US20180002435A1 - mAb-DRIVEN CHIMERIC ANTIGEN RECEPTOR SYSTEMS FOR SORTING/DEPLETING ENGINEERED IMMUNE CELLS - Google Patents

mAb-DRIVEN CHIMERIC ANTIGEN RECEPTOR SYSTEMS FOR SORTING/DEPLETING ENGINEERED IMMUNE CELLS Download PDF

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US20180002435A1
US20180002435A1 US15/546,630 US201615546630A US2018002435A1 US 20180002435 A1 US20180002435 A1 US 20180002435A1 US 201615546630 A US201615546630 A US 201615546630A US 2018002435 A1 US2018002435 A1 US 2018002435A1
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Prior art keywords
seq
epitope
epitope1
mab
specific
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US15/546,630
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Inventor
Barbara Johnson SASU
Arvind Rajpal
Philippe Duchateau
Alexandre Juillerat
Julien Valton
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Cellectis SA
Allogene Therapeutics Inc
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Cellectis SA
Rinat Neuroscience Corp
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Publication of US20180002435A1 publication Critical patent/US20180002435A1/en
Assigned to RINAT NEUROSCIENCE CORP. reassignment RINAT NEUROSCIENCE CORP. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: SASU, Barbra Johnson, RAJPAL, ARVIND
Assigned to ALLOGENE THERAPEUTICS, INC. reassignment ALLOGENE THERAPEUTICS, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: RINAT NEUROSCIENCE CORP.
Assigned to CELLECTIS reassignment CELLECTIS ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: DUCHATEAU, PHILIPPE, JUILLERAT, ALEXANDRE, VALTON, JULIEN
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N2015/1028—Sorting particles
    • G01N2015/1081—
    • G01N2015/149—

Definitions

  • the present invention relates to improved chimeric antigen receptors (CAR) to be used in immunotherapy, the extracellular binding domains (scFv) of which have been modified by insertion of a mAb-specific epitope to allow both sorting and/or depletion of the immune cells endowed with said CARs.
  • CAR chimeric antigen receptors
  • scFv extracellular binding domains
  • the present invention relates also to the immune cells expressing said CARs, to the methods of in vivo depleting and/or in vitro sorting said CAR-expressing immune cells, and is drawn to the their therapeutic use.
  • Adoptive immunotherapy which involves the transfer of autologous antigen-specific T cells generated ex vivo, is a promising strategy to treat viral infections and cancer.
  • the T cells used for adoptive immunotherapy can be generated either by expansion of antigen-specific T cells or redirection of T cells through genetic engineering (Park, Rosenberg et al. 2011). Transfer of viral antigen specific T cells is a well-established procedure used for the treatment of transplant associated viral infections and rare viral-related malignancies. Similarly, isolation and transfer of tumor specific T cells has been shown to be successful in treating melanoma.
  • CARs transgenic T cell receptors or chimeric antigen receptors
  • CARs are synthetic receptors consisting of a targeting moiety that is associated with one or more signaling domains in a single fusion molecule.
  • the binding moiety of a CAR consists of an antigen-binding domain of a single-chain antibody (scFv), comprising the light and heavy variable fragments of a monoclonal antibody joined by a flexible linker. Binding moieties based on receptor or ligand domains have also been used successfully.
  • the signaling domains for first generation CARs are derived from the cytoplasmic region of the CD3zeta or the Fc receptor gamma chains.
  • First generation CARs have been shown to successfully redirect T cell cytotoxicity, however, they failed to provide prolonged expansion and anti-tumor activity in vivo.
  • Signaling domains from co-stimulatory molecules including CD28, OX-40 (CD134), ICOS and 4-1BB (CD137) have been added alone (second generation) or in combination (third generation) to enhance survival and increase proliferation of CAR modified T cells.
  • CARs have successfully allowed T cells to be redirected against antigens expressed at the surface of tumor cells from various malignancies including lymphomas and solid tumors (Jena, Dotti et al. 2010).
  • CAR T cells can promote acute adverse events after being transferred into patients.
  • adverse events is Graft versus host disease (GvHD), on-target off-tumor activity or aberrant lymphoproliferative capacity due to vector derived insertional mutagenesis. Therefore, there is a need to develop cell specific depletion systems to prevent such deleterious events to occur in vivo.
  • Philip et al (2014) describes the RQR8 system which is being used as compact marker/suicide gene allowing selection of transduced cells.
  • RQR8 derives from the combination of target epitopes from both CD34 and CD20 antigens. This construct allows selection with the clinically approved CliniMACS CD34 system (Miltenyi). Moreover, this RQR8 construct binds the widely used pharmaceutical antibody rituximab, resulting in selective deletion of transgene-expressing cells.
  • RQR8 is co-expressed with a CAR in a retroviral vector using the foot-and-mouth disease 2A peptide, resulting thereby into the expression of 2 independent transgenes (RQR8 and CAR) on the surface of the T-cells.
  • This system presents some limitations from the industrial perspective, as first, it requires the cloning large retroviral inserts, and second, to ensure that the transformed cells express both RQR8 and CAR polypeptides, to eliminate possible “false-positive” i.e. T-cells that would not express both polypeptides, in particular the RQR8 suicide gene allowing the depletion of the engineered immune cells in the event of undesirable effects.
  • immunosuppressive drugs such as glucocorticoids or cytostatics such as alkylating agents (cyclophosphamide, nitrosoureas, platinum compounds . . . ) or antimetabolites (methotrexate, azathioprine, fluorouracil . . . ) are widely used.
  • cytostatics such as alkylating agents (cyclophosphamide, nitrosoureas, platinum compounds . . . ) or antimetabolites (methotrexate, azathioprine, fluorouracil . . . ) are widely used.
  • these drugs are not discriminative as they affect the proliferation of all T and B cells.
  • Antibodies are sometimes used as a quick and potent immunosuppressive therapy to prevent the acute rejection reactions as well as a targeted treatment of lymphoproliferative or autoimmune disorders, in particular anti-CD20 monoclonals.
  • In vivo elimination of T cell subsets was performed by Benjamin and Waldmann (1986) to determine the role of CD4+ T cells in generating antibody responses to soluble proteins, and by Cobbold et al. (1986) to determine the role of CD4+ and CD8+ T cells in rejecting bone marrow and tissue allografts.
  • In vivo depletion has been performed extensively to study varied topics including control of antiviral cytotoxic T lymphocyte (CTL) responses (Buller et al., 1987).
  • CTL cytotoxic T lymphocyte
  • the antibodies which have been used so far on T cells direct antigens (CD3, CD4, CD52) that are all broadly present on resting or activated T cells as well as on other cell types. As such, the use of such antibodies would not allow the selective elimination of the engineered immune cells endowed with CARs.
  • the inventors have sought for an “all-in-one” system which allows an optimized in vitro sorting of CAR-expressing immune cells by reducing “false-positive”, meanwhile allowing the in vivo depletion of the immune cells expressing said CARs in case of adverse clinical event.
  • the present invention is drawn to chimeric antigen receptors (CAR), which extracellular binding domain (scFv) is modified in such a way to allow both cell sorting and cell depletion (see FIG. 2 for illustrative embodiment).
  • CAR chimeric antigen receptors
  • scFv extracellular binding domain
  • mAb-driven sorting/depletion system consists in inserting a selected epitope within the scFv; this epitope having a specificity to be recognized by a specific antibody (preferably mAb).
  • mAb-driven sorting/depletion system consists in inserting a selected epitope within the scFv; this epitope having a specificity to be recognized by a specific antibody (preferably mAb).
  • mAb preferably mAb
  • the chimeric scFv of the invention which is formed of the VH and VL polypeptides and the specific epitope(s) may itself have different structures depending on the position of insertion of the epitope and the use of linkers.
  • the present invention also relates to the resulting method for sorting and/or depleting the engineered immune cells endowed with the modified CARs.
  • epitope-mAb couples can be used to generate such system; in particular those already approved for medical use, such as CD20/rituximab as a non-limiting example.
  • the epitope-specific antibody may be conjugated with a cytotoxic drug. It is also possible to promote CDC cytotoxicity by using engineered antibodies on which are grafted component(s) of the complement system.
  • the invention encompasses therapeutic methods where the activation of the engineered immune cells endowed with CARs is modulated by depleting the cells by using an antibody that directs the external ligand binding domain of said CARs.
  • a polypeptide encoding a chimeric antigen receptor (CAR) comprising at least one extracellular binding domain that comprises a scFv formed by at least a VH chain and a VL chain specific to an antigen, wherein said extracellular binding domain comprises at least one mAb-specific epitope.
  • CAR chimeric antigen receptor
  • said extracellular binding domain comprises at least one mAb-specific epitope.
  • said mAb-specific epitope is located between the VH and VL chains.
  • 3. The polypeptide according to item 1 or 2 wherein said VH and VL chains, and mAb specific-epitope are bound together by at least one linker and to the transmembrane domain of said CAR by a hinge. 4.
  • polypeptide according to item 3 wherein the mAb-epitope is joined to the VH and VL chains by two linkers. 5.
  • FIG. 1 Schematic structure of the mAb-driven sorting/depletion system of the invention using here a single-chain CAR scaffold; several configurations are presented for the chimeric scFv with different positions of the VH, VL chains and the mAb-specific epitope.
  • FIG. 2 Schematic representation of cell sorting and cell depletion functioning by using the mAb-driven system of the invention.
  • the addition of specific mAb (+/ ⁇ complement) allows purification of CAR+ T cells by recognizing its epitope within the chimeric scFv.
  • the same specific mAb (+/ ⁇ complement) by binding to its specific epitope within the chimeric scFv provokes a specific lysis of CAR+ T cells.
  • FIG. 3 Schematic representation of cell depletion using bi-specific antibody.
  • FIG. 4 CAR architecture for 10 CARs expressing anti-CD123 scFv with CD20 mimotope(s) used in Examples 1-2.
  • a series of 10 chimeric scFv are designed in which one or two copies of the CD20 mimotopes (black box named “mimotope”) are inserted between the anti-CD123 scFv and the hinge.
  • all the 10 CARs have the same hinge (CD8 hinge), transmembrane domain (CD8 TM), co-stimulatory domain (4-1BB) and stimulatory domain (ITAM CD3 zeta).
  • SEQ ID NO 1-10 comprise the leader sequence MALPVTALLLPLALLLHAARP, which is present when the CAR is initially expressed but which is not part of the CAR expressed at the surface of the cell.
  • FIG. 5 shows the cytolytic activity of T cells expressing anti-CD123 CAR of SEQ ID NO 1-4 or 142 or control T Cell not expressing any anti CD123 CAR (mock T-cell-transfection step without any mRNA).
  • the cytolytic activity is expressed as the frequency of specific cell lysis as detailed in Example 1.
  • FIG. 6 shows the result of a CDC assay where T cells expressing anti-CD123 CAR of SEQ ID NO 1-4 or control T Cell not expressing any anti CD123 CAR (mock T-cell (transfection step without any mRNA)) are incubated with Rituximab (RTX) and Baby Rabbit Complement BRC). The results are expressed as relative frequency of viable cells among anti-CD123 CAR positive T cells (with respect to control experiment) as detailed in Example 3.
  • FIGS. 7A, 7B and 7C discloses the general structure of CARs of SEQ ID NO 125 to 141 that have been designed and tested in Examples 4 to 6.
  • An anti BCMA ScFV was used in all these CARs.
