Systems and methods for targeting cancer cells

Abstract

The present disclosure provides an immune cell genetically modified to produce two antigen triggered polypeptides, each recognizing a different cell surface antigen. The present disclosure provides a system two antigen-triggered polypeptides, each recognizing a different cell surface antigen. The present disclosure provides a method of killing a target cancer cell, using a genetically modified immune cell or a system of the present disclosure. The present disclosure provides a computational method to identify target N antigen pairs on a cancer cell.

1 . An in vitro or ex vivo genetically modified cytotoxic immune cell, wherein the cytotoxic immune cell is genetically modified to produce two different polypeptides that recognize two different cell surface antigens, wherein at least one of the two different cell surface antigens is present on the surface of a target cancer cell. 
     
     
         2 . The genetically modified cytotoxic immune cell of  claim 1 , wherein the two different polypeptides comprise:
 a) a first antigen-triggered polypeptide that binds specifically to a first target cell surface antigen present on a target cancer cell; and   b) a second antigen-triggered polypeptide that binds specifically to a second target cell surface antigen.   
     
     
         3 . The genetically modified cytotoxic immune cell of  claim 1 , wherein the cytotoxic immune cell is a cytotoxic T cell or a natural killer cell. 
     
     
         4 . The genetically modified cytotoxic immune cell of  claim 1 , wherein the immune cell is activated to kill a target cancer cell only when the target cancer cell expresses both of the two different cell surface antigens on its cell surface. 
     
     
         5 . The genetically modified cytotoxic immune cell of  claim 2 , wherein the cytotoxic immune cell:
 a) is activated to kill a target cancer cell that expresses the first target cell surface antigen, but not the second target cell surface antigen, on its cell surface; and   b) is inhibited from killing a non-cancerous cell if the non-cancerous cell expresses both the first target cell surface antigen and the second target cell surface antigen on its cell surface.   
     
     
         6 . The genetically modified cytotoxic immune cell of  claim 2 , wherein the first antigen-triggered polypeptide is a synNotch receptor and the second antigen-triggered polypeptide is a chimeric antigen receptor (CAR);
 wherein the first antigen-triggered polypeptide is a synNotch receptor and the second antigen-triggered polypeptide is a T cell receptor (TCR);   wherein the first antigen-triggered polypeptide is a CAR and the second antigen-triggered polypeptide is an inhibitory CAR (iCAR);   wherein the first antigen-triggered polypeptide is a CAR and the second antigen-triggered polypeptide is a synNotch receptor;   wherein the first antigen-triggered polypeptide is a synNotch receptor and the second antigen-triggered polypeptide is a synNotch receptor: or   wherein the first antigen-triggered polypeptide is a synNotch receptor and activation of the synNotch receptor induces expression of an immune inhibitory polypeptide.   
     
     
         7 - 16 . (canceled) 
     
     
         17 . A method of killing a target cancer cell in an individual, the method comprising administering to the individual an effective number of the genetically modified cytotoxic immune cell of  claim 1 , wherein said genetically modified cytotoxic immune cell kills the target cancer cell in the individual. 
     
     
         18 . The method of  claim 17 , wherein the target cancer cell is an AML cell, an anaplastic lymphoma cell, an astrocytoma cell, a B-cell cancer cell, a breast cancer cell, a colon cancer cell, an ependymoma cell, an esophageal cancer cell, a glioblastoma cell, a glioma cell, a leiomyosarcoma cell, a liposarcoma cell, a liver cancer cell, a lung cancer cell, a mantle cell lymphoma cell, a melanoma cell, a neuroblastoma cell, a non-small cell lung cancer cell, an oligodendroglioma cell, an ovarian cancer cell, a pancreatic cancer cell, a peripheral T-Cell lymphoma cell, a renal cancer cell, a sarcoma cell or a stomach cancer cell. 
     
