Methods Of HLA Engineering and Treatments For Autoimmunity

Abstract

Methods of preventing or treating autoimmune disease are disclosed. In some cases, subjects with having or at risk of developing autoimmune disease are identified as possessing one or more autoimmunity-susceptibility HLA alleles at one or more HLA loci. In many cases, the HLA loci are selected from Class I and Class II loci, for example Class I A, B, and C, and Class II DQ, DR, and DP. In many cases, subjects suffering from or at risk of developing an autoimmune disease may be administered a plurality engineered autologous HSCs modified to carry and express a variant susceptibility allele having at least one mutation in the antigen binding cleft that alters antigen binding and/or specificity of that variant HLA molecule. In many embodiments, the engineered HSCs are CD34+ immune cells that express one or more modified HLA proteins.

What is claimed is: 
     
         1 . A method of modifying an HLA allele associated with an autoimmune disease, comprising:
 identifying an HLA gene associated with an autoimmune disease;   identifying a susceptible HLA allele of the identified HLA gene, wherein the susceptible HLA allele is associated with susceptibility to the autoimmune disease;   identifying a resistant HLA allele of the identified HLA gene, wherein the resistant HLA allele is associated with resistance to the autoimmune disease;   identifying one or more target amino acid positions within a binding cleft of an HLA protein encoded for by the susceptible HLA allele, wherein the target amino acid position has a first identity and the target amino position in the HLA protein encoded by the resistant HLA allele has a different, second identity;   modifying the susceptible HLA allele to encode an HLA protein with the target amino acid position having the second identity and with altered binding affinity for at least one self-peptide as compared to binding affinity of a HLA protein encoded for by the susceptible HLA allele for the at least one self-peptide; and thereby   modifying an HLA allele associated with an autoimmune disease.   
     
     
         2 . The method of  claim 1 , wherein the autoimmune disease is selected from rheumatoid arthritis (RA), celiac disease, diabetes mellitus type 1, systemic lupus erythematosus (SLE), multiple sclerosis (MS), myelin oligodendrocyte glycoprotein antibody disorders (MOGAD), myasthenic syndromes and neuromyelitis optica (NMO), ankylosing spondylitis, Behget's syndrome, Birdshot uveitis, narcolepsy, narcolepsy type 1 (NT1; previously termed narcolepsy with cataplexy), Kawasaki disease, Crohn's disease, psoriasis, dermatomyositis (DM), Addison's disease, irritable-bowl syndrome (IBS), Graves' disease, Henoch-Schönlein purpura (HSP), sarcoidosis, Sjögren's syndrome, eosinophilic granulomatosis with polyangiitis, Hashimoto's disease, idiopathic thrombocytopenic purpura, polymyositis (PM), paraneoplastic neurological syndromes (PNS), autoimmune encephalitis, lupus nephritis (LN), myasthenia gravis (MG), psoriatic arthritis, graft rejection, graft-versus-host disease (GVHD), an unwanted delayed-type hypersensitivity reaction, T-cell mediated pulmonary disease, neuritis, vitiligo, autoimmune pancreatitis, inflammatory bowel diseases, ulcerative colitis, glomerulonephritis, scleroderma, autoimmune thyroid diseases, asthma, autoimmune uveoretinitis, pemphigus vulgaris, pulmonary fibrosis or idiopathic pulmonary fibrosis, primary biliary cirrhosis, and pernicious anemia. 
     
     
         3 . The method of  claim 2 , wherein the target amino acid is not at the T-cell receptor binding interface. 
     
     
         4 . The method of  claim 3 , wherein the self-peptide contains at least one deiminated residue. 
     
     
         5 . The method of  claim 3 , wherein the HLA gene codes for a Class I or Class II HLA protein. 
     
     
         6 . The method of  claim 5 , wherein the HLA gene codes for HLA-A, HLA-B, or HLA-C. 
     
     
         7 . The method of  claim 6 , wherein the susceptible HLA allele is selected from A*02, A*03, and A*29. 
     
     
         8 . The method of  claim 7 , wherein the susceptible HLA allele is selected from A*02:01, A*03:01, and A*29:01. 
     
