuppressive agents, such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies, or other immunoablative agents such as CAMPATH, anti-CD3 antibodies or other antibody therapies, cytoxin, fludarabine, cyclosporin, FK506, rapamycin, mycophenolic acid, steroids, FR901228, cytokines, and irradiation, peptide vaccine, such as that described in Izumoto et al. 2008 J Neurosurg 108:963-971.
In certain instances, compounds of the present invention are combined with other therapeutic agents, such as other anti-cancer agents, anti-allergic agents, anti-nausea agents (or anti-emetics), pain relievers, cytoprotective agents, and combinations thereof.
In one embodiment, a chimeric protein-expressing cell described herein can be used in combination with a chemotherapeutic agent. Exemplary chemotherapeutic agents include an anthracycline (e.g., doxorubicin (e.g., liposomal doxorubicin)), a vinca alkaloid (e.g., vinblastine, vincristine, vindesine, vinorelbine), an alkylating agent (e.g., cy53acarbazineide, decarbazine, melphalan, ifosfamide, temozolomide), an immune cell antibody (e.g., alemtuzamab, gemtuzumab, rituximab, ofatumumab, tositumomab, brentuximab), an antimetabolite (including, e.g., folic acid antagonists, pyrimidine analogs, purine analogs and adenosine deaminase inhibitors (e.g., fludarabine)), an mTOR inhibitor, a TNFR glucocorticoid induced TNFR related protein (GITR) agonist, a proteasome inhibitor (e.g., aclacinomycin A, gliotoxin or bortezomib), an immunomodulator such as thalidomide or a thalidomide derivative (e.g., lenalidomide).
General Chemotherapeutic agents considered for use in combination therapies include busulfan (Myleran®), busulfan injection (Busulfex®), cladribine (Leustatin®), cyclophosphamide (Cytoxan® or Neosar®), cytarabine, cytosine arabinoside (Cytosar-U®), cytarabine liposome injection (DepoCyt®), daunorubicin hydrochloride (Cerubidine®), daunorubicin citrate liposome injection (DaunoXome®), dexamethasone, doxorubicin hydrochloride (Adriamycin®, Rubex®), etoposide (Vepesid®), fludarabine phosphate (Fludara®), hydroxyurea (Hydrea®), Idarubicin (Idamycin®), mitoxantrone (Novantrone®), Gemtuzumab Ozogamicin (Mylotarg®).
In embodiments, general chemotherapeutic agents considered for use in combination therapies include anastrozole (Arimidex®), bicalutamide (Casodex®), bleomycin sulfate (Blenoxane®), busulfan (Myleran®), busulfan injection (Busulfex®), capecitabine (Xeloda®), N4-pentoxycarbonyl-5-deoxy-5-fluorocytidine, carboplatin (Paraplatin®), carmustine (BiCNU®), chlorambucil (Leukeran®), cisplatin (Platinol®), cladribine (Leustatin®), cyclophosphamide (Cytoxan® or Neosar®), cytarabine, cytosine arabinoside (Cytosar-U®), cytarabine liposome injection (DepoCyt®), dacarbazine (DTIC-Dome®), dactinomycin (Actinomycin D, Cosmegan), daunorubicin hydrochloride (Cerubidine®), daunorubicin citrate liposome injection (DaunoXome®), dexamethasone, docetaxel (Taxotere®), doxorubicin hydrochloride (Adriamycin®, Rubex®), etoposide (Vepesid®), fludarabine phosphate (Fludara®), 5-fluorouracil (Adrucil®, Efudex®), flutamide (Eulexin®), tezacitibine, Gemcitabine (difluorodeoxycitidine), hydroxyurea (Hydrea®), Idarubicin (Idamycin®), ifosfamide (IFEX®), irinotecan (Camptosar®), L-asparaginase (ELSPAR®), leucovorin calcium, melphalan (Alkeran®), 6-mercaptopurine (Purinethol®), methotrexate (Folex®), mitoxantrone (Novantrone®), mylotarg, paclitaxel (Taxol®), phoenix (Yttrium90/MX-DTPA), pentostatin, polifeprosan 20 with carmustine implant (Gliadel®), tamoxifen citrate (Nolvadex®), teniposide (Vumon®), 6-thioguanine, thiotepa, tirapazamine (Tirazone®), topotecan hydrochloride for injection (Hycamptin®), vinblastine (Velban®), vincristine (Oncovin®), and vinorelbine (Navelbine®).
