Patent Application
20230158070
Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 430,675 Byte ASCII (Text) file named “2021-01-08_38569-251_SQL_ST25.txt,” created on Jan. 8, 2021.
The present invention relates to a therapeutic combination of immune cells, preferably allogeneic non-alloreactive TCR-KO immune T cells, wherein a gene coding an antigen marker X present on both T-cells and pathological cells is inactivated and a corresponding therapeutic antibody specific for said antigen marker X, method for preparing the same and use in immunotherapy.
The present invention also relates to rare cutting endonucleases (ex: Cas9/CRISPR, meganucleases, Zinc-finger nucleases or TAL nucleases, specific for the gene encoding said antigen marker, their use for making allogeneic therapeutic cells, alone or in combination with a therapeutic antibody specific for said marker antigen. The engineered cells can be used in immune T cell depleted hosts, in the presence of said corresponding therapeutic antibody. The invention opens the way to standard and affordable adoptive immunotherapy strategies using in particular T-cells resistant to treatment with anti-T cells therapeutic antibody, for treating a cancer, an infection and an auto-immune disease.
Adoptive immunotherapy, which involves the transfer of 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, see, e.g., Brenner et al., Current Opinion in Immunology, 22(2): 251-257 (2010). A Genetic modification consists in expressing chimeric antigen receptors (CARs) in immune T cells. CAR are fusion proteins comprised of an antigen recognition moiety and T cell activation domains (see, e.g., Eshhar et al., Proc. Natl. Acad. Sci. USA, 90(2): 720-724 (1993), and Sadelain et al., Current Opinion in Immunology, 21(2): 215-223 (2009)). Often, the antigen recognition moiety of a CAR consists of an antigen-binding domain of a single-chain antibody (scFv), comprising the light and 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 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), and 4-1BB (CD137) added alone (second generation) or in combination (third generation) to the cytoplasmic domain of CARSs enhance survival and increase proliferation of CAR modified T cells. Other domains seem to be determinant in the capacity of CARs to bind their target such as the hinge or stalk domain.
The current protocol for treatment of patients using adoptive immunotherapy is based on autologous cell transfer. In this approach, T lymphocytes are recovered from patients, genetically modified or selected ex vivo, cultivated and expanded in vitro in order to amplify the number of cells and finally infused into the patient. In addition to lymphocyte infusion, the host may be manipulated in other ways that support the engraftment of the T cells or their participation in an immune response, for example pre-conditioning (with radiation or chemotherapy) and administration of lymphocyte growth factors (such as IL-2). Each patient receives an individually fabricated treatment, using the patient's own lymphocytes (i.e. an autologous therapy). Autologous therapies face consequently substantial technical and logistic hurdles to practical application, their generation requires expensive dedicated facilities and expert personnel, they must be generated in a short time following a patient's diagnosis, and in many cases, pretreatment of the patient has resulted in degraded immune function, such that the patient's lymphocytes may be poorly functional and present in very low numbers. Because of these hurdles, each patient's autologous cell preparation is effectively a new product, resulting in substantial variations in efficacy and safety.
Ideally, one would like to use a standardized therapy in which allogeneic therapeutic cells could be pre-manufactured, characterized in detail, and available for immediate administration to patients. By allogeneic it is meant that the cells are obtained from individuals belonging to the same species but are genetically dissimilar. The use of allogeneic cells may nevertheless encounter many drawbacks. In immune-competent hosts allogeneic cells are rapidly rejected, a process termed host versus graft rejection (HvG), and this substantially limits the efficacy of the transferred cells. In immune-incompetent or compatible hosts, allogeneic cells are able to engraft, but their endogenous T-cell receptors (TCR) specificities may still recognize the host tissue as foreign, resulting in graft versus host disease (GvHD), which can lead to serious tissue damage and death.
In order to provide less alloreactive allogeneic T-cells, preferably allogeneic non-alloreactive TCR-KO immune T cells, the inventors previously disclosed a method to genetically engineer immune cells, in which different effector genes, in particular those encoding T-cell receptors, were inactivated by using specific TAL-nucleases, better known under the trade mark TALEN™ (Cellectis, 8, rue de la Croix Jarry, 75013 PARIS). This method has proven to be highly efficient in primary cells using RNA transfection as part of a platform allowing the mass production of allogeneic T-cells (WO 2013/176915).
Effector cells and pathological cells may express a number of common antigens such as those described in WO2015121454A1.
Thus, CD38 (cluster of differentiation 38), also known as cyclic ADP ribose hydrolase is a glycoprotein found on the surface of many immune cells (white blood cells), in particular on T-cells, including CD4+, CD8+, B lymphocytes and natural killer cells. CD38 also functions in cell adhesion, signal transduction and calcium signaling. Structural information about this protein can be found in the UniProtKB/Swiss-Prot database under reference P28907. In humans, the CD38 protein is encoded by the CD38 gene which located on chromosome 4. CD38 is a multifunctional ectoenzyme that catalyzes the synthesis and hydrolysis of cyclic ADP-ribose (cADPR) from NAD+ to ADP-ribose. These reaction products are deemed essential for the regulation of intracellular Ca2+. Also, loss of CD38 function was associated with impaired immune responses and metabolic disturbances (Malavasi F., et al. (2008). “Evolution and function of the ADP ribosyl cyclase/CD38 gene family in physiology and pathology”. Physiol. Rev. 88(3): 841-86).
CD38 protein is also a marker of HIV infection, leukemias, myelomas, solid tumors, type II diabetes mellitus and bone metabolism, as well as some other genetically determined conditions. In particular, it has been used as a prognostic marker in leukemia (Ibrahim, S. et al. (2001) CD38 expression as an important prognostic factor in B-cell chronic lymphocytic leukemia. Blood 98:181-186).
The cell surface glycoprotein CS1 (also referred in the literature as SLAMF7, CD319 or CRACC—NCBI Reference Sequence: NP_067004.3) is highly and ubiquitously expressed on the surface of non-pathological (normal) lymphocytes and myeloma cells (Hsi E D, et al. Clin Cancer Res 2008 14:2775-84). CS1 is expressed at very low levels in the majority of immune effector cells, including natural killer (NK) cells, some subsets of T cells, and normal B cells, and is almost undetectable on myeloid cells (Hsi E D, et al. Clin Cancer Res 2008 14:2775-84). Notably, CS1 is negligibly expressed in human hematopoietic stem cells (Hsi E D, et al. Clin Cancer Res 2008 14:2775-84), which can be used for stem cell transplantation to treat hematologic malignancies, including MM. The functions of CS1 in MM remain incompletely understood, and it has been documented that CS1 may play a role in myeloma cell adhesion, clonogenic growth, and tumorigenicity (Benson D M Jr, et al. J Clin Oncol 2012 30:2013-5; Tai Y T, et al. Blood 2009 113:4309-18).
Similarly, cluster of Differentiation 70 (CD70, CD27LG or TNFSF7) is a member of the tumor necrosis factor (TNF) superfamily and the ligand for CD27, a TNF superfamily receptor which is expressed on normal T cells and may be over expressed in pathological cells. The transient interaction between CD27 and CD70 provides T cell costimulation complementary to that provided by CD28. CD70 is expressed on hematological cancers such as Non-Hodgkin's Lymphoma and Hodgkin's disease as well as on solid tumors such as Glioblastoma and Renal Cell Carcinoma; with its expression on Renal Cell Carcinoma being nearly uniform (see e.g., Grewal I., et al., Expert Opinion on Therapeutic Targets, 12(3): 341-351 (2008)). CD70 antibodies are currently used to induce or produce a lymphodepletion, or to treat particular diseases (see Cancer Res 2006; 66(4): 2328-37).
Expression, even transient, of such antigens on T cells may be an obstacle during the manufacturing and production of CAR T cells due to potential target-driven T cell differentiation, exhaustion, and fratricide. To palliate this, the inventors previously disclosed genetically engineer T-cells in which, a gene encoding an antigen X expressed on both T cells and pathological cells was inactivated by using specific TAL-nucleases. In these cells, a TCR subunit may be also inactivated so that cell surface expression of endogenous TCR remains undetectable as described in WO2016142532A1 which is incorporated here in its entirety. A CAR which gene is inserted into the genome of these cells can both, inhibit cell surface expression of the TCR and specifically redirects said cells against the antigen X while providing cells with a TCR-like mediated activity.
The inventors now disclosed a combination of said engineered cell with a therapeutic antibody specific for X. The specificity of said therapeutic antibody, for the same antigen X expressed on T cells and pathological cells, targeted by the CAR and which gene is inactivated in effector allogeneic T cells makes the combination especially efficient and fast in reducing the tumoral mass as compared to either T cells or therapeutic antibody alone.
Surprisingly, the combination of drugs of the invention allows, a better circumscription of cancer cells due to the possibility of accessing different compartments in the body where cancer cells migrated and niched, as compared to individuals treated with CART cells or the antibody specific for the corresponding antigen, alone.
Targeting the same antigen marker in cancer cells using two different pathways seem also to allow reducing significantly the amount of undesired cellular immune response (such as cytokine release syndrome).
In general, the present invention discloses a combination of immune cells comprising an inactivated antigen marker X, and a therapeutic antibody specific for X, with X being expressed on both immune cell and pathological cells. This combination is provided for the treatment of a disease mediated by pathological cells or tissues expressing X or over expressing X as compared to normal tissue.
In particular embodiments, inactivated means that a gene encoding a protein (X) in immune cells is inactivated such as X is not expressed at the cell surface or is expressed and inactive. In combination with a therapeutic antibody specific for said antigen marker X, engineered immune cells are particularly efficient in reducing the tumor mass, reducing or preventing the escape or relapse of immune cells. Examples of such antigen markers X are found in Table 4 to 14. An illustration of such antigen marker is CD38, CS1 or CD70. By antigen marker is meant the whole protein or an immune-reactive fragment thereof.
The present invention provides a combination comprising an immune cell comprising at least one inactivated gene coding a cell surface antigen X, with X being expressed on both immune cell and pathological cell and a therapeutic antibody specific for said cell surface antigen X.
The present invention provides a combination comprising engineered immune cells, or a population of engineered immune cells, comprising at least one inactivated gene coding a cell surface antigen X, with X being expressed on both immune cells and pathological cells, and a therapeutic antibody specific for said cell surface antigen X, preferably a homogenous population of immune cells, more preferably a homogenous population of immune cells expressing less than 90% X at the cell surface as compared to non engineered immune cells. In preferred embodiments, the immune cells comprise an inactivated alpha and/or beta TCR gene(s) and/or inactivated beta 2 Microglobulin gene and an inactivated antigen marker X gene, and a therapeutic antibody specific for X, with X being expressed on both immune cell and pathological cells, preferably a homogenous population of immune cells, more preferably a homogenous population of immune cells expressing less than 90% alpha beta TCR and less than 90% X at the cell surface as compared to non engineered immune cells.
The combination of the invention comprises an immune cell comprising at least one inactivated gene coding a cell surface antigen, said at least one inactivated gene coding a cell surface antigen comprising a genetic modification affecting cell surface expression of said cell surface antigen and
Preferably, the present invention provides a combination comprising
The present invention provides a combination comprising:
In other embodiments the present invention provides a combination comprising
provided that said gene is not a gene coding a component of the alpha beta TCR which modification inhibits cell surface expression of the alpha beta TCR, such as a gene coding the constant part of the TCR alpha subunit (TRAC A gene), and said therapeutic antibody is not an antibody selectively binding to an antigen present at the surface of alpha beta TCR positive (αβTCR+) cells.
In another embodiment the present invention provides a combination comprising
When generating “off the shelve” engineered immune cells, the invention generally concerns a combination for immunotherapy comprising:
An allogeneic immune T cell means an alpha beta TCR deficient immune T cell or cells comprising more than 90% TCR-negative T cells, preferably said allogeneic immune T cells comprising a rare cutting endonuclease mediated TCR deficient gene, which product is not expressed at the cell surface.
In preferred embodiments, said allogeneic immune T cells comprise a TALEN-mediated TCR alpha inactivated gene, even more preferably said TALEN-mediated TCR alpha inactivated gene is inactivated by insertion of a polynucleotide into the constant part of the TCR alpha subunit (TRAC A gene), even more preferably, said TALEN®-modified endogenous αβ-TCR negative human primary T cell wherein the constant region of the genomic TCR gene (TRAC gene) comprises a genetic modification generated by a TALEN® and affecting cell surface expression of the endogenous alpha beta TCR, said genomic TRAC gene comprising from 5′ to 3′:
(a) a 5′ region of said human genomic TRAC gene upstream,
(b) a recognition domain for a TALEN®,
(c) a gap or an insertion as compared to the wild type TRAC gene affecting the cell surface expression of the extracellular domain or transmembrane domain of the alpha beta TCR, said insertion comprising an exogenous polynucleotide selected from a noncoding sequence such as, a stop codon, an IRES, a coding sequence such as a sequence coding for a self-cleaving peptide in frame with the TRAC open reading frame, a sequence coding a chimeric antigen receptor (CAR), a sequence coding a TCR, a sequence coding a protein conferring sensitivity to a drug, a sequence coding a protein conferring resistance to a drug, a cytokine, a termination sequence, a combination thereof,
(c′) optionally a second TALEN® recognition domain,
(d) a 3′ region of the genomic TRAC gene.
In more preferred embodiments said allogeneic T cell may be a human primary allogeneic T cell or a homogenous population of human primary allogeneic T cells, preferably a human primary CD8 allogeneic T cell, human primary CD4 allogeneic T cell, a combination thereof.
In even more preferred embodiments, a combination of the invention comprises a TALEN®-modified endogenous αβ-TCR negative human primary allogeneic T cell comprising a recognition domain for a TALEN® comprising any one of the following sequences ttgtcccacagATATC, ttgtcccacagATATCCAG, CCGTGTACCAGCTGAGA, a combination thereof, and a TALEN®-inactivated antigen marker X gene, and a therapeutic antibody specific for X, with X being expressed on both immune cell and pathological cells,
In another embodiment the present invention provides a combination comprising
provided that said gene is not a gene coding a component of the alpha beta TCR which modification inhibits cell surface expression of the alpha beta TCR, such as a gene coding the constant part of the TCR alpha subunit (TRAC A gene), and said therapeutic antibody is not an antibody selectively binding to an antigen present at the surface of alpha beta TCR positive (αβTCR+) cells.
Affecting cell surface expression of X means decreasing cell surface expression to undetectable level of X as compared to a positive control expressing said antigen X or inactivating the activity of said surface antigen X.
A genetic modification means a mutation, a deletion or an insertion, resulting in an inactivation (silencing) of a gene, and/or inactivation of transcription, translation, and/or inactivation of protein expression, inactivation of protein expression at the cell surface, inactivation of the activity of the protein coded by said gene.
The following embodiments of the invention are provided:
In particular embodiments said immune T cell is a population of T cells, preferably homogenous population of T cells.
A TCR negative immune cell means a cell comprising a TCR KO gene, or a TCR deficient gene, deficiency resulting in a disruption of cell surface expression of the TCR.
In the present invention alpha beta TCR deficient cells express less than 90%, preferably less than 95% alpha beta TCR at the cell surface as determined by flow cytometry.
Inhibition of cell surface expression of an antigen, means that in 80 to 90%, preferably in more than 99%, even more preferably in more than 99.9% of total cells, cell surface expression of said antigen is undetectable by flow cytometry.
Particular embodiments encompass any one of the followings:
CD70-expressing cancers that can be treated or prevented using the combination of the invention, for example, different subtypes of Non-Hodgkin's Lymphoma (indolent NHLs, follicular NHLs, small lymphocytic lymphomas, lymphoplasmacytic NHLs, or marginal zone NHLs); Hodgkin's disease (e.g., Reed-Sternberg cells); cancers of the B-cell lineage, including, e.g., diffuse large B-cell lymphomas, follicular lymphomas, Burkitt's lymphoma, mantle cell lymphomas, B-cell lymphocytic leukemias (e.g., acute lymphocytic leukemia, chronic lymphocytic leukemia); Epstein Barr Virus positive B cell lymphomas; renal cell carcinomas (e.g., clear cell and papillary); nasopharyngeal carcinomas; thymic carcinomas; gliomas; glioblastomas; neuroblastomas; astrocytomas; meningiomas; Waldenstrom macroglobulinemia; multiple myelomas; and colon, stomach, and rectal carcinomas. The cancer can be, for example, newly diagnosed, pre-treated or refractory or relapsed. In preferred embodiments, a CD38-expressing cancer has at least about 15,000, at least about 10,000 or at least about 5,000 CD38 molecules/cell.
In preferred embodiments, a CS1-expressing cancer has at least about 15,000, at least about 10,000 or at least about 5,000 CS1 molecules/cell.
In preferred embodiments, a CD70-expressing cancer has at least about 15,000, at least about 10,000 or at least about 5,000 CD70 molecules/cell.
CS 1 (also known as SLAMF7, CRACC, 19A, APEX-1, FOAP 12, and 19A; GENBANK® Accession No. NM 021181.3, Ref. Boles et al, Immunogenetics, 52:302-307 (2001); Bouchon et al, J. Immunol, 167:5517-5521 (2001); Murphy et al, Biochem. J., 361:431-436 (2002)) is a member of the CD2 subset of the immunoglobulin superfamily. Molecules of the CD2 family are involved in a broad range of immunomodulatory functions, such as co-activation, proliferation differentiation, and adhesion of lymphocytes, as well as immunoglobulin secretion, cytokine production, and NK cell cytotoxicity. Several members of the CD2 family, such as CD2, CD58, and CD 150, play a role or have been proposed to play a role in a number of autoimmune and inflammatory diseases, such as psoriasis, rheumatoid arthritis, and multiple sclerosis. It has been reported that CS 1 plays a role in NK cell-mediated cytotoxicity and lymphocyte adhesion (Bouchon, A. et al, J. Immunol, 5517-5521 (2001); Murphy, J. et al, Biochem. J., 361:431-436 (2002)).