  • One, two, three or four epitopes selected from a CD20 mimotope (black box named “mimotope”) and or a CD34 epitope (gray box named “CD34”) were included at different positions, i.e upstream to the ScFv, downstream to the ScFv or between the variable chains of the ScFv (noted as V1 and V2).
  • all the CARs have the same hinge (CD8 hinge), transmembrane domain (CD8 TM), co-stimulatory domain (4-1BB) and stimulatory domain (ITAM CD3 zeta).
  • FIGS. 8A and 8B shows the result of a CDC assay where T cells expressing anti-BCMA CAR of SEQ ID NO 125 or 130 to 141 are incubated with RTX and BRC. The results are expressed as relative frequency of viable cells among anti-BCMA CAR positive T cells (with respect to control experiment) as detailed in Example 4.
  • FIG. 9 shows the cytolytic activity of T cells expressing anti-BCMA CAR of SEQ ID NO 125 or 130 to 139 or control T Cell not expressing any anti BCMA CAR (T-cell).
  • the cytolytic activity is expressed as the frequency of viable H929 cells as detailed in Example 4.
  • FIG. 10A shows the frequency of T-cells expressing CAR of SEQ ID NO 128 comprising a CD34 epitope and two CD20 mimotopes before or after purification with CD34 MicroBead Kit or in the flow through fraction.
  • FIG. 10B shows the number of T-cells expressing CAR of SEQ ID NO 128 comprising a CD34 epitope before or after purification with CD34 MicroBead Kit or in the flow through fraction.
  • FIG. 11 shows concentration of INF gamma produced by T cell expressing anti-BCMA CAR of SEQ ID NO 125 or 130 to 139 in the presence of RTX, phytohemagglutinin (PHA) or in the absence of both RTX anf PHA.
  • PHA phytohemagglutinin
  • FIG. 12 shows the frequency of CAR positive T-Cell resulting from the detection of T Cell expressing CARs of SEQ ID NO 125 or 130 to 139 using a BCMA-Fc fusion protein and a labeled anti Fc antibody or RTX and a labeled anti Fc antibody.
  • FIG. 13 shows the frequency of CAR positive T-cells resulting from the detection of T Cell expressing CARs of SEQ ID NO 128 using RTX and a labeled anti Fc antibody or labeled QBEND-10.
  • FIGS. 14A and 14B shows the detection of T Cells expressing BCMA CARs of SEQ ID NO 145 (BC30, Wild type), 146 (LM), 147 (LML), 148 (LMLM and-149 (LMLML) containing CD20 mimotopes by flow cytometry.
  • the CAR T cells are detected by flow cytometry using either soluble biotinylated-BCMA protein followed by PE-conjugated streptavidin (sBCMA biotin (PE) or the anti-CD20 antibody rituximab followed by FITC-conjugated anti-human IgG (Rituximab (FITC)).
  • PE PE-conjugated streptavidin
  • FITC FITC-conjugated anti-human IgG
  • FIG. 15 shows the detection of T cells not transduced, transduced with a lentivirus for the coexpression of an anti BCMA CAR of SEQ ID NO 145 and RQR8 (SEQ ID NO 150) (BC30-RQR8), or BCMA CARs of SEQ ID NO 149 containing CD20 mimotopes by flow cytometry.
  • the CAR-T cells are detected by flow cytometry using either soluble biotinylated-BCMA protein followed by PE-conjugated streptavidin (sBCMA biotin (PE)) or the anti-CD20 antibody rituximab followed by FITC-conjugated anti-human IgG (Rituximab (FITC)).
  • FIG. 16 shows the result of a CDC assay where T cells expressing anti-BCMA CAR of SEQ ID NO 149 (BC30-R2), anti BCMA CAR of SEQ ID NO 145 or coexpressing an anti BCMA CAR of SEQ ID NO 145 and RQR8 (SEQ ID NO 150) (BC30-RQR8) are incubated with RTX and BRC.
  • the percentage of cytotoxicity is determined by flow cytometry analysis using biotinylated BCMA protein.
  • the results are expressed as the frequency of cell lysis among anti-BCMA CAR positive T cells with respect to control (cells incubated with BRC only).
  • FIG. 17 shows the cytolytic activity of T cells expressing anti-BCMA CAR of SEQ ID NO 149 (BC30-R2) or coexpressing an anti BCMA CAR of SEQ ID NO 145 (BC30) and RQR8 (SEQ ID NO 150) (BC30-RQR8) in the presence/absence of RTX.
  • the cytolytic activity is expressed as the percentage of cell lysis calculated as disclosed in example 7.5 and is determined at different ratio of effector (CAR T cell):target (MM1S cells expressing BCMA).
  • FIG. 18 shows the percentage of activated T cells expressing anti-BCMA CAR of SEQ ID NO 149 in the presence of PBS (control), anti-CD3 OKT3 antibody ( ⁇ CD3), or Rituximab (RTX). T cell activation is assessed by measuring the expression of the activation markers CD25 and CD69 using flow cytometry.
  • Table 1 Listing of the pharmaceutically-approved mAb with their antigenic targets. The sequences of the latter are provided, as well as epitope(s) for some of them.
  • Table 2 Listing of several mimotopes and epitopes corresponding to their mAb which are presented in Example 2.
  • Table 3 Listing of the VH & VL chains of scFv targeting the CD19, CD33, 5T4, ROR1, EGFRvIII, BCMA, CS1 and CD123 antigens.
  • the invention relates to a polypeptide encoding a chimeric antigen receptor (CAR) comprising at least one extracellular binding domain that comprises a scFv formed by at least a VH chain and a VL chain specific to an antigen, preferably a cell surface marker antigen, wherein said extracellular binding domain comprises at least one mAb-specific epitope.
  • the mAb-specific epitope is an epitope to be bound by an epitope-specific mAb for in vitro cell sorting and/or in vivo cell depletion of T cells expressing a CAR comprising such epitope.
  • the invention relates to a polypeptide encoding a chimeric antigen receptor (CAR) comprising at least one extracellular binding domain that comprises a scFv formed by at least a VH chain and a VL chain specific to a cell surface marker antigen, wherein said extracellular binding domain comprises at least one mAb-specific epitope to be bound by a epitope-specific mAb for in vitro cell sorting and/or in vivo cell depletion of T cells expressing said CAR.
  • CAR chimeric antigen receptor
  • the invention relates to a CAR comprising
  • the invention relates to a CAR comprising
  • the CAR of the invention comprises one extracellular binding domain.
  • chimeric scFv is meant a polypeptide corresponding to a single-chain variable fragment composed of heavy and light chains (V H and V L , respectively) and of an epitope, which was not originally included in said V H and V L chains.
  • the latter epitope is referred to as “mAb-specific epitope” when it has the capacity to be bound specifically by an antibody, in particular a monoclonal antibody.
  • the mAbs specific epitope is not an epitope recognized by the ScFv.
  • the mAbs specific epitope is not derived from the extracellular domain of the CAR.
  • the components of this chimeric scFv i.e.
  • the light and heavy variable fragments of the ligand binding domain and the mAb specific epitope may be joined together by at least one linker, usually a flexible linker. These components are generally joined to the transmembrane domain of the CAR by a hinge.
  • the structure of the chimeric scFv of the invention can be various as presented in the FIG. 1 depending of the position of its main components (V H and V L and m-Ab specific epitope).
  • the chimeric scFv of the invention may have several conformations, at least 9 when considering the number of possible permutations of one V H , one V L and one epitope.
  • each component (VH, VL and epitope) is interconnected with its neighbor(s) by at least one flexible linker such as presented previously.
  • the suitable combinations according to the invention are the ones which provide a good affinity/specificity in both bindings: between the mAb-specific epitope and the infused mAb, and between the VH &VL chains of the chimeric scFv and the antigen of the cell target ligand.
  • the extracellular-binding domain of the CAR comprises at least two linkers, both of them joining the epitope to the VH and VL chains; and a hinge joining the scFv-epitope to the transmembrane domain of the CAR.
  • the projected CAR conformation is such that the mAb-specific epitope is located beside the VH and VL chains
  • a screening is performed when the CAR is expressed and is tested for cytoxicity and/or mAb depletion.
  • a screening may be performed by phage display before testing and/or transient expression of the CAR construct. This may be obtained by transfection of mRNA, which is sufficient for a primary cytoxicity and/or mAb depletion test.
  • the extracellular binding domain comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 mAb-specific epitopes.
  • the extracellular binding domain comprises 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 mAb-specific epitopes.
  • the extracellular binding domain comprises 1, 2 or 3 mAb-specific epitopes.
  • the extracellular binding domain comprises several mAb-specific epitopes
  • all the mAb-specific epitopes are identical.
  • the extracellular binding domain when the extracellular binding domain comprises several mAb-specific epitopes, the mAb-specific epitopes are not identical.
  • the extracellular binding domain can comprises three mAb-specific epitopes, two of them being identical and the third one being different.
  • the extracellular binding domain comprises a VH, a VL, and one or more mAb-specific epitopes, preferably 1, 2 or 3, more preferably 2 or 3 mAb-specific epitopes.
  • the extracellular binding domain comprises the following sequence (Nterm is located on the left hand side):
  • V 1 and V 2 are V H and V L of an ScFv (i.e, V 1 is V L and V 2 is V H or V 1 is V H and V 2 is V L );
  • L 1 is any linker suitable to link the V H chain to the V L chain in an ScFv;
  • L is a linker, preferably comprising glycine and serine residues, and each occurrence of L in the extracellular binding domain can be identical or different to other occurrence of L in the same extracellular binding domain, and, x is 0 or 1 and each occurrence of x is independently from the others; and, Epitope 1, Epitope 2 and Epitope 3 are mAb-specific epitopes and can be identical or different.
  • the extracellular binding domains comprises the following sequence (Nterm is located on the left hand side):
  • L 1 is a linker comprising Glycine and/or Serine. In some embodiments, L 1 is a linker comprising the amino acid sequence (Gly-Gly-Gly-Ser) n or (Gly-Gly-Gly-Gly-Ser) n , where n is 1, 2, 3, 4 or 5. In some embodiments L 1 is (Gly 4 Ser) 4 or (Gly 4 Ser) 3 .
  • L is a flexible linker, preferably comprising Glycine and/or Serine.
  • L has an amino acid sequence selected from SGG, GGS, SGGS, SSGGS, GGGG, SGGGG, GGGGS, SGGGGS, GGGGGS, SGGGGGS, SGGGGG, GSGGGGS, GGGGGGGS, SGGGGGGG, SGGGGGGGS, or SGGGGSGGGGS preferably SGG, SGGS, SSGGS, GGGG, SGGGGS, SGGGGGS, SGGGGG, GSGGGGS or SGGGGSGGGGS.
  • all the Ls are identical.
  • the extracellular binding domain comprises several occurrences of L
  • the Ls are not all identical.
  • L is SGGGGS.
  • the extracellular binding domain comprises several occurrences of L and all the Ls are SGGGGS.
  • Epitope 1, Epitope 2 and Epitope 3 are identical or different and are selected from mAb-specific epitopes having an amino acid sequence of SEQ ID NO 35, SEQ ID NO 36, SEQ ID NO 37, SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41 or SEQ ID NO 42, SEQ ID NO 144 or SEQ ID NO 174.
  • Epitope 1, Epitope 2 and Epitope 3 are identical or different and are selected from mAb-specific epitopes specifically recognized by ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosumab, golimumab, i
  • Epitope 1 is a mAb-specific epitope having an amino acid sequence of SEQ ID NO 35.
