Methods and compositions for treating cancer

Abstract

Described are compositions and methods relating to immune cells which express both a chimeric antigen receptor which binds to the IL13 receptor α-2 (IL13Rα2) and a O 6 -methylguanine DNA methyltransferase (MGMT) protein. Viral particles containing an IL13 chimeric antigen receptor (IL13CAR) or variant thereof and an MGMT protein or variant thereof are used to transfect immune cells such as T cells, imparting to the transfected cells both IL13Rα2-targeting activity and resistance to the chemotherapeutic agent temozolomide (TMZ). The compositions and methods described are useful for cancer therapy such as the treatment of a high-grade malignant glioma.

1 . A chimeric nucleic acid sequence comprising
 a first nucleic acid sequence encoding in an IL13CAR comprising
 an IL13 ligand domain which binds the IL13α2 receptor (SEQ ID NO:44), 
 a transmembrane domain, 
 a cytoplasmic domain comprising a CD3-zeta signaling domain; and 
   a second nucleic acid sequence encoding an MGMT polypeptide, wherein the MGMT polypeptide is selected from the group consisting of SEQ ID NO:33, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, and SEQ ID NO:43.   
     
     
         2 . The chimeric nucleic acid sequence according to  claim 1 , wherein the IL13CAR further comprises a signal peptide. 
     
     
         3 . The chimeric nucleic acid sequence according to  claim 1 , wherein the IL13CAR further comprises a hinge region. 
     
     
         4 . The chimeric nucleic acid sequence according to  claim 1 , wherein the cytoplasmic domain further comprises a co-stimulatory domain selected from the group consisting of CD28, 4-1BB (CD137), and OX40 (CD134). 
     
     
         5 . The chimeric nucleic acid sequence according to  claim 4 , wherein the co-stimulatory domain comprises a CD28 co-stimulatory domain and CD28 co-stimulatory domain is at least 90% identical to SEQ ID NO:29. 
     
     
         6 . The chimeric nucleic acid sequence according to  claim 1 , wherein the CD3-zeta signaling domain is at least 90% identical to SEQ ID NO:30. 
     
     
         7 . The chimeric nucleic acid sequence according to  claim 1 , further comprising a third nucleic acid sequence encoding a self-cleaving linker peptide, wherein the third nucleic acid sequence is positioned between the first nucleic acid and second nucleic acid, and optionally wherein the chimeric nucleic acid further comprises a nucleic acid sequence encoding a linker peptide between the CD3-zeta signaling domain and the self-cleaving linker peptide. 
     
     
         8 . (canceled) 
     
     
         9 . (canceled) 
     
     
         10 . (canceled) 
     
     
         11 . The chimeric nucleic acid sequence according to  claim 1 , wherein the IL13 ligand domain comprises an amino acid sequence which is at least 90% identical to a sequence selected from the group consisting of SEQ ID NO:26, SEQ ID NO:36, and SEQ ID NO:37 and a variant thereof. 
     
     
         12 . The chimeric nucleic acid sequence according to  claim 1 , selected from the group consisting of SEQ ID NO:1 nucleotides 109 to 1839, SEQ ID NO:2 nucleotides 109 to 1839, and SEQ ID NO:3 nucleotides 109 to 1839. 
     
     
         13 . A nucleic acid sequence comprising SEQ ID NO: 1 (IL13 CAR-P140KMGMT), SEQ ID NO:2 (IL-13(E13Y) CAR-P140KMGMT), SEQ ID NO:3 (IL-13(E13K R109K) CAR-P140KMGMT), or a combination thereof. 
     
     
         14 . A vector comprising the chimeric nucleic acid sequence according to  claim 1 . 
     
     
         15 . The vector according to  claim 14 , wherein the vector is a retroviral vector. 
     
     
         16 . (canceled) 
     
     
         17 . A host cell comprising a chimeric nucleic acid sequence according to  claim 1 . 
     
     
         18 . (canceled) 
     
     
         19 . The host cell according to  claim 17 , wherein the cell is a T cell. 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . (canceled) 
     
     
         24 . A pharmaceutical composition comprising a chimeric nucleic acid sequence of  claim 1  and a carrier. 
     
     
         25 . A method for producing a mammalian cell which expresses an IL13CAR protein and an MGMT protein comprising:
 a) introducing into the cell a nucleic acid sequence of  claim 1 ; and   b) maintaining the cell under conditions in which the IL13CAR protein and the MGMT protein are expressed by the cell.   
     
     
         26 . (canceled) 
     
     
         27 . (canceled) 
     
     
         28 . A method for treating brain cancer in a subject in need thereof comprising administering to the subject one or more immune cells that express proteins encoded by
 a first nucleic acid sequence encoding in an N-terminal to C-terminal direction an IL13CAR comprising
 an IL13 ligand domain which binds the IL13α2 receptor (SEQ ID NO:44), 
 a transmembrane domain, and 
 a cytoplasmic domain comprising a CD3-zeta signaling domain; and 
   a second nucleic acid sequence encoding an MGMT polypeptide selected from the group consisting of SEQ ID NO:33, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, and SEQ ID NO:43.   
     
     
         29 . The method according to  claim 28 , wherein the brain cancer is a high-grade malignant glioma. 
     
     
         30 . The method according to  claim 28 , wherein the subject is being treated with, has been treated with, or will be treated with a DNA-methylating chemotherapeutic agent. 
     
     
         31 . The method according to  claim 30 , wherein the DNA-methylating chemotherapeutic agent is TMZ. 
     
     
         32 . (canceled)