Elotuzumab is a humanized monoclonal IgGI antibody directed against CS-1, a cell surface glycoprotein, which is highly and uniformly expressed in multiple myeloma. Elotuzumab induces significant antibody-dependent cellular cytotoxicity (ADCC) against primary multiple myeloma cells in the presence of peripheral lymphocytes (Tai et al, Blood, 112: 1329-1337 (2008)). Results of three studies that evaluated the safety and efficacy of this drug administered alone (Zonder et al, Blood, 120(3):552-559 (2012)), in combination with bortezomib (Jakubowiak et al, J. Clin. Oncol., 30(16): 1960-1965 (Jun. 1, 2012)), or lenalidomide and low-dose dexamethasone (Lonial et al, J. Clin. Oncol., 30: 1953-1959 (2012); and Richardson et al, Blood (ASH Annual Meeting Abstracts), 1 16:986 (2010) for the treatment of patients with relapsed or refractory multiple myeloma, have been reported. All three combinations showed a manageable safety profile and encouraging activity. For example, a Phase VII study evaluating the safety and efficacy of Elotuzumab in combination lenalidomide and low-dose dexamethasone for the treatment of relapsed or refractory multiple myeloma demonstrated a 33 month PFS as well as a 92% response rate for patients receiving the 10 mg/kg dose (Lonial et al., J. Clin. Oncol., 31 (2013) (Suppl., Abstr. 8542)). Phase III clinical trials of lenalidomide/dexamethasone with or without Elotuzumab in previously untreated multiple myeloma patients is ongoing, while another phase III trial designed to evaluate this same combination in the first line setting is also ongoing.
In particular embodiments a TAL-protein as any one of the TAL protein of item 54, is provided for use in the manufacturing of CART cells.
A TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; with SEQ ID NO 116 and SEQ ID NO 117; or with SEQ ID NO 118 and SEQ ID NO 119, is provided for modifying the CD38 gene.
A TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 102 and SEQ ID NO 103; with SEQ ID NO 104 and SEQ ID NO 105; or with SEQ ID NO 106 and SEQ ID NO 107, is provided for modifying the CD70 gene.
A TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 108 and SEQ ID NO 109; with SEQ ID NO 110 and SEQ ID NO 111; with SEQ ID NO 112 and SEQ ID NO 113; with SEQ ID NO 171 and SEQ ID NO 172; with SEQ ID NO 173 and SEQ ID NO 174; with SEQ ID NO 175 and SEQ ID NO 176; or with SEQ ID NO 177 and SEQ ID NO 178, is provided for modifying the CS1 gene.
A polynucleotide or a vector encoding any one of the TAL protein above is provided.
A TAL-protein comprising a sequence of SEQ ID NO 114 and SEQ ID NO 115.
A TAL-protein comprising a sequence of SEQ ID NO 116 and SEQ ID NO 117.
A TAL-protein comprising a sequence of SEQ ID NO 118 and SEQ ID NO 119.
A TAL-protein comprising a sequence of SEQ ID NO 102 and SEQ ID NO 103.
A TAL-protein comprising a sequence of SEQ ID NO 104 and SEQ ID NO 105.
A TAL-protein comprising a sequence of SEQ ID NO 106 and SEQ ID NO 107.
A TAL-protein comprising a sequence of SEQ ID NO 108 and SEQ ID NO 109.
A TAL-protein comprising a sequence of SEQ ID NO 110 and SEQ ID NO 111.
A TAL-protein comprising a sequence of SEQ ID NO 112 and SEQ ID NO 113.
A TAL-protein comprising a sequence of SEQ ID NO 171 and SEQ ID NO 172.
A TAL-protein comprising a sequence of SEQ ID NO 173 and SEQ ID NO 174.
A TAL-protein comprising a sequence of SEQ ID NO 175 and SEQ ID NO 176.
A TAL-protein comprising a sequence of SEQ ID NO 177 and SEQ ID NO 178.
A TAL-protein according to item 54 comprising a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; comprising a sequence having at least 95% homology with SEQ ID NO 116 and SEQ ID NO 117; comprising a sequence having at least 95% homology with SEQ ID NO 118 and SEQ ID NO 119; comprising a sequence having at least 95% homology with SEQ ID NO 102 and SEQ ID NO 103; comprising a sequence having at least 95% homology with SEQ ID NO 104 and SEQ ID NO 105; comprising a sequence having at least 95% homology with SEQ ID NO 106 and SEQ ID NO 107; comprising a sequence having at least 95% homology with SEQ ID NO 108 and SEQ ID NO 109; comprising a sequence having at least 95% homology with SEQ ID NO 110 and SEQ ID NO 111; comprising a sequence having at least 95% homology with SEQ ID NO 112 and SEQ ID NO 113; comprising a sequence having at least 95% homology with SEQ ID NO 171 and SEQ ID NO 172; comprising a sequence having at least 95% homology with SEQ ID NO 173 and SEQ ID NO 174; comprising a sequence having at least 95% homology with SEQ ID NO 175 and SEQ ID NO 176; or comprising a sequence having at least 95% homology with SEQ ID NO 177 and SEQ ID NO 178 for use in the manufacturing of CART cells.
A TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; with SEQ ID NO 116 and SEQ ID NO 117; with SEQ ID NO 118 and SEQ ID NO 119; is provided for modifying the CD38 gene.
A TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 102 and SEQ ID NO 103; with SEQ ID NO 104 and SEQ ID NO 105; with SEQ ID NO 106 and SEQ ID NO 107, is provided for modifying the CD70 gene.
A TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 108 and SEQ ID NO 109; with SEQ ID NO 110 and SEQ ID NO 111; with SEQ ID NO 112 and SEQ ID NO 113 with SEQ ID NO 171 and SEQ ID NO 172; with SEQ ID NO 173 and SEQ ID NO 174; with SEQ ID NO 175 and SEQ ID NO 176; or with SEQ ID NO 177 and SEQ ID NO 178 is provided for modifying the CS1 gene.
A polynucleotide or a vector encoding a protein comprising any one of the TAL protein above is provided.
A polynucleotide or a vector encoding any one of the TAL protein above is provided.
An engineered immune T cell comprising a CD38 modified gene obtained using a TAL-protein or a polynucleotide encoding a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; with SEQ ID NO 116 and SEQ ID NO 117; or with SEQ ID NO 118 and SEQ ID NO 119 is provided.
An engineered immune T cell comprising a CD70 modified gene obtained using a TAL-protein or a polynucleotide encoding a sequence having with SEQ ID NO 102 and SEQ ID NO 103; with SEQ ID NO 104 and SEQ ID NO 105; or with SEQ ID NO 106 and SEQ ID NO 107, is provided.
An engineered immune T cell comprising a CS1 modified gene obtained using a TAL-protein or a polynucleotide encoding a sequence having with SEQ ID NO 108 and SEQ ID NO 109; with SEQ ID NO 110 and SEQ ID NO 111; with SEQ ID NO 112 and SEQ ID NO 113; with SEQ ID NO 171 and SEQ ID NO 172; with SEQ ID NO 173 and SEQ ID NO 174; with SEQ ID NO 175 and SEQ ID NO 176; or with SEQ ID NO 177 and SEQ ID NO 178 is provided.
According to the invention, the immune cells are engineered in order to inactivate a gene encoding an antigen marker or several antigens markers, or to inactivate the expression of the gene which product is involved in the presentation of such antigen marker on the cell surface.
Inactivation is preferably performed by a genome modification, more particularly through the expression, preferably transient, in the cell of a specific rare-cutting endonuclease able to target a genetic locus directly or indirectly involved in the production or presentation of said antigen marker at the surface of the cell. Different types of rare-cutting endonucleases can be used, such as Meganucleases, TAL-nucleases, zing-finger nucleases (ZFN), or RNA guided endonucleases like Cas9/CRISPR. The specific rare-cutting endonucleases used here, Meganucleases, TAL-nucleases, zing-finger nucleases (ZFN), and RNA guided endonucleases like Cas9/CRISPR are part of the present invention, their use for engineering cells for immunotherapy.
According to a preferred embodiment, the immune cells defective in at least one antigen marker X are endowed with at least one chimeric antigen receptors (CAR) allowing a specific binding of target cells bearing said targeted antigen marker X and the concomitant use of a therapeutic antibody targeting X.
According to another embodiment, the immune cells can be further engineered to make them allogeneic, especially by deleting genes involved into self-recognition, such as those, for instance, encoding components of T-cell receptors (TCR) or HLA complex.
The present invention encompasses the isolated cell, or cell lines, in particular isolated T-cells, or T cell lines comprising the genetic modifications set forth in the detailed description, examples and figures, as well as any of the proteins, polypeptides or vectors useful to engineer said T-cells.
As a result of the invention, the proteins, polynucleotides, vectors and engineered-cells can be used as therapeutic products, ideally as an “off the shelf” product, in methods for treating or preventing cancer, infections or auto-immune disease.
Tables 4 to 14: Examples of antigen markers, which can be targeted with the engineered-cells of the invention for treating different types of cancer.
Table 5 to 13: Surface antigen markers expressed in T-cells, while being over-expressed in tumor cells from various types of cancer.
Table 5: colon tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 5 and a therapeutic antibody specific for X, for the treatment of colon cancer.
Table 6: breast tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 6 and a therapeutic antibody specific for X, for the treatment of breast cancer.
Table 7: digestive track tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 7 and a therapeutic antibody specific for X, for the treatment of digestive tract cancer.
Table 8: kidney tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers in table 8 and a therapeutic antibody specific for X, for the treatment of kidney cancer.
Table 9: liver tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 9 and a therapeutic antibody specific for X, for the treatment of liver cancer.
Table 10: lung tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 10 and a therapeutic antibody specific for X, for the treatment of lung cancer.
Table 11: ovary tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers in table 11 and a therapeutic antibody specific for X, for the treatment of ovary cancer.
Table 12: pancreas tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 12 and a therapeutic antibody specific for X, for the treatment of pancreas cancer.
Table 13: prostate tumor cells;
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 13 and a therapeutic antibody specific for X, for the treatment of prostate cancer.
Table 14: Main surface antigen markers expressed in T-cells, while being over-expressed in liquid tumor cells from various types of cancer (ALL, AML, CML, MDS, CLL, CTRL).
A combination comprising immune cells, comprising an inactivated antigen marker corresponding to any one of the antigen markers X in table 14 and a therapeutic antibody specific for X, for the treatment of ALL, AML, CML, MDS, CLL, CTRL.
Unless specifically defined herein, all technical and scientific terms used have the same meaning as commonly understood by a skilled artisan in the fields of gene therapy, biochemistry, genetics, and molecular biology.
All methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, with suitable methods and materials being described herein. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will prevail. Further, the materials, methods, and examples are illustrative only and are not intended to be limiting, unless otherwise specified.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Current Protocols in Molecular Biology (Frederick M. AUSUBEL, 2000, Wiley and son Inc, Library of Congress, USA); Molecular Cloning: A Laboratory Manual, Third Edition, (Sambrook et al, 2001, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Harries & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the series, Methods In ENZYMOLOGY (J. Abelson and M. Simon, eds.-in-chief, Academic Press, Inc., New York), specifically, Vols. 154 and 155 (Wu et al. eds.) and Vol. 185, “Gene Expression Technology” (D. Goeddel, ed.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); and Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).
In a general aspect, the present invention relates to new combinations of engineered immune cells with undetectable level of cell surface expression of an antigen marker X, with X usually expressed on normal non pathological immune cells, with a therapeutic antibody specific for X, for new adoptive immunotherapy strategies in treating diseases linked with the development of pathological cells expressing an antigen marker X, such as cancer cells, infected cells and cells involved in auto-immune diseases. An immune cell is a cytotoxic T cell which activation by an antigen results in lysis of the target cells.
The main objective of the invention is to target pathological cells that bear specific antigen markers in common with T-cells using two immune reagents, a therapeutic antibody and an engineered immune cell, with the particularity that both reagents target the same antigen which is normally expressed on normal immune cells and on pathological cells.
Thus, in individuals treated with the combination of the invention, an immunodepletion may be obtained but the use of immune cells may not be compromised as engineered immune cells of the present invention are resistant to the therapeutic antibody with which they are combined to and can therefore be used in an individual treated with said therapeutic antibody.
By pathological cell is meant any types of cells present in a patient, which are deemed causing health deterioration.
In general, pathological cells are malignant or infected cells that need to be reduced or eliminated to obtain remission of a patient.
Affecting cell surface expression means decreasing cell surface expression to undetectable level or inactivating the activity of said surface antigen.
In particular embodiments the invention provides a combination according to item 1 wherein said immune cell is an immune T cell, a hematopoietic stem cell, preferably a TCR negative immune T cell, a TCR negative hematopoietic stem cell.
In preferred embodiments said immune T cell is a population of T cells, preferably homogenous.
A TCR negative immune cell means a cell comprising a TCR KO gene, or a TCR deficient gene, deficiency resulting in a disruption of cell surface expression of the TCR. Preferably said TCR is an alpha beta TCR.
Inhibition of cell surface expression means that in 80 to 90%, preferably in more than 99%, even more preferably in more than 99.9% of total cells, cell surface expression of said antigen is undetectable by flow cytometry.
In particular embodiments the invention provides a combination comprising an engineered immune CD8 T cell, immune CD4 T cells, inflammatory T-cell cytotoxic T-cell, regulatory T-cell or helper T-cell. Cytotoxic CD4 T− cell, Cytotoxic CD8 T− lymphocyte.
In particular embodiments the invention provides a combination according to anyone of item 1 to 3 wherein said gene is selected from any one of the genes in Table 4 to 14. A genetic modification means a mutation, an insertion or a deletion generated using a rare cutting endonuclease. Insertion comprises a polynucleotide encoding a gene, such as a CAR, a gene conferring resistance to a drug, sensitivity to a drug, encoding a cytokine.
In particular embodiments the invention provides a combination wherein said genetic modification is generated by a TAL-Nuclease, preferably a mRNA encoding a TAL-Nuclease. In particular embodiments the invention provides a combination according to any one of item 11 wherein said immune T cell express a CAR targeting specifically CD38.
In particular embodiments the invention provides a combination according to any one of item 11 wherein said immune T cell express a CAR targeting specifically CD123.
In particular embodiments the invention provides a combination according to any one of item 11 wherein said immune T cell express a CAR targeting specifically CD22.
In particular embodiments the invention provides a combination according to any one of item 11 wherein said immune T cell express a CAR targeting specifically CS1.
In particular embodiments the invention provides a combination according to any one of item 11 wherein said immune T cell express a CAR targeting specifically CLL-1.
In particular embodiments the invention provides a combination according to any one of the above wherein said immune T cell express a recombinant TCR isolated from a tumor. In particular embodiments the invention provides a combination wherein said immune T cell express a CAR which target specifically a cell surface marker selected from BCMA, CD33, EGFRVIII, Flt3, WT1, CD70, MUC16, PRAME, TSPAN10, CLAUDIN18.2, DLL3, LY6G6D, Liv-1, CHRNA2 and ADAM10.
In particular embodiments the invention provides a combination wherein said CAR comprises an extracellular binding domain, said extracellular binding domain comprising two, or three 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, ipilimumab, ofatumumab, panitumumab, QBEND-10 and ustekinumab, preferably 2 mAb-specific epitopes specifically recognized by rituximab, or 1 mAb-specific epitopes specifically recognized by QBEND-10 and 3 mAb-specific epitopes specifically recognized by rituximab.
In most preferred embodiments the invention provides a combination according to any one of those disclosed herein wherein said immune T cell is or was further engineered by genetically inactivating at least one gene encoding a component of the T-cell receptor (TCR) and/or affecting the expression of molecule of the HLA complex.
Thus, the invention provides a combination wherein said immune T cell is engineered to be less alloreactive as compared to non-engineered cells and therefore more specific for the pathological cells intended to be treated or destroyed.
The combination according to any one of those above wherein said immune T cell is further engineered to be less alloreactive as compared to non-engineered cells, by genetically inactivating the alphaTCR and beta2microglobulin genes,
The combination according to any one of item 1 to 15 wherein said immune T cell is further engineered to be less alloreactive as compared to non-engineered cells, by genetically inactivating the alphaTCR and regulatory factor X-associated ankyrin-containing protein (RFXANK) gene,
The combination according to any one of item 1 to 15 wherein said immune T cell is further engineered to be less alloreactive as compared to non-engineered cells, by genetically inactivating the alphaTCR and regulatory factor 5 (RFX5) gene,
The combination according to any one of item 1 to 15 wherein said immune T cell is further engineered to be less alloreactive as compared to non-engineered cells, by genetically inactivating the alphaTCR and regulatory factor X-associated protein (RFXAP) gene,
The combination according to any one of item 1 to 15 wherein said immune T cell is further engineered to be less alloreactive as compared to non-engineered cells, by genetically inactivating the alphaTCR and class II transactivator (CIITA),
The combination according to any one of item 1 to 15 wherein said immune T cell is further engineered to be less alloreactive as compared to non-engineered cells, by genetically inactivating the alphaTCR and TAP-1 gene.
In particular embodiments the invention provides a combination according to any one of the above further engineered to resist hypoxia, preferably wherein said CAR or said cells comprises a domain conferring resistance to hypoxia such as at least one HIF 1 alpha domain. The combination according to the present invention further engineered to resist tumor-inducing inhibition anti-tumor activity of immune cells mediated by any one of the following molecules, Programmed Death 1 (PD-1), Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4), LAG3 Tim3, BTLA, BY55, TIGIT, B7H5, LAIR1, SIGLEC10, and 2B4.
CD70-expressing cancers that can be treated or prevented using the combination of the invention, for example, different subtypes of Non-Hodgkin's Lymphoma (indolent NHLs, follicular NHLs, small lymphocytic lymphomas, lymphoplasmacytic NHLs, or marginal zone NHLs); Hodgkin's disease (e.g., Reed-Sternberg cells); cancers of the B-cell lineage, including, e.g., diffuse large B-cell lymphomas, follicular lymphomas, Burkitt's lymphoma, mantle cell lymphomas, B-cell lymphocytic leukemias (e.g., acute lymphocytic leukemia, chronic lymphocytic leukemia); Epstein Barr Virus positive B cell lymphomas; renal cell carcinomas (e.g., clear cell and papillary); nasopharyngeal carcinomas; thymic carcinomas; gliomas; glioblastomas; neuroblastomas; astrocytomas; meningiomas; Waldenstrom macroglobulinemia; multiple myelomas; and colon, stomach, and rectal carcinomas. The cancer can be, for example, newly diagnosed, pre-treated or refractory or relapsed. In some embodiments, a CD70-expressing cancer has at least about 15,000, at least about 10,000 or at least about 5,000 CD70 molecules/cell.
Document WO2010051391 A1 is incorporated herein in its entirety as prior art allowing the combination of CS1 deficient engineered TCR negative T cells and a therapeutic antibody to be prepared and used for the treatment of NK cell lymphoma, NK or T cell lymphoma, angioimmunoblastic T-cell lymphoma (AITL), or peripheral T cell lymphoma not otherwise specified (PTCL-NOS).
