Patent Application
20250064853
The present invention relates to anti-CD84 antibodies and chimeric antigen receptors (CARs), and their use in therapy, in particular cancer therapy. The invention also relates to methods for determining CD84 levels in a sample and for identifying a subject suitable for treatment with an anti-CD84 antibody or CAR.
The human CD84 protein is a “cluster of differentiation” first identified in 1993. Sequencing of CD84 has identified it as a member of the Slam (Signaling Lymphocyte Activation Molecule) family.
The extracellular part of the CD84 receptor contains a non-canonical IgV distal domain and an IgC2g proximal domain, a structure common to all members of the SLAM family and similar to CD2. CD84 functions as an homophilic adhesion molecule; the receptor:ligand interaction involves the IgV domain and is independent of the cytoplastic domain and there are specific differences in the homophilic interfaces that prevent the binding of CD84 to other molecules of the SLAM family.
Human CD84 is expressed in various types of immune cells. Expression levels are heterogeneous depending on the cell type and its state of differentiation or activation. CD84 appears very early during haematopoietic differentiation in bone marrow progenitor cells and is expressed in most T and B cells, but with higher expression in memory T and B lymphocytes, follicular helper T cells and germinal centre B cells. Myeloid antigen-presenting cells, such as monocytes and monocyte-derived dendritic cells (DCs) are also positive for CD84. Granulocytes also express significant levels of CD84 with the highest expression on basophils and mast cells. Among all haematopoietic cells, platelets express the highest levels of CD84, which was initially proposed as an aggregation-induced signalling receptor implicated in stabilizing platelet-platelet interactions. However, studies with CD84-deficient mice indicate that it does not play a significant role in haemostatic and thrombotic function. CD84 expression is low in natural killer cells (NK) and absent in red blood cells.
CD84 signalling can activate or inhibit leukocyte function depending on the cell type and its stage of activation or differentiation. CD84-mediated signalling regulates diverse immunological processes, including T-cell cytokine secretion, natural killer-cell cytotoxicity, monocyte activation, autophagy, cognate T: B interactions and B-cell tolerance at the level of germinal centres.
Alterations in CD84 have been related to autoimmune disorders. For example, specific allelic variations in CD84 are associated with autoimmune diseases such as systemic lupus erythematosus and rheumatoid arthritis (RA). Typical treatment for such autoimmune diseases often involves disease-modifying anti-rheumatic drugs (DMARDS), which are not curative but stop or slow down symptoms and/or disease progression.
CD84 is expressed in certain cancers, in particular haematological malignancies, such as chronic lymphocytic leukaemia (CLL).
Haematological malignancies are often treated by chemotherapy or radiotherapy, which have known adverse side effects. Accordingly, there remains a significant need for improved treatments for haematological malignancies.
The inventors have determined that CD84 is overexpressed in a range of cancer cell lines derived from malignant haematological diseases, including Burkitt's lymphoma, acute myeloid leukaemia (AML), chronic myeloid leukaemia (CML), B-cell acute lymphoblastic leukaemia (B-ALL), T-cell acute lymphoblastic leukaemia (T-ALL) and histiocytic lymphoma.
The inventors have studied and developed a range of antibodies and chimeric antigen receptors (CARs) that bind CD84.
In particular, the inventors have characterised the cellular expression of the CARs and functionally characterised CAR-T cells, for example through determination of their proliferation, cytokine production and their cytotoxicity against a range of target cancer cell lines. Moreover, the inventors have demonstrated that chimeric antigen receptors of the present invention can induce cytotoxicity in cancer cells expressing CD84.
Accordingly, the present invention provides an antigen-binding domain comprising:
In some embodiments, the antigen-binding domain comprises:
Suitably, the antigen-binding domain is a CD84-binding domain.
In some embodiments, the antigen-binding domain is an scFv.
In another aspect, the invention provides an antibody comprising the antigen-binding domain of the invention.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising the antigen-binding domain of the invention.
Suitably, the antigen-binding domain, antibody or CAR of the invention binds to CD84.
In some embodiments, the CAR is an scFv CAR.
In some embodiments, the CAR comprises a CD8a or a CD28 transmembrane domain. In preferred embodiments, the CAR comprises a CD8a transmembrane domain.
The antigen-binding domain and the transmembrane domain may be connected by a spacer.
In some embodiments, the spacer comprises a CD8a hinge or a CD28 hinge. In preferred embodiments, the CAR comprises a CD8a hinge.
The CAR may comprise one or more, for example two or three, intracellular signalling domains. In preferred embodiments, the CAR comprises a CD3-zeta signalling domain.
The CAR may comprise one or more, for example two or three, co-stimulatory domains. In some embodiments, the CAR comprises one or more co-stimulatory domains selected from the group consisting of a 4-1BB co-stimulatory domain, a CD28 co-stimulatory domain, a OX40 co-stimulatory domain and an ICOS co-stimulatory domain.
In preferred embodiments, the CAR comprises a 4-1BB co-stimulatory domain. In some embodiments, the CAR comprises a CD28 co-stimulatory domain. In some embodiments, the CAR comprises an OX40 co-stimulatory domain. In some embodiments, the CAR comprises an ICOS co-stimulatory domain.
In preferred embodiments, the CAR comprises a 4-1BB co-stimulatory domain and a CD3-zeta signalling domain.
In preferred embodiments, the CAR comprises the antigen-binding domain of the invention, a CD8a transmembrane domain, a 4-1BB co-stimulatory domain and a CD3-zeta signalling domain.
In another aspect, the invention provides a polynucleotide comprising one or more nucleotide sequences encoding the antigen-binding domain, the antibody or the CAR of the invention.
In another aspect, the invention provides a vector comprising the polynucleotide of the invention.
In some embodiments, the vector is a viral vector. In some embodiments, the vector is a retroviral vector or lentiviral vector, preferably a lentiviral vector.
In another aspect, the invention provides a cell comprising the polynucleotide or the vector of the invention.
In another aspect, the invention provides a cell comprising the antigen-binding domain or the CAR of the invention.
The cell may comprise a further (second) CAR.
In another aspect, the invention provides a cell comprising a first CAR and a second CAR, wherein the first CAR is the CAR of the invention.
In another aspect, the invention provides a composition comprising a first cell and a second cell, wherein the first cell comprises a first CAR and the second cell comprises a second CAR, and wherein the first CAR is the CAR of the invention.
In some embodiments, the first CAR and the second CAR are different. In some embodiments, the first CAR and the second CAR bind to different antigens.
In another aspect, the invention provides a cell comprising a tandem CAR, wherein the tandem CAR comprises a first antigen-binding domain (e.g. scFv) and a second antigen-binding domain (e.g. scFv), and wherein the first antigen-binding domain (e.g. scFv) is the antigen-binding domain (e.g. scFv) of the invention.
In some embodiments, the first antigen-binding domain (e.g. scFv) and the second antigen-binding domain (e.g. scFv) are different. In some embodiments, the first antigen-binding domain (e.g. scFv) and the second antigen-binding domain (e.g. scFv) bind to different antigens.
In some embodiments, the second CAR is an anti-CD19 CAR, an anti-CD20 CAR or an anti-CD22 CAR (e.g. for the treatment of B-cell malignancies); an anti-CD33 CAR or an anti-CD123 CAR (e.g. for the treatment of AML); or an anti-CD7 CAR (e.g. for the treatment of T-ALL).
In some embodiments, the second antigen-binding domain (e.g. scFv) is an anti-CD19 antigen-binding domain (e.g. scFv), an anti-CD20 antigen-binding domain (e.g. scFv) or an anti-CD22 antigen-binding domain (e.g. scFv) (e.g. for the treatment of B-cell malignancies); an anti-CD33 antigen-binding domain (e.g. scFv) or an anti-CD123 antigen-binding domain (e.g. scFv) (e.g. for the treatment of AML); or an anti-CD7 antigen-binding domain (e.g. scFv) (e.g. for the treatment of T-ALL).
In some embodiments, the cell is a T cell or NK cell, preferably a T cell. In some embodiments, the T cell is an autologous or allogeneic T cell. In some embodiments, the NK cell is an autologous or allogeneic NK cell.
NK cells may, for example, be sourced from any suitable tissue sample, cell line or stem cell source. In some embodiments, the NK cell (preferably allogeneic NK cell) is from cord blood (CB), induced pluripotent stem cells (iPSCs), bone marrow (BM), human embryonic stem cells (hESCs), a cell line (e.g. NK92 or YT), or peripheral blood (PB) (e.g. autologous or allogeneic). Preferably, the NK cell is from CB.
In another aspect, the invention provides a pharmaceutical composition comprising the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector or the cell of the invention.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in therapy.
In some embodiments, the therapy is treatment of cancer.
In another aspect, the invention provides a method for treating a disease comprising administering the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention to a subject in need thereof.
In some embodiments, the disease is cancer.
In another aspect, the invention provides use of the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for the manufacture of a medicament.
In some embodiments, the medicament is for treating a disease, preferably cancer.
In preferred embodiments, the cancer is a haematological malignancy.
In preferred embodiments, the cancer cells express CD84, for example the haematological malignancy may be a CD84-expressing haematological malignancy.
In some embodiments, the cancer is selected from the group consisting of chronic lymphocytic leukaemia (CLL), B-cell lymphoma, diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, follicular lymphoma, mantle cell lymphoma, B-cell acute lymphoblastic leukaemia (B-ALL), acute myeloid leukaemia (AML), myelodysplastic syndrome, T-cell acute lymphoblastic leukaemia/lymphoma (T-ALL), chronic myeloproliferative syndrome, chronic myeloid leukaemia (CML), chronic myelomonocytic leukaemia, dendritic-cell neoplasm and histiocytic sarcoma.
In some embodiments, the cancer is selected from the group consisting of chronic lymphocytic leukaemia (CLL), diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, follicular lymphoma, mantle cell lymphoma, B-cell acute lymphoblastic leukaemia (B-ALL), T-cell acute lymphoblastic leukaemia/lymphoma (T-ALL), acute myeloid leukemia (AML) and histiocytic sarcoma.
In preferred embodiments, the cancer is selected from the group consisting of CLL, B-cell lymphoma, B-ALL, T-ALL and AML.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating AML.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating T-ALL.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating B-cell lymphoma.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating Burkitt's lymphoma.
In another aspect, the invention provides use of the antigen-binding domain or the antibody of the invention for determining CD84 expression level in a sample, optionally for analysing a CD84 expression level in a sample from a subject.
In another aspect, the invention provides a method for identifying a subject suitable for treatment with an anti-CD84 CAR or antibody, wherein the method comprises determining a CD84 expression level in a sample isolated from the subject, wherein the CD84 expression level is determined using the antigen-binding domain or the antibody of the invention.
In some embodiments, the sample is a blood sample.
The terms “comprising”, “comprises” and “comprised of” as used herein are synonymous with “including” or “includes”; or “containing” or “contains”, and are inclusive or open-ended and do not exclude additional, non-recited members, elements or steps. The terms “comprising”, “comprises” and “comprised of” also include the term “consisting of”.
CD84 (also known as LY9B and SLAMF5) is a membrane glycoprotein that is a member of the signalling lymphocyte activation molecule (SLAM) family, which itself is a subset of the larger CD2 cell-surface receptor subgroup of the Ig superfamily.
The extracellular part of the CD84 receptor contains a non-canonical IgV distal domain and an IgC2g proximal domain, a structure common to all members of the SLAM family. CD84 functions as an homophilic adhesion molecule and is expressed in numerous immune cell types. The receptor:ligand interaction involves the IgV domain and is independent of the cytoplastic domain. There are specific differences in the homophilic interfaces that prevent the binding of CD84 to other molecules of the SLAM family.
The inventors have determined that CD84 is overexpressed in a range of cell lines derived from malignant haematological diseases, including Burkitt's lymphoma, acute myeloid leukaemia (AML), chronic myeloid leukaemia (CML), B-cell acute lymphoblastic leukaemia (B-ALL), T-cell acute lymphoblastic leukaemia (T-ALL) and histiocytic lymphoma.
Studies have suggested that CD84 is overexpressed in chronic lymphocytic leukaemia (CLL).