     
         19 . A system for killing a target cancer cell, the system comprising:
 a) a first antigen-triggered polypeptide that binds specifically to a first target antigen present on the target cancer cell, or a first nucleic acid comprising a nucleotide sequence encoding the first antigen-triggered polypeptide; and   b) a second antigen-triggered polypeptide that binds specifically to a second target antigen, or a second nucleic acid comprising a nucleotide sequence encoding the second antigen-triggered polypeptide.   
     
     
         20 . The system of  claim 19 , wherein the first antigen-triggered polypeptide is a synNotch polypeptide, and the second antigen-triggered polypeptide is a chimeric antigen receptor (CAR);
 wherein the first antigen-triggered polypeptide is a synNotch polypeptide and the second antigen-triggered polypeptide is an inhibitory CAR (iCAR);   wherein the first antigen-triggered polypeptide is a synNotch polypeptide and the second antigen-triggered polypeptide is one polypeptide chain of a split CAR;   wherein the first antigen-triggered polypeptide is a synNotch polypeptide and the second antigen-triggered polypeptide is a T-cell receptor;   wherein the first antigen-triggered polypeptide is a synNotch polypeptide and the second antigen-triggered polypeptide is an immunoinhibitory polypeptide;   wherein the first antigen-triggered polypeptide is a first synNotch polypeptide and the second antigen-triggered polypeptide is a second synNotch polypeptide: or   wherein the first antigen-triggered polypeptide induces production of an antibody or cytokine upon binding to the first target antigen.   
     
     
         21 - 22 . (canceled) 
     
     
         23 . The system of  claim 19 , wherein the first target antigen and the second target antigen are both present on the surface of a target cancer cell; or
 wherein a) the first target antigen and the second target antigen are both present on the surface of a non-cancerous cell, and b) the first target antigen, but not the second target antigen, is present on the surface of a target cancer cell.   
     
     
         24 . (canceled) 
     
     
         25 . The system of  claim 19 , wherein the first target antigen and the second target antigen are selected from a target antigen pair depicted in  FIG.  1    or  FIG.  9 - 14   . 
     
     
         26 - 30 . (canceled) 
     
     
         31 . A method of killing a target cancer cell in an individual, the method comprising:
 a) introducing the system of  claim 19  into a cytotoxic T cell in vitro or ex vivo, generating a modified cytotoxic T cell; and   b) administering the modified cytotoxic T cell to the individual.   
     
     
         32 . (canceled) 
     
     
         33 . The method of  claim 31 , wherein the modified cytotoxic T cell is activated to kill the target cancer cell only when the target cancer cell expresses both the first target antigen and the second target antigen on its cell surface; or
 wherein the modified cytotoxic T cell a) is activated to kill a target cancer cell that expresses the first target cell surface antigen, but not the second target cell surface antigen, on its cell surface; and b) is inhibited from killing a non-cancerous cell if the non-cancerous cell expresses both the first target cell surface antigen and the second target cell surface antigen on its cell surface.   
     
     
         34 . (canceled) 
     
     
         35 . A method of identifying a combination of target antigens for targeting a cancer cell, the method comprising:
 a) generating a training set of target antigen parameters by determining, from a training set of expression data, pairs of antigens that discriminate between cancer cells and non-cancerous cells, thereby generating an algorithm;   b) applying the algorithm to a test set of expression data, to generate a combination of target antigens.   
     
     
         36 . The method of  claim 35 , wherein step (a) comprises selecting pairs of target antigens that comprise:
 i) a first target antigen that is expressed at a high level on cancer cells of a selected cancer cell type; and   ii) a second target antigen that is expressed at a high level on cancer cells of the selected cancer cell type; or   i) a first target antigen that is expressed at a high level on cancer cells of a selected cancer cell type and on non-cancerous cells of the same cell type; and   ii) a second target antigen that is expressed at a high level on non-cancerous cells of the same cell type but not on cancer cells of the same cell type.   
     
     
         37 . The method of  claim 35 , wherein the algorithm comprises one or more of an F1 cutoff, a precision cutoff, a recall cutoff, or combination thereof. 
     