Non-limiting examples of conditions associated with CD38 expression include but are not limited to, multiple myeloma (Jackson et al. (1988), Clin. Exp. Immunol. 72: 351-356), B-cell chronic lymphocytic leukemia (B-CLL) Durig et al. (2002), Leukemia 16: 30-5; Morabito et al. (2001), Leukemia Research 25: 927-32; Marinov et al. (1993), Neoplasma 40(6): 355-8; and Jelinek et al. (2001), Br. J. Haematol. 115: 854-61), acute lymphoblastic leukemia (Keyhani et al. (1999), Leukemia Research 24: 153-9; and Marinov et al. (1993), Neoplasma 40(6): 355-8), chronic myeloid leukemia (Marinov et al. (1993), Neoplasma 40(6): 355-8), acute myeloid leukemia (Keyhani et al. (1999), Leukemia Research 24: 153-9), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia or chronic myeloid leukemia (CML), acute myelogenous leukemia or acute myeloid leukemia (AML), acute lymphocytic leukemia (ALL), hairy cell leukemia (HCL), myelodysplasia syndromes (MDS) or chronic myelogenous leukemia (CML-BP) in blastic and all subtypes of these leukemias which are defined by morphological, histochemical and immunological techniques that are well known by those of skill in the art. “Neoplasm” or “neoplastic condition” or “cancer” refers to a condition associated with proliferation of cells characterized by a loss of normal controls that results in one re more symptoms including, unregulated growth, lack of differentiation, local tissue invasion, and metastasis. In some embodiments of the invention, the hematologic cancer expressing CD38 is a cancer selected from the group of Chronic Lymphocytic Leukemia (CLL), Chronic Myelogenous Leukemia (CML), Acute Myelogenous Leukemia (AML), and Acute Lymphocytic Leukemia (ALL). Furthermore, it is known in the art that CD38 expression is a prognostic indicator for patients with conditions such as, for example, B-cell chronic lymphocytic leukemia (Durig et al. (2002), Leukemia 16: 30-5; and Morabito et al. (2001), Leukemia Research 25: 927-32) and acute myelogenous leukemia (Keyhani et al. (1999), Leukemia Research 24: 153-9). The combination of the invention comprising CD38 negative engineered cells and anti-CD38 therapeutic antibody is intended to be administered to patients with these particular conditions.
CS 1 (also known as SLAMF7, CRACC, 19A, APEX-1, FOAP 12, and 19A; GENBANK® Accession No. NM 021181.3, Ref. Boles et al, Immunogenetics, 52:302-307 (2001); Bouchon et al, J. Immunol, 167:5517-5521 (2001); Murphy et al, Biochem. J., 361:431-436 (2002)) is a member of the CD2 subset of the immunoglobulin superfamily. Molecules of the CD2 family are involved in a broad range of immunomodulatory functions, such as co-activation, proliferation differentiation, and adhesion of lymphocytes, as well as immunoglobulin secretion, cytokine production, and NK cell cytotoxicity. Several members of the CD2 family, such as CD2, CD58, and CD 150, play a role or have been proposed to play a role in a number of autoimmune and inflammatory diseases, such as psoriasis, rheumatoid arthritis, and multiple 10 sclerosis. It has been reported that CS 1 plays a role in NK cell-mediated cytotoxicity and lymphocyte adhesion (Bouchon, A. et al, J. Immunol, 5517-5521 (2001); Murphy, J. et al, Biochem. J., 361:431-436 (2002)).
The present invention provides a TAL-protein comprising a sequence having at least 95% homology with
The invention provides a TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; with SEQ ID NO 116 and SEQ ID NO 117; with SEQ ID NO 118 and SEQ ID NO 119; with SEQ ID NO 102 and SEQ ID NO 103; with SEQ ID NO 104 and SEQ ID NO 105; with SEQ ID NO 106 and SEQ ID NO 107; with SEQ ID NO 108 and SEQ ID NO 109; with SEQ ID NO 110 and SEQ ID NO 111; with SEQ ID NO 112 and SEQ ID NO 113; with SEQ ID NO 171 and SEQ ID NO 172; with SEQ ID NO 173 and SEQ ID NO 174; with SEQ ID NO 175 and SEQ ID NO 176; or with SEQ ID NO 177 and SEQ ID NO 178 for use in the manufacturing of CART cells.
The invention provides a TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; with SEQ ID NO 116 and SEQ ID NO 117; or with SEQ ID NO 118 and SEQ ID NO 119; is provided for modifying the CD38 gene,
The invention provides a TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 102 and SEQ ID NO 103; with SEQ ID NO 104 and SEQ ID NO 105; or with SEQ ID NO 106 and SEQ ID NO 107, is provided for modifying the CD70 gene.
The invention provides a TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 108 and SEQ ID NO 109; with SEQ ID NO 110 and SEQ ID NO 111; with SEQ ID NO 112 and SEQ ID NO 113; with SEQ ID NO 171 and SEQ ID NO 172; with SEQ ID NO 173 and SEQ ID NO 174; with SEQ ID NO 175 and SEQ ID NO 176; or with SEQ ID NO 177 and SEQ ID NO 178 is provided for modifying the CS1 gene.
The invention provides a polynucleotide or a vector encoding any one of the TAL protein above.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 114 and SEQ ID NO 115.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 116 and SEQ ID NO 117.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 118 and SEQ ID NO 119.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 102 and SEQ ID NO 103.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 104 and SEQ ID NO 105.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 106 and SEQ ID NO 107.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 108 and SEQ ID NO 109.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 110 and SEQ ID NO 111.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 112 and SEQ ID NO 113.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 171 and SEQ ID NO 172.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 173 and SEQ ID NO 174.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 175 and SEQ ID NO 176.
The invention provides a TAL-protein comprising a sequence of SEQ ID NO 177 and SEQ ID NO 178.
The invention provides a TAL-protein according to item 54 comprising a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; comprising a sequence having at least 95% homology with SEQ ID NO 116 and SEQ ID NO 117; comprising a sequence having at least 95% homology with SEQ ID NO 118 and SEQ ID NO 119; comprising a sequence having at least 95% homology with SEQ ID NO 102 and SEQ ID NO 103; comprising a sequence having at least 95% homology with SEQ ID NO 104 and SEQ ID NO 105; comprising a sequence having at least 95% homology with SEQ ID NO 106 and SEQ ID NO 107; comprising a sequence having at least 95% homology with SEQ ID NO 108 and SEQ ID NO 109; comprising a sequence having at least 95% homology with SEQ ID NO 110 and SEQ ID NO 111; comprising a sequence having at least 95% homology with SEQ ID NO 112 and SEQ ID NO 113; comprising a sequence having at least 95% homology with SEQ ID NO 171 and SEQ ID NO 172; comprising a sequence having at least 95% homology with SEQ ID NO 173 and SEQ ID NO 174; comprising a sequence having at least 95% homology with SEQ ID NO 175 and SEQ ID NO 176; or comprising a sequence having at least 95% homology with SEQ ID NO 177 and SEQ ID NO 178 for use in the manufacturing of CART cells.
The invention provides a TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; with SEQ ID NO 116 and SEQ ID NO 117; or with SEQ ID NO 118 and SEQ ID NO 119; is provided for modifying the CD38 gene.
The invention provides a TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 102 and SEQ ID NO 103; with SEQ ID NO 104 and SEQ ID NO 105; or with SEQ ID NO 106 and SEQ ID NO 107, is provided for modifying the CD70 gene.
A TAL-protein comprising a sequence having at least 95% homology with SEQ ID NO 108 and SEQ ID NO 109; with SEQ ID NO 110 and SEQ ID NO 111; with SEQ ID NO 112 and SEQ ID NO 113; with SEQ ID NO 171 and SEQ ID NO 172; with SEQ ID NO 173 and SEQ ID NO 174; with SEQ ID NO 175 and SEQ ID NO 176; or with SEQ ID NO 177 and SEQ ID NO 178 is provided for modifying the CS1 gene.
The invention provides a polynucleotide or a vector encoding a protein comprising any one of the TAL protein above is provided.
A polynucleotide or a vector encoding any one of the TAL protein above is provided.
An engineered immune T cell comprising a CD38 modified gene obtained using a TAL-protein or a polynucleotide encoding a sequence having at least 95% homology with SEQ ID NO 114 and SEQ ID NO 115; with SEQ ID NO 116 and SEQ ID NO 117; or with SEQ ID NO 118 and SEQ ID NO 119 is provided.
The invention provides an engineered immune T cell comprising a CD70 modified gene obtained using a TAL-protein or a polynucleotide encoding a sequence having with SEQ ID NO 102 and SEQ ID NO 103; with SEQ ID NO 104 and SEQ ID NO 105; or with SEQ ID NO 106 and SEQ ID NO 107, is provided.
An engineered immune T cell comprising a CS1 modified gene obtained using a TAL-protein or a polynucleotide encoding a sequence having with SEQ ID NO 108 and SEQ ID NO 109; with SEQ ID NO 110 and SEQ ID NO 111; with SEQ ID NO 112 and SEQ ID NO 113; with SEQ ID NO 171 and SEQ ID NO 172; with SEQ ID NO 173 and SEQ ID NO 174; with SEQ ID NO 175 and SEQ ID NO 176; or with SEQ ID NO 177 and SEQ ID NO 178 is provided.
The T-cells according to the invention may be endowed with a chimeric antigen receptor directed the antigen marker that is commonly expressed by the pathological cells and T-cells. The expression “known to be present” means that the antigen marker is reported to be found on the surface of the T-cells grown in natural conditions in-vivo, especially in the blood, but not necessarily when they are cultured in-vitro. In any event, the method of the invention results into the absence of the antigen marker on the surface of the engineered T-cell, thereby preventing the chimeric antigen receptor from reacting with the engineered T-cell surface. In this respect, the method for preparing the T cells of the invention may include a further step of purifying the resulting T-cells by excluding the cells presenting said marker antigen on their surface.
Therapeutic Antibodies
Therapeutic antibodies used in the present study may be any therapeutic antibody specific for an antigen expressed on immune cells used for immunotherapy such as T cells of precursors, and on pathological cells preferably any one of the antigens described in tables 4 to 14 of the present invention.
As non-limiting examples of anti-CD70 therapeutic antibodies that may be used with and/or combined to engineered cells with a CD70 KO or inactivated gene, the following therapeutic antibody may be combined with cells in which the CD70 gene was inactivated:
Anti CD70 Therapeutic mAbs
In a preferred embodiment, the combination of the invention comprises CD70 KO immune cells and ARGX 110 and is used for the treatment of Renal Cell Carcinoma or for Non-hodgkin's Lymphoma.
As examples of anti-CD38 therapeutic antibodies that may be used and combined to CD38 KO engineered cells, the following may be combined with cells in which the CD38 gene was inactivated:
Anti CD38 Therapeutic mAbs
As example of anti-CS1 antibody that may be used and combined to engineered cells in which the CS1 gene was inactivated the following are preferred:
Anti CS1 Therapeutic mAbs
Elotuzumab is a humanized monoclonal IgGI antibody directed against CS-1, a cell surface glycoprotein, which is highly and uniformly expressed in multiple myeloma.
Elotuzumab induces significant antibody-dependent cellular cytotoxicity (ADCC) against primary multiple myeloma cells in the presence of peripheral lymphocytes (Tai et al, Blood, 112: 1329-1337 (2008)). Results of three studies that evaluated the safety and efficacy of this drug administered alone (Zonder et al, Blood, 120(3):552-559 (2012)), in combination with bortezomib (Jakubowiak et al, J. Clin. Oncol., 30(16): 1960-1965 (Jun. 1, 2012)), or lenalidomide and low-dose dexamethasone (Lonial et al, J. Clin. Oncol., 30: 1953-1959 (2012); and Richardson et al, Blood (ASH Annual Meeting Abstracts), 1 16:986 (2010) for the treatment of patients with relapsed or refractory multiple myeloma, have been reported. All three combinations showed a manageable safety profile and encouraging activity. For example, a Phase VII study evaluating the safety and efficacy of Elotuzumab in combination lenalidomide and low-dose dexamethasone for the treatment of relapsed or refractory multiple myeloma demonstrated a 33 month PFS as well as a 92% response rate for patients receiving the 10 mg/kg dose (Lonial et al., J. Clin. Oncol., 31 (2013) (Suppl., Abstr. 8542)). Phase III clinical trials of lenalidomide/dexamethasone with or without Elotuzumab in previously untreated multiple myeloma patients is ongoing, while another phase III trial designed to evaluate this same combination in the first line setting is also ongoing. Accordingly, the invention provides a combination of CS-1 deficient engineered cells and a therapeutic antibody specific for CS1 namely in combination with bortezomib or lenalidomide and low-dose dexamethasone for the treatment of patients with relapsed or refractory multiple myeloma.
Combination—Step of Combining
Combining said engineered T cells with a therapeutic antibody specific for said antigen marker, may mean that cells and antibody are incubated together so that said therapeutic antibody binds to cells in which the antigen is still expressed. The therapeutic antibody is therefore bound to engineered cells that express the antigen marker. Incubation with appropriate reagent allows an antibody mediated purification in vitro or in vivo of engineered cells that do not express the marker antigen. An appropriate reagent may be beads, preferably magnetic beads coated with a protein that binds to antibodies, such as G or A proteins or protein of the complement. Purification may be performed in vivo or in vitro. A therapeutic antibody is an antibody with therapeutic activity, preferably approved by health authorities. Therapeutic activity means an activity that improves health condition in a patient suffering a disease.
All these examples of therapeutically effective antibody are administered in individual in need thereof. A skilled person will administered it in combination with engineered cells accordingly to the present invention, each at the efficient doses to improve the health condition.
In certain embodiments of the present invention, engineered cells are administered to a patient in conjunction with (e.g., before, simultaneously or following) the therapeutic antibody targeting the cell surface antigen marker which expression is inactivated in said cells.
The active dose(s) of antibody and of engineered immune cells and route of injection are known of the skilled person. The present invention provide a combination adapted to the patients so that the first injection of the combination allows 1) immunodepleting the patient in T cells, 2) grafting said patient with engineered cells 3) destroying pathological cells and/or avoiding relapse refractory forms of said pathological cells.
As shown in Table 4, this invention is applicable to an important number of antigen marker candidates reported to be expressed by tumor cells, but also by T-cells. Some of them, like CD38, have been used as specific markers in diagnostic methods for a while, especially with respect to Leukemia pathological cells, but not in therapy. Indeed, although these markers were identified in the art as quite specific markers, they could not be used as targets for immunotherapy because antibodies directed against these markers would have destroyed or interfered with patients' T-cells.
According to a preferred embodiment of the invention, the gene mutation or inactivation of step a) of the above method is performed using a rare-cutting endonuclease.
By inactivating a gene it is intended that the gene of interest is not expressed in a functional protein form. In particular embodiments, the genetic modification of the method relies on the expression, in provided cells to engineer, of a rare-cutting endonuclease such that same catalyzes cleavage in one targeted gene thereby inactivating said targeted gene. The nucleic acid strand breaks caused by the endonuclease are commonly repaired through the distinct mechanisms of homologous recombination or non-homologous end joining (NHEJ). However, NHEJ is an imperfect repair process that often results in changes to the DNA sequence at the site of the cleavage. Mechanisms involve rejoining of what remains of the two DNA ends through direct re-ligation (Critchlow and Jackson 1998) or via the so-called microhomology-mediated end joining (Betts, Brenchley et al. 2003; Ma, Kim et al. 2003). Repair via non-homologous end joining (NHEJ) often results in small insertions or deletions and can be used for the creation of specific gene knockouts. Said modification may be a substitution, deletion, or addition of at least one nucleotide. Cells in which a cleavage-induced mutagenesis event, i.e. a mutagenesis event consecutive to an NHEJ event, has occurred can be identified and/or selected by well-known method in the art.
The term “rare-cutting endonuclease” refers to a wild type or variant enzyme capable of catalyzing the hydrolysis (cleavage) of bonds between nucleic acids within a DNA or RNA molecule, preferably a DNA molecule. Particularly, said nuclease can be an endonuclease, more preferably a rare-cutting endonuclease which is highly specific, recognizing nucleic acid target sites ranging from 10 to 45 base pairs (bp) in length, usually ranging from 10 to 35 base pairs in length, more usually from 12 to 20 base pairs. The endonuclease according to the present invention recognizes at specific polynucleotide sequences, further referred to as “target sequence” and cleaves nucleic acid inside these target sequences or into sequences adjacent thereto, depending on the molecular structure of said endonuclease. The rare-cutting endonuclease can recognize and generate a single- or double-strand break at specific polynucleotides sequences.
In a particular embodiment, said rare-cutting endonuclease according to the present invention is a RNA-guided endonuclease such as the Cas9/CRISPR complex. RNA guided endonucleases constitute a new generation of genome engineering tool where an endonuclease associates with a RNA molecule. In this system, the RNA molecule nucleotide sequence determines the target specificity and activates the endonuclease (Gasiunas, Barrangou et al. 2012; Jinek, Chylinski et al. 2012; Cong, Ran et al. 2013; Mali, Yang et al. 2013).
Cas 9
Cas9, also named Csn1 (COG3513) is a large protein that participates in both crRNA biogenesis and in the destruction of invading DNA. Cas9 has been described in different bacterial species such as S. thermophiles, Listeria innocua (Gasiunas, Barrangou et al. 2012; Jinek, Chylinski et al. 2012) and S. pyogenes (Deltcheva, Chylinski et al. 2011). The large Cas9 protein (>1200 amino acids) contains two predicted nuclease domains, namely HNH (McrA-like) nuclease domain that is located in the middle of the protein and a splitted RuvC-like nuclease domain (RNase H fold) (Makarova, Grishin et al. (2006).
By “Cas9” is meant an engineered endonuclease or a homologue of Cas9 which is capable of processing target nucleic acid sequence. In particular embodiment, Cas9 can induce a cleavage in the nucleic acid target sequence which can correspond to either a double-stranded break or a single-stranded break. Cas9 variant can be a Cas9 endonuclease that does not naturally exist in nature and that is obtained by protein engineering or by random mutagenesis. Cas9 variants according to the invention can for example be obtained by mutations i.e. deletions from, or insertions or substitutions of at least one residue in the amino acid sequence of a S. pyogenes Cas9 endonuclease (COG3513). In the frame aspects of the present invention, such Cas9 variants remain functional, i.e. they retain the capacity of processing a target nucleic acid sequence. Cas9 variant can also be homologues of S. pyogenes Cas9 which can comprise deletions from, or insertions or substitutions of, at least one residue within the amino acid sequence of S. pyogenes Cas9. Any combination of deletion, insertion, and substitution may also be made to arrive at the final construct, provided that the final construct possesses the desired activity, in particular the capacity of binding a guide RNA or nucleic acid target sequence.
