Treatment of cancer using a cll-1 chimeric antigen receptor

Abstract

The invention provides compositions and methods for treating diseases associated with expression of CLL-1. The invention also relates to chimeric antigen receptor (CAR) specific to CLL-1, vectors encoding the same, and recombinant cells comprising the CLL-1 CAR. The invention also includes methods of administering a genetically modified cell expressing a CAR that comprises a CLL-1 binding domain.

1 - 50 . (canceled) 
     
     
         51 . A method of treating a mammal having a disease associated with expression of CLL-1, comprising administering to the mammal an effective amount of a cell, comprising an isolated nucleic acid molecule encoding a chimeric antigen receptor (CAR), wherein the CAR comprises an anti-CLL-1 binding domain, a transmembrane domain, and an intracellular signaling domain, and wherein said anti-CLL-1 binding domain comprises a heavy chain complementary determining region 1 (HC CDR1), a heavy chain complementary determining region 2 (HC CDR2), and a heavy chain complementary determining region 3 (HC CDR3) of any anti-CLL-1 heavy chain binding domain amino acid sequences listed in Table 2, 5, 7, or 3. 
     
     
         52 . The method of  claim 51 , wherein the disease associated with CLL-1 expression is:
 (i) a cancer or malignancy, or a precancerous condition chosen from one or more of a myelodysplasia, a myelodysplastic syndrome or a preleukemia, or   (ii) a non-cancer related indication associated with expression of CLL-1.   
     
     
         53 . The method of  claim 51 , wherein the disease is a hematologic cancer. 
     
     
         54 . The method of  claim 51 , wherein the disease is an acute leukemia chosen from one or more of acute myeloid leukemia (AML); acute lymphoblastic B-cell leukemia (B-cell acute lymphoid leukemia, BALL), acute lymphoblastic T-cell leukemia (T-cell acute lymphoid leukemia (TALL), B-cell prolymphocytic leukemia, chronic lymphocytic leukemia, chronic myeloid leukemia (CML), myelodysplastic syndrome, plasma cell myeloma, or a combination thereof. 
     
     
         55 . The method of  claim 51 , wherein the cell is administered in combination with one or more of:
 (i) an agent that increases the efficacy of the cell comprising the CAR nucleic acid or CAR polypeptide;   (ii) an agent that ameliorates one or more side effects associated with administration of the cell comprising the CAR nucleic acid or CAR polypeptide; or   (iii) an agent that treats the disease associated with the expression of CLL-1.   
     
     
         56 - 57 . (canceled) 
     
     
         58 . The method of  claim 51 , wherein the cell comprising an isolated nucleic acid molecule encoding the CAR further expresses an inhibitory molecule that comprises a first polypeptide that comprises at least a portion of an inhibitory molecule, associated with a second polypeptide that comprises a positive signal from an intracellular signaling domain, wherein the inhibitory molecule comprises first polypeptide that comprises at least a portion of PD1 and a second polypeptide comprising a costimulatory domain and primary signaling domain. 
     
     
         59 . (canceled) 
     
     
         60 . The method of  claim 55 , wherein the agent is an mTOR inhibitor and the subject is administered a low, immune enhancing, dose of an mTOR inhibitor. 
     
     
         61 - 64 . (canceled) 
     
     
         65 . The method of  claim 51 , wherein a chemotherapeutic agent is administered prior to administration of the cell, and optionally, wherein the chemotherapeutic agent increases CLL-1 expression on the cancer cell or wherein the chemotherapeutic agent is cytarabine. 
     
     
         66 . The method of  claim 51 , wherein said anti-CLL-1 binding domain further comprises a light chain complementary determining region 1 (LC CDR1), a light chain complementary determining region 2 (LC CDR2), and a light chain complementary determining region 3 (LC CDR3) of any anti-CLL-1 light chain binding domain amino acid sequences listed in Table 2, 6, 8, or 4. 
     
     
         67 . The method of  claim 51 , wherein the isolated nucleic acid molecule which encodes a CAR comprising:
 (a)
 (i) the amino acid sequence of any light chain variable region listed in Table 2; 
 (ii) an amino acid sequence having at least one, two, or three modifications but not more than 30, 20, or 10 modifications of the amino acid sequence of any of the light chain variable regions provided in Table 2; or 
 (iii) an amino acid sequence with 95-99% identity to the amino acid sequence of any of the light chain variable regions provided in Table 2; and/or 
   (b)
 (i) the amino acid sequence of any heavy chain variable region listed in Table 2; 
 (ii) an amino acid sequence having at least one, two or three modifications but not more than 30, 20 or 10 modifications of the amino acid sequence of any of the heavy chain variable regions provided in Table 2: or 
 (iii) an amino acid sequence with 95-99% identity to the amino acid sequence of any of the heavy chain variable regions provided in Table 2. 
   