Treatments can be evaluated, for example, by tumor regression, tumor weight or size shrinkage, time to progression, duration of survival, progression free survival, overall response rate, duration of response, quality of life, protein expression and/or activity. Approaches to determining efficacy of the therapy can be employed, including for example, measurement of response through radiological imaging.
TCR Incorporated Antigen Agnostic Receptors (TIAARs)
Table 2 provides exemplary, non-limiting examples of components of TCR incorporated antigen agnostic receptors (TIAARs) of the invention. Table 3 shows exemplary arrangements of the components.
Constitutive Costimulatory Proteins
Table 4 provides exemplary, non-limiting examples of components of constitutive costimulatory proteins of the invention. Table 5 shows the exemplary arrangements of the components.
Inducible Costimulatory Receptors
Table 6 provides exemplary, non-limiting examples of inducible costimulatory receptors of the invention. Table 7 shows exemplary arrangements of the components.
The following sequences in the below table include complete components and are non-limiting. Components may include a signal peptide (SP), a TCR clustering domain (CD) and/or a signaling domain (SD). It will be understood that whereas certain proteins may comprise N-terminal signal peptides when expressed, those signal peptides are cleaved and may be imprecisely cleaved when the proteins are expressed, and that the resulting proteins from which signal peptides are removed comprise binding domains having variation of up to about five amino acids in the location of the N-terminal amino acid.
In some embodiments, any one or more of the arrangements below are contemplated:
Although the present invention and its advantages have been described in detail, it should be understood that various changes, substitutions and alterations can be made herein without departing from the spirit and scope of the invention as defined in the appended claims.
The present invention will be further illustrated in the following Examples which are given for illustration purposes only and are not intended to limit the invention in any way.
Coculture assay set up. T cells from 2 healthy donors were either modified to express the constructs tested or left non-transduced (NTD) at MOI 10. One day prior to coculture set up, effector T cells were thawed and resuspended at 1×106 cells/mL in T cell media (TCM) without IL2 and incubated overnight at 37° C. with 5% CO2. On the day of coculture, T cells (effectors) and Ba/F3-OKT3 targets were collected and counted using a ViCELL BLU as per manufacturer's instructions. T cells were then cocultured with B a/F3 OKT3 targets at the 10:1, 1:1 and 1:10 E:T (effector:target) ratios overnight. For the inducible costimulatory protein constructs tested (i.e., pIB1097 to pIB1102), an additional set of wells were setup to which 10 μg/mL pembrolizumab was added in addition to Ba/F3 OKT3 targets. Each condition was performed in duplicates. Unstimulated T cells served as negative controls. Two sets of each E:T ratio as well as the T cell only control plates were set up. Brefeldin A was added at 1:1000 dilution to one set of plates to assess cytokine production by intracellular cytokine staining (ICS) using a flow cytometer after overnight co-culture. The second set was incubated for 5 days following which T cell counts and activation marker expression (i.e., 41BB and CD69) was assessed by flow cytometry.
The invention includes modifying components of the TCR complex and associated signaling adaptors (such as, for example, in a TCR incorporated antigen agnostic receptor “TIAAR”), identifying transmembrane domains (TMDs) and modifications that enable constitutive activation of receptors (“constitutive”) and utilizing antibodies to induce activation of the receptor (“inducible”).
scFV targeting co-stimulatory or inhibitor receptors and ligands. The scFV are derived from antibodies targeting co-stimulatory or inhibitory molecules expressed on immune cells.