RuvC/RNaseH motif includes proteins that show wide spectra of nucleolytic functions, acting both on RNA and DNA (RNaseH, RuvC, DNA transposases and retroviral integrases and PIWI domain of Argonaut proteins). In the present invention the RuvC catalytic domain of the Cas9 protein can be characterized by the sequence motif: D-[I/L]-G-X-X-S-X-G-W-A, wherein X represents any one of the natural 20 amino acids and [I/L] represents isoleucine or leucine. In other terms, the present invention relates to Cas9 variant which comprises at least D-[I/L]-G-X-X-S-X-G-W-A sequence, wherein X represents any one of the natural 20 amino acids and [I/L] represents isoleucine or leucine.
HNH motif is characteristic of many nucleases that act on double-stranded DNA including colicins, restriction enzymes and homing endonucleases. The domain HNH (SMART ID: SM00507, SCOP nomenclature: HNH family) is associated with a range of DNA binding proteins, performing a variety of binding and cutting functions. The ones with known function are involved in a range of cellular processes including bacterial toxicity, homing functions in groups I and II introns and inteins, recombination, developmentally controlled DNA rearrangement, phage packaging, and restriction endonuclease activity (Dalgaard, Klar et al. 1997). These proteins are found in viruses, archaebacteria, eubacteria, and eukaryotes. Interestingly, as with the LAGLI-DADG and the GIY-YIG motifs, the HNH motif is often associated with endonuclease domains of self-propagating elements like inteins, Group I, and Group II introns (Dalgaard, Klar et al. 1997). The HNH domain can be characterized by the presence of a conserved Asp/His residue flanked by conserved His (amino-terminal) and His/Asp/Glu (carboxy-terminal) residues at some distance. A substantial number of these proteins can also have a CX2C motif on either side of the central Asp/His residue. Structurally, the HNH motif appears as a central hairpin of twisted p-strands, which are flanked on each side by an a helix (Kleanthous, Kuhlmann et al. 1999). In the present invention, the HNH motif can be characterized by the sequence motif: Y-X-X-D-H-X-X-P-X-S-X-X-X-D-X-S, wherein X represents any one of the natural 20 amino acids. The present invention relates to a Cas9 variant which comprises at least Y-X-X-D-H-X-X-P-X-S-X-X-X-D-X-S sequence wherein X represents any one of the natural 20 amino acids.
This invention can be of particular interest to easily do targeted multiplex gene modifications and to create an inducible nuclease system by introduction of the guide RNA to the Cas9 cells. For the purpose of the present invention, the inventors have established that Cas9 protein can be divided into two separate split Cas9 RuvC and HNH domains which can process target nucleic acid sequence together or separately with the guide RNA.
Also the RuvC and HNH domains from different RNA guided endonucleases or Cas homologues may be assembled to improve nuclease efficiency or specificity. The domains from different species can be either split into two proteins or fused to each other to form a variant Cas protein. The Cas9 split system is deemed particularly suitable for an inducible method of genome targeting and to avoid the potential toxic effect of the Cas9 overexpression within the cell. Indeed, a first split Cas9 domain can be introduced into the cell, preferably by stably transforming said cell with a transgene encoding said split domain. Then, the complementary split part of Cas9 can be introduced into the cell, such that the two split parts reassemble into the cell to reconstitute a functional Cas9 protein at the desired time.
The reduction of the size of the split Cas9 compared to wild type Cas9 ease the vectorization and the delivery into the cell, for example, by using cell penetrating peptides. Re-arranging domains from different Cas proteins, allows to modulate the specificity and nuclease activity, for instance, by targeting PAM motifs that are slightly different from S. pyogenes Cas9
Split Cas9 System
The previous characterization of the RuvC and HNH domains has prompted the inventors to engineer Cas9 protein to create split Cas9 protein. Surprisingly, the inventors showed that these two split Cas9 could process together or separately the nucleic acid target. This observation allows developing a new Cas9 system using split Cas9 protein. Each split Cas9 domains can be prepared and used separately. Thus, this split system displays several advantages for vectorization and delivery of the RNA guided endonuclease in T-cells, allowing delivering a shorter and/or inactive protein, and is particularly suitable to induce genome engineering in T-cells at the desired time and thus limiting the potential toxicity of an integrated Cas9 nuclease.
By “Split Cas9” is meant here a reduced or truncated form of a Cas9 protein or Cas9 variant, which comprises either a RuvC or HNH domain, but not both of these domains. Such “Split Cas9” can be used independently with guide RNA or in a complementary fashion, like for instance, one Split Cas9 providing a RuvC domain and another providing the HNH domain. Different split RNA guided endonucleases may be used together having either RuvC and/or NHN domains.
Each Cas9 split domain can be derived from the same or from different Cas9 homologues. Many homologues of Cas9 have been identified in genome databases.
Said Cas9 split domains (RuvC and HNH domains) can be simultaneously or sequentially introduced into the cell such that said split Cas9 domain(s) process the target nucleic acid sequence in the cell. Said Cas9 split domains and guide RNA can be introduced into the cell by using cell penetrating peptides or other transfection methods as described elsewhere.
In another aspect of the invention, only one split Cas9 domain, referred to as compact Cas9 is introduced into said cell. Indeed, surprisingly the inventors showed that the split Cas9 domain comprising the RuvC motif as described above is capable of cleaving a target nucleic acid sequence independently of split domain comprising the HNH motif. Thus, they could establish that the guideRNA does not need the presence of the HNH domain to bind to the target nucleic acid sequence and is sufficiently stable to be bound by the RuvC split domain. In a preferred embodiment, said split Cas9 domain alone is capable of nicking said target nucleic acid sequence.
Each split domain can be fused to at least one active domain in the N-terminal and/or C-terminal end, said active domain can be selected from the group consisting of: nuclease (e.g. endonuclease or exonuclease), polymerase, kinase, phosphatase, methylase, demethylase, acetylase, desacetylase, topoisomerase, integrase, transposase, ligase, helicase, recombinase, transcriptional activator (e.g. VP64, VP16), transcriptional inhibitor (e. g; KRAB), DNA end processing enzyme (e.g. Trex2, Tdt), reporter molecule (e.g. fluorescent proteins, lacZ, luciferase).
HNH domain is responsible for nicking of one strand of the target double-stranded DNA and the RuvC-like RNaseH fold domain is involved in nicking of the other strand (comprising the PAM motif) of the double-stranded nucleic acid target (Jinek, Chylinski et al. 2012). However, in wild-type Cas9, these two domains result in blunt cleavage of the invasive DNA within the same target sequence (proto-spacer) in the immediate vicinity of the PAM (Jinek, Chylinski et al. 2012). Cas 9 can be a nickase and induces a nick event within different target sequences.
As non-limiting example, Cas9 or split Cas9 can comprise mutation(s) in the catalytic residues of either the HNH or RuvC-like domains, to induce a nick event within different target sequences. As non-limiting example, the catalytic residues of the Cas9 protein are those corresponding to amino acids D10, D31, H840, H868, N882 and N891 or aligned positions using CLUSTALW method on homologues of Cas Family members. Any of these residues can be replaced by any other amino acids, preferably by alanine residue. Mutation in the catalytic residues means either substitution by another amino acids, or deletion or addition of amino acids that induce the inactivation of at least one of the catalytic domain of cas9. (cf. In a particular embodiment, Cas9 or split Cas9 may comprise one or several of the above mutations. In another particular embodiment, split Cas9 comprises only one of the two RuvC and HNH catalytic domains. In the present invention, Cas9 from different species, Cas9 homologues, Cas9 engineered and functional variant thereof can be used. The invention envisions the use of any RNA guided endonuclease or split RNA guided endonucleases variants to perform nucleic acid cleavage in a genetic sequence of interest.
Preferably, the Cas9 variants according to the invention have an amino acid sequence sharing at least 70%, preferably at least 80%, more preferably at least 90%, and even more preferably 95% identity with Cas9 of S. pyogenes (COG3513).
Meganucleases
Rare-cutting endonuclease can also be a homing endonuclease, also known under the name of meganuclease. Such homing endonucleases are well-known to the art (Stoddard 2005). Homing endonucleases are highly specific, recognizing DNA target sites ranging from 12 to 45 base pairs (bp) in length, usually ranging from 14 to 40 bp in length. The homing endonuclease according to the invention may for example correspond to a LAGLIDADG endonuclease, to a HNH endonuclease, or to a GIY-YIG endonuclease. Preferred homing endonuclease according to the present invention can be an I-CreI variant. A “variant” endonuclease, i.e. an endonuclease that does not naturally exist in nature and that is obtained by genetic engineering or by random mutagenesis can bind DNA sequences different from that recognized by wild-type endonucleases (see international application WO2006/097854).
Said rare-cutting endonuclease can be a modular DNA binding nuclease. By modular DNA binding nuclease is meant any fusion proteins comprising at least one catalytic domain of an endonuclease and at least one DNA binding domain or protein specifying a nucleic acid target sequence. The DNA binding domain is generally a RNA or DNA-binding domain formed by an independently folded polypeptide or protein domain that contains at least one motif that recognizes double- or single-stranded polynucleotides. Many such polypeptides have been described in the art having the ability to bind specific nucleic acid sequences. Such binding domains often comprise, as non-limiting examples, helix-turn helix domains, leucine zipper domains, winged helix domains, helix-loop-helix domains, HMG-box domains, Immunoglobin domains, B3 domain or engineered zinc finger domain.
The present invention provides a rare-cutting endonuclease for inactivating a gene which product is expressed or overexpressed on pathological cells and normal T cell and which product is expressed on the surface of normal T-cells selected from any one of those discloses in table 4 to table 14.
In preferred embodiment the rare-cutting endonuclease of the invention is specific for the CD38 gene or for the CD70 gene or for the CS1 gene.
The rare-cutting endonuclease as above is provided and selected from a Meganuclease, a transcription activator-like (TAL)-nuclease, a zing-finger nuclease (ZFN), or a RNA/DNA guided endonucleases.
The rare-cutting endonuclease as above is provided and selected from a Meganuclease, a transcription activator-like (TAL)-nuclease, a zing-finger nuclease (ZFN), or a RNA/DNA guided endonucleases.
The rare-cutting endonuclease provided here is a transcription activator-like effector (TALE)-nuclease specific for CD38, CD70 or CS-1 gene.
The rare-cutting endonuclease of the invention may be for example specific for one of the following SEQ ID NO. 1, SEQ ID NO. 4, SEQ ID NO. 7, SEQ ID NO. 63, SEQ ID NO. 66, SEQ ID NO. 69, SEQ ID NO. 72, SEQ ID NO. 75, SEQ ID NO. 78, SEQ ID NO. 167, SEQ ID NO. 168, SEQ ID NO. 169 or SEQ ID NO. 170.
The present invention encompasses TAL-nucleases having at least 95% homology with any one of the TAL-nucleases comprising SEQ ID NO 114 and SEQ ID NO 115; SEQ ID NO 116 and SEQ ID NO 117; SEQ ID NO 118 and SEQ ID NO 119; SEQ ID NO 102 and SEQ ID NO 103; SEQ ID NO 104 and SEQ ID NO 105; SEQ ID NO 106 and SEQ ID NO 107; SEQ ID NO 108 and SEQ ID NO 109; SEQ ID NO 110 and SEQ ID NO 111; SEQ ID NO 112 and SEQ ID NO 113; SEQ ID NO 171 and SEQ ID NO 172; SEQ ID NO 173 and SEQ ID NO 174; SEQ ID NO 175 and SEQ ID NO 176; or SEQ ID NO 177 and SEQ ID NO 178.
Zinc-Finger Nucleases
Initially developed to cleave DNA in vitro, “Zinc Finger Nucleases” (ZFNs) are a fusion between the cleavage domain of the type IIS restriction enzyme, FokI, and a DNA recognition domain containing 3 or more C2H2 zinc finger motifs. The heterodimerization at a particular position in the DNA of two individual ZFNs in precise orientation and spacing leads to a double-strand break (DSB) in the DNA. The use of such chimeric endonucleases have been extensively reported in the art as reviewed by Urnov et al. (Genome editing with engineered zinc finger nucleases (2010) Nature reviews Genetics 11:636-646).
Standard ZFNs fuse the cleavage domain to the C-terminus of each zinc finger domain. In order to allow the two cleavage domains to dimerize and cleave DNA, the two individual ZFNs bind opposite strands of DNA with their C-termini a certain distance apart. The most commonly used linker sequences between the zinc finger domain and the cleavage domain requires the 5′ edge of each binding site to be separated by 5 to 7 bp.
The most straightforward method to generate new zinc-finger arrays is to combine smaller zinc-finger “modules” of known specificity. The most common modular assembly process involves combining three separate zinc fingers that can each recognize a 3 base pair DNA sequence to generate a 3-finger array that can recognize a 9 base pair target site. Numerous selection methods have been used to generate zinc-finger arrays capable of targeting desired sequences. Initial selection efforts utilized phage display to select proteins that bound a given DNA target from a large pool of partially randomized zinc-finger arrays. More recent efforts have utilized yeast one-hybrid systems, bacterial one-hybrid and two-hybrid systems, and mammalian cells.
TAL-Nucleases
“TALE-nuclease” or “MBBBD-nuclease” refers to engineered proteins resulting from the fusion of a DNA binding domain typically derived from Transcription Activator Like Effector proteins (TALE) or Modular Base-per-Base Binding domain (MBBBD), with a catalytic domain having endonuclease activity. Such catalytic domain usually comes from enzymes, such as for instance I-Tevl, ColE7, NucA and Fok-I. TALE-nuclease can be formed under monomeric or dimeric forms depending of the selected catalytic domain (WO2012138927). Such engineered TALE-nucleases are commercially available under the trade name TALEN™ (Cellectis, 8 rue de la Croix Jarry, 75013 Paris, France).
According to a preferred embodiment of the invention, the DNA binding domain is derived from a Transcription Activator like Effector (TALE), wherein sequence specificity is driven by a series of 33-35 amino acids repeats originating from Xanthomonas or Ralstonia bacterial proteins AvrBs3, PthXo1, AvrHah1, PthA, Tal1c as non-limiting examples.
These repeats differ essentially by two amino acids positions that specify an interaction with a base pair (Boch, Scholze et al. 2009; Moscou and Bogdanove 2009). Each base pair in the DNA target is contacted by a single repeat, with the specificity resulting from the two variant amino acids of the repeat (the so-called repeat variable dipeptide, RVD). TALE binding domains may further comprise an N-terminal translocation domain responsible for the requirement of a first thymine base (TO) of the targeted sequence and a C-terminal domain that containing a nuclear localization signals (NLS). A TALE nucleic acid binding domain generally corresponds to an engineered core TALE scaffold comprising a plurality of TALE repeat sequences, each repeat comprising a RVD specific to each nucleotides base of a TALE recognition site. In the present invention, each TALE repeat sequence of said core scaffold is made of 30 to 42 amino acids, more preferably 33 or 34 wherein two critical amino acids (the so-called repeat variable dipeptide, RVD) located at positions 12 and 13 mediates the recognition of one nucleotide of said TALE binding site sequence; equivalent two critical amino acids can be located at positions other than 12 and 13 specially in TALE repeat sequence taller than 33 or 34 amino acids long. Preferably, RVDs associated with recognition of the different nucleotides are HD for recognizing C, NG for recognizing T, NI for recognizing A, NN for recognizing G or A. In another embodiment, critical amino acids 12 and 13 can be mutated towards other amino acid residues in order to modulate their specificity towards nucleotides A, T, C and G and in particular to enhance this specificity. A TALE nucleic acid binding domain usually comprises between 8 and 30 TALE repeat sequences. More preferably, said core scaffold of the present invention comprises between 8 and 20 TALE repeat sequences; again more preferably 15 TALE repeat sequences. It can also comprise an additional single truncated TALE repeat sequence made of 20 amino acids located at the C-terminus of said set of TALE repeat sequences, i.e. an additional C-terminal half-TALE repeat sequence.
Other engineered DNA binding domains can be used as alternative sequences to form so-called modular base-per-base specific nucleic acid binding domains (MBBBD) as described in WO 2014/018601. Said MBBBD can be engineered, for instance, from newly identified proteins, namely EAV36_BURRH, E5AW43_BURRH, E5AW45_BURRH and E5AW46_BURRH proteins from the recently sequenced genome of the endosymbiont fungi Burkholderia rhizoxinica (Lackner, Moebius et al. 2011). These nucleic acid binding polypeptides comprise modules of about 31 to 33 amino acids that are base specific. These modules display less than 40% sequence identity with Xanthomonas TALE common repeats and present more polypeptides sequence variability. The different domains from the above proteins (modules, N and C-terminals) from Burkholderia and Xanthomonas are useful to engineer new proteins or scaffolds having binding properties to specific nucleic acid sequences and may be combined to form chimeric TALE-MBBBD proteins.
In a preferred embodiment, a TAL nuclease of the invention comprises a sequence selected from any one the following pair of sequences: SEQ ID NO 102 and SEQ ID NO 103, SEQ ID NO 104 and SEQ ID NO 105, SEQ ID NO 106 and SEQ ID NO 107, SEQ ID NO 108 and SEQ ID NO 109, SEQ ID NO 110 and SEQ ID NO 111, SEQ ID NO 112 and SEQ ID NO 113, SEQ ID NO 114 and SEQ ID NO 115, SEQ ID NO 116 and SEQ ID NO 117, SEQ ID NO 118 and SEQ ID NO 119, SEQ ID N0171 and SEQ ID NO 172, SEQ ID NO 173 and SEQ ID NO 174, SEQ ID NO 175 and SEQ ID NO 176, SEQ ID NO 177 and SEQ ID NO 178; or a sequence having least 95% homology with any one of said pair of sequences.