  • Epitope 2 is a mAb-specific epitope having an amino acid sequence of SEQ ID NO 35.
  • Epitope 3 is a mAb-specific epitope having an amino acid sequence of SEQ ID NO 35.
  • Epitope 4 is a mAb-specific epitope having an amino acid sequence of SEQ ID NO 35.
  • Epitope 2 is a mAb-specific epitope having an amino acid sequence of SEQ ID NO 35 and Epitope 3 is an mAb-specific epitope having an amino acid sequence of SEQ ID NO 144.
  • one of Epitope 1, Epitope 2, Epitope 3 and Epitope 4 is a CD34 epitope, preferably an epitope of SEQ ID 144.
  • one of Epitope1, Epitope 2, Epitope 3 and Epitope 4 is a CD34 epitope, preferably an epitope of SEQ ID 144 and the other mAb specific epitopes are CD20 mimotopes, preferably mimotope of SEQ ID NO 35.
  • the epitope to be inserted within the chimeric scFv is specific to the monoclonal antibody (mAb) which is used for cell sorting and/or cell depletion processes.
  • mAb monoclonal antibody
  • the introduced epitope within chimeric scFv is chosen as part of a mAb-specific epitope/epitope-specific mAb couple, in the basis of their approval by National Health Agencies in terms of regulatory/safety.
  • Such couples are presented in the following table 1.
  • the epitope introduced within the chimeric scFv is the CD20 antigen, preferably SEQ ID NO 35 and the infused mAb which is being used to target it—for sorting and/or depletion purpose(s) is rituximab.
  • the mAb-specific epitope has an amino acid sequence of SEQ ID NO 35, SEQ ID NO 36, SEQ ID NO 37, SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO 41, SEQ ID NO 42, SEQ ID NO 144 or SEQ ID NO 174.
  • the extracellular binding domain of the CAR of the invention comprises one mAb-specific epitope of SEQ ID NO 35, two mAb-specific epitopes of SEQ ID NO 35, three mAb-specific epitopes of SEQ ID NO 35, one mAb-specific epitope of SEQ ID NO 35 and one mAb-specific epitope of SEQ ID NO 144, two mAb-specific epitopes of SEQ ID NO 35 and one mAb-specific epitope of SEQ ID NO 144, three mAb-specific epitopes of SEQ ID NO 35 and one mAb-specific epitope of SEQ ID NO 144.
  • the epitope is a mimotope.
  • the mimotope As a macromolecule, often a peptide, which mimics the structure of an epitope, the mimotope has the advantage to be smaller than conventional epitope, and therefore may be beneficial for a non-conformational sequence and easier to reproduce in a long polypeptide such a CAR.
  • Mimotopes are known for several pharmaceutically-approved mAb such as two 10 amino acid peptides for cetuximab (Riemer et al., 2005), or a 24 aa for palivizumab (Arbiza et al, 1992).
  • these mimotopes can be identified by phage display, it is possible to try several of them in order to obtain a sequence which does not perturb the scFv for the same mAb. Furthermore, their use can enhance a complement-dependent cytotoxicity (CDC).
  • CDC complement-dependent cytotoxicity
  • extracellular ligand-binding domain is defined as an oligo- or polypeptide that is capable of binding a ligand. Preferably, said domain is sought for being capable of interacting with a cell surface molecule.
  • the extracellular ligand-binding domain may be chosen to recognize a ligand that acts as a cell surface marker on target cells associated with a particular disease state.
  • cell surface markers that may act as ligands include those associated with viral, bacterial and parasitic infections, autoimmune disease and cancer cells.
  • the extracellular ligand-binding domain can comprise an antigen binding domain derived from an antibody against an antigen of the target.
  • the antigen of the target can be a tumor-associated surface antigen as described above.
  • the extracellular binding domain is an extracellular ligand-binding domain as defined above.
  • said extracellular ligand-binding domain is a single chain antibody fragment (scFv) comprising the light (V L ) and the heavy (V H ) variable fragment of a target antigen specific monoclonal antibody, and an mAb epitope specific antigen.
  • the extracellular binding domain comprises a single chain antibody fragment (scFv) comprising the light (V L ) and the heavy (V H ) variable fragment of a cell surface target antigen specific monoclonal antibody.
  • binding domain than scFv can also be used for predefined targeting of lymphocytes, such as camelid single-domain antibody fragments, receptor ligands like a vascular endothelial growth factor polypeptide, an integrin-binding peptide, heregulin or an IL-13 mutein, antibody binding domains, antibody hypervariable loops or CDRs as non-limiting examples.
  • said extracellular binding domain can be a DARPin (designed ankyrin repeat protein).
  • DARPins are genetically engineered antibody mimetic proteins typically exhibiting highly specific and high-affinity target protein binding. They are derived from natural ankyrin proteins and comprise at least three, usually four or five repeat motifs of these proteins. DARPins are small, single domain proteins which can be selected to bind any given target protein with high affinity and specificity (Epa, Dolezal et al. 2013; Friedrich, Hanauer et al. 2013; Jost, Schilling et al. 2013). According to the present invention, DARPins can be engineered to comprise multiple antigen recognition sites.
  • the present invention relates to a method comprising providing an immune cell, and expressing at the surface of said immune cell chimeric antigen receptor which comprises a designed ankyrin repeat protein capable of recognizing at least one specific ligand, preferably at two specific ligands.
  • the ligand of the target or the antigen recognized by the extracellular binding domain can be a tumor-associated surface antigen, such as ErbB2 (HER2/neu), carcinoembryonic antigen (CEA), epithelial cell adhesion molecule (EpCAM), epidermal growth factor receptor (EGFR), EGFR variant III (EGFRvIII), CD19, CD20, CD30, CD40, disialoganglioside GD2, GD3, C-type lectin-like molecule-1 (CLL-1), ductal-epithelial mucine, gp36, TAG-72, glycosphingolipids, glioma-associated antigen, ⁇ -human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carb
  • HER2/neu human telomerase reverse transcripta
  • the ligand that the chimeric antigen receptor recognizes is present on the surface of a target cell, particularly cancer cell or viral cell. In some embodiments, the ligand that the chimeric antigen receptor recognizes is present in a tumor microenvironment. In some aspects of the invention, the ligand that the chimeric antigen receptor recognizes is a growth factor.
  • said VH and VL chains have as antigenic target sequence of over 80% identity, preferably over 90%, and more preferably over 95% with SEQ ID NO 43 (CD19 antigen), SEQ ID NO 44 (CD38 antigen), SEQ ID NO 45 (CD123 antigen), SEQ ID NO 46 (CS1 antigen), SEQ ID NO 47 (BCMA antigen), SEQ ID NO 48 (FLT-3 antigen), SEQ ID NO 49 (CD33 antigen), SEQ ID NO 50 (CD70 antigen), SEQ ID NO 51 (EGFR-3v antigen), SEQ ID NO 52 (WT1 antigen).
  • said VH and VL chains have as antigenic target sequence of over 80% identity, preferably over 90%, and more preferably over 95% with or identical to SEQ ID NO 53-64 (CD19 antigen), SEQ ID NO 65-76 (CD33 antigen), SEQ ID NO 77-84 (5T4 antigen), SEQ ID NO 85-90 (ROR1 antigen), SEQ ID NO 91-94 (EGFRvIII antigen), SEQ ID NO 95-102 (BCMA antigen), SEQ ID NO 103-112 (CS1 antigen) and SEQ ID NO 113-124 (CD123 antigen) as follows in Table 3.
  • the antigen recognized by the extracellular binding domain preferably by the ScFv is selected from SEQ ID NO 43 (CD19 antigen), SEQ ID NO 44 (CD38 antigen), SEQ ID NO 45 (CD123 antigen), SEQ ID NO 46 (CS1 antigen), SEQ ID NO 47 (BCMA antigen), SEQ ID NO 48 (FLT-3 antigen), SEQ ID NO 49 (CD33 antigen), SEQ ID NO 50 (CD70 antigen), SEQ ID NO 51 (EGFR-vIII antigen) or SEQ ID NO 52 (WT1 antigen).
  • the extracellular binding domain comprises:
  • said VH and VL chains have as epitope target sequence of over 80% identity, preferably over 90%, and more preferably over 95% with SEQ ID NO 11 (CD20 antigen).
  • the extracellular ligand-binding domain can also comprise a peptide binding an antigen of the target, a peptide or a protein binding an antibody that binds an antigen of the target, a peptide or a protein ligand such as a growth factor, a cytokine or a hormone as non-limiting examples binding a receptor on the target, or a domain derived from a receptor such as a growth factor receptor, a cytokine receptor or a hormone receptor as non-limiting examples, binding a peptide or a protein ligand on the target.
  • the target is a cell or a virus.
  • the antigen binding domain of the CAR can be any domain that binds to the cell target antigen including but not limited to a monoclonal antibody, a recombinant antibody, a human antibody, a humanized antibody, and a functional fragment thereof.
  • a humanized antibody can be produced using a variety of techniques known in the art, including but not limited to, CDR-grafting (see, e.g., European Patent No. EP 239,400; International Publication No. WO 91/09967; and U.S. Pat. Nos. 5,225,539, 5,530,101, and 5,585,089, each of which is incorporated herein in its entirety by reference), veneering or resurfacing (see, e.g., European Patent Nos.
  • framework substitutions are identified by methods well-known in the art, e.g., by modeling of the interactions of the CDR and framework residues to identify framework residues important for antigen binding and sequence comparison to identify unusual framework residues at particular positions. (See, e.g., Queen et al., U.S. Pat. No. 5,585,089; and Riechmann et al., 1988, Nature, 332:323, which are incorporated herein by reference in their entireties.).
  • the scFv may be nanobodies (natural single domain antibodies) which can be obtained by immunization of dromedaries, camels, llamas, alpacas or sharks.
  • Peptide linkers can vary from 10 to 25 amino acids in length and are typically, but not always, composed of hydrophilic amino acids such as glycine (G) and serine (S). Peptide linkers of shorter lengths (0-4 amino acids) have also been used. However, scFv bearing shorter linkers can form multimers. Generally, the (GGGGS) 3 peptide is used as an scFv peptide linker.
  • This 15-amino acid linker sequence [designated as the (GGGGS) 3 linker] is used in the Recombinant Phage Antibody System (RPAS kit) commercially available from Amersham.
  • RPAS kit Recombinant Phage Antibody System
  • linkers suitable within the present invention are the 15-mer peptide linker (RGRGRGRGRSRGGGS) (Zhihong Shen, Heping Yan, Ying Zhang, Raymond L. Mernaugh, and Xiangqun Zeng (2008), Anal Chem. 80(6): 1910-1917).
  • the “linker” as used in the context of a scFv refers to a peptide linker that consists of amino acids such as glycine and/or serine residues used alone or in combination, to link variable heavy and variable light chain regions together.
  • the flexible polypeptide linker is a Glycine/Serine linker and comprises the amino acid sequence (Gly-Gly-Gly-Ser) n or (Gly-Gly-Gly-Gly-Ser) n , where n is a positive integer equal to or greater than 1.
  • the flexible polypeptide linkers include, but are not limited to, (Gly 4 Ser) 4 or (Gly 4 Ser) 3 .
  • the CAR according to the invention are sought for enabling engineered immune cells to trigger the destruction of pathological cells, in particular malignant cells. They may be designed according to single-chain or multi-chain architectures.
