Gene-regulating compositions and methods for improved immunotherapy

Abstract

The present disclosure provides methods and compositions related to the modification of immune effector cells to increase therapeutic efficacy. In some embodiments, immune effector cells modified to reduce expression of one or more endogenous target genes, or to reduce one or more functions of an endogenous protein to enhance effector functions of the immune cells are provided. In some embodiments, immune effector cells further modified by introduction of transgenes conferring antigen specificity, such as exogenous T cell receptors (TCRs) or chimeric antigen receptors (CARs) are provided. Methods of treating a cell proliferative disorder, such as a cancer, using the modified immune effector cells described herein are also provided.

1 - 288 . (canceled) 
     
     
         289 . A method of treating cancer in a subject in need thereof, the method comprising:
 administering to the subject a composition comprising a therapeutically effective amount of modified human immune cells,   wherein the modified human immune cells comprise an insertion, deletion, or mutation in an endogenous ZC3H12A gene, and endogenous ZC3H12A gene expression is reduced in the modified human immune cells, relative to unmodified human immune cells obtained from the subject, and   wherein modified human immune cells are autologous to the subject.   
     
     
         290 . The method of  claim 289 , wherein the modified human immune cells further comprise an engineered immune receptor or a chimeric antigen receptor (CAR) or an engineered T cell receptor (TCR). 
     
     
         291 . The method of  claim 289 , wherein the modified human immune cells are T cells. 
     
     
         292 . The method of  claim 289 , wherein the modified human immune cells are tumor infiltrating lymphocytes. 
     
     
         293 . The method of  claim 289 , wherein the modified human immune cells further comprise an exogenous transgene expressing an immune activating molecule, and the immune activating molecule is selected from the group consisting of a cytokine, a chemokine, a co-stimulatory molecule, an activating peptide, and an antibody or an antigen-binding fragment thereof. 
     
     
         294 . The method of  claim 289 , wherein the cancer is selected from a leukemia, a lymphoma, and a solid tumor. 
     
     
         295 . The method of  claim 292 , wherein the cancer is a melanoma. 
     
     
         296 . The method of  claim 292 , wherein the cancer is a head and neck cancer. 
     
     
         297 . The method of  claim 292 , wherein the cancer is a lung cancer. 
     
     
         298 . The method of  claim 289 , wherein the modified human immune cells further comprise an insertion, deletion, or mutation in an endogenous gene selected from ANKRD11, BCL2L11, BCOR, CALM2, CBLB, CHIC2, CTLA4, DHODH, E2F8, FL11, FOXP3, GATA3, GNAS, IKZF1, HAVCR2, IKZF2, IKZF3, LAG3, NFKBIA BCL3, NRP1, PBRM1, PCBP1, PDCD1, PPP2R2D, PTPN6, RBM39, RC3H1, SEMA7A, SERPINA3, SMAD2, TANK, TGFBR1, TGFBR2, TIGIT, TNFAIP3, TNIP1, TRAF6, UMPS, and WDR6. 
     
     
         299 . A method of treating cancer in a subject in need thereof, the method comprising:
 modifying an endogenous ZC3H12A gene in human immune cells obtained from the subject to produce modified human immune cells, wherein the modified human immune cells comprise an insertion, deletion, or mutation in the endogenous ZC3H12A gene, and endogenous ZC3H12A gene expression is reduced in the modified human T cells, relative to unmodified human immune cells obtained from the subject; and   administering to the subject a composition comprising a therapeutically effective amount of the modified human immune cells.   
     
     
         300 . The method of  claim 299 , further comprising obtaining the human immune cells from the subject prior to the modifying. 
     
     
         301 . The method of  claim 299 , wherein the modified human immune cells further comprise an engineered immune receptor. 
     
     
         302 . The method of  claim 301 , wherein the engineered immune receptor is a chimeric antigen receptor (CAR) or an engineered T cell receptor (TCR). 
     
     
         303 . The method of  claim 299 , wherein the modified human immune cells are T cells. 
     
     
         304 . The method of  claim 299 , wherein the modified human immune cells are tumor infiltrating lymphocytes. 
     
     
         305 . The method of  claim 299 , wherein the modified human immune cells further comprise an exogenous transgene expressing an immune activating molecule, and the immune activating molecule is selected from the group consisting of a cytokine, a chemokine, a co-stimulatory molecule, an activating peptide, and an antibody or an antigen-binding fragment thereof. 
     
     
         306 . The method of  claim 299 , wherein the cancer is selected from a leukemia, a lymphoma, and a solid tumor. 
     
     
         307 . The method of  claim 304 , wherein the cancer is selected from a melanoma, a head and neck cancer, and a lung cancer. 
     
     
         308 . The method of  claim 299 , wherein the modified human immune cells further comprise an insertion, deletion, or mutation in an endogenous gene selected from ANKRD11, BCL2L11, BCOR, CALM2, CBLB, CHIC2, CTLA4, DHODH, E2F8, FL11, FOXP3, GATA3, GNAS, IKZF1, HAVCR2, IKZF2, IKZF3, LAG3, NFKBIA BCL3, NRP1, PBRM1, PCBP1, PDCD1, PPP2R2D, PTPN6, RBM39, RC3H1, SEMA7A, SERPINA3, SMAD2, TANK, TGFBR1, TGFBR2, TIGIT, TNFAIP3, TNIP1, TRAF6, UMPS, and WDR6.