Delivery Methods
The inventors have considered any means known in the art to allow delivery inside cells or subcellular compartments of said cells the polynucleotides expressing the endonucleases, their possible co-effectors (e.g. guide RNA, . . . ) as well as the chimeric antigen receptors. These means include viral transduction, electroporation and also liposomal delivery means, polymeric carriers, chemical carriers, lipoplexes, polyplexes, dendrimers, nanoparticles, emulsion, natural endocytosis or phagocytose pathway as non-limiting examples.
As a preferred embodiment of the invention, polynucleotides encoding the endonucleases of the present invention are transfected under mRNA form in order to obtain transient expression and avoid chromosomal integration of foreign DNA, for example by electroporation. The inventors have determined different optimal conditions for mRNA electroporation in T-cell displayed in Table 1. The inventor used the cytoPulse technology which allows, by the use of pulsed electric fields, to transiently permeabilize living cells for delivery of material into the cells (U.S. Pat. No. 6,010,613 and WO 2004/083379). Pulse duration, intensity as well as the interval between pulses can be modified in order to reach the best conditions for high transfection efficiency with minimal mortality. Basically, the first high electric field pulses allow pore formation, while subsequent lower electric field pulses allow to moving the polynucleotide into the cell. In one aspect of the present invention, the inventor describe the steps that led to achievement of >95% transfection efficiency of mRNA in T cells, and the use of the electroporation protocol to transiently express different kind of proteins in T cells. In particular the invention relates to a method of transforming T cell comprising contacting said T cell with RNA and applying to T cell an agile pulse sequence consisting of:
In particular embodiment, the method of transforming T cell comprising contacting said T cell with RNA and applying to T cell an agile pulse sequence consisting of:
Any values included in the value range described above are disclosed in the present application. Electroporation medium can be any suitable medium known in the art. Preferably, the electroporation medium has conductivity in a range spanning 0.01 to 1.0 milliSiemens.
Viral Transduction
According to the present invention, the use of retroviral vectors and more preferably of lentiviral vectors is particularly suited for expressing the chimeric antigen receptors into the T-cells. In a preferred embodiment the use of adeno associated viral vectors and more preferably of AAV6, or AAV9 vectors is particularly suited for expressing a gene including chimeric antigen receptors into the T-cells. Methods for viral transduction are well known in the art (Walther et al. (2000) Viral Vectors for Gene Transfer. Drugs. 60(2):249-271). Integrative viral vectors allow the stable integration of the polynucleotides in the T-cells genome and to expressing the chimeric antigen receptors over a longer period of time.
Non Alloreactive T Cells:
Although the method of the invention could be carried out in-vivo as part of a gene therapy, for instance, by using viral vectors targeting T-cells in blood circulation, which would include genetic sequences expressing a specific rare-cutting endonuclease along with other genetic sequences expressing a CAR, the method of the invention is more generally intended to be practiced ex-vivo on cultured T-cells obtainable from patients or donors. The engineered T-cells engineered ex-vivo can be either re-implanted into a patient from where they originate, as part of an autologous treatment, or to be used as part of an allogeneic treatment. In this later case, it is preferable to further engineer the cells to make them non-alloreactive to ensure their proper engraftment. Accordingly, the method of the invention may include additional steps of procuring the T-cells from a donor and to inactivate genes thereof involved in MHC recognition and or being targets of immunosuppressive drugs such as described for instance in WO 2013/176915.
T cell receptors (TCR) are cell surface receptors that participate in the activation of T cells in response to the presentation of antigen. The TCR is generally made from two chains, alpha and beta, which assemble to form a heterodimer and associates with the CD3-transducing subunits to form the T-cell receptor complex present on the cell surface. Each alpha and beta chain of the TCR consists of an immunoglobulin-like N-terminal variable (V) and constant (C) region, a hydrophobic transmembrane domain, and a short cytoplasmic region. As for immunoglobulin molecules, the variable region of the alpha and beta chains are generated by V(D)J recombination, creating a large diversity of antigen specificities within the population of T cells. However, in contrast to immunoglobulins that recognize intact antigen, T cells are activated by processed peptide fragments in association with an MHC molecule, introducing an extra dimension to antigen recognition by T cells, known as MHC restriction. Recognition of MHC disparities between the donor and recipient through the T cell receptor leads to T cell proliferation and the potential development of GVHD. It has been shown that normal surface expression of the TCR depends on the coordinated synthesis and assembly of all seven components of the complex (Ashwell and Klusner 1990). The inactivation of TCRalpha or TCRbeta can result in the elimination of the TCR from the surface of T cells preventing recognition of alloantigen and thus GVHD.
Thus, still according to the invention, engraftment of the allogeneic T-cells may be improved by inactivating at least one gene encoding a TCR component. TCR is rendered not functional in the cells by inactivating TCR alpha gene and/or TCR beta gene(s), preferably by inserting a sequence into the endogenous TCR gene (genomic TCR gene), by using a viral vector preferably an adeno associated virus.
With respect to the use of Cas9/CRISPR system, the inventors have determined appropriate target sequences within the 3 exons encoding TCR, allowing a significant reduction of toxicity in living cells, while retaining cleavage efficiency. The preferred target sequences are noted in Table 2 (+ for lower ratio of TCR negative cells, ++ for intermediate ratio, +++ for higher ratio).
MHC antigens are also proteins that played a major role in transplantation reactions. Rejection is mediated by T cells reacting to the histocompatibility antigens on the surface of implanted tissues, and the largest group of these antigens is the major histocompatibility antigens (MHC). These proteins are expressed on the surface of all higher vertebrates and are called HLA antigens (for human leukocyte antigens) in human cells. Like TCR, the MHC proteins serve a vital role in T cell stimulation. Antigen presenting cells (often dendritic cells) display peptides that are the degradation products of foreign proteins on the cell surface on the MHC. In the presence of a co-stimulatory signal, the T cell becomes activated, and will act on a target cell that also displays that same peptide/MHC complex. For example, a stimulated T helper cell will target a macrophage displaying an antigen in conjunction with its MHC, or a cytotoxic T cell (CTL) will act on a virally infected cell displaying foreign viral peptides.
Thus, in order to provide less alloreactive T-cells, the method of the invention can further comprise the step of inactivating or mutating one HLA gene.
The class I HLA gene cluster in humans comprises three major loci, B, C and A, as well as several minor loci. The class II HLA cluster also comprises three major loci, DP, DQ and DR, and both the class I and class II gene clusters are polymorphic, in that there are several different alleles of both the class I and II genes within the population. There are also several accessory proteins that play a role in HLA functioning as well. The TapI and Tap2 subunits are parts of the TAP transporter complex that is essential in loading peptide antigens on to the class I HLA complexes, and the LMP2 and LMP7 proteosome subunits play roles in the proteolytic degradation of antigens into peptides for display on the HLA. Reduction in LMP7 has been shown to reduce the amount of MHC class I at the cell surface, perhaps through a lack of stabilization (Fehling et al. (1999) Science 265:1234-1237). In addition to TAP and LMP, there is the tapasin gene, whose product forms a bridge between the TAP complex and the HLA class I chains and enhances peptide loading. Reduction in tapasin results in cells with impaired MHC class I assembly, reduced cell surface expression of the MHC class I and impaired immune responses (Grandea et al. (2000) Immunity 13:213-222 and Garbi et al. (2000) Nat. Immunol. 1:234-238). Any of the above genes may be inactivated as part of the present invention as disclosed, for instance in WO 2012/012667.
The present invention provides an engineered T cell comprising any one of the genetic modification to a sequence as shown in SEQ ID NO. 1, SEQ ID NO. 4, or SEQ ID NO. 7 of the CD38 gene, of SEQ ID NO. 63, SEQ ID NO. 66, SEQ ID NO. 69, SEQ ID NO. 167, SEQ ID NO. 168, SEQ ID NO. 169 or SEQ ID NO. 170 of the CS1 gene or of SEQ ID NO. 72, SEQ ID NO. 75 or SEQ ID NO. 78 of the CD70 gene.
The present invention provides a combination comprising an engineered T cell comprising any one of the genetic modification to a sequence as shown in SEQ ID NO. 1, SEQ ID NO. 4, SEQ ID NO. 7 of the CD38 gene and a therapeutic antibody specific for the antigen marker encoded by the CD38 gene.
The present invention provides a combination comprising an engineered T cell comprising any one of the genetic modification to a sequence as shown in SEQ ID NO. 63, SEQ ID NO. 66, SEQ ID NO. 69, SEQ ID NO. 167, SEQ ID NO. 168, SEQ ID NO. 169 or SEQ ID NO. 170 of the CS1 gene and a therapeutic antibody specific for the antigen marker encoded by the CS1 gene.
The present invention provides a combination comprising an engineered T cell comprising any one of the genetic modification to a sequence as shown in SEQ ID NO. 72, SEQ ID NO. 75 or SEQ ID NO. 78 of the CD70 gene and a therapeutic antibody specific for the antigen marker encoded by the CD70 gene.
The engineered T cell according to the above comprises a genetic modification to a sequence of SEQ ID NO. 1 by a TAL protein comprising a sequence SEQ ID NO 114 and SEQ ID NO 115, a genetic modification to a sequence of SEQ ID NO. 4 by a TALEN comprising a SEQ ID No 116 and SEQ ID NO 117, or a genetic modification to a sequence of SEQ ID NO. 7 by a TAL protein comprising a sequence SEQ ID No 118 and SEQ ID NO 119; and/or a genetic modification to a sequence of SEQ ID NO. 63 by a TAL protein of sequence SEQ ID NO 108 and SEQ ID NO 109, a genetic modification to a sequence of SEQ ID NO. 66 by a TAL protein of sequence SEQ ID NO 110 and SEQ ID NO 111, a genetic modification to a sequence of SEQ ID NO. 69 by a TAL protein of sequence SEQ ID NO 112 and SEQ ID NO 113, a genetic modification to a sequence of SEQ ID NO. 167 by a TAL protein of sequence SEQ ID NO 171 and SEQ ID NO 172, a genetic modification to a sequence of SEQ ID NO. 168 by a TAL protein of sequence SEQ ID NO 173 and SEQ ID NO 174, or a genetic modification to a sequence of SEQ ID NO. 169 by a TAL protein of sequence SEQ ID NO 171 and SEQ ID NO 172; and/or a genetic modification to a sequence of SEQ ID NO. 72 by a TAL protein of sequence SEQ ID NO 102 and SEQ ID NO 103, a genetic modification to a sequence of SEQ ID NO. 75 by a TAL protein of sequence SEQ ID NO 104 and SEQ ID NO 105, a genetic modification to a sequence of SEQ ID NO. 78 by a TAL protein of sequence SEQ ID NO 106 and SEQ ID NO 107.
The engineered T cell according to the above comprising an insertion of a polynucleotide sequence encoding a gene, preferably a CAR, preferably at the locus described above, into the TRAC gene and at least one a genetic inactivation to a sequence of SEQ ID NO. 1 by a TAL protein comprising a sequence SEQ ID NO 114 and SEQ ID NO 115; a genetic modification to a sequence of SEQ ID NO. 4 by a TALEN comprising a SEQ ID NO 116 and SEQ ID NO 117, a genetic modification to a sequence of SEQ ID NO. 7 by a TAL protein comprising a sequence SEQ ID NO 118 and SEQ ID NO 119, a genetic modification to a sequence of SEQ ID NO. 63 by a TAL protein of sequence SEQ ID NO 108 and SEQ ID NO 109, a genetic modification to a sequence of SEQ ID NO. 66 by a TAL protein of sequence SEQ ID NO 110 and SEQ ID NO 111, a genetic modification to a sequence of SEQ ID NO. 69 by a TAL protein of sequence SEQ ID NO 112 and SEQ ID NO 113, of the CS1 gene, a genetic modification to a sequence of SEQ ID NO. 72 by a TAL protein of sequence SEQ ID NO 102 and SEQ ID NO 103, a genetic modification to a sequence of SEQ ID NO. 75 by a TAL protein of sequence SEQ ID NO 104 and SEQ ID NO 105, a genetic modification to a sequence of SEQ ID NO. 78 of the CD70 gene by a TAL protein of sequence SEQ ID NO 106 and SEQ ID NO 107.
The TAL-nuclease of the invention as any one of the above is provided for use as a medicament, alone or in combination with an therapeutic antibody specific for the same gene.
The combination of the invention as any one of the above and below is provided for the treatment of cancer, infections or auto-immune disease.
Method of Engineering Drug-Resistant T-Cells:
To improve cancer therapy and selective engraftment of allogeneic T-cells, drug resistance can be conferred to the engineered T-cells to protect them from the toxic side effects of chemotherapy or immunosuppressive agents. Indeed, most patients were treated with chemotherapy and immune depleting agents as a standard of care, prior to receiving T-cell immunotherapy. One could take advantage of these treatments to help the selection of the engineered T-cells, either by adding chemotherapy drugs in culture media for expansion of the cells ex-vivo prior to treatment, or by obtaining a selective expansion of the engineered T-cells in-vivo in patients under chemotherapy or immunosuppressive treatments.
Also the drug resistance of T-cells also permits their enrichment in or ex vivo, as T-cells which express the drug resistance gene, will survive and multiply relative to drug sensitive cells. In particular, the present invention relates to a method of engineering allogeneic and drug resistance T-cells resistant for immunotherapy comprising:
Drug resistance can be conferred to a T-cell by inactivating one or more gene(s) responsible for the cell's sensitivity to the drug (drug sensitizing gene(s)), such as the hypoxanthine-guanine phosphoribosyl transferase (HPRT) gene (Genbank: M26434.1). In particular HPRT can be inactivated in engineered T-cells to confer resistance to a cytostatic metabolite, the 6-thioguanine (6TG) which is converted by HPRT to cytotoxic thioguanine nucleotide and which is currently used to treat patients with cancer, in particular leukemias (Hacke, Treger et al. 2013). Another example if the inactivation of the CD3 normally expressed at the surface of the T-cell can confer resistance to anti-CD3 antibodies such as teplizumab.
Drug resistance can also be conferred to a T-cell by expressing a drug resistance gene. Said drug resistance gene refers to a nucleic acid sequence that encodes “resistance” to an agent, such as a chemotherapeutic agent (e.g. methotrexate). In other words, the expression of the drug resistance gene in a cell permits proliferation of the cells in the presence of the agent to a greater extent than the proliferation of a corresponding cell without the drug resistance gene. A drug resistance gene of the invention can encode resistance to antimetabolite, methotrexate, vinblastine, cisplatin, alkylating agents, anthracyclines, cytotoxic antibiotics, anti-immunophilins, their analogs or derivatives, and the like.
Variant alleles of several genes such as dihydrofolate reductase (DHFR), inosine monophosphate dehydrogenase 2 (IMPDH2), calcineurin or methylguanine transferase (MGMT) have been identified to confer drug resistance to a cell. Said drug resistance gene can be expressed in the cell either by introducing a transgene encoding said gene into the cell or by integrating said drug resistance gene into the genome of the cell by homologous recombination. Several other drug resistance genes have been identified that can potentially be used to confer drug resistance to targeted cells (Takebe, Zhao et al. 2001; Sugimoto, Tsukahara et al. 2003; Zielske, Reese et al. 2003; Nivens, Felder et al. 2004; Bardenheuer, Lehmberg et al. 2005; Kushman, Kabler et al. 2007).
DHFR is an enzyme involved in regulating the amount of tetrahydrofolate in the cell and is essential to DNA synthesis. Folate analogs such as methotrexate (MTX) inhibit DHFR and are thus used as anti-neoplastic agents in clinic. Different mutant forms of DHFR which have increased resistance to inhibition by anti-folates used in therapy have been described. In a particular embodiment, the drug resistance gene according to the present invention can be a nucleic acid sequence encoding a mutant form of human wild type DHFR (GenBank: AAH71996.1) which comprises at least one mutation conferring resistance to an anti-folate treatment, such as methotrexate. In particular embodiment, mutant form of DHFR comprises at least one mutated amino acid at position G15, L22, F31 or F34, preferably at positions L22 or F31 ((Schweitzer, Dicker et al. 1990); International application WO 94/24277; U.S. Pat. No. 6,642,043).
As used herein, “antifolate agent” or “folate analogs” refers to a molecule directed to interfere with the folate metabolic pathway at some level. Examples of antifolate agents include, e.g., methotrexate (MTX); aminopterin; trimetrexate (Neutrexin™); edatrexate; N10-propargyl-5,8-dideazafolic acid (CB3717); ZD1694 (Tumodex), 5,8-dideazaisofolic acid (IAHQ); 5,10-dideazatetrahydrofolic acid (DDATHF); 5-deazafolic acid; PT523 (N alpha-(4-amino-4-deoxypteroyl)-N delta-hemiphthaloyl-L-ornithine); 10-ethyl-10-deazaaminopterin (DDATHF, lomatrexol); piritrexim; 10-EDAM; ZD1694; GW1843; Pemetrexate and PDX (10-propargyl-10-deazaaminopterin).
Another example of drug resistance gene can also be a mutant or modified form of ionisine-5′-monophosphate dehydrogenase II (IMPDH2), a rate-limiting enzyme in the de novo synthesis of guanosine nucleotides. The mutant or modified form of IMPDH2 is a IMPDH inhibitor resistance gene. IMPDH inhibitors can be mycophenolic acid (MPA) or its prodrug mycophenolate mofetil (MMF). The mutant IMPDH2 can comprises at least one, preferably two mutations in the MAP binding site of the wild type human IMPDH2 (NP_000875.2) that lead to a significantly increased resistance to IMPDH inhibitor. The mutations are preferably at positions T333 and/or S351 (Yam, Jensen et al. 2006; Sangiolo, Lesnikova et al. 2007: Jonnalagadda, Brown et al. 2013). In a particular embodiment, the threonine residue at position 333 is replaced with an isoleucine residue and the serine residue at position 351 is replaced with a tyrosine residue.
Another drug resistance gene is the mutant form of calcineurin. Calcineurin (PP2B) is an ubiquitously expressed serine/threonine protein phosphatase that is involved in many biological processes and which is central to T-cell activation. Calcineurin is a heterodimer composed of a catalytic subunit (CnA; three isoforms) and a regulatory subunit (CnB; two isoforms). After engagement of the T-cell receptor, calcineurin dephosphorylates the transcription factor NFAT, allowing it to translocate to the nucleus and active key target gene such as IL2. FK506 in complex with FKBP12, or cyclosporine A (CsA) in complex with CyPA block NFAT access to calcineurin's active site, preventing its dephosphorylation and thereby inhibiting T-cell activation (Brewin, Mancao et al. 2009). The drug resistance gene of the present invention can be a nucleic acid sequence encoding a mutant form of calcineurin resistant to calcineurin inhibitor such as FK506 and/or CsA. In a particular embodiment, said mutant form can comprise at least one mutated amino acid of the wild type calcineurin heterodimer a at positions: V314, Y341, M347, T351, W352, L354, K360, preferably double mutations at positions T351 and L354 or V314 and Y341. Correspondence of amino acid positions described herein is frequently expressed in terms of the positions of the amino acids of the form of wild-type human calcineurin heterodimer (GenBank: ACX34092.1).