An example amino acid sequence of CD84 is:
An antigen-binding domain may be a protein or peptide that possesses the ability to recognise and bind to an antigen. The antigen-binding domain includes any naturally occurring, synthetic, semi-synthetic or recombinantly produced binding partner for an antigen of interest.
Illustrative antigen-binding domains include antibodies or antibody fragments or derivatives, extracellular domains of receptors (e.g. TCRs), ligands for cell surface molecules/receptors, or receptor binding domains thereof.
In preferred embodiments, the antigen-binding domain is, or is derived from, an antibody. An antibody-derived domain can be a fragment of an antibody or a genetically engineered product of one or more fragments of the antibody, which fragment is involved in binding with the antigen. Examples include a variable region (Fv), a complementarity determining region (CDR), a Fab, a single chain variable fragment (scFv), a heavy chain variable region (VH), a light chain variable region (VL) and a camelid antibody (VHH).
The antigen-binding domain may be non-human (e.g. murine), chimeric, humanised or fully human.
In preferred embodiments, the antigen-binding domain is a single chain variable fragment (scFv). The scFv may be, for example, a murine, human or humanised scFv.
The term “complementarity determining region” (CDR) with regard to an antibody or antigen-binding fragment thereof refers to a highly variable loop in the variable region of the heavy chain or the light chain of an antibody. CDRs can interact with the antigen conformation and largely determine binding to the antigen (although some framework regions are known to be involved in binding). The heavy chain variable region and the light chain variable region each contain three CDRs.
“Heavy chain variable region” (VH) refers to the variable fragment of the heavy chain of an antibody that contains three CDRs interposed between flanking stretches known as framework regions, which are more highly conserved than the CDRs and form a scaffold to support the CDRs.
“Light chain variable region” (VL) refers to the variable fragment of the light chain of an antibody that contains three CDRs interposed between framework regions.
“Fv” refers to the smallest fragment of an antibody to bear the complete antigen-binding site. An Fv consists of the variable region of a single light chain bound to the variable region of a single heavy chain.
“Single chain variable fragment” (scFv) refers to an engineered antibody consisting of a light chain variable region (VL) and a heavy chain variable region (VH) connected to one another directly or via a peptide linker sequence.
The antigen-binding domain may specifically bind to the antigen, for example bind to the antigen but not bind to other peptides, or bind at a lower affinity to other peptides.
The binding affinity between two molecules (e.g. an antigen-binding domain and an antigen) may be quantified, for example, by determination of the dissociation constant (KD). The Kp can be determined by measurement of the kinetics of complex formation and dissociation between the antigen-binding domain and antigen, e.g. using a technique such as surface plasmon resonance (SPR). The rate constants corresponding to the association and the dissociation of a complex are referred to as the association rate constant ka (or kon) and dissociation rate constant kd (or koff), respectively. KD is related to ka and kd through the equation KD=kd/ka.
Suitably, the antigen-binding domain is a CD84-binding domain.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-NYWIN (SEQ ID NO: 1); CDR2-DIYPVSGTTNYNEKFKR (SEQ ID NO: 2); and CDR3-GTGRFAY (SEQ ID NO: 3); or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RASQSVSTSSYSYMH (SEQ ID NO: 4); CDR2-FASNLES (SEQ ID NO: 5); and CDR3-QHSWEIPYT (SEQ ID NO: 6); or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-NYWLG (SEQ ID NO: 7); CDR2-DIYPGGGYTNYIEKFKG (SEQ ID NO: 8); and CDR3-YEGGYYGNYDAMDY (SEQ ID NO: 9), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RASESVDNYGISFMN (SEQ ID NO: 10); CDR2-AASNQGS (SEQ ID NO: 11); and CDR3-QQSKAVPRT (SEQ ID NO: 12), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-GFTFSSYA (SEQ ID NO: 13); CDR2-ISGSGGST (SEQ ID NO: 14); and CDR3-AKWDCSDGRCYWAY (SEQ ID NO: 15), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-NIESKD (SEQ ID NO: 16); CDR2-DDA (SEQ ID NO: 17); and CDR3-QVWDSSSDHVV (SEQ ID NO: 18), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-GFTFSSYP (SEQ ID NO: 19); CDR2-ISYHGRNK (SEQ ID NO: 20); and CDR3-ARDRDATPGGTGVGNHGMAV (SEQ ID NO: 21), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-QSLLHSSGYNY (SEQ ID NO: 22); CDR2-MGS (SEQ ID NO: 23); and CDR3-MQGLQTPPT (SEQ ID NO: 24), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-GFTFSDNA (SEQ ID NO: 25); CDR2-ISGTGRTT (SEQ ID NO: 26); and CDR3-AKWDCSDGRCYWAY (SEQ ID NO: 27), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-QSLVYSDGDTY (SEQ ID NO: 28); CDR2-KVS (SEQ ID NO: 29); and CDR3-MQGTHWPPNT (SEQ ID NO: 30), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-TSGMGVG (SEQ ID NO: 31); CDR2-HIWWDDVKRYNPALKS (SEQ ID NO: 32); and CDR3-MRTSYYFDY (SEQ ID NO: 33), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RASENIFSSLA (SEQ ID NO: 34); CDR2-NAKTLAE (SEQ ID NO: 35); and CDR3-QHHYATPFT (SEQ ID NO: 36), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-SYWIN (SEQ ID NO: 37); CDR2-DIYLGSGSTNYNEKFKS (SEQ ID NO: 38); and CDR3-SGGYLGY (SEQ ID NO: 39), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RASQSVSTSSYSYMH (SEQ ID NO: 40); CDR2-FASNLES (SEQ ID NO: 41); and CDR3-QHSWEIPYT (SEQ ID NO: 42), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-NYWIG (SEQ ID NO: 43); CDR2-DIYPGGGYTNYNENFKG (SEQ ID NO: 44); and CDR3-STTYYSSYWCFDV (SEQ ID NO: 45), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-KSSQSLLNSGNQANYLA (SEQ ID NO: 46); CDR2-GASTRES (SEQ ID NO: 47); and CDR3-QNDHSYPFT (SEQ ID NO: 48), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-RYWMS (SEQ ID NO: 49); CDR2-EINPDSSTINYTPSLKD (SEQ ID NO: 50); and CDR3-PGPTVVATYWYFDV (SEQ ID NO: 51), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RSSQSIVHSNGNTYLE (SEQ ID NO: 52); CDR2-KVSSRFS (SEQ ID NO: 53); and CDR3-FQGSHVPRT (SEQ ID NO: 54), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-RYWIN (SEQ ID NO: 55); CDR2-DIYPGSGSTNYNEKFKS (SEQ ID NO: 56); and CDR3-DTTIAY (SEQ ID NO: 57), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RASQSVTTSRYSYMH (SEQ ID NO: 58); CDR2-FASNLES (SEQ ID NO: 59); and CDR3-QHSWEIPYT (SEQ ID NO: 60), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-GYNMN (SEQ ID NO: 131); CDR2-NIDPYYGGTNYNQKFKG (SEQ ID NO: 132); and CDR3-GLLSGSFPY (SEQ ID NO: 133), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RASENIYSYLA (SEQ ID NO: 134); CDR2-NAKTLAE (SEQ ID NO: 135); and CDR3-QHHYGSPLT (SEQ ID NO: 136), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-RSWMS (SEQ ID NO: 137); CDR2-EINPDSSTINYTPSLKD (SEQ ID NO: 138); and CDR3-FYDGYSIYWYFDV (SEQ ID NO: 139), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RSSQSIVHSNGDTYLE (SEQ ID NO: 140); CDR2-KVSNRFS (SEQ ID NO: 141); and CDR3-FQGSHVPRT (SEQ ID NO: 142), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-TSGMGVG (SEQ ID NO: 143); CDR2-HIWWDDVKRYNPALRS (SEQ ID NO: 144); and CDR3-IAVTYFFDF (SEQ ID NO: 145), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-RASENIFSSFA (SEQ ID NO: 146); CDR2-NARTLAE (SEQ ID NO: 147); and CDR3-QHHYASPFT (SEQ ID NO: 148), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-TSGMGVG (SEQ ID NO: 149); CDR2-HIWWDDVKRYNPALKS (SEQ ID NO: 150); and CDR3-MSTSYYFDY (SEQ ID NO: 151), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-KASQSLFTSVA (SEQ ID NO: 152); CDR2-SASYRYT (SEQ ID NO: 153); and CDR3-QQHYSSPFT (SEQ ID NO: 154), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a heavy chain variable region (VH) having complementarity determining regions (CDRs) with the sequences: CDR1-IYAMN (SEQ ID NO: 155); CDR2-RIRSKSNNYARFYADSVKD (SEQ ID NO: 156); and CDR3-PLRSYFSMDY (SEQ ID NO: 157), or variants thereof each having up to three amino acid substitutions, additions or deletions; and a light chain variable region (VL) having CDRs with the sequences: CDR1-KASENVDTYVS (SEQ ID NO: 158); CDR2-GASNRYT (SEQ ID NO: 159); and CDR3-GQTYSYPWT (SEQ ID NO: 160), or variants thereof each having up to three amino acid substitutions, additions or deletions.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 61; and a VL domain having the sequence of SEQ ID NO: 62 or 108, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 63; and a VL domain having the sequence of SEQ ID NO: 64 or 109, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 65; and a VL domain having the sequence of SEQ ID NO: 66, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 68; and a VL domain having the sequence of SEQ ID NO: 69, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 71; and a VL domain having the sequence of SEQ ID NO: 72, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 74; and a VL domain having the sequence of SEQ ID NO: 75, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 76; and a VL domain having the sequence of SEQ ID NO: 77, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 78; and a VL domain having the sequence of SEQ ID NO: 79, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 80; and a VL domain having the sequence of SEQ ID NO: 81, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 82; and a VL domain having the sequence of SEQ ID NO: 83, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 161; and a VL domain having the sequence of SEQ ID NO: 162, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 163; and a VL domain having the sequence of SEQ ID NO: 164, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 165; and a VL domain having the sequence of SEQ ID NO: 166, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 167; and a VL domain having the sequence of SEQ ID NO: 168, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In some embodiments, the antigen-binding domain comprises a VH domain having the sequence of SEQ ID NO: 169; and a VL domain having the sequence of SEQ ID NO: 170, or variants thereof each having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
The CD84-binding domain may be a scFv. A scFv may comprise the heavy variable region (VH) and light chain variable region (VL) of an antibody, connected with a short linker peptide, for example of about 10 to 25 amino acids. The scFv may be in the orientation (from N- to C-terminus) VH-VL or VL-VH. In some embodiments, the scFv is in the orientation (from N- to C-terminus) VH-VL. In some embodiments, the scFv is in the orientation (from N- to C-terminus) VL-VH.
Example linker sequences for connecting VH and VL domains include:
The antigen-binding domain may comprise or consist of the sequence of any one of SEQ ID NOs: 61, 63, 112-125 or 181-184, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
Suitably, the variant may bind to CD84 at least as well as the corresponding antigen-binding domain shown as SEQ ID NO: 61, 63, 112-125 or 181-184. For example, the variant may specifically bind to CD84 with a binding affinity which is at least equivalent to the binding affinity between the corresponding antigen-binding domain shown as SEQ ID NO: 61, 63, 112-125 or 181-184 and CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 61, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 63, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 112, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 113, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 114, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 115, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 116, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 117, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 118, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 119, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 120, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 121, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 122, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 123, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 124, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 125, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 181, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 182, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 183, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
In some embodiments, the antigen-binding domain comprises or consists of the sequence of SEQ ID NO: 184, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto, and preferably retaining the ability to bind to CD84.
The antigen-binding domain may be comprised in a chimeric antigen receptor (CAR).
“Chimeric antigen receptor” (CAR or CARs) as used herein refers to engineered receptors which can confer an antigen specificity onto cells (for example, T cells, such as naive T cells, central memory T cells, effector memory T cells or combinations thereof). CARs are also known as artificial T-cell receptors, chimeric T-cell receptors or chimeric immunoreceptors. CARs can also confer an antigen specificity onto other immune cells such as NK cells (e.g. from cord blood (CB), induced pluripotent stem cells (iPSCs), bone marrow (BM), human embryonic stem cells (hESCs), a cell line (e.g. NK92 or YT), or peripheral blood (PB) (Mehta et al. (2018) Front. Immunol. 9:283; Liu et al. (2020) N. Engl. J. Med. 382:545-553). CARs used in NK cells may have other transmembrane domains (such as NKG2D or DAP12) and other co-stimulatory domains (such as NKG2D or 2B4) and they may incorporate genes for IL-2 or IL-15 within the CAR construct to constantly provide cytokine support to the CAR-NK cells.