  • the extracellular ligand-binding domain, transmembrane domain, and intracellular signaling domain are in one polypeptide, i.e., in a single chain.
  • Multi-chain architectures are more particularly disclosed in WO2014039523.
  • a multi-chain CAR is typically formed of different polypeptides such as:
  • the signaling polypeptide is responsible for the activation of at least one of the normal functions of the engineered immune cell.
  • the function of a T cell can be a cytolytic activity or helper activity including the secretion of cytokines.
  • the term “signaling protein” refers to a protein which transduces the transmitter domain function signal and directs the cell to perform a specialized function.
  • said transmitter domain can be a signaling protein. Transmission of the signals can result from: protein/protein interactions, protein/DNA interaction, protein/RNA interaction, protein/small molecule interaction, post translational protein modification, conformational change, subcellular relocalization.
  • the signaling protein can activate a gene in the nucleus.
  • Examples of signaling protein can be members of NFAT transcription factor family which are inducible factor that could bind the interleukin-2 promoter in activated T cells.
  • the regulation of NFAT proteins involves metabolites and proteins such as calcium, calcineurin and Homer scaffolding proteins.
  • Said signaling protein can be an activated engineered form of NFAT avoiding regulation by calcineurin and Homer proteins.
  • Said signaling protein can be a NF- ⁇ B engineered to avoid sequestration in the cytoplasm by I ⁇ b allowing activation of T cells.
  • Said signaling protein can also be the expression of the three IKK subunits (IKK ⁇ , IKK ⁇ , IKK ⁇ ).
  • Reconstituted IKK complex activated NF- ⁇ B pathway, by triggering the ubiquitination of the I ⁇ B.
  • the activation of the JNK signaling could be triggered through the direct expression of signaling protein AP-1 (transcription factor).
  • Said signaling protein can be an engineered transcription activator like effector (TALE) binding domain that will specifically target and activate transcription of the same gene as for the N FAT and NF-kb.
  • TALE transcription activator like effector
  • said signaling protein can inhibit a signaling pathway through protein-protein interaction or can activate a gene in the nucleus to inhibit a signaling pathway.
  • Said signaling protein can be vaccinia H1 related proteins (VHR) a member of the mitogen-activated protein kinase phosphatases (MKPs) family which dephosphorylates and inactivates an extracellular signal regulated kinases (ERK) signaling proteins.
  • VHR vaccinia H1 related proteins
  • MKPs mitogen-activated protein kinase phosphatases
  • signal transducing domain for use in a CAR can be the cytoplasmic sequences of the T cell receptor and co-receptors that act in concert to initiate signal transduction following antigen receptor engagement, as well as any derivate or variant of these sequences and any synthetic sequence that has the same functional capability.
  • Signal transduction domain may comprise two distinct classes of cytoplasmic signaling sequence, those that initiate antigen-dependent primary activation, and those that act in an antigen-independent manner to provide a secondary or co-stimulatory signal.
  • the signal transduction domain of the CAR of the present invention comprises a co-stimulatory signal molecule.
  • a co-stimulatory molecule is a cell surface molecule other than an antigen receptor or their ligands that is required for an efficient immune response.
  • Co-stimulatory ligand refers to a molecule on an antigen presenting cell that specifically binds a cognate co-stimulatory molecule on a T cell, thereby providing a signal which, in addition to the primary signal provided by, for instance, binding of a TCR/CD3 complex with an MHC molecule loaded with peptide, mediates a T cell response, including, but not limited to, proliferation activation, differentiation and the like.
  • a “co-stimulatory molecule” refers to the cognate binding partner on a T cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the cell, such as, but not limited to proliferation.
  • Co-stimulatory molecules include, but are not limited to an MHC class I molecule, BTLA and Toll ligand receptor.
  • a multi-chain CAR can be derived from the structure of a Fc receptor, preferably Fc ⁇ RI, and comprise at least two of the following components:
  • these different polypeptides multimerize together spontaneously to form dimeric, trimeric or tetrameric structures that arise at the cell surface in a juxtamembrane position.
  • the invention relates to an immune cell comprising a single-chain CAR as well defined in the prior art, as well as in any of U.S. Pat. No. 7,446,190, WO2008/121420, U.S. Pat. No. 8,252,592, US20140024809, WO2012/079000, WO2014153270, WO2012/099973, WO2014/011988, WO2014/011987, WO2013/067492, WO2013/070468, WO2013/040557, WO2013/126712, WO2013/126729, WO 2013/126726, WO2013/126733, U.S. Pat. No.
  • the invention relates to a CAR comprising
  • the transmembrane domain comprises the transmembrane region(s) of the alpha, beta or zeta chain of the T-cell receptor, PD-1, 4-1BB, OX40, ICOS, CTLA-4, LAG3, 2B4, BTLA4, TIM-3, TIGIT, SIRPA, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 or CD154.
  • the hinge is an IgG4 hinge or a CD8 alpha hinge, preferably a CD8 alpha hinge.
  • transmembrane domains comprise the ability to be expressed at the surface of a cell, preferably in the present invention an immune cell, in particular lymphocyte cells or Natural killer (NK) cells, and to interact together for directing cellular response of immune cell against a predefined target cell.
  • the transmembrane domain can be derived either from a natural or from a synthetic source.
  • the transmembrane domain can be derived from any membrane-bound or transmembrane protein.
  • the transmembrane polypeptide can be a subunit of the T cell receptor such as ⁇ , ⁇ , ⁇ or ⁇ , polypeptide constituting CD3 complex, IL2 receptor p55 ( ⁇ chain), p75 ( ⁇ chain) or ⁇ chain, subunit chain of Fc receptors, in particular Fc ⁇ receptor III or CD proteins.
  • the transmembrane domain can be synthetic and can comprise predominantly hydrophobic residues such as leucine and valine.
  • said transmembrane domain is derived from the human CD8 alpha chain (e.g. NP_001139345.1).
  • Said transmembrane domain can also be a CD8 transmembrane domain (alpha and beta chains).
  • Said Transmembrane domain can be engineered to create obligated hetero or homodimers.
  • said CARs can comprise transmembrane domains or intracellular domains which can only dimerize after ligand recognition.
  • Another example of transmembrane domain can be NKG2-D receptor.
  • NKG2D natural killer cell group 2D
  • NKG2D is a C-type lectin-like receptor expressed on NK cells, ⁇ -TcR + T cells, and CD8 + ⁇ -TcR + T cells (Bauer, Groh et al., 1999, Science 285(5428):727-9.
  • NKG2D is associated with the transmembrane adapter protein DAP10 (Wu, Song et al. 1999, Science 285(5428):730-2), whose cytoplasmic domain binds to the p 85 subunit of the PI-3 kinase.
  • Said transmembrane domain can also be an integrin.
  • Integrins are heterodimeric integral membrane proteins composed of a ⁇ and ⁇ chains which combined together form the LFA-1 (integrin lymphocyte function-associated antigen-1) which is expressed on all leukocytes.
  • LFA-1 plays a central role in leukocyte intercellular adhesion through interactions with its ligand, ICAMs 1-3 (intercellular adhesion molecules 1 through 3), and also it has an important role in lymphocyte co-stimulatory signaling (Chen and Flies 2013, Nat Rev Immunol 13(4):227-42).
  • the molecular details of the binding of LAF-1 to its immunoglobulin ICAM-1 are quite known allowing a careful engineering of LAF-1 binding site.
  • ⁇ L domain for ICAM-1 is regulated by the displacement of its C-terminal helix which is conformational linked to alterations of specific loops in LAF-1.
  • the active and low conformations differ of 500 and 10,000 folds.
  • two types of antagonists are known for LFA-1 and their mechanism of action is known.
  • Integrin cell surface adhesion receptors can transmit a signal from the outside to inside but also vice-versa.
  • There are cytoskeletal proteins as Talin which binds to the integrin tail LFA-1 to transfer a message from inside to outside.
  • the transmembrane domain comprises the transmembrane region of PD-1 or the transmembrane region(s) of CD8 alpha.
  • the transmembrane domain is attached to the extracellular domain of the CAR via a hinge e.g., a hinge from a human protein.
  • a hinge e.g., a hinge from a human protein.
  • the hinge can be a human Ig (immunoglobulin) hinge, e.g., a PD-1 hinge, an IgG4 hinge, or a CD8alpha hinge.
  • the hinge of the CAR is a human immunoglobulin hinge.
  • the hinge of the CAR is an IgG4 hinge or a CD8 alpha hinge.
  • the hinge is an Fc ⁇ RIII alpha hinge.
  • the hinge is a CD8 alpha hinge.
  • the hinge is a CD8 alpha hinge has amino acid sequence with at least about 70%, preferably at least 80%, more preferably at least 90%, 95%, 97%, or 99% sequence identity with an amino acid sequence shown in SEQ. ID NO: 179, 180 or 181.
  • stalk region generally means any oligo- or polypeptide that functions to link the transmembrane domain to the extracellular ligand-binding domain.
  • stalk region are used to provide more flexibility and accessibility for the extracellular ligand-binding domain.
  • a stalk region may comprise up to 300 amino acids, preferably 10 to 100 amino acids and most preferably 25 to 50 amino acids.
  • Stalk region may be derived from all or part of naturally occurring molecules, such as from all or part of the extracellular region of CD8, CD4, CD28 or RTK, or from all or part of an antibody constant region.
  • the stalk region may be a synthetic sequence that corresponds to a naturally occurring stalk sequence, or may be an entirely synthetic stalk sequence.
  • the intracellular domain (also referred to herein as a “cytoplasmic signaling domain” or “an intracellular signaling domain”) comprises a functional signaling domain derived from a stimulatory molecule as defined below.
  • the stimulatory molecule is the zeta chain associated with the T-cell receptor complex.
  • the cytoplasmic signaling domain further comprises one or more functional signaling domains derived from at least one costimulatory molecule as defined below.
  • the costimulatory molecule is chosen from 4-1BB (i.e., CD137), CD27 and/or CD28.
  • the term “stimulatory molecule,” refers to a molecule expressed by a T-cell that provides the positive cytoplasmic signaling sequence(s) that regulate positive activation of the TCR complex in a stimulatory way for at least some aspect of the T-cell signaling pathway.
  • the positive signal is initiated by, for instance, binding of a TCR/CD3 complex with an MHC molecule loaded with peptide, and which leads to mediation of a T-cell response, including, but not limited to, proliferation, activation, differentiation, and the like.
  • a positive cytoplasmic signaling sequence (also referred to as a “positive signaling domain” or positive intracellular signaling domain) that acts in a stimulatory manner may contain a signaling motif which is known as immunoreceptor tyrosine-based activation motif or ITAM.
  • ITAM immunoreceptor tyrosine-based activation motif
  • Examples of an ITAM containing positive cytoplasmic signaling sequence includes, but is not limited to, those derived from TCR zeta (or CD3zeta), FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b, CD278 (also known as “ICOS”) and CD66d.
  • the intracellular signaling domain of the CAR can comprise the CD3 ⁇ (zeta) signaling domain which has amino acid sequence with at least about 70%, preferably at least 80%, more preferably at least 90%, 95%, 97%, or 99% sequence identity with an amino acid sequence shown in SEQ. ID NO: 175.
  • the intracellular signaling domain of the CAR generates a signal that promotes an immune effector function of the CAR containing cell.
  • immune effector function e.g., in a CAR T-cell
  • helper activity including the secretion of cytokines.