In another particular embodiment, said mutant form can comprise at least one mutated amino acid of the wild type calcineurin heterodimer b at positions: V120, N123, L124 or K125, preferably double mutations at positions L124 and K125. Correspondence of amino acid positions described herein is frequently expressed in terms of the positions of the amino acids of the form of wild-type human calcineurin heterodimer b polypeptide (GenBank: ACX34095.1).
Another drug resistance gene is 0(6)-methylguanine methyltransferase (MGMT) encoding human alkyl guanine transferase (hAGT). AGT is a DNA repair protein that confers resistance to the cytotoxic effects of alkylating agents, such as nitrosoureas and temozolomide (TMZ). 6-benzylguanine (6-BG) is an inhibitor of AGT that potentiates nitrosourea toxicity and is co-administered with TMZ to potentiate the cytotoxic effects of this agent. Several mutant forms of MGMT that encode variants of AGT are highly resistant to inactivation by 6-BG, but retain their ability to repair DNA damage (Maze, Kurpad et al. 1999). In a particular embodiment, AGT mutant form can comprise a mutated amino acid of the wild type AGT position P140 (UniProtKB: P16455).
Another drug resistance gene can be multidrug resistance protein 1 (MDR1) gene. This gene encodes a membrane glycoprotein, known as P-glycoprotein (P-GP) involved in the transport of metabolic byproducts across the cell membrane. The P-Gp protein displays broad specificity towards several structurally unrelated chemotherapy agents. Thus, drug resistance can be conferred to cells by the expression of nucleic acid sequence that encodes MDR-1 (NP_000918).
Drug resistance gene can also be cytotoxic antibiotics, such as ble gene or mcrA gene. Ectopic expression of ble gene or mcrA in an immune cell gives a selective advantage when exposed to the chemotherapeutic agent, respectively the bleomycine or the mitomycin C.
The T-cells can also be made resistant to immunosuppressive agents. An immunosuppressive agent is an agent that suppresses immune function by one of several mechanisms of action. In other words, 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. As non-limiting example, an immunosuppressive agent can be a calcineurin inhibitor, a target of rapamycin, an interleukin-2 α-chain blocker, an inhibitor of inosine monophosphate dehydrogenase, an inhibitor of dihydrofolic acid reductase, a corticosteroid or an immunosuppressive antimetabolite. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. The method according to the invention allows conferring immunosuppressive resistance to T cells for immunotherapy by inactivating the target of the immunosuppressive agent in T cells. As non-limiting examples, targets for immunosuppressive agent can be a receptor for an immunosuppressive agent such as: CD52, glucocorticoid receptor (GR), a FKBP family gene member and a cyclophilin family gene member.
In immunocompetent hosts, allogeneic cells are normally rapidly rejected by the host immune system. It has been demonstrated that, allogeneic leukocytes present in non-irradiated blood products will persist for no more than 5 to 6 days. Thus, to prevent rejection of allogeneic cells, the host's immune system must be effectively suppressed. Glucocorticoidsteroids are widely used therapeutically for immunosuppression. This class of steroid hormones binds to the glucocorticoid receptor (GR) present in the cytosol of T cells resulting in the translocation into the nucleus and the binding of specific DNA motifs that regulate the expression of a number of genes involved in the immunologic process. Treatment of T cells with glucocorticoid steroids results in reduced levels of cytokine production leading to T cell anergy and interfering in T cell activation. Alemtuzumab, also known as CAMPATH1-H, is a humanized monoclonal antibody targeting CD52, a 12 amino acid glycosylphosphatidyl-inositol-(GPI) linked glycoprotein (Waldmann and Hale, 2005). CD52 is expressed at high levels on T and B lymphocytes and lower levels on monocytes while being absent on granulocytes and bone marrow precursors. Treatment with Alemtuzumab, a humanized monoclonal antibody directed against CD52, has been shown to induce a rapid depletion of circulating lymphocytes and monocytes. It is frequently used in the treatment of T cell lymphomas and in certain cases as part of a conditioning regimen for transplantation. However, in the case of adoptive immunotherapy the use of immunosuppressive drugs will also have a detrimental effect on the introduced therapeutic T cells. Therefore, to effectively use an adoptive immunotherapy approach in these conditions, the introduced cells would need to be resistant to the immunosuppressive treatment.
As a preferred embodiment of the above steps, said gene of step (b), specific for an immunosuppressive treatment, is CD52, and the immunosuppressive treatment of step (d) comprises a humanized antibody targeting CD52 antigen. As another embodiment, said gene of step (b), specific for an immunosuppressive treatment, is a glucocorticoid receptor (GR) and the immunosuppressive treatment of step d) comprises a corticosteroid such as dexamethasone. As another embodiment, said target gene of step (b), specific for an immunosuppressive treatment, is a FKBP family gene member or a variant thereof and the immunosuppressive treatment of step (d) comprises FK506 also known as Tacrolimus or fujimycin. As another embodiment, said FKBP family gene member is FKBP12 or a variant thereof. As another embodiment, said gene of step (b), specific for an immunosuppressive treatment, is a cyclophilin family gene member or a variant thereof and the immunosuppressive treatment of step (d) comprises cyclosporine.
In a particular embodiment of the invention, the genetic modification step of the method relies on the inactivation of an antigen marker X expressed on both T cell and pathological cells and of at least two genes selected from the group consisting of CD52, dCK, GR, TCR alpha, TCR beta, a combination thereof. The inventor succeeded in engineering at least 5 genes in a primary cell as disclosed in PA 201670503.
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 using at least two RNA guides targeting the different genes.
In a particular embodiment of the invention, the genetic modification step of the method relies on the inactivation of two genes selected from the group consisting of dCK and GR, dCK and TCR alpha, dCK 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 using at least two RNA guides targeting the different genes.
Engineering Highly Active T Cells for Immunotherapy
According to the present invention, the cells can be selected from the group consisting of T-cells, preferably inflammatory T-lymphocytes, cytotoxic T-lymphocytes, regulatory T-lymphocytes or helper T-lymphocytes. In another embodiment, said cell can be from the group consisting of CD4+ T-lymphocytes and CD8+T-lymphocytes. They can be extracted from blood or derived from stem cells. The cells may also be stem cells preferably cells can be adult stem cells, embryonic stem cells. In another embodiments cells may be non-human stem cells, cord blood stem cells, progenitor cells, bone marrow stem cells, induced pluripotent stem cells, totipotent stem cells or hematopoietic stem cells. Representative human cells are CD34+ cells, or CD8+ cells. Prior to expansion and genetic modification of the cells of the invention, a source of cells can be obtained from a subject through a variety of non-limiting methods. T-cells can be obtained from a number of non-limiting sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors. In certain embodiments of the present invention, any number of T cell lines available and known to those skilled in the art, may be used. In another embodiment, said cell can be derived from a healthy donor, from a patient diagnosed with cancer or from a patient diagnosed with an infection. In another embodiment, said cell is part of a mixed population of cells which present different phenotypic characteristics. In the scope of the present invention is also encompassed a cell line obtained from a transformed T-cell according to the method previously described.
The cells used here may have been already engineered, that is to say inactivated by deleting a TCR subunit, preferably a TCR alpha subunit, made resistant to PNA by inactivating the dCK gene, made resistant to alentuzumab by deleting the D52 gene as described in WO2015075195A1, or in Valton J, Guyot V, Marechal A, et al. A Multidrug-resistant Engineered CAR T Cell for Allogeneic Combination Immunotherapy. Molecular Therapy. 2015; 23(9):1507-1518. doi:10.1038/mt.2015.104.
As a further aspect of the invention, the T-cells according to the invention may be further engineered, preferably genetically engineered, to enhance their activity and/or activation, especially by modulating the expression of proteins involved in overall T-cell regulation, referred to as “immune-checkpoints”.
Immune Check Points
It will be understood by those of ordinary skill in the art, that the term “immune checkpoints” means a group of molecules expressed by T cells. These molecules effectively serve as “brakes” to down-modulate or inhibit an immune response. Immune checkpoint molecules include, but are not limited to Programmed Death 1 (PD-1, also known as PDCD1 or CD279, accession number: NM_005018), Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4, also known as CD152, GenBank accession number AF414120.1), LAG3 (also known as CD223, accession number: NM_002286.5), Tim3 (also known as HAVCR2, GenBank accession number: JX049979.1), BTLA (also known as CD272, accession number: NM_181780.3), BY55 (also known as CD160, GenBank accession number: CR541888.1), TIGIT (also known as IVSTM3, accession number: NM_173799), LAIR1 (also known as CD305, GenBank accession number: CR542051.1, {Meyaard, 1997 #122}), SIGLEC10 (GeneBank accession number: AY358337.1), 2B4 (also known as CD244, accession number: NM_001166664.1), PPP2CA, PPP2CB, PTPN6, PTPN22, CD96, CRTAM, SIGLEC7 {Nicoll, 1999 #123}, SIGLEC9 {Zhang, 2000 #124; Ikehara, 2004 #125}, TNFRSF10B, TNFRSF10A, CASP8, CASP10, CASP3, CASP6, CASP7, FADD, FAS, TGFBRII, TGFRBRI, SMAD2, SMAD3, SMAD4, SMAD10, SKI, SKIL, TGIF1, IL10RA, IL10RB, HMOX2, IL6R, IL6ST, EIF2AK4, CSK, PAG1, SIT1, FOXP3, PRDM1, BATF {Quigley, 2010 #121}, GUCY1A2, GUCY1A3, GUCY1B2, GUCY1B3 which directly inhibit immune cells. For example, CTLA-4 is a cell-surface protein expressed on certain CD4 and CD8 T cells; when engaged by its ligands (B7-1 and B7-2) on antigen presenting cells, T-cell activation and effector function are inhibited. Thus the present invention relates to a method of engineering T-cells, especially for immunotherapy, comprising genetically modifying T-cells by inactivating at least one protein involved in the immune checkpoint, in particular PD1 and/or CTLA-4 or any immune-checkpoint proteins referred to in Table 3.
Engineered cells encompasses an engineered immune cell comprising at least one inactivated gene X and expressing a chimeric antigen receptor (CAR) or a component of a recombinant T-cell receptor; wherein said cell has been genetically modified to reduce or inactivate the expression of at least one additional endogenous polynucleotide sequence selected from:
Engineered T-Cells Expressing Chimeric Antigen Receptors Against Pathological Cells
The chimeric antigen receptors introduced into the T-cells according to the invention can adopt different design such as single-chain or multi-chain CARs. These different designs allow various strategies for improving specificity and binding efficiency towards the targeted pathological cells. Some of these strategies are illustrated in the figures of the present application. Single-chain CARs are the most classical version in the art. Multi-chain CAR architectures were developed by the applicant as allowing modulation of the activity of T-cells in terms of specificity and intensity. The multiple subunits can shelter additional co-stimulation domains or keep such domains at a distance, as well as other types of receptors, whereas classical single chain architecture can sometimes be regarded as too much sensitive and less permissive to multispecific interactions.
Single-Chain CAR
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.
Novel specificities in T cells have been successfully generated through the genetic transfer of transgenic T cell receptors or chimeric antigen receptors (CARs) (Jena, Dotti et al. 2010). CARs are synthetic receptors consisting of a targeting moiety that is associated with one or more signaling domains in a single fusion molecule. In general, the binding moiety of a CAR consists of an antigen-binding domain of a single-chain antibody (scFv), comprising the light and 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), 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).
In addition to the CAR targeting the antigen marker, which is common to the pathological cells and the T-cells, such as CD38, it is envisioned to express further CARs directed towards other antigen markers not necessarily expressed by the T-cells, so as to enhancing T-cells specificity.
Examples of chimeric antigen receptor that can be further expressed by the T-cells to create multi-specific cells, are antigen receptors directed against multiple myeloma or lymphoblastic leukemia antigen markers, such as TNFRSF17 (UNIPROT Q02223), SLAMF7 (UNIPROT Q9NQ25), GPRC5D (UNIPROT Q9NZD1), FKBP11 (UNIPROT Q9NYL4), KAMP3, ITGA8 (UNIPROT P53708), and FCRL5 (UNIPROT Q68SN8).
As further examples, the antigen of the target can be from any cluster of differentiation molecules (e.g. CD16, CD64, CD78, CD96, CLL1, CD116, CD117, CD71, CD45, CD71, CD123 and CD138), 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, ductal-epithelial mucine, gp36, TAG-72, glycosphingolipids, glioma-associated antigen, β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut hsp70-2, M-CSF, prostase, prostase specific antigen (PSA), PAP, NY-ESO-1, LAGA-1a, p53, prostein, PSMA, surviving and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrin B2, CD22, insulin growth factor (IGF1)-I, IGF-II, IGFI receptor, mesothelin, a major histocompatibility complex (MHC) molecule presenting a tumor-specific peptide epitope, 5T4, ROR1, Nkp30, NKG2D, tumor stromal antigens, the extra domain A (EDA) and extra domain B (EDB) of fibronectin and the A1 domain of tenascin-C (TnC A1) and fibroblast associated protein (fap); a lineage-specific or tissue specific antigen such as CD3, CD4, CD8, CD24, CD25, CD33, CD34, CD133, CD138, CTLA-4, B7-1 (CD80), B7-2 (CD86), GM-CSF, cytokine receptors, endoglin, a major histocompatibility complex (MHC) molecule, BCMA (CD269, TNFRSF 17), or a virus-specific surface antigen such as an HIV-specific antigen (such as HIV gp120); an EBV-specific antigen, a CMV-specific antigen, a HPV-specific antigen, a Lasse Virus-specific antigen, an Influenza Virus-specific antigen as well as any derivate or variant of these surface markers. Antigens are not necessarily surface marker antigens but can be also endogenous small antigens presented by HLA class I at the surface of the cells.
Multi-Subunit CAR
Chimeric antigen receptors from the prior art introduced in T-cells have been formed of single chain polypeptides that necessitate serial appending of signaling domains. However, by moving signaling domains from their natural juxtamembrane position may interfere with their function. To overcome this drawback, the applicant recently designed a multi-chain CAR derived from FcεRI to allow normal juxtamembrane position of all relevant signaling domains. In this new architecture, the high affinity IgE binding domain of FcεRI alpha chain is replaced by an extracellular ligand-binding domain such as scFv to redirect T-cell specificity against cell targets and the N and/or C-termini tails of FcεRI beta chain are used to place costimulatory signals in normal juxtamembrane positions.
Accordingly, the CAR expressed by the engineered T-cell according to the invention can be a multi-chain chimeric antigen receptor (CAR) particularly adapted to the production and expansion of engineered T-cells of the present invention. Such multi-chain CARs comprise at least two of the following components:
According to such architectures, ligands binding domains and signaling domains are born on separate polypeptides. The different polypeptides are anchored into the membrane in a close proximity allowing interactions with each other. In such architectures, the signaling and co-stimulatory domains can be in juxtamembrane positions (i.e. adjacent to the cell membrane on the internal side of it), which is deemed to allow improved function of co-stimulatory domains. The multi-subunit architecture also offers more flexibility and possibilities of designing CARs with more control on T-cell activation. For instance, it is possible to include several extracellular antigen recognition domains having different specificity to obtain a multi-specific CAR architecture. It is also possible to control the relative ratio between the different subunits into the multi-chain CAR. This type of architecture has been recently described by the applicant in PCT/US2013/058005.
The assembly of the different chains as part of a single multi-chain CAR is made possible, for instance, by using the different alpha, beta and gamma chains of the high affinity receptor for IgE (FcεRI) (Metzger, Alcaraz et al. 1986) to which are fused the signaling and co-stimulatory domains. The gamma chain comprises a transmembrane region and cytoplasmic tail containing one immunoreceptor tyrosine-based activation motif (ITAM) (Cambier 1995).
The multi-chain CAR can comprise several extracellular ligand-binding domains, to simultaneously bind different elements in target thereby augmenting immune cell activation and function. In one embodiment, the extracellular ligand-binding domains can be placed in tandem on the same transmembrane polypeptide, and optionally can be separated by a linker. In another embodiment, said different extracellular ligand-binding domains can be placed on different transmembrane polypeptides composing the multi-chain CAR. In another embodiment, the present invention relates to a population of multi-chain CARs comprising each one different extracellular ligand binding domains. In a particular, the present invention relates to a method of engineering immune cells comprising providing an immune cell and expressing at the surface of said cell a population of multi-chain CAR each one comprising different extracellular ligand binding domains. In another particular embodiment, the present invention relates to a method of engineering an immune cell comprising providing an immune cell and introducing into said cell polynucleotides encoding polypeptides composing a population of multi-chain CAR each one comprising different extracellular ligand binding domains. In a particular embodiment the method of engineering an immune cell comprises expressing at the surface of the cell at least a part of FcεRI beta and/or gamma chain fused to a signal-transducing domain and several part of FcεRI alpha chains fused to different extracellular ligand binding domains. In a more particular embodiment, said method comprises introducing into said cell at least one polynucleotide which encodes a part of FcεRI beta and/or gamma chain fused to a signal-transducing domain and several FcεRI alpha chains fused to different extracellular ligand binding domains. By population of multi-chain CARs, it is meant at least two, three, four, five, six or more multi-chain CARs each one comprising different extracellular ligand binding domains. The different extracellular ligand binding domains according to the present invention can preferably simultaneously bind different elements in target thereby augmenting immune cell activation and function.
The present invention also relates to an isolated immune cell which comprises a population of multi-chain CARs each one comprising different extracellular ligand binding domains.
The signal transducing domain or intracellular signaling domain of the multi-chain CAR of the invention is responsible for intracellular signaling following the binding of extracellular ligand binding domain to the target resulting in the activation of the immune cell and immune response. In other words, the signal transducing domain is responsible for the activation of at least one of the normal effector functions of the immune cell in which the multi-chain CAR is expressed. For example, the effector function of a T cell can be a cytolytic activity or helper activity including the secretion of cytokines.