     
         38 . The method of  claim 35 , wherein step (a) comprises training a computer software with the training set, and wherein step (b) comprises applying the algorithm using the trained computer software. 
     
     
         39 - 45 . (canceled) 
     
     
         46 . The in vitro or ex vivo genetically modified cytotoxic immune cell of  claim 1 , wherein the two different polypeptides comprise a first polypeptide that recognizes a first cell surface antigen present on the surface of a target cancer cell and a second polypeptide that recognizes a second cell surface antigen present on the surface of a non-target cell. 
     
     
         47 . The genetically modified cytotoxic immune cell of  claim 46 , wherein the non-target cell is a cell of a normal tissue. 
     
     
         48 . The genetically modified cytotoxic immune cell of  claim 47 , wherein the normal tissue is brain tissue. 
     
     
         49 . The genetically modified cytotoxic immune cell of  claim 47 , wherein the second cell surface antigen is selected from the group consisting of: OPALIN, TMEM235, GABRA1, KCNJ9, GRM3, SEZ6, NTSR2, KCNK4, SLCO1A2, SLC24A2, MOG, GABRG1, GABRG2, CNTNAP4, DSCAM, CACNG3, CRB1, CDH10, HRH3, GRIK1, SLC39A12, GPR158, CACNG2, SYT3, HTR5A, CACNG7, GPR37L1, LRRTM3, GLRA2, CHRNB2, KCNQ2, JPH3, GPR19, ADCY8, SPOCK3, SLC32A1, OPCML, GABRA3, GRM5, SCN1A, SLC5A11, KCNC1, SLC12A5, GRM4, GRM1, GRIA4, MEGF11, CACNA1B, LYPD1, GRID2, SCN2A, NKAIN2, UNC5A, SLC4A10, TMEFF2, CSMD3, PPAPDC1A, HAPLN4, GPR85, ANTXR2, CACNG4, CSPG5, KCNK10, CHRNA4, CNTNAP2, KCNJ10, GABRB2, GRIN1, CRB2, SHISA7, NKAIN4, HTR2C, CACNG8, NRG3, ABCG4, CDH8, GABRD, KIRREL3, GABRB1, KCNA2, CDH20, IGDCC3, KCNJ6, CNIH2, KCNK12, CDH18, CSMD2, SYT4, OR2L13, CDH9, GABRA2, KCNF1, MAG, CALN1, GRIN2B, GRM7, VSTM2A, GPR61, OMG, KCNA1, GPR83, ATP8A2, GABBR2, GPR12, TRPM3, SLC8A3, KCND2, GSG1L, SLC30A10, ASTN1, GPR179, LRFN2, CACNAlE, CALY, SLC6A15, KIAA0319, SYT6, PTPRR, KCTD8, GPR22, SLC4A8, LAMP5, MEGF10, FXYD7, KCNK9, SLC1A6, MLC1, OPRK1, ATP2B2, ACSL6, THBD, PTPRT, PCDHGC4, CLDN10, KCNV1, LPPR3, SLCO1C1, PCDH8, ANO4, LRRTM4, PCDH15, CCKBR, GABRA5, SLC6A12, GRIN2A, SLC1A2, SLC43A1, KCNC2, ELFN2, ATP7A, GRIK4, LRRC55, HCN2, NKAIN1, DPP10, AJAP1, NPFFR1, TRPC3, TGFBI, SLC6A7, GABRA4, SLC13A5, GRIN2C, HCN1, SLC26A8, PPIC, NETO1, TNFRSF10B, CDH22, SLC6A13, DISP2, SLC6A11, CD93, EPHA10, PHLDB2, OXTR, WNT7A, GYPC, KCNA4, PCDHAC2, HGFAC, DRD1, SHISA9, SCN8A, ICAM1, PIRT, A4GALT, MRGPRF, CD248, CD58, CD44, EPHA2 and PROCR. 
     
     
         50 - 59 . (canceled)