  • costimulatory molecule refers to the cognate binding partner on a T-cell that specifically binds with a costimulatory ligand, thereby mediating a costimulatory response by the T-cell, such as, but not limited to, proliferation.
  • Costimulatory molecules are cell surface molecules other than antigen receptors or their ligands that are required for an efficient immune response.
  • Costimulatory molecules include, but are not limited to an MHC class I molecule, BTLA and a Toll ligand receptor, as well as OX40, CD2, CD27, CD28, CDS, ICAM-1, LFA-1 (CD11a/CD18) and 4-IBB (CD137).
  • a costimulatory intracellular signaling domain can be the intracellular portion of a costimulatory molecule.
  • a costimulatory molecule can be represented in the following protein families: TNF receptor proteins, Immunoglobulin-like proteins, cytokine receptors, integrins, signaling lymphocytic activation molecules (SLAM proteins), and activating NK cell receptors.
  • the intracellular signaling domain of the CAR of the invention comprises amino acid sequence which comprises at least 70%, preferably at least 80%, more preferably at least 90%, 95%, 97%, or 99% sequence identity with an amino acid sequence shown in SEQ. ID NO: 176 and SEQ. ID NO: 177.
  • CARs and immune cells comprising them have been extensively disclosed and can be prepared by the skilled person according to known methods.
  • methodologies to prepare CARs and cells comprising such CARs are disclosed in U.S. Pat. No. 7,446,190, WO2008/121420, U.S. Pat. No. 8,252,592, US20140024809, WO2012/079000, WO2014153270, WO2012/099973, WO2014/011988, WO2014/011987, WO2013/067492, WO2013/070468, WO2013/040557, WO2013/126712, WO2013/126729, WO 2013/126726, WO2013/126733, U.S. Pat. No.
  • the present invention encompasses a recombinant DNA construct comprising sequences encoding an CAR as defined above, wherein the CAR comprises an extracellular domain such as an antibody fragment that binds specifically to cell target antigen, and wherein the sequence of the extracellular domain is contiguous with and in the same reading frame as a nucleic acid sequence encoding a transmembrane domain and an intracellular domain.
  • An exemplary CAR construct may comprise an optional leader sequence, an extracellular cell target antigen binding domain, a hinge, a transmembrane domain, and an intracellular inhibitory signaling domain
  • the invention relates to a recombinant DNA construct comprising sequences encoding a CAR as defined above.
  • the CAR comprises an extracellular domain comprising
  • the invention relates to a method for in vitro sorting CAR-expressing immune cell, comprising contacting a population of said engineered immune with antigen-specific antibody (preferably monoclonal Abs) to collect only cells expressing CAR.
  • antigen-specific antibody preferably monoclonal Abs
  • the invention relates to a method for in vitro sorting CAR-expressing immune cell, wherein said CAR comprises at least one extracellular binding domain comprising at least one mAb-specific epitope as described above, comprising
  • the invention relates to a method for in vitro sorting CAR-expressing immune cells, wherein said CAR comprises at least one extracellular binding domain comprising at least one mAb-specific epitope, comprising
  • said monoclonal antibody specific for said mAb-specific epitope is conjugated to a fluorophore and the step of selecting the cells that bind to the monoclonal antibody is done by Fluorescence Activated Cell Sorting (FACS).
  • FACS Fluorescence Activated Cell Sorting
  • said monoclonal antibody specific for said mAb-specific epitope is conjugated to a magnetic particle and the step of selecting the cells that bind to the monoclonal antibody is done by Magnetic Activated Cell Sorting (MACS).
  • MCS Magnetic Activated Cell Sorting
  • the extracellular binding domain of the CAR comprises a mAb-specific epitope of SEQ ID NO 144.
  • the extracellular binding domain of the CAR comprises a mAb-specific epitope of SEQ ID NO 144 and the antibody used to contact the population of immune cells is QBEND-10.
  • the extracellular binding domain of the CAR comprises a mAb-specific epitope of SEQ ID NO 35.
  • the extracellular binding domain of the CAR comprises a mAb-specific epitope of SEQ ID NO 35 and the antibody used to contact the population of immune cells is Rituximab.
  • the population CAR-expressing immune cells obtained when using the method for in vitro sorting CAR-expressing immune cells described above comprises at least 70%, 75%, 80%, 85%, 90%, 95% of CAR-expressing immune cells. In some embodiments, the population CAR-expressing immune cells obtained when using the method for in vitro sorting CAR-expressing immune cells described above, comprises at least 85% CAR-expressing immune cells.
  • the population of CAR-expressing immune cells obtained when using the method for in vitro sorting CAR-expressing immune cells described above shows increased cytotoxic activity in vitro compared with the initial (non-sorted) cell population using the protocol described in Example 7.5.
  • said cytotoxic activity in vitro is increased by 10%, 20%, 30% or 50%.
  • the mAbs are previously bound onto a support such as a column or on beads such as routinely realized by the skilled in the art.
  • immune cells are T-cells.
  • cells to be administered to the recipient may be enriched in vitro from the source population.
  • Methods of expanding source populations are well known in the art, and may include selecting cells that express an antigen such as CD34 antigen, using combinations of density centrifugation, immuno-magnetic bead purification, affinity chromatography, and fluorescent activated cell sorting, known to those skilled in the art.
  • flow cytometry is widely used in the art and is a method well known to one of ordinary skill to sort and quantify specific cell types within a population of cells.
  • flow cytometry is a method for quantitating components or structural features of cells primarily by optical means. Since different cell types can be distinguished by quantitating structural features, flow cytometry and cell sorting can be used to count and sort cells of different phenotypes in a mixture.
  • a flow cytometric analysis involves two basic steps: 1) labeling selected cell types with one or more labeled markers, and T) determining the number of labeled cells relative to the total number of cells in the population.
  • the primary method of labeling cell types is by binding labeled antibodies to markers expressed by the specific cell type.
  • the antibodies are either directly labeled with a fluorescent compound or indirectly labeled using, for example, a fluorescent-labeled second antibody which recognizes the first antibody.
  • the method used for sorting T cells expressing CAR is the Magnetic-Activated Cell Sorting (MACS).
  • MCS Magnetic-Activated Cell Sorting
  • Magnetic-activated cell sorting is a method for separation of various cell populations depending on their surface antigens (CD molecules) by using superparamagnetic nanoparticles and columns. It takes only a few simple steps to get pure cell populations
  • Cells in a single-cell suspension are magnetically labeled with microbeads.
  • the sample is applied to a column composed of ferromagnetic spheres, which are covered with a cell-friendly coating allowing fast and gentle separation of cells.
  • the unlabeled cells pass through while the magnetically labeled cells are retained within the column. The flow-through can be collected as the unlabeled cell fraction.
  • the column is removed from the separator, and the magnetically labeled cells are eluted from the column.
  • FACS is a technique of choice to purify cell populations of known phenotype as very high purity of the desired population can be achieved, or when the target cell population expresses a very low level of the identifying marker, or when cell populations require separation based on differential marker density.
  • FACS is the only available purification technique to isolate cells based on internal staining or intracellular protein expression, such as a genetically modified fluorescent protein marker.
  • FACS allows the purification of individual cells based on size, granularity and fluorescence. In order to purify cells of interest, they are first stained with fluorescently-tagged monoclonal antibodies (mAb), which recognize specific surface markers on the desired cell population.
  • mAb monoclonal antibodies
  • the mAb used in the method for sorting T cells expressing the CAR is chosen amongst ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosumab, golimumab, ipilimumab
  • said mAb is rituximab.
  • said mAb is QBEND-10.
  • in vivo depletion is meant in the present invention the administration of a treatment to a mammalian organism aiming to stop the proliferation of CAR-expressing immune cells by inhibition or elimination.
  • One aspect of the invention is related to a method for in vivo depleting an engineered immune cell expressing a CAR comprising an m-Ab specific epitope as previously described, comprising contacting said engineered immune cell or said CAR-expressing immune cell with at least one epitope-specific mAbs.
  • Another aspect of the invention relates to a method for in vivo depleting immune CAR-expressing immune cell which comprises the above chimeric scFv (formed by insertion of a mAb-specific epitope) by contacting said engineered immune cell with epitope-specific antibodies.
  • said immune cells are T-cells and/or the antibodies are monoclonal.
  • the in vivo depletion of immune engineered cell is performed on engineered immune cell which has been previously sorted using the in vitro method of the present invention. In this case, this will be the same infused mAb used.
  • the mAb-specific antigen is CD20 antigen and the epitope-specific mAb is rituximab.
  • the invention relates to a method for in vivo depleting an engineered immune cell expressing a CAR comprising an mAb-specific epitope (CAR-expressing immune cell) as previously described, in a patient comprising contacting said CAR-expressing immune cell with at least one epitope-specific mAb.
  • CAR-expressing immune cell mAb-specific epitope
  • the mAb used in the method for depleting an engineered immune cell expressing a CAR is chosen amongst ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosumab, golimumab, ip
  • said mAb-specific epitope is a CD20 epitope or mimotope, preferably SEQ ID NO 35 and the epitope-specific mAbs is rituximab.
  • the step of contacting said engineered immune cell or said CAR-expressing immune cell with at least one epitope-specific mAb comprises infusing the patient with epitope-specific mAb, preferably rituximab.
  • the amount of epitope-specific mAb administered to the patient is sufficient to eliminate at least 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% of the CAR-expressing immune cell in the patient.
  • the step of contacting said engineered immune cell or said CAR-expressing immune cell with at least one epitope-specific mAb comprises infusing the patient with 375 mg/m 2 of rituximab, once or several times, preferably once weekly.
  • the amount of viable CAR-expressing immune cells decreases, preferably by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90%.
  • the CDC assay is the assay disclosed in Example 3, Example 4 or Example 7.4.
  • said mAb-specific epitope is a CD20 epitope or mimotope, preferably SEQ ID NO 35 and the epitope-specific mAbs is rituximab.
  • the in vivo depletion of CAR-engineered immune cells is performed by infusing bi-specific antibodies.
  • a bispecific monoclonal antibody (BsAb) is an artificial protein that is composed of fragments of two different monoclonal antibodies and consequently binds to two different types of antigen.
  • effector cell includes immune cells such as lymphocytes, macrophages, dendritic cells, natural killer cells (NK Cell), cytotoxic T lymphocytes (CTL).
  • immune cells such as lymphocytes, macrophages, dendritic cells, natural killer cells (NK Cell), cytotoxic T lymphocytes (CTL).
  • the infused bi-specific mAb is able to bind both the mAb-specific epitope borne on engineered immune cells expressing the chimeric scFv and to a surface antigen on an effector and cytotoxic cell.
  • FIG. 3 This aspect is presented in FIG. 3 .
  • ADCC antibody-dependent cellular cytotoxicity
  • a cytotoxic drug is coupled to the epitope-specific mAbs which are used in to deplete CAR-expressing immune cells.
  • ADC antibody-drug conjugate
  • the epitope-specific mAb to be infused is conjugated beforehand with a molecule able to promote complement dependent cytotoxicity (CDC). Therefore, the complement system helps or complements the ability of antibodies to clear pathogens from the organism. When stimulated by one of several, is triggered an activation cascade as a massive amplification of the response and activation of the cell-killing membrane attack complex.