In the present application, the term “signal transducing domain” refers to the portion of a protein which transduces the effector signal function signal and directs the cell to perform a specialized function.
Preferred examples of signal transducing domain for use in single or multi-chain CAR can be the cytoplasmic sequences of the Fc receptor or 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 as the same functional capability. Signal transduction domain comprises 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. Primary cytoplasmic signaling sequence can comprise signaling motifs which are known as immunoreceptor tyrosine-based activation motifs of ITAMs. ITAMs are well defined signaling motifs found in the intracytoplasmic tail of a variety of receptors that serve as binding sites for syk/zap70 class tyrosine kinases. Examples of ITAM used in the invention can include as non-limiting examples those derived from TCRzeta, FcRgamma, FcRbeta, FcRepsilon, CD3gamma, CD3delta, CD3epsilon, CD5, CD22, CD79a, CD79b and CD66d. In a preferred embodiment, the signaling transducing domain of the multi-chain CAR can comprise the CD3zeta signaling domain, or the intracytoplasmic domain of the FcεRI beta or gamma chains.
In particular embodiment the signal transduction domain of the multi-chain 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.
Ligand binding-domains can be any antigen receptor previously used, and referred to, with respect to single-chain CAR referred to in the literature, in particular scFv from monoclonal antibodies. Bispecific or multi-specific CARs as described in WO 2014/4011988 are incorporated by reference.
The combination of the invention comprises an engineered T cell according to the above endowed with at least one chimeric antigen receptor (CAR) or exogenous TCR.
The combination of the invention comprises an engineered allogeneic T cell according to the above, engineered to be less alloreactive, by engineering or deleting genes encoding components of the HLA complex, either to inactivated cell surface expression, by deleting genes encoding components of the HLA complex, or modifying the sequence to match MHC molecules to those of the patient.
The combination of the invention comprises an engineered allogeneic T cell according to the above, engineered to be less alloreactive, by engineering or deleting genes encoding components of the HLA complex, selected from beta2microglobulin, regulatory factor X-associated ankyrin-containing protein (RFXANK), regulatory factor 5 (RFX5), regulatory factor X-associated protein (RFXAP), and class II transactivator (CIITA), TAP-1, a combination thereof.
The engineered T cell of the combination of the invention according to the above wherein said CAR is specific for: a cluster of differentiation molecule, a tumor-associated surface antigen, a lineage-specific or tissue specific antigen or a virus-specific surface antigen is provided. The engineered T cell according to the above may comprise a CAR wherein said CAR is targeting (and specific for) any of the following antigen surface marker: CD16, CD64, CD78, CD96, CLL1, CD116, CD117, CD71, CD45, CD71, CD123 and CD138; or 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, ductal-epithelial mucine, gp36, TAG-72, glycosphingolipids, glioma-associated antigen, β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut hsp70-2, M-CSF, prostase, prostase specific antigen (PSA), PAP, NY-ESO-1, LAGA-1a, p53, prostein, PSMA, surviving and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrin B2, CD22, insulin growth factor (IGF1)-I, IGF-II, IGFI receptor, mesothelin, a major histocompatibility complex (MHC) molecule presenting a tumor-specific peptide epitope, 5T4, ROR1, Nkp30, NKG2D, tumor stromal antigens, the extra domain A (EDA) and extra domain B (EDB) of fibronectin and the A1 domain of tenascin-C (TnC A1) and fibroblast associated protein (fap); or CD3, CD4, CD8, CD24, CD25, CD33, CD34, CD38, CD133, CD138, CTLA-4, B7-1 (CD80), B7-2 (CD86), GM-CSF, cytokine receptors, endoglin, a major histocompatibility complex (MHC) molecule, BCMA (CD269, TNFRSF17); or HIV-specific antigen (such as HIV gp120); an EBV-specific antigen, a CMV-specific antigen, a HPV-specific antigen, a Lasse Virus-specific antigen, an Influenza Virus-specific antigen, as the therapeutic antibody combined. The CAR endowed in the engineered cells in the combination of the invention may be specific for (e.g. CD16, CD19, CD20, CD22, CD30, CD38, CD40, CD64, CD70, CD78, CD79a CD79b, CD96, CLL1, CD116, CD117, CD71, CD45, CD123 and CD138), CS1, 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), disialoganglioside GD2, o-acethyl GD2, GD3, mesothelin, ductal-epithelial mucine, gp36, TAG-72, glycosphingolipids, glioma-associated antigen, β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RUI, RU2 (AS), intestinal carboxyl esterase, hsp70-2, HSP70, Flt3, WT1, MUC16, PRAME, TSPAN10, CLAUDIN18.2, DLL3, LY6G6D, Liv-1, CHRNA2, ADAM10, M-CSF, prostase, prostase specific antigen (PSA), PAP, NY-ESO-1, LAGA-Ia, p53, prostein, PSMA, surviving and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrin B2, insulin growth factor (IGF1)-I, IGF-II, IGFI receptor, mesothelin, a major histocompatibility complex (MHC) molecule presenting a tumor-specific peptide epitope, 5T4, RORI, Nkp30, NKG2D, tumor stromal antigens, the extra domain A (EDA) and extra domain B (EDB) of fibronectin and the A1 domain of tenascin-C (TnC A1) and fibroblast associated protein (fap); a lineage-specific or tissue specific antigen such as CD3, CD4, CD8, CD24, CD25, CD33, CD34, CD133, CD138, CTLA-4, B7-1 (CD80), B7-2 (CD86), GM-CSF, CD123, HSP70, FAP, HER2, CD79a, CD79b, CD123, MUC-1, and CS1, a cytokine receptor, endoglin, a major histocompatibility complex (MHC) molecule, BCMA (CD269, TNFRSF 17), or a virus-specific surface antigen such as an HIV specific antigen (such as HIV gp120, NEF, gp41); an EBV-specific antigen, a CMV-specific antigen, a HPV-specific antigen, a Lasse Virus-specific antigen, an Influenza Virus-specific antigen as well as any derivate or variant of these surface markers. an endogenous small antigen presented by HLA class I at the surface of the cells.
The combination of the invention may comprise an immune T cell expressing a CAR which targets specifically a cell surface marker selected from CD19, CD38, HSP70, CD30, FAP, HER2, CD79a, CD79b, CD123, CD22, CLL-1, MUC-1, GD2, O-acetyl-GD2, GD3, ROR 1, and CS1.
The combination of the invention may comprise an immune T cell expressing a CAR which targets specifically a cell surface marker selected from any cluster of differentiation molecules (e.g. CD16, CD20, CD22, CD30, CD38, CD40, CD64, CD78, CD79a CD79b, CD96, CLL1, CD116, CD117, CD71, CD45, CD123 and CD138), CS1, a tumor-associated surface antigen, such as ErbB2 (HER2/neu), carcinoembryonic antigen (CEA), epithelial cell adhesion molecule (EpCAM), epidermal growth factor receptor (EGFR), disialoganglioside GD2, o-acethyl GD2, GD3, mesothelin, ductal-epithelial mucine, gp36, TAG-72, glycosphingolipids, glioma-associated antigen, β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RUI, RU2 (AS), intestinal carboxyl esterase, hsp70-2, HSP70, M-CSF, prostase, prostase specific antigen (PSA), PAP, NY-ESO-1, LAGA-Ia, p53, prostein, PSMA, surviving and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrin B2, insulin growth factor (IGF1)-I, IGF-II, IGFI receptor, mesothelin, a major histocompatibility complex (MHC) molecule presenting a tumor-specific peptide epitope, 5T4, RORI, Nkp30, NKG2D, tumor stromal antigens, the extra domain A (EDA) and extra domain B (EDB) of fibronectin and the A1 domain of tenascin-C (TnC A1) and fibroblast associated protein (fap); a lineage-specific or tissue specific antigen such as CD3, CD4, CD8, CD24, CD25, CD34, CD133, CD138, CTLA-4, B7-1 (CD80), B7-2 (CD86), GM-CSF, CD123, FAP, HER2, CD79a, CD79b, CD123, MUC-1, and CS1, cytokine receptors, endoglin, a major histocompatibility complex (MHC) molecule, or a virus-specific surface antigen such as an HIV specific antigen (such as HIV gp120); an EBV-specific antigen, a CMV-specific antigen, a HPV-specific antigen, a Lasse Virus-specific antigen, an Influenza Virus-specific antigen as well as any derivate or variant of these surface markers. an endogenous small antigen presented by HLA class I at the surface of the cells.
The combination of the invention may comprise an immune T cell expressing a CAR which targets specifically a cell surface marker selected from BCMA, CD33, EGFRVIII, Flt3, WT1, CD70, MUC16, PRAME, TSPAN10, CLAUDIN18.2, DLL3, LY6G6D, Liv-1, CHRNA2, ADAM10.
Activation and Expansion of T Cells
The method according to the invention generally includes a further step of activating and/or expanding the T-cells. This can be done prior to or after genetic modification of the T cells, using the methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and U.S. Patent Application Publication No. 20060121005. According to these methods, the T cells of the invention can be expanded by contact with a surface having attached thereto an agent that stimulates a CD3 TCR complex associated signal and a ligand that stimulates a co-stimulatory molecule on the surface of the T cells.
In particular, T cell populations may be stimulated in vitro such as by contact with an anti-CD3 antibody, or antigen-binding fragment thereof, or an anti-CD2 antibody immobilized on a surface, or by contact with a protein kinase C activator (e.g., bryostatin) in conjunction with a calcium ionophore. For co-stimulation of an accessory molecule on the surface of the T cells, a ligand that binds the accessory molecule is used. For example, a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells. To stimulate proliferation of either CD4+ T cells or CD8+ T cells, an anti-CD3 antibody and an anti-CD28 antibody. For example, the agents providing each signal may be in solution or coupled to a surface. As those of ordinary skill in the art can readily appreciate, the ratio of particles to cells may depend on particle size relative to the target cell. In further embodiments of the present invention, the cells, such as T cells, are combined with agent-coated beads, the beads and the cells are subsequently separated, and then the cells are cultured. In an alternative embodiment, prior to culture, the agent-coated beads and cells are not separated but are cultured together. Cell surface proteins may be ligated by allowing paramagnetic beads to which anti-CD3 and anti-CD28 are attached (3×28 beads) to contact the T cells. In one embodiment the cells (for example, 4 to 10 T cells) and beads (for example, DYNABEADS® M-450 CD3/CD28 T paramagnetic beads at a ratio of 1:1) are combined in a buffer, preferably PBS (without divalent cations such as, calcium and magnesium). Again, those of ordinary skill in the art can readily appreciate any cell concentration may be used. The mixture may be cultured for several hours (about 3 hours) to about 14 days or any hourly integer value in between. In another embodiment, the mixture may be cultured for 21 days. Conditions appropriate for T cell culture include an appropriate media (e.g., Minimal Essential Media or RPMI Media 1640 or, X-vivo 5, (Lonza)) that may contain factors necessary for proliferation and viability, including serum (e.g., fetal bovine or human serum), interleukin-2 (IL-2), insulin, IFN-g, 1L-4, 1L-7, GM-CSF, -10, -2, 1L-15, TGFp, and TNF- or any other additives for the growth of cells known to the skilled artisan. Other additives for the growth of cells include, but are not limited to, surfactant, plasmanate, and reducing agents such as N-acetyl-cysteine and 2-mercaptoethanoi. Media can include RPMI 1640, A1M-V, DMEM, MEM, a-MEM, F-12, X-Vivo 1, and X-Vivo 20, Optimizer, with added amino acids, sodium pyruvate, and vitamins, either serum-free or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones, and/or an amount of cytokine(s) sufficient for the growth and expansion of T cells. Antibiotics, e.g., penicillin and streptomycin, are included only in experimental cultures, not in cultures of cells that are to be infused into a subject. The target cells are maintained under conditions necessary to support growth, for example, an appropriate temperature (e.g., 37° C.) and atmosphere (e.g., air plus 5% C02). T cells that have been exposed to varied stimulation times may exhibit different characteristics
In another particular embodiment, said cells can be expanded by co-culturing with tissue or cells. Said cells can also be expanded in vivo, for example in the subject's blood after administrating said cell into the subject.
Therapeutic Applications
The combination of the invention as described above are intended to be used as a medicament for treating, among others, cancer, infections or immune diseases in a patient in need thereof.
Said treatment can be ameliorating, curative or prophylactic. It may be either part of an autologous immunotherapy or part of an allogenic immunotherapy treatment. By 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. By allogeneic is meant that the cells or population of cells used for treating patients are not originating from said patient but from a donor.
The combination of the above comprises T cells according to one of the previous methods may be pooled, frozen, and administrated to one or several patients. When they are made non-alloreactive, they are available as an “off the shelf” therapeutic product, which means that they can be universally infused to patients in need thereof in combination with a therapeutic antibody directed against the antigen deleted in cells with which Ab are combined of the invention.
Said treatments are primarily intended to patients diagnosed with cancer, viral infection, autoimmune disorders or Graft versus Host Disease (GvHD). Cancers are preferably leukemias and lymphomas, which have liquid tumors, but may also concern solid tumors. Types of cancers to be treated with the CARs of the invention include, but are not limited to, carcinoma, blastoma, and sarcoma, and certain leukemia or lymphoid malignancies, benign and malignant tumors, and malignancies e.g., sarcomas, carcinomas, and melanomas. Adult tumors/cancers and pediatric tumors/cancers are also included.
The present invention provides in Tables 4 to 14 with examples of antigen markers, which can be targeted with the combination of the invention for treating different types of cancer as illustrated in table 5 to 14.
Preferred antigen markers used for the immunotherapy of the present invention are more particularly those of table 5 to 14.
Pathological Conditions
The following pathological conditions may be treated efficiently with the combination of the invention: Multiple myeloma (MM), Acute myeloid leukemia (AML), Chronic myeloid leukemia (CML), Acute lymphoblastic leukemia (ALL), Hodgkin lymphoma (HL) (relapsed, refractory), Non-Hodgkin lymphoma (NHL) (relapsed, refractory), Neuroblastoma, Ewing sarcoma, Myelodysplastic syndromes, BPDCN.
The combination or the pharmaceutical composition of the invention is also especially efficient in the treatment or prophylaxis of Gliomas, pancreatic cancer, lung cancer, bladder cancer, colon cancer, breast cancer.
The combination or the pharmaceutical composition of the invention is adapted for the treatment of Non-Hodgkin's Lymphoma (indolent NHLs, follicular NHLs, small lymphocytic lymphoma, lymphoplasmacytic NHL, or marginal zone NHL); Hodgkin's disease (e.g., Reed-Sternberg cells); a cancer of the B-cell lineage, including, e.g., diffuse large B-cell lymphoma, follicular lymphoma, Burkitt's lymphoma, mantle cell lymphoma, Cutaneous T cell lymphoma, B-cell lymphocytic leukemia (e.g., acute lymphocytic leukemia, chronic lymphocytic leukemia); Epstein Barr Virus positive B cell lymphoma; renal cell carcinoma (e.g., clear cell and papillary); nasopharyngeal carcinoma; thymic carcinoma; glioma; glioblastoma; neuroblastoma; astrocytoma; meningioma; Waldenstrom macroglobulinemia; multiple myeloma; colon cancer, stomach cancer, and rectal carcinoma.
A combination comprising an immune T cell with a genetic modification of the CD70 gene affecting cell surface expression of CD70 and an anti-CD70 therapeutic antibody ARGX 110, is used in the treatment of Cutaneous T cell lymphoma.
A combination comprising an immune T cell with a genetic modification of the CD70 gene affecting cell surface expression of CD70 and an anti-CD70 therapeutic antibody MDX 1203 is intended for its use in the treatment of Renal Cell Carcinoma or Non-hodgkin's Lymphoma.
The combination directed to CS1 is used for the treatment of carcinoma, blastoma, and sarcoma, preferably MM, leukemia, melanoma, relapse or refractory CS-1 expressing MM or a complication related to CS-1 expressing MM.
The combination directed to CS1 is used for the treatment of any one of the following CS1 expressing cancers: Multiple Myeloma, Acute Myeloid Leukemia, Myelodysplastic Syndrome, Smoldering Multiple Myeloma, monoclonal gammopathy of unknown significance (MGUS), plasma cell leukemia, Non-Hodgkin's Lymphoma.
The combination directed to CS1 expressing cancers is used for the treatment of Multiple Myeloma, Non-Hodgkin Lymphoma, Diffuse Large B Cell Lymphoma, Mantle-Cell Lymphoma, Follicular Lymphoma, Indolent B Cell Lymphoma, Primary Mediastinal Lymphoma, Lymphoplasmacytic Lymphoma.
The combination directed to CS1 may be used for the treatment of any one of the following CS1 expressing cancers: NK cell lymphoma, NK or T cell lymphoma, angioimmunoblastic T-cell lymphoma (AITL), or peripheral T cell lymphoma not otherwise specified (PTCL-NOS).
The combination directed to CD38 comprising an immune T cell with a genetic modification of the CD38 gene affecting cell surface expression of CD38 and an anti-CD38 therapeutic antibody HuMax-CD38—Isatuximab is for example for the treatment of Prostate Cancer, Non-small Cell Lung Cancer, Plasma Cell Myeloma, MM, T-cell Type Acute Leukemia, Precursor T-Iymphoblastic Lymphoma or Leukaemia, prostate cancer, Non-small Cell Lung Cancer.
The combination comprising an immune T cell with a genetic modification of the CD38 gene affecting cell surface expression of CD38 and an anti-CD38 therapeutic antibody HuMax-CD38—Daratumumab may be used for the treatment of Microsatellite Unstable Colorectal Cancer, Microsatellite Stable Colorectal Cancer, Mismatch Repair Proficient Colorectal Cancer, Mismatch Repair Deficient Colorectal Cancer, Waldenstrom Macroglobulinemia, Malignant Neoplasms of Male Genital Organs, Prostate Cancer, Hematopoietic Cancer, Acute Myelogenous Leukemia, High-Risk Myelodysplastic Syndrome, Plasma cell myeloma, Monoclonal Gammopathy, Smoldering Multiple Myeloma, Membranoproliferative Glomerulonephritis, Multiple Myeloma.
The combination comprising an immune T cell with a genetic modification of the CD38 gene affecting cell surface expression of CD38 and Isatuximab, for the treatment of T-cell Type Acute Leukemia-Precursor T, lymphoblastic Lymphoma, Leukaemia is provided.