Cytokine production (Bcl-xL, IL2, IFNgamma and TNFalpha) from genetically modified and non-transduced T cells (NTD) after overnight stimulation with either Ba/F3 OKT3 targets or left unstimulated (i.e., T cells only) (
Proliferation (T cell counts from CD45+ (TIARR)) and activation marker expression (41BB from CD45+ and CD69 from CD45+) from genetically modified and non-transduced T cells (NTD) after 5-day co-culture with either Ba/F3 OKT3 targets or left unstimulated (i.e., T cells only) (
Cytokine production (Bcl-xL, IL2, IFNgamma and TNFalpha) from genetically modified and non-transduced T cells (NTD) after overnight stimulation with either Ba/F3 OKT3 targets or left unstimulated (i.e., T cells only) (
Proliferation (T cell counts from CD45+(LZ)) and activation marker expression (41BB from CD45+ and CD69 from CD45+) from genetically modified and non-transduced T cells (NTD) after 5-day co-culture with either Ba/F3 OKT3 targets or left unstimulated (i.e., T cells only) (
Cytokine production (Bcl-xL, IL2, IFNg and TNFa) from genetically modified and non-transduced T cells (NTD) after overnight stimulation with either Ba/F3 OKT3 targets or Ba/F3 OKT3 targets with 10 ug/mL pembrolizumab or left unstimulated (i.e., T cells only) (
Proliferation (T cell counts from CD45+(Inducible)) and activation marker expression (41BB from CD45+ and CD69 from CD45+) from genetically modified and non-transduced T cells (NTD) after 5-day co-culture with either Ba/F3 OKT3 targets or Ba/F3 OKT3 targets with 10 ug/mL pembrolizumab or left unstimulated (i.e., T cells only) (
An engineered protein having the sequence of SEQ ID NO: 166 will be transfected into a Tumor Infiltrating Lymphocyte (TIL) cell using standard procedures by incorporating vectors. This cell will then be used to generate a population of TIL cells expressing those proteins. The population will be derived through detecting expression of the protein on the surface of the cells transfected to express the two proteins, and selecting cells which are identified as expressing those proteins. Through this process, the population of cells will be enriched for those expressing the protein. Following enrichment, the TIL cells will be administered at a therapeutic amount to a patient as a therapeutic treatment for cancer.
Transduction of CoStAR Constructs into TIL Cells
CoStAR constructs were transduced into TIL cells from tumor digests. The efficiency of CEA or FOLR expression on tumor digests at Day 1 is as shown in
The efficiency of CEA or FOLR expression by Day 21 is as shown in
On day 1, the tumor digest was thawed (no stimulation) in media 1. There were a total of 15 tumor digests, and comprised pancreatic, CRC, NSCLC, ovarian, melanoma, and cervical tumors (
TCM base media: GMP/TCM media+25 mM HEPES+25 μM 2-Mercaptoethanol
Media 1: TCM base media+10% FBS, 1× Gentamycin/Amphotericin (500× stock)+50 ug/mL vancomycin+3000 IU/mL IL2
Media 2: TCM base media+10% FBS, 2× Gentamicin/Amphotericin B (500× stock)+100 ug/mL vancomycin+6000 IU/mL IL2
Media 3: TCM base media+8% human AB serum, 3000 IU/mL IL2
Day 1: Thaw frozen tumor digest
Day 3: TIL Transduction During Outgrowth
Day 4: TIL Second Transduction
Day 8: Outgrowth Feed
Day 10: Static REP
Day 15: Dynamic REP
Day 18: Dynamic REP Maintenance
Notes:
Day 21: Harvest
TIL cells expressing CoStAR constructs then underwent a screen to assess function. The results of this screen are as shown in
On day 1, TIL cells were thawed. On day 2, CoStAR-modified TILS were sorted, then ran on fortessa. On day 4, the media change was completed, and the cells were stained and ran on fortessa. On day 6, the TCM media was changed to exclude IL2. On day 7, the co-culture and serial stimulation assay was set up. As can be seen in
Methodology: TCM Media with IL2
To a bottle of 500 mL RPMI 1640, add: 50 mL FBS, 5 mL pen/strep, 5 mL HEPES, 500 uL 2-mercaptoethanol, and 1 uL/mL of IL-2 stock (3e6 U/mL). The final concentration of the media should be 3000 U/mL.
Day 1: Thaw TILS
Day 2: Sort CoStAR-modified TILS
Day 4: Complete media change
Day 6: Change to media without IL2
Day 7: Set up co-culture
TIL cells expressing CoStAR constructs then underwent a serial stimulation assay. The results of the stimulation assay are as shown in
Day 1:
Day 6, 13, 20, 27, and 34: Collect cells for cell count
Day 7, 14, 21, 28, and 35: re-stimulation of cells with targets
Having thus described in detail preferred embodiments of the present invention, it is to be understood that the invention defined by the above paragraphs is not to be limited to particular details set forth in the above description as many apparent variations thereof are possible without departing from the spirit or scope of the present invention.
This application claims the benefit of priority of PCT Patent Application Serial No. PCT/US2022/073741, filed Jul. 14, 2022, which claims priority to U.S. Provisional Application Ser. No. 63/222,916, filed Jul. 16, 2021, both of which are hereby expressly incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63222916 | Jul 2021 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US2022/073741 | Jul 2022 | US |
| Child | 17822251 | US |