CARs may, for example, comprise an antigen-binding domain, a transmembrane domain and an intracellular signaling domain (endodomain).
In some embodiments, the CAR comprises a CD84-binding domain, a transmembrane domain and an intracellular signaling domain. The CAR may comprise one or more co-stimulatory domain.
The antigen-binding domain (e.g. CD84-binding domain) of the CAR may be an antigen-binding domain as disclosed herein.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of any one of SEQ ID NOs: 172-180, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
Suitably, the variant may function at least as well as the corresponding CAR shown as SEQ ID NO: 172-180. For example, the variant may specifically bind to CD84 with a binding affinity which is at least equivalent to the binding affinity between the corresponding CAR shown as SEQ ID NO: 172-180 and CD84.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 172, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 173, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 174, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 175, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 176, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 177, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 178, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 179, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
In another aspect, the invention provides a chimeric antigen receptor (CAR) comprising or consisting of the sequence of SEQ ID NO: 180, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
The CAR may comprise a transmembrane domain.
The transmembrane domain may comprise the transmembrane sequence from any protein which has a transmembrane domain, including any of the type I, type II or type III transmembrane proteins. The transmembrane domain of the CAR may also comprise an artificial hydrophobic sequence. The transmembrane domains of the CAR may be selected so as not to dimerise.
Examples of transmembrane (TM) regions used in CAR constructs are: a) the CD28 TM region (Pulè et al., Mol Ther, 2005 November; 12 (5): 933-41; Brentjens et al., CCR, 2007 September 15; 13 (18 Pt 1): 5426-35; Casucci et al., Blood, 2013 November 14; 122 (20): 3461-72.); b) the OX40 TM region (Pulè et al., Mol Ther, 2005 November; 12 (5): 933-41); c) the 4-1BB™ region (Brentjens et al, CCR, 2007 September 15; 13 (18 Pt 1): 5426-35); d) the CD3-zeta™ region (Pulè et al., Mol Ther, 2005 November; 12 (5): 933-41; Di Stasi et al. Blood, 2009 June 18; 113 (25): 6392-402.); e) the CD8a TM region (Maher et al., Nat Biotechnol, 2002 January; 20 (1): 70-5.; Imai C et al., Leukemia, 2004, April; 18 (4): 676-84; Brentjens et al., CCR, 2007 September 15; 13 (18 Pt 1): 5426-35; Milone et al., Mol Ther, 2009 August; 17 (8): 1453-64.); f) the DAP12 TM region (Müller, N. et al. J. Immunother. 2015 June 01; 38, 197); g) the 2B4 TM region (Altvater, B. et al. Clin. Cancer Res, 2009 July 22; (15) 4857-4866) and h) the NKG2D TM region (Li, Y et al, Cell Stem Cell, 2018 August 2; (23): 181-192).
Additional transmembrane domains will be apparent to those of skill in the art.
An example amino acid sequence of a CD8a transmembrane domain is:
An example amino acid sequence of a CD28 transmembrane domain is:
In some embodiments, the transmembrane domain comprises or consists of the sequence of SEQ ID NO: 127 or 128, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
The CAR may comprise a signal peptide such that when the CAR is expressed in a cell the protein is directed to the endoplasmic reticulum and subsequently to the cell surface.
Signal peptides may be recognised and cleaved by a signal peptidase during or after translocation to generate a mature protein.
In some embodiments, the signal peptide is a CD8a signal peptide.
The CAR may comprise a spacer that joins the antigen-binding domain to the transmembrane domain.
The spacer sequence may, for example, comprise an IgG1 Fc region, an IgG1 hinge or a human or mouse CD8 stalk.
In some embodiments, the CAR comprises a CD8a stalk.
The intracellular domain may provide for signal-transmission in a CAR.
The intracellular signalling domain may comprise one or more immunoreceptor tyrosine-based activation motif (ITAM), which is a conserved sequence of four amino acids repeated twice in the cytoplasmic tails of certain cell-surface proteins of the immune system. The motif contains a tyrosine separated from a leucine or isoleucine by any two other amino acids (YxxL/I). The tyrosine residues of these motifs may be phosphorylated following interaction of the receptor molecules with their ligands and may form binding sites for other proteins involved in signalling pathways.
The intracellular signalling domain may comprise or consist of the CD3-zeta endodomain, which contains three ITAMs. The CD3-zeta endodomain may transmit an activation signal to the T cell after the antigen is bound.
The CAR may comprise one or more co-stimulatory domain. For example, 4-1BB (also known as CD137) can be used with CD3-zeta, or CD28, OX40 and/or ICOS can be used with CD3-zeta to transmit a proliferative/survival signal. Also NKG2D, 2B4 (also known as CD244), DAP12 and/or DAP10 can be used with CD3-zeta to transmit a proliferative/survival signal.
In some embodiments, the CAR comprises a CD3-zeta signalling domain and lacks any co-stimulatory domains. In some embodiments, the CAR comprises a CD3-zeta signalling domain and one or more co-stimulatory domain.
In some embodiments, the CAR comprises one or more co-stimulatory domains selected from the group consisting of a 4-1BB co-stimulatory domain, a CD28 co-stimulatory domain and an OX40 co-stimulatory domain.
In preferred embodiments, the CAR comprises a 4-1BB co-stimulatory domain. In some embodiments, the CAR comprises a CD28 co-stimulatory domain. In some embodiments, the CAR comprises a OX40 co-stimulatory domain.
In preferred embodiments, the CAR comprises a 4-1BB co-stimulatory domain and a CD3-zeta signalling domain.
An example amino acid sequence of a CD3-zeta signalling domain is:
In some embodiments, the signalling domain comprises or consists of the sequence of SEQ ID NO: 129, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
An example amino acid sequence of a 4-1BB co-stimulatory domain is:
An example amino acid sequence of a CD28 co-stimulatory domain is:
In some embodiments, the co-stimulatory domain comprises or consists of the sequence of SEQ ID NO: 130 or 171, or a variant thereof having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, preferably at least 90%, sequence identity thereto.
Polynucleotides of the invention may comprise DNA or RNA, preferably DNA. They may be single-stranded or double-stranded. Preferably the polynucleotides are isolated polynucleotides. It will be understood by a skilled person that numerous different polynucleotides 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 of the invention to reflect the codon usage of any particular host organism in which the polypeptides of the invention are to be expressed.
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 lifespan of the polynucleotides of the invention.
Polynucleotides such as DNA polynucleotides may be produced recombinantly, synthetically or by any means available to those of skill in the art. They may also be cloned by standard techniques.
Longer polynucleotides will generally be produced using recombinant means, for example using polymerase chain reaction (PCR) cloning techniques. This will involve making a pair of primers (e.g. of about 15 to 30 nucleotides) flanking the target sequence which it is desired to clone, bringing the primers into contact with mRNA or cDNA obtained from an animal or human cell, performing a PCR under conditions which bring about amplification of the desired region, isolating the amplified fragment (e.g. by purifying the reaction mixture with an agarose gel) and recovering the amplified DNA. The primers may be designed to contain suitable restriction enzyme recognition sites so that the amplified DNA can be cloned into a suitable vector.
The polynucleotide may comprise a promoter and/or enhancer operably linked to the one or more nucleotide sequence encoding the antigen-binding domain, antibody or CAR of the invention. The term “operably linked”, as used herein, may mean that two components are linked together in a manner, which enables both to carry out their function substantially unhindered. For example, the promoter and/or enhancer may facilitate and/or enhance expression of the antigen-binding domain, antibody or CAR.
In some embodiments, the promoter is a EF1α promoter.
In some embodiments, the polynucleotide is a vector.
Preferably the vector is a viral vector, such as a retroviral vector, lentiviral vector, adeno-associated viral (AAV) vector or adenoviral vector. In some embodiments the polynucleotide is a viral genome.
In another aspect the invention provides a viral vector comprising the polynucleotide of the invention.
In some embodiments the viral vector is in the form of a viral vector particle.
A vector is a tool that allows or facilitates the transfer of an entity from one environment to another. In accordance with the invention, and by way of example, some vectors used in recombinant nucleic acid techniques allow entities, such as a segment of nucleic acid (e.g. a heterologous DNA segment, such as a heterologous cDNA segment), to be transferred into a target cell. The vector may serve the purpose of maintaining the heterologous nucleic acid (DNA or RNA) within the cell, facilitating the replication of the vector comprising a segment of nucleic acid and/or facilitating the expression of the protein encoded by a segment of nucleic acid.
Vectors comprising polynucleotides used in the invention may be introduced into cells using a variety of techniques known in the art, such as transfection, transduction and transformation.
Transfection may refer to a general process of incorporating a nucleic acid into a cell and includes a process using a non-viral vector to deliver a polynucleotide to a cell. Transduction may refer to a process of incorporating a nucleic acid into a cell using a viral vector.
A retroviral vector may be derived from or may be derivable from any suitable retrovirus. A large number of different retroviruses have been identified. Examples include murine leukaemia virus (MLV), human T-cell leukaemia virus (HTLV), mouse mammary tumour virus (MMTV), Rous sarcoma virus (RSV), Fujinami sarcoma virus (FuSV), Moloney murine leukaemia virus (Mo-MLV), FBR murine osteosarcoma virus (FBR MSV), Moloney murine sarcoma virus (Mo-MSV), Abelson murine leukaemia virus (A-MLV), avian myelocytomatosis virus-29 (MC29) and avian erythroblastosis virus (AEV). A detailed list of retroviruses may be found in Coffin, J. M. et al. (1997) Retroviruses, Cold Spring Harbour Laboratory Press, 758-63.
Retroviruses may be broadly divided into two categories, “simple” and “complex”. Retroviruses may be even further divided into seven groups. Five of these groups represent retroviruses with oncogenic potential. The remaining two groups are the lentiviruses and the spumaviruses.
The basic structures of retrovirus and lentivirus genomes share many common features such as a 5′ LTR and a 3′ LTR. Between or within these are located a packaging signal to enable the genome to be packaged, a primer-binding site, integration sites to enable integration into a host cell genome, and gag, pol and env genes encoding the packaging components—these are polypeptides required for the assembly of viral particles. Lentiviruses have additional features, such as rev and RRE sequences in HIV, which enable the efficient export of RNA transcripts of the integrated provirus from the nucleus to the cytoplasm of an infected target cell.
In the provirus, these genes are flanked at both ends by regions called long terminal repeats (LTRs). The LTRs are responsible for proviral integration and transcription. LTRs also serve as enhancer-promoter sequences and can control the expression of the viral genes.
The LTRs themselves are identical sequences that can be divided into three elements: U3, R and U5. U3 is derived from the sequence unique to the 3′ end of the RNA. R is derived from a sequence repeated at both ends of the RNA. U5 is derived from the sequence unique to the 5′ end of the RNA. The sizes of the three elements can vary considerably among different retroviruses.
In a defective retroviral vector genome gag, pol and env may be absent or not functional.
In a typical retroviral vector, at least part of one or more protein coding regions essential for replication may be removed from the virus. This makes the viral vector replication-defective.
Lentivirus vectors are part of the larger group of retroviral vectors. A detailed list of lentiviruses may be found in Coffin, J. M. et al. (1997) Retroviruses, Cold Spring Harbour Laboratory Press, 758-63. In brief, lentiviruses can be divided into primate and non-primate groups. Examples of primate lentiviruses include but are not limited to human immunodeficiency virus (HIV), the causative agent of human acquired immunodeficiency syndrome (AIDS); and simian immunodeficiency virus (SIV). Examples of non-primate lentiviruses include the prototype “slow virus” visna/maedi virus (VMV), as well as the related caprine arthritis-encephalitis virus (CAEV), equine infectious anaemia virus (EIAV), and the more recently described feline immunodeficiency virus (FIV) and bovine immunodeficiency virus (BIV).