     
     
         68 . The method of  claim 51 , wherein the encoded anti-CLL-1 binding domain comprises:
 (a) an amino acid sequence:
 (i) selected from a group consisting of SEQ ID NO:47, 44, 48, 49, 50, 39, 40, 41, 42, 43, 45, 46, 51, 73, 70, 74, 75, 76, 65, 66, 67, 68, 69, 71, 72, 77, 195, 86, 83, 87, 88, 89, 78, 79, 80, 81, 82, 84, 85, 90, or 196; 
 (ii) having at least one, two or three modifications but not more than 30, 20 or 10 modifications to any of SEQ ID NO: 47, 44, 48, 49, 50, 39, 40, 41, 42, 43, 45, 46, 51, 73, 70, 74, 75, 76, 65, 66, 67, 68, 69, 71, 72, 77, 195, 86, 83, 87, 88, 89, 78, 79, 80, 81, 82, 84, 85, 90, or 196; or 
 (iii) with 95-99% identity to any of SEQ ID NO: 47, 44, 48, 49, 50, 39, 40, 41, 42, 43, 45, 46, 51, 73, 70, 74, 75, 76, 65, 66, 67, 68, 69, 71, 72, 77, 195, 86, 83, 87, 88, 89, 78, 79, 80, 81, 82, 84, 85, 90, or 196; or 
   (b) a nucleotide sequence selected from a group consisting of SEQ ID NO: 60, 44, 61, 62, or 63, or a sequence with 95-99% identity thereof.   
     
     
         69 . The method of  claim 51 , wherein the encoded CAR includes a transmembrane domain that comprises:
 (i) a transmembrane domain of a protein selected from the group consisting of the alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and CD154;   (ii) the encoded transmembrane domain comprises the amino acid sequence of SEQ ID NO: 6, an amino acid sequence comprises at least one, two, or three modifications but not more than 20, 10, or 5 modifications of the amino acid sequence of SEQ ID NO:6, or a sequence with 95-99% identity to the amino acid sequence of SEQ ID NO:6; and/or   (iii) the nucleic acid sequence encoding the transmembrane domain comprises a sequence of SEQ ID NO:17, or a sequence with 95-99% identity thereof.   
     
     
         70 . The method of  claim 51 , wherein the encoded CLL-1 binding domain is connected to the transmembrane domain by a hinge region, wherein:
 (i) the encoded hinge region comprises the amino acid sequence of SEQ ID NO:2, or a sequence with 95-99% identity thereof; or   (ii) the nucleic acid sequence encoding the hinge region comprises the nucleotide sequence of SEQ ID NO: 13, or a sequence with 95-99% identity thereof.   
     
     
         71 . The method of  claim 51 , wherein the CAR further comprises a costimulatory domain, wherein the costimulatory domain:
 (i) is a functional signaling domain obtained from a protein selected from the group consisting of a MHC class I molecule, TNF receptor proteins, Immunoglobulin-like proteins, cytokine receptors, integrins, signaling lymphocytic activation molecules (SLAM proteins), activating NK cell receptors, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD11a/CD18), 4-1BB (CD137), B7-H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, CD19a, and a ligand that specifically binds with CD83;   (ii) comprises the amino acid sequence of SEQ ID NO:7, or an amino acid sequence having at least one, two, or three modifications but not more than 20, 10, or 5 modifications of the amino acid sequence of SEQ ID NO:7, or a sequence with 95-99% identity to the amino acid sequence of SEQ ID NO:7; and/or   (iii) is encoded by a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:18, or a sequence with 95-99% identity thereof.   
     
     
         72 . The method of  claim 51 , wherein the encoded intracellular signaling domain:
 (i) comprises a functional signaling domain of 4-1BB and/or a functional signaling domain of CD3 zeta;   (ii) comprises the amino acid sequence of SEQ ID NO: 7 and/or the sequence of SEQ ID NO:9 or SEQ ID NO:10; or an amino acid sequence having at least one, two, or three modifications but not more than 20, 10, or 5 modifications of the amino acid sequence of SEQ ID NO:7 and/or the amino acid sequence of SEQ ID NO:9 or SEQ ID NO:10; or a sequence with 95-99% identity to the amino acid sequence of SEQ ID NO:7 and/or the amino acid sequence of SEQ ID NO:9 or SEQ ID NO:10;   (iii) comprises the sequence of SEQ ID NO:7 and the sequence of SEQ ID NO:9 or SEQ ID NO:10, wherein the sequences comprising the intracellular signaling domain are expressed in the same frame and as a single polypeptide chain; and/or   (iv) comprises the sequence of SEQ ID NO:18, or a sequence with 95-99% identity thereof, and/or the sequence of SEQ ID NO:20 or SEQ ID NO:21, or a sequence with 95-99% identity thereof.   
     
     
         73 . The method of  claim 51 , further comprising a leader sequence which encodes the amino acid sequence of SEQ ID NO:1. 
     
     
         74 . The method of  claim 51 , wherein the CAR comprises:
 (a) an amino acid sequence:
 (i) of any of SEQ ID NOs:99, 96, 100, 101, 102, 91, 92, 93, 94, 95, 97, 98, 103, or 197; 
 (ii) having at least one, two or three modifications but not more than 30, 20 or 10 modifications to any of SEQ ID NOs: 99, 96, 100, 101, 102, 91, 92, 93, 94, 95, 97, 98, 103, or 197; or 
 (iii) with 95-99% identity to any of SEQ ID NOs: 99, 96, 100, 101, 102, 91, 92, 93, 94, 95, 97, 98, 103, or 197; or 
   (b) the nucleotide sequence of any of SEQ ID NOs: 112, 109, 113, 114, 115, 104, 105, 106, 107, 108, 110, 111, 116, or 198, or a nucleotide sequence with 95-99% identity to any of SEQ ID NOs: 112, 109, 113, 114, 115, 104, 105, 106, 107, 108, 110, 111, 116, or 198.