Allogeneic cell therapy of b cell malignancies using genetically engineered t cells targeting cd19

Abstract

A population of genetically engineered immune cells (e.g., T cells), which express a chimeric antigen receptor (CAR) specific to CD19 and contain a disrupted TRAC gene, a disrupted B2M gene, or both, for use in treating a B cell malignancy.

1 . A method for treating a B-cell malignancy in a human patient, the method comprising:
 (i) subjecting a human patient having a B-cell malignancy to a lymphodepletion treatment; and   (ii) administering to the human patient a population of genetically engineered T cells after step (i), wherein the population of genetically engineered T cells comprising T cells that comprise:
 (a) a disrupted T cell receptor alpha constant (TRAC) gene, 
 (b) a nucleic acid coding for a chimeric antigen receptor (CAR) that binds CD19, wherein the CAR comprises an anti-CD19 single chain variable fragment (scFv) that comprises a heavy chain variable region set forth in SEQ ID NO: 51, and a light chain variable region set forth in SEQ ID NO: 52, and wherein the nucleic acid is inserted in the disrupted TRAC gene, and 
 (c) a disrupted beta 2-microglobulin (β2M) gene; 
   
       wherein the population of genetically engineered T cells is administered to the human patient at a dose of about 1×10 7  to about 1×10 9  CAR +  T cells. 
     
     
         2 . The method of  claim 1 , wherein the disrupted TRAC gene comprises a deletion of a fragment comprising the nucleotide sequence of SEQ ID NO: 26, 
     
     
         3 . The method of  claim 1 , wherein the population of genetically engineered T cells administered to the human patient per dose contains no more than 7×10 4  TCR +  T cells/kg. 
     
     
         4 . The method of  claim 1 , wherein the lymphodepletion treatment in step (i) comprises co-administration to the human patient fludarabine at about 30 mg/m 2  and cyclophosphamide at about 500-750 mg/m 2  per day for three days. 
     
     
         5 . The method of  claim 4 , wherein the lymphodepletion treatment in step (i) comprises co-administration to the human patient fludarabine at about 30 mg/m 2  and cyclophosphamide at about 500 mg/m 2  per day for three days, or fludarabine at about 30 mg/m 2  and cyclophosphamide at about 750 mg/m 2  per day for three days. 
     
     
         6 . The method of  claim 1 , wherein the population of genetically engineered T cells is administered to the human patient at a dose of about 1×10 7 , about 3×10 7 , about 1×10 8 , about 3×10 8 , or about 1×10 9  CAR′ T cells. 
     
     
         7 . The method of  claim 1 , wherein prior to step (i), the human patient does not show one or more of the following features:
 (a) significant worsening of clinical status,   (b) requirement for supplemental oxygen to maintain a saturation level of greater than 91%,   (c) uncontrolled cardiac arrhythmia,   (d) hypotension requiring vasopressor support,   (e) active infection, and   (f) grade ≥2 acute neurological toxicity.   
     
     
         8 . The method of  claim 1 , wherein step (i) is performed about 2-7 days prior to step (ii). 
     
     
         9 . The method of  claim 1 , wherein after step (i) and prior to step (ii), the human patient does not show one or more of the following features:
 (a) active uncontrolled infection;   (b) worsening of clinical status compared to the clinical status prior to step (i); and   (c) grade ≥2 acute neurological toxicity.   
     
     
         10 . The method of  claim 1 , further comprising (iii) monitoring the human patient for development of acute toxicity after step (ii); and (iv) managing the acute toxicity if occurs. 
     
     
         11 . The method of  claim 10 , wherein step (iii) is performed for at least 28 days after administration of the population of genetically engineered T cells. 
     
     
         12 . The method of  claim 10 , wherein the acute toxicity comprises tumor lysis syndrome (TLS), cytokine release syndrome (CRS), immune effector cell-associated neurotoxicity syndrome (ICANS), B cell aplasia, hemophagocytic lymphohistiocytosis (HLH), cytopenia, graft-versus-host disease (GvHD), hypertension, renal insufficiency, or a combination thereof. 
     
     
         13 . The method of  claim 1 , wherein the B cell malignancy is non-Hodgkin lymphoma, which optionally is selected from the group consisting of diffuse large B cell lymphoma (DLBCL), high grade B cell lymphoma with MYC and BCL2 and/or BCL6 rearrangement, transformed follicular lymphoma (FL), and grade 3b FL. 
     
     
         14 . The method of  claim 13 , wherein DLBCL is DLBCL not otherwise specified (NOS). 
     
     
         15 . The method of  claim 1 , wherein the human patient has at least one measurable lesion that is fluorodeoxyglucose positron emission tomography (PET)-positive. 
     
     
         16 . The method of  claim 1 , wherein the B cell malignancy is refractory and/or relapsed. 
     
     
         17 . The method of  claim 1 , wherein the human patient has undergone one or more lines of prior anti-cancer therapies. 
     
     
         18 . The method of  claim 17 , wherein the human patient has undergone two or more lines of prior anti-cancer therapies. 
     