The lentivirus family differs from retroviruses in that lentiviruses have the capability to infect both dividing and non-dividing cells (Lewis, P et al. (1992) EMBO J. 11:3053-8; Lewis, P. F. et al. (1994) J. Virol. 68:510-6). In contrast, other retroviruses, such as MLV, are unable to infect non-dividing or slowly dividing cells such as those that make up, for example, muscle, brain, lung and liver tissue.
A lentiviral vector, as used herein, is a vector, which comprises at least one component part derivable from a lentivirus. Preferably, that component part is involved in the biological mechanisms by which the vector infects cells, expresses genes or is replicated.
The lentiviral vector may be a “primate” vector. The lentiviral vector may be a “non-primate” vector (i.e. derived from a virus which does not primarily infect primates, especially humans). Examples of non-primate lentiviruses may be any member of the family of lentiviridae, which does not naturally infect a primate.
As examples of lentivirus-based vectors, HIV-1- and HIV-2-based vectors are described below.
The HIV-1 vector contains cis-acting elements that are also found in simple retroviruses. It has been shown that sequences that extend into the gag open reading frame are important for packaging of HIV-1. Therefore, HIV-1 vectors often contain the relevant portion of gag in which the translational initiation codon has been mutated. In addition, most HIV-1 vectors also contain a portion of the env gene that includes the RRE. Rev binds to RRE, which permits the transport of full-length or singly spliced mRNAs from the nucleus to the cytoplasm. In the absence of Rev and/or RRE, full-length HIV-1 RNAs accumulate in the nucleus. Alternatively, a constitutive transport element from certain simple retroviruses such as Mason-Pfizer monkey virus can be used to relieve the requirement for Rev and RRE. Efficient transcription from the HIV-1 LTR promoter requires the viral protein Tat.
Most HIV-2-based vectors are structurally very similar to HIV-1 vectors. Similar to HIV-1-based vectors, HIV-2 vectors also require RRE for efficient transport of the full-length or singly spliced viral RNAs.
Preferably, the viral vector used in the present invention has a minimal viral genome.
By “minimal viral genome” it is to be understood that the viral vector has been manipulated so as to remove the non-essential elements and to retain the essential elements in order to provide the required functionality to infect, transduce and deliver a nucleotide sequence of interest to a target host cell. Further details of this strategy can be found in WO 1998/017815.
Preferably, the plasmid vector used to produce the viral genome within a host cell/packaging cell will have sufficient lentiviral genetic information to allow packaging of an RNA genome, in the presence of packaging components, into a viral particle which is capable of infecting a target cell, but is incapable of independent replication to produce infectious viral particles within the final target cell. Preferably, the vector lacks a functional gag-pol and/or env gene and/or other genes essential for replication.
However, the plasmid vector used to produce the viral genome within a host cell/packaging cell will also include transcriptional regulatory control sequences operably linked to the lentiviral genome to direct transcription of the genome in a host cell/packaging cell. These regulatory sequences may be the natural sequences associated with the transcribed viral sequence (i.e. the 5′ U3 region), or they may be a heterologous promoter, such as another viral promoter (e.g. the CMV promoter).
The vectors may be self-inactivating (SIN) vectors in which the viral enhancer and promoter sequences have been deleted. SIN vectors can be generated and transduce non-dividing cells in vivo with an efficacy similar to that of wild-type vectors. The transcriptional inactivation of the long terminal repeat (LTR) in the SIN provirus should prevent mobilisation by replication-competent virus. This should also enable the regulated expression of genes from internal promoters by eliminating any cis-acting effects of the LTR.
The vectors may be integration-defective. Integration defective lentiviral vectors (IDLVs) can be produced, for example, either by packaging the vector with catalytically inactive integrase (such as an HIV integrase bearing the D64V mutation in the catalytic site; Naldini, L. et al. (1996) Science 272:263-7; Naldini, L. et al. (1996) Proc. Natl. Acad. Sci. USA 93:11382-8; Leavitt, A. D. et al. (1996) J. Virol. 70:721-8) or by modifying or deleting essential att sequences from the vector LTR (Nightingale, S. J. et al. (2006) Mol. Ther. 13:1121-32), or by a combination of the above.
In another aspect the invention provides a cell comprising the polynucleotide, the vector, the antigen-binding domain or the CAR of the invention.
In some embodiments the cell is a T cell, lymphocyte or stem cell, such as a hematopoietic stem cell, cord blood stem cell (CB) or induced pluripotent stem cell (iPSC).
For example, the cell may be selected from the group consisting of CD4 cells, CD8 cells, Th0 cells, Tc0 cells, Th1 cells, Tc1 cells, Th2 cells, Tc2 cells, Th17 cells, Th22 cells, gamma/delta T cells, natural killer (NK) cells, natural killer T (NKT) cells, double-negative T cells, naive T cells, memory stem T cells, central memory T cells, effector memory T cells, effector T cells, cytokine-induced killer (CIK) cells, hematopoietic stem cells and induced pluripotent stem cells (iPSC).
In some embodiments, the cell is a T cell or NK cell, preferably a T cell. In some embodiments, the T cell is an autologous or allogeneic T cell.
The cell may have been isolated from a subject.
The cell of the invention may be provided for use in adoptive cell transfer. As used herein the term “adoptive cell transfer” refers to the administration of a cell population to a patient. Typically, the cells are T cells isolated from a subject and then genetically modified and cultured in vitro before being administered to the patient.
Adoptive cell transfer may be allogenic or autologous.
By “autologous cell transfer” it is to be understood that the starting population of cells (which are then transduced with a polynucleotide or vector according to the invention) is obtained from the same subject as that to which the transduced cell population is administered. Autologous transfer is advantageous as it avoids problems associated with immunological incompatibility and is available to subjects irrespective of the availability of a genetically matched donor.
By “allogeneic cell transfer” it is to be understood that the starting population of cells (which are then transduced with a polynucleotide or vector according to the invention) is obtained from a different subject as that to which the transduced cell population is administered. Preferably, the donor will be genetically matched to the subject to which the cells are administered to minimise the risk of immunological incompatibility. Alternatively, the donor may be mismatched and unrelated to the patient.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in therapy.
In some embodiments, the therapy is treatment of cancer.
In preferred embodiments, the cancer is a haematological malignancy.
In preferred embodiments, the cancer cells express CD84, for example the haematological malignancy may be a CD84-expressing haematological malignancy.
In some embodiments, the cancer is selected from the group consisting of chronic lymphocytic leukaemia (CLL), B-cell lymphoma, diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, follicular lymphoma, mantle cell lymphoma, B-cell acute lymphoblastic leukaemia (B-ALL), acute myeloid leukaemia (AML), myelodysplastic syndrome, T-cell acute lymphoblastic leukaemia/lymphoma (T-ALL), chronic myeloproliferative syndrome, chronic myeloid leukaemia (CML), chronic myelomonocytic leukaemia, dendritic-cell neoplasm and histiocytic sarcoma.
In some embodiments, the cancer is selected from the group consisting of chronic lymphocytic leukaemia (CLL), diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, follicular lymphoma, mantle cell lymphoma, B-cell acute lymphoblastic leukaemia (B-ALL), T-cell acute lymphoblastic leukaemia/lymphoma (T-ALL), acute myeloid leukemia (AML) and histiocytic sarcoma.
In preferred embodiments, the cancer is selected from the group consisting of CLL, B-cell lymphoma, B-ALL, T-ALL and AML.
In preferred embodiments, the cancer is selected from the group consisting of B-cell lymphoma, B-ALL, T-ALL and AML.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating AML.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating T-ALL.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating B-cell lymphoma.
In another aspect, the invention provides the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention for use in treating Burkitt's lymphoma.
In some embodiments, the cancer is not a T-cell lymphoma. In some embodiments, the cancer is not a mature T-cell lymphoma. In some embodiments, the cancer is not CLL. In some embodiments, the cancer is not a solid tumour.
The treatment of mammals, particularly humans, is preferred. Both human and veterinary treatments are within the scope of the invention.
Although the agents for use in the invention can be administered alone, they will generally be administered in admixture with a pharmaceutical carrier, excipient or diluent, particularly for human therapy.
The medicaments, for example cells or vector particles, of the invention may be formulated into pharmaceutical compositions. These compositions may comprise, in addition to the medicament, a pharmaceutically acceptable carrier, diluent, excipient, buffer, stabiliser or other materials well known in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material may be determined by the skilled person according to the route of administration, e.g. intravenous or intra-arterial.
The pharmaceutical composition is typically in liquid form. Liquid pharmaceutical compositions generally include a liquid carrier such as water, petroleum, animal or vegetable oils, mineral oil or synthetic oil. Physiological saline solution, magnesium chloride, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol may be included. In some cases, a surfactant, such as pluronic acid (PF68) 0.001% may be used. In some cases, serum albumin may be used in the composition.
For injection, the active ingredient may be in the form of an aqueous solution, which is pyrogen-free, and has suitable pH, isotonicity and stability. The skilled person is well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection or Lactated Ringer's Injection. Preservatives, stabilisers, buffers, antioxidants and/or other additives may be included as required.
For delayed release, the medicament may be included in a pharmaceutical composition which is formulated for slow release, such as in microcapsules formed from biocompatible polymers or in liposomal carrier systems according to methods known in the art.
Handling of the cell therapy products is preferably performed in compliance with FACT-JACIE International Standards for cellular therapy.
In some embodiments, the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention is administered to a subject systemically.
In some embodiments, the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention is administered to a subject locally.
The term “systemic delivery” or “systemic administration” as used herein means that the agent of the invention is administered into the circulatory system, for example to achieve broad distribution of the agent. In contrast, topical or local administration restricts the delivery of the agent to a localised area.
In some embodiments, the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention is administered intravascularly, intravenously or intra-arterially.
In preferred embodiments, the antigen-binding domain, the antibody, the CAR, the polynucleotide, the vector, the cell or the pharmaceutical composition of the invention is administered intravenously.
The skilled person can readily determine an appropriate dose of an agent of the invention to administer to a subject. Typically, a physician will determine the actual dosage which will be most suitable for an individual patient and it will depend on a variety of factors including the activity of the specific compound employed, the metabolic stability and length of action of that compound, the age, body weight, general health, sex, diet, mode and time of administration, rate of excretion, drug combination, the severity of the particular condition, and the individual undergoing therapy. There can of course be individual instances where higher or lower dosage ranges are merited, and such are within the scope of the invention.
The term “subject” as used herein refers to either a human or non-human animal.
Examples of non-human animals include vertebrates, for example mammals, such as non-human primates (particularly higher primates), dogs, rodents (e.g. mice, rats or guinea pigs), pigs and cats. The non-human animal may be a companion animal.
Preferably, the subject is human.
In addition to the specific proteins and nucleotides mentioned herein, the invention also encompasses variants, derivatives, analogues, homologues and fragments thereof.
In the context of the invention, a “variant” of any given sequence is a sequence in which the specific sequence of residues (whether amino acid or nucleic acid residues) has been modified in such a manner that the polypeptide or polynucleotide in question retains at least one of its endogenous functions. A variant sequence can be obtained by addition, deletion, substitution, modification, replacement and/or variation of at least one residue present in the naturally occurring polypeptide or polynucleotide.
The term “derivative” as used herein in relation to proteins or polypeptides of the invention includes any substitution of, variation of, modification of, replacement of, deletion of and/or addition of one (or more) amino acid residues from or to the sequence, providing that the resultant protein or polypeptide retains at least one of its endogenous functions.
The term “analogue” as used herein in relation to polypeptides or polynucleotides includes any mimetic, that is, a chemical compound that possesses at least one of the endogenous functions of the polypeptides or polynucleotides, which it mimics.
Typically, amino acid substitutions may be made, for example from 1, 2 or 3, to 10 or 20 substitutions, provided that the modified sequence retains the required activity or ability. Amino acid substitutions may include the use of non-naturally occurring analogues.
Proteins used in the invention may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent protein. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues as long as the endogenous function is retained. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include asparagine, glutamine, serine, threonine and tyrosine.