  • CDC complement dependent cytotoxicity
  • glycans Different molecule may be used to conjugate the mAb, such as glycans [Courtois, A, Gac-Breton, S., Berthou, C., Guézennec, J., Bordron, A. and Boisset, C. (2012), Complement dependent cytotoxicity activity of therapeutic antibody fragments is acquired by immunogenic glycan coupling, Electronic Journal of Biotechnology ISSN: 0717-3458; http://www.ejbiotechnology.info DOI: 10.2225/vol15-issue5).
  • the epitope-specific mAb used in the method for sorting and depleting an engineered immune cell expressing a CAR is the same and is chosen amongst ibritumomab, tiuxetan, muromonab-CD3, tositumomab, abciximab, basiliximab, brentuximab vedotin, cetuximab, infliximab, rituximab, alemtuzumab, bevacizumab, certolizumab pegol, daclizumab, eculizumab, efalizumab, gemtuzumab, natalizumab, omalizumab, palivizumab, ranibizumab, tocilizumab, trastuzumab, vedolizumab, adalimumab, belimumab, canakinumab, denosuma
  • the extracellular binding domain comprises at least one epitope specifically bound by rituximab such as an mAb-specific epitope having an amino acid sequence of SEQ ID NO 35 and at least one epitope specifically bound by QBEND10 such as SEQ ID NO 144 and the mAb used for sorting the cells is QBEND10 and the mAb used to deplete the cell is rituximab.
  • the inventors developed methods of engineering immune cells expressing a chimeric antigen receptor (CAR), preferably a CAR as described above, with all components necessary to trigger a cell surface target antigen and to expand/amplify. Further, this CAR has the particularity of to carry a chimeric scFv wherein the scFv is modified to include an epitope able to be specifically recognized by an antibody for cell sorting and/or cell depletion purposes.
  • CAR chimeric antigen receptor
  • the method for engineering an immune cell chimeric antigen receptor comprising at least one extracellular binding domain that comprises a scFv formed by at least a VH chain and a VL chain specific to a cell surface marker antigen and one mAb-specific epitope to be bound by a epitope-specific mAb, comprising:
  • the method for engineering an immune cell expressing a chimeric antigen receptor (CAR) as described above, preferably comprising at least one extracellular binding domain that comprises a scFv formed by at least a VH chain and a VL chain specific to a cell surface marker antigen and one mAb-specific epitope to be bound by a epitope-specific mAb comprises:
  • CARs and immune cells comprising them have been extensively disclosed and can be prepared by the skilled person according to known methods. For example, methodologies to prepare CAR and cells comprising such CARs are disclosed earlier. Immune cells comprising a CAR can be prepared by the skilled person according to the methodologies disclosed in the above mentioned references. In a preferred embodiment, immune cells comprising a CAR can be prepared by the skilled person according to the methodologies disclosed in WO2013/176915.
  • the immune cell can be derived from an inflammatory T-lymphocyte, a cytotoxic T-lymphocyte, a regulatory T-lymphocyte, or a helper T-lymphocyte.
  • immune cell is obtained from a healthy donor. In some embodiments, the immune cell is obtained from a patient.
  • the method to engineer cell of the invention further comprises one or more additional genomic modification step.
  • additional genomic modification step can be intended the introduction into cells to engineer of one or more protein of interest.
  • Said protein of interest can be a CAR.
  • the method of engineering T-cells of invention can comprise:
  • an immunosuppressive agent is an agent that suppresses immune function by one of several mechanisms of action.
  • an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response.
  • an immunosuppressive agent can be a calcineurin inhibitor, a target of rapamycin, an interleukin-2 u-chain blocker, an inhibitor of inosine monophosphate dehydrogenase, an inhibitor of dihydrofolic acid reductase, a corticosteroid or an immunosuppressive antimetabolite.
  • the genetic modification step of the method relies on the inactivation of one gene selected from the group consisting of CD52, GR, TCR alpha and TCR beta. In another embodiment, the genetic modification step of the method relies on the inactivation of two genes selected from the group consisting of CD52 and GR, CD52 and TCR alpha, CDR52 and TCR beta, GR and TCR alpha, GR and TCR beta, TCR alpha and TCR beta. In another embodiment, the genetic modification step of the method relies on the inactivation of more than two genes. The genetic modification is preferably operated ex-vivo.
  • the rare-cutting endonucleases used for inactivating the genes in T-cells are preferably Transcription Activator like Effector (TALE), but may be also a Cas9 coupled to a RNA guide as respectively described in WO 2013/176915 and WO 2014/191128.
  • TALE Transcription Activator like Effector
  • CAR at the surface of a cell.
  • said CAR can be expressed by introducing the latter into a cell.
  • CARs can be introduced as transgene encoded by one plasmid vector.
  • Said plasmid vector can also contain a selection marker which provides for identification and/or selection of cells which received said vector.
  • Polypeptides may be synthesized in situ in the cell as a result of the introduction of polynucleotides encoding said polypeptides into the cell. Alternatively, said polypeptides could be produced outside the cell and then introduced thereto.
  • Methods for introducing a polynucleotide construct into cells are known in the art and including as non-limiting examples stable transformation methods wherein the polynucleotide construct is integrated into the genome of the cell, transient transformation methods wherein the polynucleotide construct is not integrated into the genome of the cell and virus mediated methods.
  • Said polynucleotides may be introduced into a cell by for example, recombinant viral vectors (e.g.
  • retroviruses adenoviruses
  • liposome adenoviruses
  • transient transformation methods include for example microinjection, electroporation or particle bombardment.
  • Said polynucleotides may be included in vectors, more particularly plasmids or virus, in view of being expressed in cells.
  • said isolated cell according to the present invention comprises a polynucleotide encoding the chimeric antigen receptor carrying the chimeric scFv.
  • the present invention also relates to polynucleotides, vectors encoding the above described CAR according to the invention.
  • the polynucleotide may consist in an expression cassette or expression vector (e.g. a plasmid for introduction into a bacterial host cell, or a viral vector such as a baculovirus vector for transfection of an insect host cell, or a plasmid or viral vector such as a lentivirus for transfection of a mammalian host cell).
  • an expression cassette or expression vector e.g. a plasmid for introduction into a bacterial host cell, or a viral vector such as a baculovirus vector for transfection of an insect host cell, or a plasmid or viral vector such as a lentivirus for transfection of a mammalian host cell.
  • the nucleic acid sequences of the present invention are codon-optimized for expression in mammalian cells, preferably for expression in human cells. Codon-optimization refers to the exchange in a sequence of interest of codons that are generally rare in highly expressed genes of a given species by codons that are generally frequent in highly expressed genes of such species, such codons encoding the amino acids as the codons that are being exchanged.
  • isolated cell or immune cell expressing a CAR as described herein obtained by the different methods or cell line derived from said isolated cell as previously described can be used as a medicament.
  • said medicament can be used for treating pathologies such as cancer in a patient in need thereof.
  • said isolated cell or immune cell expressing a CAR as described herein I according to the invention or cell line derived from said isolated cell can be used in the manufacture of a medicament for treatment of a pathology such as a cancer in a patient in need thereof.
  • the present invention relies on methods for treating patients in need thereof, said method comprising at least one of the following steps:
  • said immune cell, preferably T cells, of the invention can undergo robust in vivo T cell expansion and can persist for an extended amount of time.
  • Said treatment can be ameliorating, curative or prophylactic. It may be either part of an autologous immunotherapy or part of an allogenic immunotherapy treatment.
  • autologous it is meant that cells, cell line or population of cells used for treating patients are originating from said patient or from a Human Leucocyte Antigen (HLA) compatible donor.
  • HLA Human Leucocyte Antigen
  • allogeneic is meant that the cells or population of cells used for treating patients are not originating from said patient but from a donor.
  • Said treatment can be used to treat patients diagnosed with cancer, viral infection, autoimmune disorders or Graft versus Host Disease (GvHD).
  • Cancers that may be treated include tumors that are not vascularized, or not yet substantially vascularized, as well as vascularized tumors.
  • the cancers may comprise non solid tumors (such as hematological tumors, for example, leukemias and lymphomas) or may comprise solid tumors.
  • Types of cancers to be treated with the CAR of the invention include, but are not limited to, carcinoma, blastoma, and sarcoma, and certain leukemia or lymphoid malignancies, benign and malignant tumors, and malignancies e.g., sarcomas, carcinomas, and melanomas.
  • sarcomas e.g., sarcomas, carcinomas, and melanomas.
  • Adult tumors/cancers and pediatric tumors/cancers are also included.
  • It can be a treatment in combination with one or more therapies against cancer selected from the group of antibodies therapy, chemotherapy, cytokines therapy, dendritic cell therapy, gene therapy, hormone therapy, laser light therapy and radiation therapy.
  • therapies against cancer selected from the group of antibodies therapy, chemotherapy, cytokines therapy, dendritic cell therapy, gene therapy, hormone therapy, laser light therapy and radiation therapy.
  • the administration of the cells or population of cells according to the present invention may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation.
  • the compositions described herein may be administered to a patient subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous or intralymphatic injection, or intraperitoneally.
  • the cell compositions of the present invention are preferably administered by intravenous injection.
  • the administration of the cells or population of cells can consist of the administration of 10 4 -10 9 cells per kg body weight, preferably 10 5 to 10 6 cells/kg body weight including all integer values of cell numbers within those ranges.
  • the cells or population of cells can be administrated in one or more doses.
  • said effective amount of cells are administrated as a single dose.
  • said effective amount of cells are administrated as more than one dose over a period time. Timing of administration is within the judgment of managing physician and depends on the clinical condition of the patient.
  • the cells or population of cells may be obtained from any source, such as a blood bank or a donor. While individual needs vary, determination of optimal ranges of effective amounts of a given cell type for a particular disease or conditions within the skill of the art.
  • An effective amount means an amount which provides a therapeutic or prophylactic benefit.
  • the dosage administrated will be dependent upon the age, health and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment and the nature of the effect desired.
  • said effective amount of cells or composition comprising those cells are administrated parenterally.
  • Said administration can be an intravenous administration.
  • Said administration can be directly done by injection within a tumor.
  • cells are administered to a patient in conjunction with (e.g., before, simultaneously or following) any number of relevant treatment modalities, including but not limited to treatment with agents such as antiviral therapy, cidofovir and interleukin-2, Cytarabine (also known as ARA-C) or nataliziimab treatment for MS patients or efaliztimab treatment for psoriasis patients or other treatments for PML patients.
  • agents such as antiviral therapy, cidofovir and interleukin-2, Cytarabine (also known as ARA-C) or nataliziimab treatment for MS patients or efaliztimab treatment for psoriasis patients or other treatments for PML patients.
  • the T cells of the invention may be used in combination with chemotherapy, radiation, immunosuppressive agents, such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies, or other immunoablative agents such as CAMPATH, anti-CD3 antibodies or other antibody therapies, cytoxin, fludaribine, cyclosporin, FK506, rapamycin, mycoplienolic acid, steroids, FR901228, cytokines, and irradiation.
  • immunosuppressive agents such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies
  • immunoablative agents such as CAMPATH, anti-CD3 antibodies or other antibody therapies
  • cytoxin fludaribine
  • cyclosporin FK506, rapamycin
  • mycoplienolic acid steroids
  • steroids FR901228
  • cytokines irradiation
  • the cell compositions of the present invention are administered to a patient in conjunction with (e.g., before, simultaneously or following) bone marrow transplantation, T cell ablative therapy using either chemotherapy agents such as, fludarabine, external-beam radiation therapy (XRT), cyclophosphamide, or antibodies such as OKT3 or CAMPATH,
  • the cell compositions of the present invention are administered following B-cell ablative therapy such as agents that react with CD20, e.g., Rituxan.