     
         19 . The method of  claim 17 , wherein the prior anti-cancer therapies comprise an anti-CD20 antibody, an anthracycline-containing regimen, or a combination thereof. 
     
     
         20 . The method of  claim 17 , wherein the human patient has refractory or relapsed transformed FL and has undergone at least one line of chemotherapy for disease after transformation to DLBCL. 
     
     
         21 . The method of  claim 16 , wherein the B cell malignancy is refractory, and the human patient has progressive disease on last therapy, or has stable disease following at least two cycles of therapy with duration of stable disease of up to 6 months. 
     
     
         22 . The method of  claim 1 , wherein the human patient has failed prior autologous hematopoietic stem cell transplantation (HSCT) or ineligible for prior autologous HSCT. 
     
     
         23 . The method of  claim 1 , wherein the human patient is subject to an additional anti-cancer therapy after treatment with the population of genetically engineered T cells. 
     
     
         24 . The method of  claim 1 , wherein the human patient has one or more of the following features:
 (a) has an Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1;   (b) adequate renal, liver, cardiac, and/or pulmonary function;   (c) free of prior gene therapy or modified cell therapy;   (d) free of prior treatment comprising an anti-CD19 antibody;   (e) free of prior allogeneic HSCT;   (f) free of detectable malignant cells from cerebrospinal fluid;   (g) free of brain metastases;   (h) free of prior central nervous system disorders;   (i) free of unstable angina, arrhythmia, and/or myocardial infarction;   (j) free of uncontrolled infection;   (k) free of immunodeficiency disorders or autoimmune disorders that require immunosuppressive therapy; and   (l) free of infection by human immunodeficiency virus, hepatitis B virus, or hepatitis C virus.   
     
     
         25 . The method of  claim 1 , wherein the anti-CD19 scFv comprises the amino acid sequence of SEQ ID NO: 47. 
     
     
         26 . The method of  claim 25 , wherein the CAR that binds CD19 comprises the amino acid sequence of SEQ ID NO: 40. 
     
     
         27 . The method of  claim 1 , wherein the nucleic acid encoding the anti-CD19 CAR is inserted at the site of deletion in the disrupted TRAC gene. 
     
     
         28 . The method of  claim 1 , wherein the disrupted TRAC gene comprises the nucleotide sequence of SEQ ID NO: 54. 
     
     
         29 . The method of  claim 1 , wherein the disrupted 32M gene in the population of genetically engineered T cells comprises at least one of the nucleotide sequence set forth in SEQ ID NOs: 9-14. 
     
     
         30 . The method of  claim 1 , wherein the population of genetically engineered T cells is allogeneic. 
     
     
         31 . The method of  claim 1 , wherein at least 90% of the T cells in the population of genetically engineered T cells do not express a detectable level of TCR surface protein. 
     
     
         32 . The method of  claim 1 , wherein at least 70% of the T cells in the population of genetically engineered T cells do not express a detectable level of TCR surface protein, wherein at least 50% of the T cells in the population of genetically engineered T cells do not express a detectable level of B2M surface protein; and/or wherein at least 30% of the T cells in the population of genetically engineered T cells express a detectable level of the CAR. 
     
     
         33 . The method of  claim 32 , wherein at least 99.5% of the T cells in the population of genetically engineered T cells do not express a detectable level of TCR surface protein. 
     
     
         34 . The method of  claim 1 , wherein at least 70% of the T cells in the population of genetically engineered T cells do not express a detectable level of B2M surface protein. 
     
     
         35 . The method of  claim 34 , wherein at least 85% of the T cells in the population of the genetically engineered T cells do not express a detectable level of B2M surface protein. 
     
     
         36 . The method of  claim 1 , wherein at least 50% of the T cells in the population of genetically engineered T cells express a detectable level of the CAR. 
     
     
         37 . The method of  claim 36 , wherein at least 70% of the T cells in the population of genetically engineered T cells express a detectable level of the CAR. 
     
     
         38 . The method of  claim 1 , wherein the population of genetically engineered T cells are administered to the human patient via intravenous infusion. 
     
     
         39 . The method of  claim 1 , wherein the population of genetically engineered T cells are suspended in a cryopreservation solution. 
     
     
         40 . A pharmaceutical composition for use in treating a B-cell malignancy, the pharmaceutical composition comprising a population of genetically engineered T cells that comprises:
 (a) a disrupted T cell receptor alpha constant (TRAC) gene, which optionally comprises a deletion of a fragment comprising the nucleotide sequence of SEQ ID NO: 26,   (b) a nucleic acid coding for a chimeric antigen receptor (CAR) that binds CD19, wherein the CAR comprises an anti-CD19 single chain variable fragment (scFv) that comprises a heavy chain variable region set forth in SEQ ID NO: 51 and a light chain variable region set forth in SEQ ID NO: 52, and wherein the nucleic acid is inserted in the disrupted TRAC gene, and   (c) a disrupted beta 2-microglobulin (32M) gene;   wherein the composition comprises about 1×10 7  to about 1×10 9  CAR +  T cells.   
     
     
         41 - 42 . (canceled)