Conservative substitutions may be made, for example according to the table below. Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other:
The term “homologue” as used herein means an entity having a certain homology with the wild type amino acid sequence or the wild type nucleotide sequence. The term “homology” can be equated with “identity”.
In the present context, a homologous sequence is taken to include an amino acid sequence which may be at least 50%, 55%, 65%, 75%, 85% or 90% identical, preferably at least 95%, 96% or 97% or 98% or 99% identical to the subject sequence. Typically, the homologues will comprise the same active sites etc. as the subject amino acid sequence. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of the present invention it is preferred to express homology in terms of sequence identity.
In the present context, a homologous sequence is taken to include a nucleotide sequence which may be at least 50%, 55%, 65%, 75%, 85% or 90% identical, preferably at least 95%, 96% or 97% or 98% or 99% identical to the subject sequence. Although homology can also be considered in terms of similarity, in the context of the present invention it is preferred to express homology in terms of sequence identity.
Preferably, reference to a sequence which has a percent identity to any one of the SEQ ID NOs detailed herein refers to a sequence which has the stated percent identity over the entire length of the SEQ ID NO referred to.
Homology comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate percent homology or identity between two or more sequences.
Percent homology may be calculated over contiguous sequences, i.e. one sequence is aligned with the other sequence and each amino acid or nucleotide in one sequence is directly compared with the corresponding amino acid or nucleotide in the other sequence, one residue at a time. This is called an “ungapped” alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues.
Although this is a very simple and consistent method, it fails to take into consideration that, for example, in an otherwise identical pair of sequences, one insertion or deletion in the amino acid or nucleotide sequence may cause the following residues or codons to be put out of alignment, thus potentially resulting in a large reduction in percent homology when a global alignment is performed. Consequently, most sequence comparison methods are designed to produce optimal alignments that take into consideration possible insertions and deletions without penalising unduly the overall homology score. This is achieved by inserting “gaps” in the sequence alignment to try to maximise local homology.
However, these more complex methods assign “gap penalties” to each gap that occurs in the alignment so that, for the same number of identical amino acids or nucleotides, a sequence alignment with as few gaps as possible, reflecting higher relatedness between the two compared sequences, will achieve a higher score than one with many gaps. “Affine gap costs” are typically used that charge a relatively high cost for the existence of a gap and a smaller penalty for each subsequent residue in the gap. This is the most commonly used gap scoring system. High gap penalties will of course produce optimised alignments with fewer gaps. Most alignment programs allow the gap penalties to be modified. However, it is preferred to use the default values when using such software for sequence comparisons. For example, when using the GCG Wisconsin Bestfit package the default gap penalty for amino acid sequences is −12 for a gap and −4 for each extension.
Calculation of maximum percent homology therefore firstly requires the production of an optimal alignment, taking into consideration gap penalties. A suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, USA; Devereux et al. (1984) Nucleic Acids Research 12:387). Examples of other software that can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al. (1999) ibid-Ch. 18), FASTA (Atschul et al. (1990) J. Mol. Biol. 403-410) and the GENEWORKS suite of comparison tools. Both BLAST and FASTA are available for offline and online searching (see Ausubel et al. (1999) ibid, pages 7-58 to 7-60). However, for some applications, it is preferred to use the GCG Bestfit program. Another tool, BLAST 2 Sequences, is also available for comparing protein and nucleotide sequences (FEMS Microbiol. Lett. (1999) 174:247-50; FEMS Microbiol. Lett. (1999) 177:187-8).
Although the final percent homology can be measured in terms of identity, the alignment process itself is typically not based on an all-or-nothing pair comparison. Instead, a scaled similarity score matrix is generally used that assigns scores to each pairwise comparison based on chemical similarity or evolutionary distance. An example of such a matrix commonly used is the BLOSUM62 matrix (the default matrix for the BLAST suite of programs). GCG
Wisconsin programs generally use either the public default values or a custom symbol comparison table if supplied (see the user manual for further details). For some applications, it is preferred to use the public default values for the GCG package, or in the case of other software, the default matrix, such as BLOSUM62.
Once the software has produced an optimal alignment, it is possible to calculate percent homology, preferably percent sequence identity. The software typically does this as part of the sequence comparison and generates a numerical result.
“Fragments” are also variants and the term typically refers to a selected region of the polypeptide or polynucleotide that is of interest either functionally or, for example, in an assay. “Fragment” thus refers to an amino acid or nucleic acid sequence that is a portion of a full-length polypeptide or polynucleotide.
Such variants may be prepared using standard recombinant DNA techniques such as site-directed mutagenesis. Where insertions are to be made, synthetic DNA encoding the insertion together with 5′ and 3′ flanking regions corresponding to the naturally-occurring sequence either side of the insertion site may be made. The flanking regions will contain convenient restriction sites corresponding to sites in the naturally-occurring sequence so that the sequence may be cut with the appropriate enzyme(s) and the synthetic DNA ligated into the cut. The DNA is then expressed in accordance with the invention to make the encoded protein. These methods are only illustrative of the numerous standard techniques known in the art for manipulation of DNA sequences and other known techniques may also be used.
The polynucleotides used in the invention may be codon-optimised. Codon optimisation has previously been described in WO 1999/41397 and WO 2001/79518. Different cells differ in their usage of particular codons. This codon bias corresponds to a bias in the relative abundance of particular tRNAs in the cell type. By altering the codons in the sequence so that they are tailored to match with the relative abundance of corresponding tRNAs, it is possible to increase expression. By the same token, it is possible to decrease expression by deliberately choosing codons for which the corresponding tRNAs are known to be rare in the particular cell type. Thus, an additional degree of translational control is available. Codon usage tables are known in the art for mammalian cells, as well as for a variety of other organisms.
The skilled person will understand that they can combine all features of the invention disclosed herein without departing from the scope of the invention as disclosed.
Preferred features and embodiments of the invention will now be described by way of non-limiting examples.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of chemistry, biochemistry, molecular biology, microbiology and immunology, which are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature. See, for example, Sambrook, J., Fritsch, E. F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press; Ausubel, F. M. et al. (1995 and periodic supplements) Current Protocols in Molecular Biology, Ch. 9, 13 and 16, John Wiley & Sons; Roe, B., Crabtree, J. and Kahn, A. (1996) DNA Isolation and Sequencing: Essential Techniques, John Wiley & Sons; Polak, J. M. and McGee, J.O′D. (1990) In Situ Hybridization: Principles and Practice, Oxford University Press; Gait, M. J. (1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press; and Lilley, D. M. and Dahlberg, J. E. (1992) Methods in Enzymology: DNA Structures Part A: Synthesis and Physical Analysis of DNA, Academic Press. Each of these general texts is herein incorporated by reference.
We have observed that CD84 is overexpressed in a range of malignant haematological diseases. Using GEPIA, an interactive web server for analysing the RNA sequencing expression data of 9,736 tumours and 8,587 normal samples from the TCGA and the GTEx projects (http://gepia.cancer-pku.cn/index.html; Tang et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017; 10.1093/nar/gkx247) we have found that:
We also interrogated the Cancer Cell Line Encyclopaedia (CCLE) dataset, which contains mRNA expression data for a panel of more than 1,100 cell lines derived from different types of solid and haematological tumours (https://portals.broadinstitute.org/ccle). Both RNAseq and Affymetrix analysis of mRNA expression showed that CD84 is expressed at high levels in cell lines derived from Burkitt's lymphoma, acute myeloid leukaemia (AML), B-cell lymphomas, chronic myeloid leukaemia (CML), B-cell acute lymphoblastic leukaemia (B-ALL) and T-cell acute lymphoblastic leukaemia (T-ALL), but not in T-cell lymphomas or solid tumours (
We then assessed the expression of CD84 on the surface of cell lines derived from different haematological malignancies. Table 1 shows the cell lines that were used, the haematological malignancy from which they originate and a qualitative assessment of CD84 expression based on the cytometry analysis shown in
We analysed the expression of CD84 in 9 samples from patients with CLL by flow cytometry. Table 2 shows a qualitative assessment of CD84 expression based on the cytometry analysis shown in
While certain genomic databases suggest that CD84 is overexpressed at mRNA level in AML, we sought to confirm if CD84 is expressed on the surface of malignant cells from patients (n=10) diagnosed with AML (Table 3).
Two representative examples of flow cytometry data are shown in
We studied and determined the sequences of two anti-CD84 mouse monoclonal antibodies (152-1D5 and 153-4D9; Engel et al. B-cell antigens section report, in Schlossman S (ed): Leucocyte Typing V. Oxford, UK, Oxford University Press, 1995, page 483; Palou et al. Genomic characterization of CD84 reveals the existence of five isoforms differing in their cytoplasmic domains. Tissue Antigens. 2000; 55 (2): 118-27).
In addition, we generated a number of new anti-CD84 mouse monoclonal antibodies as described in the Methods by immunizing BALB/c mice with the human CD84 protein. Table 3 summarizes the features of these antibodies, characterized as described in Methods. Binding to 300.19-CD84+, Raji and Ramos cells, lymphocytes and monocytes was carried out using hybridoma supernatants with equal amounts/concentration of anti-CD84 antibody.
The sequence corresponding to the variable region from the light chain (VL) and the sequence corresponding to the variable region from the heavy chain (VH) were determined from the different hybridomas using the Mouse Ig-Primer Set (Novagen). Sanger sequencing of this region was carried out by AbsoluteAntibody (United Kingdom). The antibody-sequence analysis was performed as follows: the complementarity-determining regions (CDR) and framework regions (FR) were identified using Abysis (sequences were defined by the Kabat-numbered scheme), IMGT and IgBLAST databases.
Table 5 shows the VH and VL sequence of these antibodies. The three CDRs in each sequence are highlighted in bold and underlined.
STSSYSYMH
WYQQKPGQPPKLLIKFASNL
NYNEKFKR
KATLTVDTSSSTGNMQLSSLA
ES
GVPARFSGSGSGTDFTLNIHPVEEEDT
DNYGISFMN
WFQQKPGQPPKLLIYAASNQ
NYIEKFKG
KATLTADTSSSTAYMQLSSLT
GS
GVPARFSGSGSGTDFSLNIHPMEEDDT
FSSLA
WYQQRQGKSPQLLVYNAKTLAEGV
KRYNPALKS
RLTISKDTSSSQVFLKIASV
STSSYSYMH
WYQQKPGQPPKLLIKFASNL
NYNEKFKS
KATLTVDTSSSSAYMQLSSLV
ES
GVPARFSGSGSGTDFTLNIHPVEEEDT
LNSGNQANYLA
WYQQKPGQPPKLLINGAS
NYNENFKG
KATLTADTSSSTAYMQLSSLT
TRES
GVPDRFTGSGSGTDFTLTISSVQAE
VHSNGNTYLE
WYLQKPGQSPKLLIYKVSS
NYTPSLKD
KFIISRDNAKNTLYLQMSKVR
RFS
GVPDRFSGSASGTDFTLKISRVEAED
TTSRYSYMH
WYQQKPGQPPKLLIKFASNL
NYNEKFKS
KATLTVDTSSSTAYMQLSRLA
ES
GVPARFSGSGSGTDFTLNIHPVEEEDT
YSYLA
WYQQKQGKSPQLLVYNAKTLAEGV
NYNQKFKG
KATLTVDKSSSTAYMQLKSLT
VHSNGDTYLE
WYLQKPGQSPKLLIYKVSN
NYTPSLKD
KFIISRDNAKNTLFLQMSKVR
RFS
GVPDRFSGSGSGTDFTLKISRVEAED
FSSFA
WYQQKRGRSPQLLVYNARTLAEGV
KRYNPALRS
RLTISKDTSSSQVELNIASV
FTSVA
WYQQKPGQSPKLLIYSASYRYTGV
KRYNPALKS
RLTISKDTSSSQVFLKIASV
DTYVS
WYQQKPEQSPKLLIYGASNRYTGV
ARFYADSVKD
RFTISRDDSQSMLYLQMNN
Human scFvs
Phage display screening was used to identify novel human scFvs that bind to CD84. Three different scFvs were identified (R3-B3, R3-G7 and R3-H3); the sequence of the CDR and FR in the variable domains of the heavy (VH) and light (VL) chains is shown in Table 6.