  • subjects may undergo standard treatment with high dose chemotherapy followed by peripheral blood stem cell transplantation.
  • subjects receive an infusion of the expanded immune cells of the present invention.
  • expanded cells are administered before or following surgery.
  • Viral vectors include retrovirus, adenovirus, parvovirus (e. g. adenoassociated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e. g., influenza virus), rhabdovirus (e. g., rabies and vesicular stomatitis virus), paramyxovirus (e. g. measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e. g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.
  • orthomyxovirus e. g., influenza virus
  • rhabdovirus e. g., rabies and vesicular stomatitis virus
  • paramyxovirus e. g. measles and Sendai
  • viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example.
  • retroviruses include: avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
  • the invention comprises further features which will emerge from the following examples illustrating the method of in vitro sorting or in vivo depleting immune cells expressing CAR for immunotherapy, as well as the appended drawings.
  • the DNA construct of the 10 CARs are transcribed into their corresponding mRNA via in vitro transcription and used to transfect by electroporation primary T cells freshly isolated from buffy coat via a standard ficoll procedure. One day post transfection, T cells were recovered and used to performed a flow based cytotoxicity assay as described as follows.
  • primary T cells are first purified from buffy-coat samples and activated using Dynabeads human T activator CD3/CD28. 3 days post activation, 1 million of activated T cells are transduced with lentiviral vectors harboring an anti-CD123 CAR expression cassette under the control of the Ef1 ⁇ promoter, at the multiplicity of infection (MOI) of 1. T cells are kept in culture at 37° C. in the presence of 5% CO 2 , 20 ng/ml IL-2 (final concentration) and 5% human AB serum in X-vivo-15 media (Lonza) for further characterization. 5 days post transduction, cells are used to perform the flow-based cytotoxicity assay.
  • MOI multiplicity of infection
  • the cytolytic activity and specificity of anti-CD123 CAR T cell are assessed according to the flow cytometry-based cytotoxicity assay as routinely performed (see for example Valton. et Al (2015) Mol Ther; 23(9):1507-1518).
  • This assay consists of labeling 10 4 CD123 positive tumor cells and 10 4 CD123-negative control cells with 0.5 mM CellTraceTM CFSE and 0.5 mM CellTraceTM violet (Life Technology) and co-incubating them with 10 5 effector CAR T cells (E/T ratio of 10:1) in a final volume of 100 ⁇ l X-Vivo-15 media, for 5 H at 37° C.
  • Cells are then recovered and labeled with eFluor780 viability marker before being fixed by 4% PFA as described above. Fixed cells are then analysed by flow cytometry to determine their viability. The frequency of specific cell lysis is calculated and displayed in the following:
  • Via CD123+ with T and Via CD123 ⁇ with T correspond respectively to the % of viable CD123+ cells and CD123 ⁇ cells obtained after 5 H in the presence of CAR T cells and where Via CD123+ cells and Via CD123 ⁇ cells correspond respectively to the % of CD123+ cells and CD123 ⁇ cells obtained after 5 H in the absence of CAR T cells.
  • results from flow-based cytotoxicity assays described above showed that T cells expressing SEQ ID 1-4 displayed the same activity than T cells expressing unmodified anti-CD123 CAR SEQ ID 142 ( FIG. 5 ).
  • results from flow-based cytotoxicity assays described above showed that T cells expressing SEQ ID 1-4 displayed the same activity than T cells expressing unmodified anti-CD123 CAR SEQ ID 142 ( FIG. 5 ).
  • insertion of CD20 mimotope in the sequence of the anti-CD123 CAR SEQ ID 142
  • the CARs of the invention comprising one of two mAb-specific epitope, preferably of SEQ ID NO 35 are able to specifically recognize the antigen targeted by the CAR and to kill cells expressing said antigen.
  • transfected CAR T cells are tested for their capacity to degranulate when exposed to a CD123 recombinant protein coated on a 96 well plate.
  • our experiments are designed to show that insertion of CD20 mimotope in the sequence of the anti-CD123 CAR does not significantly impair its ability to specifically recognize the CD123 antigen.
  • transfected T cells are incubated in the presence of CD123-positive tumor cells, in the presence or in the absence of rituximab and baby rabbit-complement.
  • the objective is to show that the cytotoxic activity and degranulation capacity of transfected T cells are impaired in the presence of rituximab and baby rabbit complement, indicating further that efficient recognition of engineered anti-CD123 CAR by rituximab leads to T cell depletion.
  • transduced T cell expressing a CAR of SEQ ID NO 1, 2, 3 or 4 or an unmodified anti-CD123 CAR were subjected to a complement dependant cytotoxicity assay (CDC).
  • the CDC assay consisted in incubating 0.2 10 6 transduced T cells either alone, or in the presence of Rituximab (RTX, ROCHE, 400 ng) and Babby Rabbit Complement (BRC, AbD Serotec, ref# C12CA, 100 ⁇ L of the solution diluted according to the manufacturer protocol) for 3 hours at 37° C. in a final volume of 400 ⁇ L of Xvivo 10% FBS.
  • anti CD123-CAR T cells were recovered and labeled with recombinant CD123 protein fused to an FC fragment (SEQ ID 143) and a PE labeled anti-FC secondary monoclonal antibody (Jackson ImmunoResearch, ref#115-115-164, diluted 1/200).
  • the flow cytometry gating strategy consisted of determining the viability of anti-CD123 CAR positive T cells (PE positive cells) among the singlet found in the total population of cells. This analysis was performed on cells incubated alone and in the presence of RTX and BRC. Results are expressed as the ratio named “Relative frequency of viable cells among anti-CD123 CAR positive T cells (with respect to control experiment)” described below:
  • CARs of the invention having architectures illustrated by FIG. 4 allow rituximab dependent depletion of CAR T cells.
  • CAR of the invention comprising at least 2 mAb-specific epitopes, preferably having CAR architecture of SEQ ID NO 3 or 4 are particularly efficiently depleted.
  • Example 4 Efficiency of the mAb-Driven Depletion System in Cells Expressing an Anti-BCMA CAR Comprising One or More mAbs Specific Epitopes in the Extracellular Domain
  • CAR architectures SEQ ID 125-139, FIG. 7 . These architectures were designed to contain 1, 2 or 3 CD20 mimotopes localized at different portions of the extracellular domain of the anti-BCMA CAR (SEQ ID NO 125), i.e in the N terminal domain, in the linker domain separating the V1 and V2 of the ScFv or upstream to the CD8 hinge linking the ScFv to the transmembrane domain of the CAR.
  • primary T cells were first purified from buffy-coat samples and activated using Dynabeads human T activator CD3/CD28. 3 days post activation, 5 million of activated T cells were transfected with either 15 or 30 g of poly adenylated mRNA encoding the different anti-BCMA CAR architectures (SEQ ID 125-139, FIG. 7 ). T cells were then kept in culture at 37° C. in the presence of 5% CO 2 , 20 ng/ml IL-2 (final concentration) and 5% human AB serum in X-vivo-15 media (Lonza) for further characterization. One day post transfection, cells were used to perform the CDC assay, a flow based cytotoxicity assay, a detection assay and an Interferon ⁇ (IFN ⁇ ) release assay.
  • IFN ⁇ Interferon ⁇
  • the CDC assay consisted in incubating 0.2 10 6 transfected cells either alone, or in the presence of Rituximab (RTX, ROCHE, 400 ng) and Babby Rabbit Complement (BRC, AbD Serotec, ref#C12CA, 100 ⁇ L of the solution diluted according to the manufacturer protocol) for 2 hours at 37° C. in a final volume of 400 ⁇ L of Xvivo 10% FBS.
  • anti BCMA-CAR T cells were recovered and labeled with recombinant BCMA protein fused to an FC fragment (SEQ ID NO 151) and a PE labeled anti-FC secondary monoclonal antibody (Jackson ImmunoResearch, ref#115-115-164, diluted 1/200).
  • the cytolytic activity and specificity of anti-BCMA CAR T cell were assessed according to the flow cytometry-based cytotoxicity assay reported in Valton. et Al (2015) Mol Ther; 23(9):1507-1518.
  • This assay consisted of labeling BCMA positive tumor target cell (T, H929) with 0.5 mM CellTraceTM CFSE (Life Technology, incubation 10 min 37° C. according to manufacturer protocol) and co-incubate them with 10 5 anti BCMA CAR T effector (E) cells (E/T ratio of 10:1) in a final volume of 100 ⁇ l X-Vivo-15 media, for 5 H at 37° C. Cells were then recovered and labeled with eFluor780 viability marker before being fixated by 4% PFA. Fixated cells were then analysed by flow cytometry to determine their viability.
  • T cell expressing various anti-BCMA CAR comprising RTX specific epitopes by clinically relevant dose of RTX, primary T cells transfected with mRNA encoding SEQ ID 125, 130-139 were incubated, one day post transfection, for 72 hours in X-vivo-15 medium supplemented with 5% AB serum, 20 ng/mL IL2 in the absence or in the presence of 500 ⁇ g/mL RTX at a concentration of 0.1 10 6 cells/wells in a final volume of 100 ⁇ l.
  • CAR T cells were then spun down, the supernatant was recovered and analysed by ELISA (using the Human IFN-gamma Quantikine ELISA Kit, RandD systems, ref # DIF50) to determine the amount of IFN ⁇ released in the culture media.
  • ELISA using the Human IFN-gamma Quantikine ELISA Kit, RandD systems, ref # DIF50
  • PHA phytohemagglutinin
  • T cells expressing SEQ ID 126-139 were all depleted to different extents by BRC and RTX in contrast to the unmodified anti-BCMA CAR (SEQ ID NO 125) that was not markedly depleted ( FIG. 8A ).
  • the results show that efficiency of depletion increase along with the number of CD20 mimotopes present in the CAR architecture.
  • results show that separating multiple CD20 mimotopes by domain larger than GS linkers, increased the efficiency of depletion as seen when comparing the extents of depletion obtained with T cells expressing SEQ ID NO 127 and SEQ ID NO 137 containing 3 CD20 mimotopes, as well as SEQ ID NO 139 and SEQ ID NO 136 containing 2 CD20 mimotopes ( FIG. 7-8A ).
  • the CAR of the invention having CAR architecture of SEQ ID NO126-139 allow rituximab dependent depletion of CAR T cell.
  • the CAR of the invention having CAR architecture such as in SEQ ID, 136, 137, 138, i.e where the CAR comprises at least two identical mAb specific epitope separated by one or more other domains (such as VH, VL, VH-L1-VL . . . ) are particularly efficiently depleted.
  • the flow-based cytotoxicity assay results indicated that all architectures (SEQ ID 126-139) were able to recognize and kill BCMA-expressing H929 tumor cells to a similar extent than T cells expressing the unmodified version of anti-BCMA CAR architecture (SEQ ID NO 125, FIG. 9 ). Consistent with the results obtained in Example 1, the presence of 1, 2 or 3 mAb specific epitopes and in particular 1, 2 or 3 CD20 mimotopes inside the CAR architecture, did not significantly influence the cytolytic activity of anti-BCMA CAR T cells.
  • the CARs of the invention having CAR architectures of SEQ ID NO126-139 have similar cytotoxic activity as compared to a CAR without mAb-specific epitope such as a CAR of SEQ ID 125.