The combination comprising an immune T cell with a genetic modification of the CD38 gene affecting cell surface expression of CD38 and Isatuximab, for the treatment of a CD38-expressing or CD 38 over expressing hematologic cancer selected from the group of Chronic Lymphocytic Leukemia (CLL), Chronic Myelogenous Leukemia (CML), Acute Myelogenous Leukemia (AML), and Acute Lymphocytic Leukemia (ALL), multiple myeloma (MM).
The combination comprising an immune T cell with a genetic modification of the CD38 gene affecting cell surface expression of CD38 and Isatuximab, for the treatment of hematologic cancer selected from the group of leukemia, lymphoma and multiple myeloma (MM).
The combination comprising an immune T cell with a genetic modification of the CD38 gene affecting cell surface expression of CD38 and Isatuximab, (directed to CD38) for the treatment of hematologic cancer selected from the group of B-cell chronic lymphocytic leukemia (B-CLL), acute lymphoblastic leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia or chronic myeloid leukemia (CML), acute myelogenous leukemia or acute myeloid leukemia (AML), acute lymphocytic leukemia (ALL), hairy cell leukemia (HCL), myelodysplasia syndromes (MDS) or chronic myelogenous leukemia (CML-BP) and any subtypes of chronic myelogenous leukemia (CML-BP).
The combination directed to CD38 for the treatment of Microsatellite Unstable Colorectal Cancer, Microsatellite Stable Colorectal Cancer, Mismatch Repair Proficient Colorectal Cancer, Mismatch Repair Deficient Colorectal Cancer, Waldenstrom Macroglobulinemia, Malignant Neoplasms of Male Genital Organs, Prostate Cancer, Hematopoietic Cancer, Acute Myelogenous Leukemia, High-Risk Myelodysplastic Syndrome, Plasma cell myeloma, Monoclonal Gammopathy, Smoldering Multiple Myeloma, Membranoproliferative Glomerulonephritis, Multiple Myeloma.
The combination as above directed to CD38 for the treatment of T-cell Type Acute Leukemia-Precursor T, lymphoblastic Lymphoma, Leukaemia.
The combination directed to CD38 for the treatment of a CD38-expressing or CD 38 over expressing hematologic cancer selected from the group of Chronic Lymphocytic Leukemia (CLL), Chronic Myelogenous Leukemia (CML), Acute Myelogenous Leukemia (AML), and Acute Lymphocytic Leukemia (ALL), multiple myeloma (MM).
The combination directed to CD38 for the treatment of hematologic cancer selected from the group of leukemia, lymphoma and multiple myeloma (MM).
The combination directed to CD38 for the treatment of hematologic cancer selected from the group of B-cell chronic lymphocytic leukemia (B-CLL), acute lymphoblastic leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia or chronic myeloid leukemia (CML), acute myelogenous leukemia or acute myeloid leukemia (AML), acute lymphocytic leukemia (ALL), hairy cell leukemia (HCL), myelodysplasia syndromes (MDS) or chronic myelogenous leukemia (CML-BP) and any subtypes of chronic myelogenous leukemia (CML-BP), leukemia, lymphoma and multiple myeloma.
The present combination of the invention, when armed with specific CARs directed against patient's own immune cells, especially T-cells, allow the inhibition or regulation of said cells, which is a key step for treating auto-immune disease, such as rheumatoid polyarthritis, systemic lupus erythematosus, Sjogren's syndrome, scleroderma, fibromyalgia, myositis, ankylosing spondylitis, insulin dependent diabetes of type I, Hashimoto's thyroiditis, Addison's disease, Crohn's disease, Celiac's disease, amyotrophic lateral sclerosis (ALS) and multiple sclerosis (MS). Accordingly the present invention encompass a method for treating an immune disease by directing engineered T-cells and therapeutic antibody as previously described against patient's own T-cells.
The above combination can take place in combination with one or more therapies selected from the group of antibodies therapy, chemotherapy, cytokines therapy, dendritic cell therapy, gene therapy, hormone therapy, laser light therapy and radiation therapy.
The combination of the invention may comprise allogeneic cells made resistant to chemotherapy drugs and immunosuppressive drugs that are used as standards of care, especially methotrexate and the combination of fludarabine and Cyclophosphamide, are particularly suited for treating various forms of cancer. Indeed, the present invention preferably relies on cells or population of cells, comprising a dCK inactivated gene. As with the therapeutic antibody of the combination disclosed here as an invention, it is expected that the chemotherapy and/or immunosuppressive treatment should help the selection and expansion of the engineered T-cells in-vivo.
In certain embodiments of the present invention, cells are administered to a patient in conjunction with (e.g., before, simultaneously or following) a therapeutic antibody and 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. In further embodiments, 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. These drugs inhibit either the calcium dependent phosphatase calcineurin (cyclosporine and FK506) or inhibit the p70S6 kinase that is important for growth factor induced signaling (rapamycin) (Liu et al., Cell 66:807-815, 1 1; Henderson et al., Immun. 73:316-321, 1991; Bierer et al., Citrr. Opin. mm n. 5:763-773, 93). In a further embodiment, 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, In another embodiment, the cell compositions of the present invention are administered following B-cell ablative therapy such as agents that react with CD20, e.g., Rituxan. For example, in one embodiment, subjects may undergo standard treatment with high dose chemotherapy followed by peripheral blood stem cell transplantation. In certain embodiments, following the transplant, subjects receive an infusion of the expanded immune cells of the present invention. In an additional embodiment, expanded cells are administered before or following surgery. Said modified cells obtained by any one of the methods described here can be used in a particular aspect of the invention for treating patients in need thereof against Host versus Graft (HvG) rejection and Graft versus Host Disease (GvHD); therefore in the scope of the present invention is a method of treating patients in need thereof against Host versus Graft (HvG) rejection and Graft versus Host Disease (GvHD) comprising treating said patient by administering to said patient an effective amount of modified cells comprising inactivated TCR alpha and/or TCR beta genes.
According to one embodiment, said combination of the invention can undergo robust in vivo T cell expansion upon administration to a patient, and can persist in the body fluids for an extended amount of time, preferably for a week, more preferably for 2 weeks, even more preferably for at least one month. Although the T-cells of the combination of the invention according to the invention are expected to persist during these periods, their life span into the patient's body are intended not to exceed a year, preferably 6 months, more preferably 2 months, and even more preferably one month.
The administration of the cells or population of cells and therapeutic antibody 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. In one embodiment, 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 104-109 cells per kg body weight, preferably 105 to 106 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. In another embodiment, said effective amount of cells are administrated as a single dose. In another embodiment, said effective amount of cells are administrated as more than one dose over a period time. Timing of administration of the combination of the invention is within the judgment of managing physician and depends on the clinical condition of the patient. While individual needs vary, determination of optimal ranges of effective amounts of a given cell type and of a given antibody of the combination, 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 with administered. 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.
In another embodiment, 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.
The cells or population of cells may be obtained from any source, such as a blood bank or a donor.
Identification of Surface Antigen Marker Expressed on the Surface of T-Cells, while being Overexpressed in Solid Tumors Involved into Different Types of Cancer (Tables 5 to 13)
We used BioGPS microarray data from a panel of normal tissues (Human U133A/GNF1H Gene Atlas) cancer microarray data that also can be downloaded from BioGPS (Human Primary Tumors (U95)) uniprot data that contains the subcellular localization.
We drew the distribution of values coming from normal tissues and determined a threshold value of 5 for the relative expression.
We browsed all the genes assayed with microarrays (44.000 probes representing about 13 000 genes) and checked their localization in the membrane (protein not referred to as being a membrane protein were discarded). Expression in CD8+ T-cells was checked from the BioGPS database. The genes were listed according to the type of cancer where the corresponding expression was the highest (Tables 5 to 13).
Identification of Surface Antigen Marker Expressed on the Surface of T-Cells, while being Overexpressed in Different Liquid Blood Tumors (Table 14)
For that study, no RNA-seq data were available and thus we used microarray data that were obtained from a large study from the MILE consortium (Microarray Innovations in Leukemia), involving 11 laboratories (http://www.ngrl.org.uk/wessex/downloads/tm08/TM08-S4-1_KenMills.pdf—Haferlach et al. 2010, http://www.ncbi.nlm.nih.gov/pubmed/20406941). This raw data include results for ALL (acute lymphoblastic leukemia), AML (acute myelogenous leukemia), CLL (chronic lymphoblastic leukemia) and CML (chronic myelogenous leukemia) and MDS (myelodysplastic syndrome). We also used uniprot data for subcellular localization as usual.
We first drew the overall distribution of values from all genes on all studied tissues. Then, to have an idea of the level necessary for expression, we took a list of genes which are expressed in some liquid tumors and for which therapeutic antibodies are available (CD52, CD 20, CD33, CD19, CD25, CD44, CD47, CD96, CD116, CD117, CD135, TIM-3). For each gene, we looked at the value obtained in the tumor in which it is expressed. Then, we computed the average for each tumor and gene pair for which the gene seems to give a cell membrane protein (cell membrane localization+description of at least one transmembrane domain in the protein). We discarded genes for which the expression in all the tissues was below this threshold of 0.15. We listed and ranked in Table 14, those genes which relative expression in T-cells was above 0.2. Thus, Table 4 provides putative antigen marker candidates for targeting liquid tumor cells as per the invention, in particular for treating ALL, AML, CLL, CML and MDS.
Therapeutic antibody specific for an the antigen identified, when available, and already under clinic phase below, were used.
Several administration protocols were tested first in an animal model of CD38 expressing pathological tissues.
Under these experimental conditions, the dose of Ab and cells necessary to obtained optimized reduction of pathological cells was estimated.
In human subjects, the amount of Ab and cells was determined based on clinical data (Drent E, Groen R W J, Noort W A, et al. Pre-clinical evaluation of CD38 chimeric antigen receptor engineered T cells for the treatment of multiple myeloma. Haematologica. 2016; 101(5):616-625. doi:10.3324/haematol.2015.137620).
Additionally, cells were engineered to be less alloreactive and/or be used in lymphodepleted individuals (TCR-negative and MHC-negative).
Example of Method to Engineer T-Cells According to the Invention for Immunotherapy
For a better understanding of the invention, it is provided below an example of the steps to follow to produce T-cells directed against leukemia CD38 positive cells:
Inactivation of the TCR alpha in said cells was performed as previously described to eliminate the TCR from the surface of the cell and prevent recognition of host tissue as foreign by TCR of allogenic and thus to avoid GvHD by following the protocols set forth in WO 2013/176915. Thus, cells were also engineered to inactivate the TCR alpha subunit and alter the alpha beta TCR expression at the cell surface.
It is also possible to inactive one gene encoding target for an immunosuppressive agent or a chemotherapy drug to render said cells resistant to immunosuppressive or chemotherapy treatment to prevent graft rejection without affecting transplanted T cells. In this example, target of immunosuppressive agents is dCK and immunosuppressive agent is a PNA or a combination of fludarabine and cytarabine as described in WO 2013/176915.
Gene Inactivation is performed by electroporation of T cells with mRNA encoding specific TAL-endonuclease (TALEN™—Cellectis, 8 rue de la Croix Jarry, France). Inactivated T cells are sorted using magnetic beads. For example, T cells still expressing the targeted gene (e.g. CD38) can be removed by fixation on a solid surface, and inactivated cells are not exposed of the stress of being passed through a column. This gentle method increases the concentration of properly engineered T-cells.
Expansion in vitro of engineered T-cells prior to administration to a patient or in vivo following administration to a patient through stimulation of CD3 complex. Before administration step, patients can be subjected to an additional immunosuppressive treatment such as CAMPATH1-H, a humanized monoclonal anti-CD52 antibody, in combination with the therapeutic Ab of the combination disclosed here (eg anti-CD70 Ab).
Optionally exposed said cells with bispecific antibodies ex vivo prior to administration to a patient or in vivo following administration to a patient to bring the engineered cells into proximity to a target antigen.
Functional Analysis of the Engineered T-Cells Electroporated with a Monocistronic mRNA Encoding for an Anti-CD38 Single Chain Chimeric Antigen Receptor (CAR CD38):
To verify that genome engineering did not affect the ability of the engineered T-cells to present anti-tumor activity, especially when provided with a chimeric antigen receptor (CAR CD38), The engineered anti-CD38 CAR T-cells were incubated for 4 hours with Daudi cells expressing CD38 on their surface. The cell surface upregulation of CD107a, a marker of cytotoxic granule release by T lymphocytes (called degranulation) was measured by flow cytometry analysis (Betts, Brenchley et al. 2003).
24 hours post electroporation, cells were stained with a fixable viability dye eFluor-780 and a PE-conjugated goat anti mouse IgG F(ab′)2 fragment specific to assess the cell surface expression of the CAR on the live cells. The vast majority of the live T-cells genetically disrupted for CD38, express the anti-CD38 CAR on their surface. T cells were co-cultured with Daudi (CD38+) cells for 6 hours and analyzed by flow cytometry to detect the expression of the degranulation marker CD107a at their surface (Betts, Brenchley et al. 2003).
The results showed that CD38 disrupted T-cells kept the same ability to degranulate in response to PMA/ionomycin (positive control) or CD38+ Daudi cells. CD107 upregulation is dependent on the presence of a CD38+. These data suggest that the genome engineering of the present T-cells had no negative impact on the ability of T cells to mount a controlled anti-tumor response.
Combination with Therapeutic Anti-CD38 Ab.
The following anti-CD38 Ab were combined with CD38-negative, anti-CD38 CAR allogeneic (TCR KO) T engineered cells: Daratumumab (DARZALEX), Isatuximab or MOR-03087).
The combination of the invention of CD38 KO immune cells and therapeutic anti-CD38 MOR202 or DARZALEX (daratumumab) antibody were used for the treatment of MM.
The resulting data show that daratumumab at the dose of 8 mg/kg of body weight, administered as an intravenous infusion for 8 weeks weekly or bi weekly in combination with anti-CD38 CAR T cells administered the last week, and a second time, significantly reduce tumor mass volume in all patients, with no relapse observed at 24 weeks as compared to individual treated with Ab alone or engineered cells alone.
Examples of TAL Proteins Inactivating the CD70 Gene
A mRNA encoding a TALE-nuclease cleaving the following CD70 genomic sequence were synthesized from plasmid carrying the coding sequences (SEQ ID NO. 104-105, or SEQ ID NO. 106-107) downstream from a T7 promoter, using mMESSAGE mMACHINE™ T7 ULTRA Transcription Kit according to manufacturer's protocol (Ambion™). T lymphocytes isolated from peripheral blood were activated using anti-CD3/CD28 activator beads (Life technologies) and 5 million cells were then transfected by electroporation with 10 μg of each of 2 mRNAs encoding both half TALE-nuclease (or non coding RNA as controls) using a CytoLVT-P instrument. A sample of engineered T-cells were harvested on the day of electroporation and at one, two, five and height days post electroporation, the remaining T-cells were grown in culture media (REF). Fourteen days post electroporation, all T-cells were harvested. For each time point, the harvested T cells were labeled with fluorochrome-conjugated anti-CD70 monoclonal antibody (ref. 130-104-357, Miltenyi Biotec and according to manufacturer's protocol) and analyzed by flow cytometry for the presence of CD70 at their cell surface. At day 5 post electroporation, genomic DNA was also extracted on harvested T-cells and Polymerase Chain Reactions (PCR) were performed to amplify the targeted CD70 loci (Exon 1 for SEQ ID NO. 104-105 or Exon2 for SEQ ID NO. 106-107), these PCR were then submitted to the T7 Endonuclease 1 assay [New England Biolabs, see Vouillot et al. (2015) Comparison of T7E1 and Surveyor Mismatch Cleavage Assays to Detect Mutations Triggered by Engineered Nucleases. G3. 5(3): 407-415.] allowing the quantification of nucleases activity.
The results show that all TALE-nucleases specific for the CD70 gene showed cleavage activity using T7 Endonuclease 1 assay at day 5 post electroporation (
In addition, TALE-nucleases T02 and T03 were also able to decrease either the percentage of CD70 positive cells and/or the intensity of the labelling measured by the Median Fluorescence Intensity as compared to mock engineered cells (controls) (
In one example (T01), CD70 at cell surface was inactivated (inactive) although partly still expressed at the cell surface. This is presenting another advantage as compared to CD70 deficient cells, probably by disrupting the signaling properties of CD70.
Cells obtained then, were combined with an anti-CD70 therapeutic antibody (CD70 Ab).
The anti-CD70 Ab was the following: Vorsetuzumab (or SGN-70 or h1F6) as disclosed in WO200473656, preferably (h1F6 clone) as disclosed in WO2006113909 which is a humanized h1F6, ARGX 110, SGN CD70A, SGN-CD70A, Vorsetuzumab mafodotin (SGN-75), and MDX 1203 (BMS-936561). The dose chosen was half of the dose giving 50 activity.
In another combination for the study above, the Ab was ARGX 2, at a dose of 5, and 10 mg/kg 3 weeks every 3 weeks with 5×105 and 5×106 cells at the same time, or at the end of the 3 weeks (Clin Cancer Res Oct. 4, 2017 DOI: 10.1158/1078-0432.CCR-17-0613).
Anti-CD70 Ab was used to selectively destroy anti-CD70 expressing cells in individuals suffering a cancer. The cells expressed a CAR allowing the cancer to be targeted and could resist the treatment with anti-CD70 Ab. The amount of engineered cells was also divided by 2 as compared to the effective dose 50 or used at the effective dose 50.
The results surprisingly showed that the combination of the invention was 7 to 10 times more efficient in reducing the tumor mass than either one of the component (engineered cells alone or anti-CD70 Ab alone) of the combination (engineered cells alone or antibody alone). Moreover, individuals receiving both components of the combination had significantly slower relapse and less refractory events than individuals treated with one component of the combination of this invention. The lymphodepletion induced by the CD70 Ab in these individuals and the in vivo selection of more active CD70 negative immune cells used for therapy (by in vivo depletion of any CD70 positive cells) account for these results.
In one arm, cells were engineered to alter cell surface expression of alpha beta TCR as previously described and combined with a CD70 cell surface depletion.
| Number | Date | Country | Kind |
|---|---|---|---|
| PA201870063 | Jan 2018 | DK | national |
This application is a national phase application under 35 U.S.C. § 371 of PCT International Application No. PCT/EP2019/052229, filed Jan. 30, 2019, which claims the benefit of Denmark Application No. PA201870063, filed Jan. 30, 2018, each of which is herein incorporated by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2019/052229 | 1/30/2019 | WO |