We engineered several anti-CD84 CAR constructs (CAR84). The complete CAR84 sequence was cloned into the third-generation lentiviral vector pCCL (Dull et al. A Third-Generation Lentivirus Vector with a Conditional Packaging System. J. Virol. 1998:72:8463-8471), including the signal peptide, the scFv specific for CD84, the CD8a hinge and transmembrane regions, the co-stimulatory domain 4-1BB and the signalling domain CD3-zeta, under the control of an EF1α promoter (
Different versions of the scFv domain were designed based on the antibodies described above. These scFv differ in the order of VH and VL sequences (with some versions having only the VH chain) and in the linker used between the VH and VL, which uses either three (S3) or four (S4) motifs (Gly-Gly-Gly-Gly-Ser). The name attributed to each CAR version reflects the design of the scFv. The sequences of the different scFv domains synthesized and cloned in the pCCL vector are listed in Table 7.
Complete CAR sequences are shown in Table 8.
Lentiviruses (LV) containing the different versions of the pCCL-EF1α-CD84 vectors were produced in HEK293-T cells and the number of transducing units was determined by the limiting dilution method. The lentiviruses were then used to transduce T cells isolated from whole blood. These CAR-T cells were then expanded for 6 to 8 days.
The following tables (Tables 9-11) summarize the number of T cells obtained after three different transductions for the different CARTs, as well as the percentage of these T cells that expressed the CD84 CAR on their surface.
The following CAR LVs did not lead to an efficient expansion of CAR-positive T cells: 152.1, 153.1, 153.2, B3.4 and B3.5. The 152.1 and 153.1 CARs were not used in further experiments.
To assess the ability of each CART cell to release cytokines, the supernatant of the effector-target cell co-cultures were collected. The CD84high cell line Ramos was used as the target cell at a 2:1 effector:target cell ratio. The levels of IFN-γ (
These results showed that CART cells with the R3-B3 scFv CAR binding domain lack cytokine release activity and therefore were not used in subsequent experiments. On the other hand, CART cells with the R3-H3 scFv CAR binding domain released a high amount of cytokines, with these two CART cells (H3.4 and H3.5) being the ones with the largest proinflammatory profile (based on TNF-α secretion), followed by CART cells with the 152-1D5 antibody CAR binding domain, which also show a high cytokine release profile. The 152-1D5 CART cells showed a similar profile independently of the scFv design (VH-VL order and linker length). CART cells based on the 153-4D9 and R3-G7 antibodies have a similar profile, with lower cytokine release in comparison to R3-H3 and 152-1D5 CART cells, except for 153.3 CART cells, which barely secrete cytokines.
To evaluate the efficacy of the CART84 cells in vitro, we performed cytotoxicity assays of each CART cell against several GFP-expressing target cell lines with different levels of CD84 expression and from both lymphoid (Ramos, NALM6 and MOLT-4 cell lines) and myeloid origin (K562 and MOLM-13 cell lines). CART cytotoxicity was assessed after a 24-hour co-culture by determining the percentage of live GFP-positive cells by cytometry. Effector:target cell ratios of 4:1, 2:1. 1:1 and 0.5:1 were tested.
First, we tested all the CARs against the CD84high Ramos cell line (
Next, we tested all the CARs against K562, a myeloid cell line with a low expression of CD84 (
Based on the cytotoxicity against Ramos and K562, we selected the following CART cells for additional characterization: 152.3, 153.4, 153.5, G7.5 and H3.5. We assessed the cytotoxicity of these CART cells at four effector:target ratios (4:1, 2:1, 1:1 and 0.5:1) against several cell lines after 24 and 48 hours of co-culture. Ramos is an aggressive B-cell lymphoma cell line (
As shown for the 2:1 ratio (
All the selected CARs showed cytotoxic activity against MOLM-13, with CARs based on 152.1D5 and 153.4D9 with a higher cytotoxic effect than those based on R3-G7 and R3-H3 antibodies (
CARs based on 152.1D5 and 153.4D9 antibodies showed a higher cytotoxic activity against NALM-6 cell line than CARs based on R3-G7 and R3-H3 scFv (
We assessed CD84 expression in the different cell populations of PBMCs by flow cytometry, and obtained results similar to what has been previously described. Monocytes show high CD84 expression, similar to that observed in the Ramos cell line. B cells display moderate CD84 expression. Both CD4 and CD8 T cells have two distinct subpopulations with regards to CD84 expression (positive and negative), with moderate CD84 expression levels on the positive population (
We assessed the cytotoxic activity of CD84 CART against PBMCs. For each experiment, both effector cells (i.e. the CART84 cells) and the target cells (PBMCs) were obtained from the same donor. The mean of three independent experiments of three different donors are shown. CART cells did not display statistically significant cytotoxic activity against their own PBMCs. However, these CART cells did show statistically significant cytotoxic activity against Ramos cells in a parallel experiment (
BALB/c mice were immunized three to four times, at 3-week intervals, with 300.19 cells stably transfected with the CD84 full-length DNA (de la Fuente M A et al. CD84 leukocyte antigen is a new member of the Ig superfamily. Blood. 1997; 15; 90 (6): 2398-405). The first intraperitoneal (i.p.) injection consisted of 20×106 cells in 300 μl PBS, the second consisted of 20×106 cells in 300 μl of PBS and the final injection consisted of 30×106 cells in 300 μl in PBS. Mice were euthanized on the third day after the final boost and the splenocytes were harvested to perform the cell fusion.
NS1 myeloma cells (European Collection of Cell Cultures, Salisbury, UK) were fused with spleen cells by incubating them at a ratio of 4:1 (splenocytes:NS1) at 37° C., centrifuging for 10 minutes at RT and adding 1 mL of warm PEG solution to the cell pellet while constantly swirling. Cells were slowly resuspended in RPMI culture medium, centrifuged and incubated at 37° C. in 5% CO2 in a humidified incubator.
Screening was carried out 10 days after fusion by analysing 50 μl of hybridoma supernatant by flow cytometry with 300.19-CD84 cells, using untransfected 300.19 cells as a negative control. Hybridomas that tested positive to 300.19-CD84 and negative to 300.19 cells were transferred to 24-well plates, grown until confluent and then transferred to T75 flasks. Single hybridoma clones producing antibodies of interest were then isolated by limited dilution. For each hybridoma, 10 single clones were retested by flow cytometry with 300.19-CD84 cells. The cloning protocol was repeated with one of the positive clones.
For each antibody, isotype (class and subclass) was determined by ELISA using anti-IgG coated plates to which the antibodies were added and then incubating the plates with an anti-mouse HRP antibody. To determine which of the two CD84 extracellular domains is recognized by the antibody, flow cytometry analysis was carried out with COS cells expressing a chimeric CD84 extracellular domain in which the domain 1 (D1) and 2 (D2) sequence is either human or murine.
Identification of Fully Human Anti-CD84 scFv
Human CD84 produced by mammalian cells (checked by SDS-PAGE;
For the biopanning rounds, tubes were coated with antigen, blocked, washed and incubated with the phage library. After washing, elution of phage binders was done with Glycine HCl followed by neutralization.
To determine the concentration of the eluted phages, these were added to E. coli TG1 cells which were then poured onto plates and cultured upside down. The calculation of PFU (plaque-forming units) was based on the number of plaques (i.e. dead TG1) on a plate.
To amplify the eluted phages, these were added to E. coli TG1 cells which were then infected by helper phage and culture. Phage precipitation was carried out with PEG/NaCl followed by resuspension and the amplified phages used in the next biopanning round of ELISA analysis.
This analysis showed significant enrichment over the rounds (Table 12) and since round 3 output already showed excellent enrichment, no additional biopanning rounds to prevent decrease in phage diversity.
Phages from round 3 were selected for monoclonal ELISA analysis. Single E. coli TG1 clones were picked and cultured with helper phage. Following centrifugation, supernatants containing phages were collected.
Plates were coated with either antigen or buffer, washed, blocked and washed again. Phages were then added to plates and incubated. Plates were washed and then an anti-phage horseradish peroxidase (HRP) antibody was added, followed by washing and incubation of TMB followed by HCl. Plates were read at 450 nm.
After sequencing of positive clones, 3 different unique sequences were identified. The 3 unique clones identified were then re-tested by ELISA to ensure clone specificity. All phages were tested at the same concentration. Plates were either covered with antigen (Ag) or with buffer (NC). The results clearly confirmed that the 3 clones specifically bind to the CD84 antigen (Table 13).
Healthy donor blood buffy-coats were obtained from the reference blood bank Banc de Sang i Teixits, Barcelona (Spain).
Ramos, Raji, NALM6, K562, MOLM-13, Kasumi-6, THP-1, and U937 were purchased from the American Type Culture Collection (ATCC). Ramos, Raji, NALM6, K562, NS1 and THP-1 cell lines were cultured in RPMI medium (ThermoFisher) supplemented with 10% foetal bovine serum (FBS, Merck) and penicillin-streptomycin (Labclinics), 300.19 cells were supplemented also with 1% L-glutamine (Gibco) and 0.1% 2-Beta-Mercaptoethanol (Sigma). The HEK293T and the COS cell line was cultured in DMEM medium (Gibco) supplemented with 10% FBS (Merck) and penicillin-streptomycin (Labclinics) and with 1% L-glutamine (Gibco). All cell lines were grown at 37° C. and 5% CO2.
HEK293-T cells were transfected with our transfer vector pCCL-EF1α-CD84 together with the packaging plasmids pRSV-Rev (Addgene, 12253), pMDLg/Prre (Addgene, 12251), and envelope plasmid pCMV-VSV-G (Addgene, 12259) using linear polyethylenimine (PEI, molecular weight 25000, Polysciences Inc 23966-1). Lentiviral supernatant was collected 48 hours later and concentrated with LentiX-Concentrator (Clontech, Takara) following the manufacturer's protocol. Concentrated lentivirus was stored at −80° C. until use.
The number of transducing units (TU/mL) was determined by the limiting dilution method.
HEK293T cells were seeded 24 h before transduction and 1:10 dilutions of the viral supernatant were prepared and added in DMEM medium (Gibco) supplemented with polybrene (Sigma-Aldrich) at 8 mg/mL. Cells were trypsinyzed 48 h later and labelled with AffiniPure F(ab′)2 fragment goat anti-mouse immunoglobulin G (IgG) allophycocyanin (APC)-conjugated (JacksonImmuno Research Laboratories, 115-136-072). A dilution corresponding to 2%-20% of positive cells was used to calculate viral titer.
T cells were isolated from whole blood during density gradient centrifugation with Ficoll-Paque™ by RosetteSep™ (RosetteSep Human T cell Enrichment cocktail from StemCell). T cells were cultured in X-Vivo 15 Serum Free Cell Medium (Lonza) supplemented with 5% AB human serum (Sigma H4522), penicillin-streptomycin (ThermoFisher, 100 mg/mL), and IL-2 at 50 IU/mL (Miltenyi). Cells were then activated using beads conjugated with CD3 and CD28 mAbs (Dynabeads Human T-Activator CD3/CD28 Gibco, 11131D). Twenty-four hours later they were transduced with the lentivirus in the presence of polybrene (Sigma-Aldrich) at 8 ug/mL. An expansion of 6 to 8 days was required before conducting the experiments.
CAR84 was detected with a recombinant CD84-His protein (R&D, 1855-CD) and a secondary His Tag APC-conjugated antibody (R&D, IC050A) and with a biotinSP-conjugated AffiniPure F(ab′)2-fragment goat-anti-mouse IgG (Jackson ImmunoResearch Laboratories, 115-065-072) or with a biotin SP-conjugated AffiniPure F(ab′)2-fragment goat-anti-human IgG (Jackson ImmunoResearch Laboratories, 109-065-006) with a BV421-conjugated streptavidin (BD Horizon, 563259). The following mAbs against human proteins were used: CD3-APC, CD4-PE-Cy7, CD4-Alexa Fluor-488, CD19-PE, CD8-APC-H7, PD-1-PE-Cy7, TIM-3-BB515, CD69-PerCP-Cy™5.5, LAG-3-BV-605, CD62L-FITC, CCR7-PerCP-Cy™5.5, CD84-PE, CD4-PE-Cy™7, CD45RA-APC (Becton Dickinson), CD84-APC and CD84-PE (BioLegend). Samples were run through the flow cytometer BD FACSCanto II (BD Biosciences), LSR II Fortessa 4L with HTS (BD), and Attune NxT 4L cytometer (ThermoFisher). For ELISA the following mAbs were used: an anti-mouse IgG-HRP (anti-mouse IgG-peroxidase antibody produced in goat, Sigma, cat: A3673-1ML) and an anti-mouse IgG coating (anti-mouse IgG antibody produced in goat (sigma, cat: M2650-1ML) Data were analysed using the FlowJo Software 10.7.1.