  • the ELISA assay results showed that the presence of one or multiple CD20 mimotopes within the CAR architecture did not influence the propensity of CAR T cells to be activated by RTX ( FIG. 11 ). Indeed The results showed that the level of IFN ⁇ released by all architectures in the presence of RTX were similar to the basal level of IFN ⁇ released in the absence of RTX.
  • FIG. 7C Two new hybrid CAR architectures SEQ ID NO 140 and 141 ( FIG. 7C ) were designed. These two architectures contained three CD20 mimotopes separated from one another by protein domains and one CD34 epitope. Their ability to be depleted by RTX and BRC was assessed by CDC assay according to the protocol described in Example 4. The results showed that these two architectures were efficiently depleted to a similar extent than T cells expressing SEQ ID 137 ( FIG. 8B ). Their cytolytic properties were also assessed using the flow-based assay described earlier.
  • the CAR of the invention having CAR architecture such as in SEQ ID 140, 141 i.e where the CAR comprises at three identical mAb-specific epitope recognized by an approved antibody such as rituximab which can be used for depletion of the cells and one mAb specific epitope which can be used for purification are particularly efficiently depleted and can also be efficiently purified.
  • CARs based on the architecture of SEQ ID NO 140 and 141 but comprising VH and VL of ScFv specific for CD19 (CAR of SEQ ID NO 162-163 and 168-169), CD123 (CAR of SEQ ID NO 164-165), CD20 (CAR of SEQ ID NO 166-167) were assembled according to the protocol described in Example 4. Their ability to be depleted by RTX and BRC can be assessed by CDC assay according to the protocol described in Example 4.
  • Results were compared side by side with detection performed with recombinant BCMA protein fused to an FC fragment (SEQ ID NO 151) and a PE labeled anti-FC secondary monoclonal antibody (Jackson ImmunoResearch, ref#115-115-164, diluted 1/200).
  • CD20 mimotope-containing CARs are codon-optimized, synthesized and subcloned into the lentiviral vector pLVX-EF1a-IRES-Puro (Clontech) using the EcoRI (5′) and MluI (3′) restriction sites (thus removing the IRES-Puro cassette).
  • Lentiviruses are produced using psPAX2, an HIV-1 gag-pol packaging plasmid, and pMD2.G, a VSV-G expression plasmid.
  • BC30 (SEQ ID NO 145) comprises the following domains:
  • BC30-LM (SEQ ID NO 146) comprises the following domains:
  • BC30-LML (SEQ ID NO 147) comprises the following domains:
  • BCMA30 VH and BCMA30 VL are respectively SEQ ID NO 97 and SEQ ID NO 98 and the mimotope is SEQ ID NO35.
  • BC30-LMLM (SEQ ID NO 148) comprises the following domains:
  • BC30-LMLML (SEQ ID NO 149) comprises the following domains:
  • Untouched T cells are isolated from human peripheral blood mononuclear cells (PBMCs) using the Pan T Cell isolation kit (Miltenyi Biotec) and activated for three days with antibodies against human CD2, CD3, and CD28 (T Cell activation/expansion kit—Miltenyi Biotec).
  • Lentiviral vectors are produced by transient transfection of sub-confluent HEK-293T/17 (American Type Culture Collection (ATCC)) cells in 6-well plates. Briefly, pLVX, psPAX2, and pMD2.G plasmids are transfected at a 4:3:1 ratio, respectively, using Lipofectamine 2000 (Invitrogen) following the manufacturer's instructions.
  • T cell culture medium 5% human AB serum in X-vivo-15 medium (Lonza)
  • X-vivo-15 medium Lonza
  • Activated T cells are seeded at 0.25 ⁇ 10 6 cells/mL in T cell culture medium containing 40 ng/ml IL-2 and transduced by adding an equal volume of fresh LV supernatant.
  • Cells are cultured at 37° C. and 5% CO2 for three days and used for flow cytometry analysis or expanded in fresh T cell medium containing 20 ng/ml IL-2.
  • FIGS. 14A and 14 B show that T cells transduced with the different CD20-mimotope-containing CARs are detected with comparable efficiency by flow cytometry using biotinylated-BCMA followed by PE-conjugated streptavidin.
  • Detection of intra CAR CD20 mimotope(s) with rituximab is weak in cells transduced with the LM construct (15.5%) but very high in all other formats tested.
  • the LMLML CAR is detected in 85.6% of the cells, indicating that this format allows the identification of virtually all cells expressing the CAR ( FIGS. 14A and 14B ).
  • the presence of two CD20 epitopes separated by flexible linkers allows for enhanced binding to rituximab and provides an optimum system to detect CAR+ cells.
  • the functionality of intra CAR CD20 epitopes for CAR-T cell detection is assessed by comparison with the RQR8 marker/suicide gene system (SEQ ID NO 150), which consists of a compact protein containing two CD20 epitopes and a CD34 epitope that is normally co-expressed with the CAR (Philip, Blood 2014).
  • SEQ ID NO 150 RQR8 marker/suicide gene system
  • T cells are transduced with a lentivirus that allows the co-expression of the BCMA30 CAR (SEQ ID NO 145) and the RQR8 protein (SEQ ID NO 150) (BC30-RQR8 construct).
  • FIG. 15 aims to show that incorporating the CD20 epitopes in the CAR molecule significantly improves detection of CAR-T cells with the anti-CD20 antibody rituximab.
  • increased transduction efficiency and CAR expression is observed in cells transduced with the BC30-R2 construct compared with those transduced with the vector encoding RQR8 and the CAR, as indicated by flow cytometry analysis with biotinylated BCMA ( FIG. 15 ).
  • insertion of CD20 epitopes into the CAR molecule enables enhanced transduction, improved detection, and absolute correlation between CAR expression and mAb specific epitope(s) expression.
  • the ability of intra CAR CD20 epitopes to enable selective elimination of CAR-T cells is evaluated in vitro using a CDC assay.
  • the objective is to show that the presence of CD20 epitopes in the CAR molecule renders CAR-T cells highly susceptible to rituximab-mediated depletion.
  • T cells transduced with either the BC30-R2 construct or the BC30-RQR8 construct are mixed with 25% baby-rabbit complement (AbD serotec) in the presence or absence of rituximab (100 ⁇ g/mL) and incubated at 37° C. and 5% CO2 for 4 hours.
  • Selective deletion of CAR-T cells is determined by flow cytometry analysis using biotinylated BCMA protein.
  • FIG. 16 shows that while both the RQR8 and intra CAR CD20 epitope suicide gene systems enable CAR-T cell depletion, cells transduced with the BC30-R2 construct are depleted more efficiently than those expressing RQR8. As expected, T cells expressing the BCMA30 CAR but no CD20 epitopes (BC30 construct) are spared. These differences may be due to the high expression of the BC30-R2 CAR and the absolute correlation between CAR expression and suicide gene expression.
  • T cells expressing either the BC30-R2 construct or the BC30-RQR8 construct are incubated with Luciferase-positive MM1S target cells at different ratios.
  • Luciferase-positive MM1S target cells For these killing assays, cells are seeded in 96-well white opaque tissue culture plates in a final volume of 100 ⁇ l of 5% human AB serum in X-vivo-15 medium (Lonza). After 4 hours, cells are equilibrated to room temperature and one volume of Bright-GloTM Reagent (Promega) is added to each well. Luminescence is measured in a GLOMAX 96 microplate luminometer (Promega) and percentage of cell lysis is calculated according to the following formula:
  • BC30-R2 CAR-T cells effectively eliminate BCMA-expressing MM1S cells in vitro ( FIG. 17 ).
  • the cytolytic activity of BC30-R2 CAR-T cells is not influenced by rituximab (100 ⁇ g/mL), which is added to the effector cell population 2 h before these cells are mixed with the target cells ( FIG. 17 ).
  • This experiment aims to demonstrate that insertion of CD20 epitopes into the BC30 CAR molecule does not affect its ability to mediate killing of BCMA+ target cells, even in the presence of rituximab.
  • BC30-R2 CAR-T cells are grown in the presence of rituximab.
  • the anti-CD3 OKT3 antibody (eBioscience) causes crosslinking of the T cell receptor (TCR) resulting in cellular activation and proliferation and is used as a positive control.
  • TCR T cell receptor
  • BC30-R2 CAR-T cells are cultured in T cell medium in the presence/absence of rituximab for three days. T cell activation is then assessed by measuring the expression of the activation markers CD25 and CD69 using flow cytometry.
  • a polypeptide encoding a chimeric antigen receptor (CAR) comprising at least one extracellular binding domain that comprises a scFv formed by at least a VH chain and a VL chain specific to a cell surface marker antigen, wherein said extracellular binding domain includes at least one mAb-specific epitope to be bound by a epitope-specific mAb for in vitro cell sorting and/or in vivo cell depletion of the immune cells expressing said CAR.
  • CAR chimeric antigen receptor
  • a polypeptide according to embodiment 1 or 2 wherein said VH and VL chains, and mAb specific-epitope are bound together by at least one linker and to the transmembrane domain of said CAR by a hinge. 4. A polypeptide according to embodiment 3, wherein the mAb-epitope is joined to the VH and VL chains by two linkers. 5. A polypeptide according to anyone of embodiment 1 to 4, wherein the mAb-epitope is from one polypeptide selected from those listed in Table 1. 6.
  • VH and VL chains have as antigenic target sequence of over 80% identity, preferably over 90%, and more preferably over 95% with SEQ ID NO 53-64 (CD19 antigen), SEQ ID NO 65-76 (CD33 antigen), SEQ ID NO 77-84 (5T4 antigen), SEQ ID NO 85-90 (ROR1 antigen), SEQ ID NO 91-94 (EGFRvIII antigen), SEQ ID NO 95-102 (BCMA antigen), SEQ ID NO 103-112 (CS1 antigen) and SEQ ID NO 113-124 (CD123 antigen).
  • An expression vector comprising a nucleic acid of embodiment 12.
  • An engineered immune cell expressing at its cell surface a chimeric antigen receptor according to anyone of embodiments 1 to 12.
  • An engineered immune cell according to embodiment 14 derived from inflammatory T-lymphocytes, cytotoxic T-lymphocytes, regulatory T-lymphocytes or helper T-lymphocytes. 16.
  • a method for engineering an immune cell of anyone of embodiment 14-16 comprising: (a) Providing an immune cell; (b) Introducing into said cell at least one polynucleotide encoding the chimeric antigen receptor according to anyone of embodiment 1-12. (c) Expressing said polynucleotide into said cell. 18.
  • a method for sorting CAR-expressing immune cells comprising contacting a population of immune cells engineered according to anyone of embodiment 14-16 with antigen-specific mAbs in order to collect CAR-expressing immune cells only.
  • 26. A method for depleting immune cell CAR-expressing immune cell according to anyone of embodiment 22-25, comprising contacting said immune cell or CAR-expressing immune cell with bi-specific mAb (BsAb) able to bind both the mAb-specific epitope borne on said cells and to an surface antigen borne on an effector (and cytotoxic) cell.
  • BsAb bi-specific mAb
  • Method for regulating the activation of an engineered immune cell comprising at least the step of: (i) Endowing said immune cell with a CAR, which extracellular binding domain comprises a scFv recognizing a cell surface marker linked to a mAb specific epitope (ii). Expanding said immune cell expressing said CAR and said mAb epitope on its surface (iii) Contacting the resulting immune cells with the mAb specific to said epitope to immobilize said immune cells.

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