     
         9 . The method of  claim 6 , wherein the susceptible HLA allele is selected from B*07, B*08, B*27, B*51, B*54, and B*57. 
     
     
         10 . The method of  claim 9 , wherein the susceptible HLA allele is selected from B*07:02, B*08:01, B*27:03 B*27:05, B*27:09, B*51:01, B*54:01, and B*57:01. 
     
     
         11 . The method of  claim 10 , wherein the target amino acid position is position 59 or position 116, or both, and the second identity is histidine. 
     
     
         12 . The method of  claim 6 , wherein the susceptible HLA allele is selected from C*06 and C*18. 
     
     
         13 . The method of  claim 12 , wherein the susceptible HLA allele is selected from C*06:02 and C*18:01. 
     
     
         14 . The method of  claim 5 , wherein the HLA gene codes for one of HLA-DPA, HLA-DPB, HLA-DQA, HLA-DQB, HLA-DRA, AND HLA-DRB. 
     
     
         15 . The method of  claim 14 , wherein the susceptible HLA allele is DPA*02. 
     
     
         16 . The method of  claim 15 , wherein the susceptible HLA allele is DPA*02:01. 
     
     
         17 . The method of  claim 14 , wherein the susceptible HLA allele is DPB*13. 
     
     
         18 . The method of  claim 17 , wherein the susceptible HLA allele is DPB*13:01. 
     
     
         19 . The method of  claim 14 , wherein the susceptible HLA allele is selected from DQA1*01, DQA1*02, DQA1*03, and DQA1*05. 
     
     
         20 . The method of  claim 19 , wherein the susceptible HLA allele is selected from DQA1*01:01, DQA1*01:02, DQA1*02:01, DQA1*03:01, DQA1*05:01 and DQA1*05:05. 
     
     
         21 . The method of  claim 14 , wherein the susceptible HLA allele is selected from DQB1*02, DQB1*03, DQB1*05, and DQB1*06. 
     
     
         22 . The method of  claim 21 , wherein the susceptible HLA allele is selected from DQB1*02:01, DQB1*03:01, DQB1*03:02, DQB1*05:01, DQB1*06:01 and DQB1*06:02. 
     
     
         23 . The method of  claim 22 , wherein the target amino acid position is position 57 or position 71, or both, and the second identity is selected from aspartic acid, glutamic acid, and tyrosine. 
     
     
         24 . The method of  claim 14 , wherein the susceptible HLA allele is selected from DRB1*01, DRB1*03, DRB1*04, DRB1*07, DRB1*08, DRB1*09, DRB1*10, DRB1*11, DRB1*12, DRB1*13, DRB1*14, DRB1*15, DRB1*16, DRB3*01, DRB3*02, DRB3*03, DRB4*01, and DRB5*01. 
     
     
         25 . The method of  claim 24 , wherein the susceptible HLA allele is selected from DRB1*01:01, DRB1*01:03, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:03, DRB1*04:04, DRB1*04:05, DRB1*04:08, DRB1*07:01, DRB1*08:01, DRB1*09:01, DRB1*10:01, DRB1*11:02, DRB1*11:03, DRB1*12:01, DRB1*13:01, DRB1*14:01, DRB1*15:01, DRB1*15:02, DRB1*16:01, DRB3*01:01, DRB3*02:02, DRB3*03:01, DRB4*01:03, and DRB5*01:01. 
     
     
         26 . The method of  claim 25 , wherein the modifying the susceptible HLA allele comprises using an RNA-guided gene editing system. 
     
     
         27 . The method of  claim 25 , wherein the target amino acid position is selected from 47, 67, 70, 71, 74, 85, 86, and 71, and the second identity is selected from isoleucine, aspartic acid, alanine, valine, leucine, methionine, tyrosine, arginine, and phenylalanine. 
     
     
         28 . An engineered immune cell comprising the engineered HLA allele of  claim 27 . 
     
     
         29 . A protein coded for by the engineered HLA allele of  claim 27 . 
     
     
         30 . A mammalian expression vector comprising the engineered HLA allele of  claim 27 .