The cytotoxicity of CART cells was assessed using different effector:target ratios and at different time-points. Target cells used in these assays were modified with a lentiviral vector to over-express GFP-firefly luciferase (GFP-ffLuc) as previously described (Shah et al. Antigen Presenting Cell-Mediated Expansion of Human Umbilical Cord Blood Yields Log-Scale Expansion of Natural Killer Cells with Anti-Myeloma Activity. PLOS One. 2013; 8 (10)). The percentage of remaining alive GFP+ tumour cells was analysed by flow cytometry and calculated using the following formula: % of live cell =100×(number of GFP+ cells with T cells at time x/number of GFP+ cells alone at time x).
CART84 cell proliferation in response to CD84 antigen was measured using a CFSE assay (Castella, M. et al. (2019) Mol. Ther.-Methods Clin. Dev. 12:134-144). CART cells were stained with CellTrace CFSE (Invitrogen, ThermoFisher, 15598431) before being co-cultured with or without stimuli for 96 hours. Proliferation was analyzed by flow cytometry and proliferating index (PI) was calculated (PI=sum of number of cells in different generations/number of cells).
IFN-γ, TNF-α, IL-6, IL-1β cytokines were quantified by Enzyme-Linked ImmunoSorbent Assay (DuoSet ELISA, R&D systems) following manufacturer's protocol.
All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the disclosed antigen-binding domains, antibodies, chimeric antigen receptors, uses and methods of the invention will be apparent to the skilled person without departing from the scope and spirit of the invention. Although the invention has been disclosed in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the disclosed modes for carrying out the invention, which are obvious to the skilled person, are intended to be within the scope of the following claims.
We engineered several anti-CD84 CAR constructs based on the antibodies GYCD84.1-7, GYCD84.1-226 and GYCD84.3-89. The complete CAR84 sequence was cloned into the third-generation lentiviral vector pCCL (Dull et al. A Third-Generation Lentivirus Vector with a Conditional Packaging System. J. Virol. 1998:72:8463-8471), including the signal peptide, the scFv specific for CD84, the CD8a hinge and transmembrane regions, the co-stimulatory domain 4-1BB and the signalling domain CD3-Z, under the control of an EF1α promoter (
Two different scFv were designed based on the antibody GYCD84.1-7, differing in the order of VH and VL sequences. All these CARs contain a linker with four (S4) motifs (Gly-Gly-Gly-Gly-Ser). The name attributed to each CAR version reflects the design of the scFv. The sequences of the different scFv domains synthesized and cloned in the pCCL vector are listed in Table 14.
We analysed the expression of CD84 on the surface of leukemic cells from patients diagnosed with AML or with T-ALL by flow cytometry. Table 15 and 16 summarize the qualitative assessment of CD84 expression on AML and T-ALL cells, respectively. Two representative examples of flow cytometry analysis of primary leukemic cells of AML samples are shown in
Lentiviruses (LV) containing the CART84 1.7.3, 1.226.5 and 3.89.5 pCCL-EF1α-CD84 vectors were produced in HEK293-T cells and the number of transducing units per mL was determined by the limiting dilution method. The lentiviruses were used to transduce T cells isolated from whole blood and these CAR-T cells were then expanded for 6 to 8 days.
Table 17 summarizes the number of T cells obtained after three different transductions, as well as the percentage of T cells that expressed the CD84 CAR on their surface.
Expansion of CART84 1.7.3, 1.226.5 and 3.89.5, as well as further analysis of expansion of 152.3, 153.5 and H3.5, for 6-7 days after transduction is shown in
Based on the cytotoxicity results obtained against Ramos, K562, MOLM-13, NALM6 and MOLT-4 cells, CART84 152.3, 153.5 and H3.5 were selected for additional characterization and compared with 1.7.3 and 1.226.5 and 3.89.5. We assessed their cytotoxicity against Ramos, MOLM-13, U937 and MOLT-4 cells after 24-hour or 48-hour co-culture by determining the percentage of live GFP-positive cells by cytometry, at effector:target cell ratios of 4:1, 2:1, 1:1 and 0.5:1. CD84 expression on these cells is shown in
All CART84 exerted a high cytotoxic effect against Ramos cells (CD84high), which was statistically significant in comparison with UT (
Against MOLM-13 (CD84moderate) and U937 (CD84low) AML cells, CART84 152.3, 153.5, 1.7.3, 1.226.5 and 3.89.5 displayed a high cytotoxic effect, which was statistically significant in comparison with UT (
Finally, we assessed the cytotoxicity of CART84 152.3, 153.5, 1.7.5, 1.226.5 and 3.89.5 towards MOLT-4 cells (CD84high), observing the same pattern seen with U937 cells, i.e., all CART cells, except H3.5, exerted a high cytotoxic effect that increased over time, and which was statistically significant in comparison with UT (
We assessed the cytotoxicity of CART84 cells 152.3, 153.5, G7.5 and H.3.5 against primary AML cells from patient samples obtained from the Haematology Department of Hospital Clínic de Barcelona (HCB). CD84 expression was assessed on the primary blasts, which were then stained with CFSE and co-cultured with the effector cells (CART/UT) at effector:target cell ratios of 4:1, 2:1, 1:1 and 0.5:1 during 24 h and 48 h. After this period, cells were stained with LIVE/Dead™ Fixable Aqua to differentiate live/dead cells. CART cells 152.3 and 153.5 displayed the highest cytotoxic activity towards AML blasts, which was statistically significant in comparison with the effect of UT. CARTs H3.5 and G7.5 exerted a low cytotoxic effect. The cytotoxic effect induced by all CARTs increased over time (
We also assessed the cytotoxicity of CART84 cells 152.3, 153.5, 1.7.3, 1.226.5 and 3.89.5 against primary T-ALL patient samples obtained from the Haematology Department of Hospital Clínic de Barcelona (HCB). The experiment was carried out as described above for AML samples. Cytotoxicity of CARTs 152.3, 153.5 and 1.7.3 was higher than that of CARTs 1.226.5 and 3.89.5 (
To assess the ability of each CART cell to release cytokines, the supernatant of the effector-target cell co-cultures were collected. Ramos, MOLM-13 and MOLT-4 were used as the target cell at a 2:1 effector:target cell ratio. The levels of IFN-γ (
IFN-γ and granzyme B are cytotoxic cytokines, whereas TNF-α is a proinflammatory one. CART84 H3.5 displayed the highest cytokine production of all CART84 tested when co-cultured with Ramos. The cytokine profile of CART84 1.7.3 was similar to that of H3.5 after being co-cultured with MOLM-13 and MOLT-4 cells. All other CART cells tested produced similar levels of cytokines. These results suggest that both H3.5 and 1.7.3 CART cells may have tonic signaling, i.e. constitutive or chronic activation in the absence of the ligand.
To assess the ability of each CART84 cell to specifically proliferate upon antigen CD84 binding, CFSE proliferation assays were performed. Briefly, on day 0 CART cells were stained with CellTrace™ CFSE. Four conditions were tested: Cells (UT or CART cells) at day 0; cells alone cultured with media at day 4; cells stimulated with an unspecific stimulus of IL-2 (50 Ul/mL) at day 4; and cells stimulated with the specific antigen at day 4, that is, with MOLM-13 cells, at an effector:target ratio of 0.5:1. We were able to prove that CART84 152.3, 153.5 and 1.226.5 proliferated more when exposed to CD84 antigen than when incubated with medium only or with IL-2 (
CD84 is expressed on malignant cells from several haematological malignancies. Among these is AML, where CD84 expression is shared between myeloid leukemic blasts and, to a lower extent, haematopoietic progenitor stem cells (HPSC). The same occurs CD33 and CD123, both of which are targets for CART products in development for treatment of AML.
To assess the potential myelotoxicity of CART84, their cytotoxicity towards HPSC was examined on CD34+ HPSC obtained from two different sources: cord blood units (CBU, from BST) and the apheresis product from a healthy donor that had been mobilized with G-CSF for an allogeneic stem cell transplant (also from BST). CD34+ cells from the apheresis product represent the ideal model to study myelotoxicity; however, it is more common to use CD34+ cells from CBU to study this type of on-target/off-tumour toxicity
Purified CD34+ cells from CBU were co-cultured for 24 hours with CART84 152.3, 153.5, 1.7.3, 1.229 and 3.89.5 at an effector:target cell ratio of 4:1 and 2:1. CART84 152.3, 153.5, 1.7.3 and 1.226.5 displayed low to moderate cytotoxic activity against CD34+ cells from CBU, with that of CART84 3.89.5 being the highest.
For the cytotoxicity assays against CD34+ HPSC from the apheresis product, 3 different donor buffy coats were used to generate the CART84. Surprisingly, the cytotoxicity of CART84 against these cells was relatively low. Although CART cytotoxicity increased after 48 hours, so did that of UT, which is unspecific (
Since CD84 is expressed on T cells, we studied the potential CART84 toxicity towards them. T cells were isolated directly from donor whole blood; half of them were activated and transduced to generate CART cells, and the other half was cryopreserved until the CART cells were available (i.e., for 6-7 days). T cells were stained with CFSE and then, co-cultured with the CART84.
To further understand which specific T-cell fraction was being targeted by CART84, the effect on the following T-cell subsets was analyzed: naïve, central-memory, effector-memory, and effector CD4/CD8 T cells. The different T-cell subpopulations were studied by flow cytometry on: 1) target T cells before the assay and 2) on surviving T cells after co-culture with the different CART84 as indicated in
The efficacy of several CART84 cells was tested in three different experiments in NOD scid gamma (NSG) immunodeficient mice using MOLM-13 AML cells, modified to express GFP-firefly Luciferase (GFPffLuc). The CART84 with the best in vitro efficacy and safety profile were selected for testing in vivo: 152.3, 153.5, H3.5, 1.7.3 and 1.226.5.
In the first and second experiments, 1×106 or 0.25×106 MOLM-13 GFP-ffLuc cells were intravenously (i.v.) injected into NSG mice at day 0, respectively (
In the experiment shown in
The bone marrow and the spleen of mice euthanized at experiment endpoint were collected and analysed by flow cytometry in order to quantify the presence of tumour cells (MOLM-13-GFPffLuc), human CD3+ T cells or CART cells. In both experiments, CART84-treated mice had a significantly lower number of tumour cells in both bone marrow and spleen when compared to UT-treated mice (
In summary, 152.3 and 153.5 were able to consistently control AML disease progression and increased survival of treated animals.
The efficacy of CART84 cells was tested in two different experiments in NOD scid gamma (NSG) mice using MOLT-4 T-ALL cells modified to express GFP-ffLuc. The following CART84 were tested: 152.3, 153.5, 1.7.3 and 1.226.5.
In the experiment shown in
In the experiment shown in
The bone marrow and spleen of mice euthanized at the experiment endpoint were analysed by flow cytometry to quantify the presence of tumour cells (MOLT-4), human CD3+ T cells and CART cells. In this case, there were no statistically significant differences in the number of tumour cells found in the bone marrow and spleen of animals from different groups (
CART84 152.3 and 153.5 were the most efficacious in terms of controlling T-ALL disease and prolonging survival in both T-ALL experiments.
To assess potential on-target/off-tumor toxicity, human primary cells were studied for CD84 expression and afterwards, the potential cytotoxic effect induced by CART84. The following human cells were studied: human coronary artery endothelial cells (HCAEC), human small airway epithelial cells (HsaEpC), human cardiac myocytes (HCM), human renal epithelial cells (HREpC) and human uterine fibroblasts (HUF). Using flow cytometry, we were able to prove that CD84 is not expressed on the surface of these cells (
In XCELLigence assays, we found that CART84 152.3 and 153.5 were not cytotoxic towards HsaEpC, HCM, HREpC nor HUF. However, some cytotoxic effect was observed towards HCAEC, despite their lack of CD84 expression, suggesting that this effect is not antigen-specific. In order to confirm this, we compared the cytotoxic activity of CART84 with that of a CART that targets CD123, since this antigen is expressed on the surface of endothelial cells. Cytotoxicity induced by the CD123-directed CART cells was significantly higher than that induced by CART84 152.3 or 153.5 (
We engineered an anti-CD123 CAR construct based on the IL3scfv-IgG4 (L235E)-CD28gg-zeta (26292) CAR from US 2014/0271582. The CAR sequence was cloned into the third-generation lentiviral vector pCCL (Dull et al. A Third-Generation Lentivirus Vector with a Conditional Packaging System. J. Virol. 1998:72:8463-8471), including the signal peptide (GMCSFR alpha), the 26292 scFv (VH-linker-VL), the IgG4-Fc hinge and the CD28-transmembrane region, the co-stimulatory domain CD28 and the signaling domain CD3-4, under the control of an EF1α promoter.
The positive CAR fraction of T cells was detected with Biotin-SP (long spacer) AffiniPure Goat Anti-Mouse IgG, F(ab′)2 fragment goat-anti-mouse IgG (Jackson ImmunoResearch) or with a biotin SP-conjugated AffiniPure F(ab′)2-fragment goat-anti-human IgG (Jackson ImmunoResearch), washed and then incubated with a BV421/PE-conjugated streptavidin (eBioscience) and with the antibodies required to study each panel of proteins as described below.
The following mAbs against human proteins were used to study CAR T-cell phenotype: CD197-BV510 (CCR7), CD62L-FITC, CD4-Pecy7, CD8-APCH7, CD45RA-APC, (Becton Dickinson).
The following mAbs against human proteins were used to study the different population cells present in AML/T-ALL samples: CD11-APC, CD19-Fitc, HLA-DR-A450, CD45-PerCPCy5.5, CD34-PerCPCy5.5, CD3-APC, CD3-APCH7, CD33-Fitc, CD14-Fitc, CD14-APCH7, CD13-PE, CD13-BV421 (Becton Dickinson), CD84-APC, CD84-PE (BioLegend), CD45-A750, CD117-PeCy7 (Beckman Coulter), CD123-PECy7 (eBiosciences).
The following mAbs against human proteins were used to study the different population of mononuclear cells present in peripheral blood: CD3-BV421, CD14-APCH7, CD19-FITC, CD33-APC, CD34-PerCPCy5.5, CD38-APC, CD84-PE (BioLegend), CD123-PECy7 (eBiosciences) and HLA-DR-BV450 (Becton Dickinson)
The following mAbs against proteins were used in the in vivo experiments carried out in the MOLM-13 model: anti-human CD3-APCH7, anti-human CD33-APC, anti-human CD45-PerCP-Cy5.5, anti-mouse CD45-PECy7, Streptavidin-BV421 (Becton Dickinson). The following mAbs against proteins were used in the in vivo experiments carried out in the MOLT-4 model: anti-human CD3-APC, anti-human CD45-PerCP-Cy5.5, anti-mouse CD45 Pe-Cy7, Streptavidin-BV421 (Becton Dickinson).
All samples were run through a BD FACSCanto™ II, LSRFortessa™ 4L (DB Biosciences) or Attune™ NXT (Invitrogen) flow cytometer and analyzed with FlowJo v10.8.0 Software (BD Biosciences).
In vitro cytotoxicity assays against primary leukemic blasts from AML and T-ALL patients Primary blasts were stained with CFSE (ThermoFisher) and co-cultured with effector cells (CART/UT) at effector:target cell ratios 4:1, 2:1, 1:1 and 0.5:1 for 24 h and 48 h. After this period, co-cultured cells were stained with LIVE/Dead™ Fixable Aqua (ThermoFisher) to differentiate live/dead cells. The percentage of remaining live blasts was determined by flow cytometry and calculated using the following formula: % of live cell =100×(number of negative LIVE/Dead-positive CFSE cells with CART cells at time x/number of negative LIVE/Dead-positive CFSE cells alone at time x).
Haematopoietic progenitor stem cells (CD34+) were obtained from two sources: cord blood units (CBU, from the blood bank Banc de Sang i Teixits de Barcelona, BST) and from an apheresis product from a healthy donor that had been mobilized with G-CSF for an allogeneic stem cell transplant (also obtained from BST).
CD34+ cells were isolated from CBU by first, Ficoll-Paque density-gradient centrifugation and second, purifying the CD34+ haematopoietic progenitor stem cells by magnetic separation with a human CD34-MicroBead kit (Miltenyi Biotec, positive selection). To isolate CD34+ cells from the apheresis product, cells were directly purified with the CD34-magnetic beads.
To assess CD84 CART cytotoxicity towards CD34+ cells, CD34+ cells were co-cultured with effector cells (CART/UT) at effector:target cell ratios 4:1, 2:1 for 24 h and 48 h. After this period, co-cultured cells were stained with APC-conjugated CD3 and PE-conjugated CD34 antibodies to differentiate effector from target cells and with LIVE/Dead Fixable Aqua to differentiate live/dead cells.
T cells were isolated during Ficoll-Paque density-gradient centrifugation from donor buffy coats using an immune-cell isolation reagent from RosetteSep™. Half of the T cells obtained in the process were activated and transduced to generate CART cells, and the other half was cryopreserved to be used as target cells until the CART cells were available (i.e. for 8 days). To perform the cytotoxicity assay, T cells were thawed and stained with CFSE before being co-cultured with the CART cells at different effector:target ratios. After 24 hours, both effector and target cells were fixed and stained with LIV/Dead Fixable Aqua cell stain kit.
The percentage of remaining live T cells was determined by flow cytometry and calculated using the following formula: % of live cell =100×(number of negative LIVE/Dead-positive CFSE cells with CART cells at time x/number of negative LIVE/Dead-positive CFSE cells alone at time x).
To study the remaining live T-cell subsets, these were also stained with human mAbs from the phenotype panel, as explained in the flow cytometry section.
Eight- to 12-week-old non obese diabetic-Cg-Prkdcscid II2rgtm 1Wjl/SzJ (NSG) mice (Charles River) were bred and housed under pathogen-free conditions in the animal facility of the Faculty of Medicine and Health Sciences of University of Barcelona. Between 0.1 and 1×106 GFPffLuc-expressing MOLM-13 or GFPffLuc-MOLT-4 cells were resuspended in saline and infused intravenously (IV) into each NSG mouse at day 0. Between 3 and 5×106 UT or CD84 CARTs were intravenously (i.v.) infused 2 to 9 days after tumour-cells infusion. Tumour progression was monitored by bioluminescence using the Xenogen IVIS 50 Imaging System (PerkinElmer). To measure bioluminescence, 100 μL of XenoLight D-Luciferin (Perkin Elmer Ref. 122799) were administered intraperitoneally into each mouse, and tumour burden was monitored weekly. Living Image software (PerkinElmer) was used to visualize and calculate total luminescence flux. Mice were euthanized when presenting signs of humane endpoint criteria. The bone marrow and the spleen were extracted and analysed by flow cytometry to quantify the presence of tumour cells, T cells and CART cells.
All procedures were performed in compliance with the institutional animal care committee of the Faculty of Medicine and Health Sciences of University of Barcelona.
The following primary human cells were acquired from PromoCell: human coronary artery endothelial cells (HCAEC), human small airway epithelial cells (HSAEpC), human uterine fibroblasts (HUF), human cardiac myocytes (HCM) and human renal epithelial cells (HREpC). Cells were cultured at 37° C. and 5% CO2 with the specific medium and supplements (also from PromoCells) as indicated in their data sheet.
In Vitro Cytotoxicity Assays with Adherent Cells
To assess CART cytotoxicity towards adherent cells, an xCELLigence instrument was used that allows real-time measurements of live cell proliferation by impedance. Target cells were seeded in RTCA E-Plates for xCELLigence (16 wells) and cell index was monitored during 24 h using the xCELLigence RTCA multiple plate monitoring system. At this point, 100 ml of either growth medium or T cells (untransduced T cells or CART cells at a 4:1 effector:target ratio) were added to each well. Data acquired from each well (cell index) was normalized to 1 and cell growth monitored during 72 h. Data were analysed using the xCELLigence RTCA Software Lite 2.0.0.1301.
The efficacy of several CART84 cells was tested in an in vivo experiment in NOD scid gamma (NSG) mice using Ramos (Burkitt lymphoma) cells modified to express GFP-ffLuc. The following CART84 were tested: 152.3, 153.5 and H3.5.
In the experiment shown in
Various features and embodiments of the present invention will now be described with reference to the following numbered paragraphs:
1. An antigen-binding domain comprising:
2. The antigen-binding domain of paragraph 1, wherein the antigen-binding domain comprises:
3. An antibody comprising the antigen-binding domain of paragraph 1 or 2.
4. A chimeric antigen receptor (CAR) comprising the antigen-binding domain of paragraph 1 or 2, optionally wherein
5. A polynucleotide comprising one or more nucleotide sequences encoding the antigen-binding domain of paragraph 1 or 2, the antibody of paragraph 3, or the CAR of paragraph 4.
6. A vector comprising the polynucleotide of paragraph 5.
7. A cell comprising the polynucleotide of paragraph 5 or the vector of paragraph 6.
8. A cell comprising the antigen-binding domain of paragraph 1 or 2, or the CAR of paragraph 4.
9. A cell comprising a first CAR and a second CAR, wherein the first CAR is the CAR of paragraph 4, optionally wherein the second CAR is an anti-CD19 CAR, an anti-CD20 CAR, an anti-CD22 CAR, an anti-CD33 CAR, an anti-CD123 CAR; or an anti-CD7 CAR.
10. The cell of any one of paragraphs 7 to 9, wherein the cell is a T cell or NK cell, optionally wherein the cell is an autologous or allogeneic cell.
11. A pharmaceutical composition comprising the antigen-binding domain of paragraph 1 or 2, the antibody of paragraph 3, the CAR of paragraph 4, the polynucleotide of paragraph 5, the vector of paragraph 6, or the cell of any one of paragraphs 7 to 10.
12. The antigen-binding domain of paragraph 1 or 2, the antibody of paragraph 3, the CAR of paragraph 4, the polynucleotide of paragraph 5, the vector of paragraph 6, the cell of any one of paragraphs 7 to 10, or the pharmaceutical composition of paragraph 11 for use in therapy, optionally wherein the therapy is treatment of cancer.
13. The antigen-binding domain, antibody, CAR, polynucleotide, vector, cell, or pharmaceutical composition for use according to paragraph 12, wherein the cancer is a haematological malignancy, optionally a CD84-expressing haematological malignancy, and/or wherein the cancer is selected from the group consisting of chronic lymphocytic leukaemia (CLL), B-cell lymphoma, diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, follicular lymphoma, mantle cell lymphoma, B-cell acute lymphoblastic leukaemia (B-ALL), acute myeloid leukaemia (AML), myelodysplastic syndrome, T-cell acute lymphoblastic leukaemia/lymphoma (T-ALL), chronic myeloproliferative syndrome, chronic myeloid leukaemia (CML), chronic myelomonocytic leukaemia, dendritic-cell neoplasm and histiocytic sarcoma.
14. Use of the antigen-binding domain of paragraph 1 or 2, or the antibody of paragraph 3, for determining CD84 expression level in a sample, optionally for analysing a CD84 expression level in a sample from a subject.
15. A method for identifying a subject suitable for treatment with an anti-CD84 CAR or antibody, wherein the method comprises determining a CD84 expression level in a sample isolated from the subject, wherein the CD84 expression level is determined using the antigen-binding domain of paragraph 1 or 2, or the antibody of paragraph 3.
| Number | Date | Country | Kind |
|---|---|---|---|
| 22382003.6 | Jan 2022 | EP | regional |
| 22205399.3 | Nov 2022 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2023/050194 | 1/5/2023 | WO |
