Engineered HLA Alleles for Treating 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 variant HLA protein comprising:
 an amino acid sequence at least 95% identical to a wild-type HLA protein selected from the group consisting of HLA-A, HLA-B, HLA-C, HLA-DQA, HLA-DQB, HLA-DRA, HLA-DRB, HLA-DPA, and HLA-DPB; and   at least one amino acid substitution within an antigen binding cleft, wherein the variant HLA protein has an antigen binding affinity different than antigen binding affinity of the wild-type HLA protein; and   wherein the variant HLA protein is engineered.   
     
     
         2 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-A and the at least one amino acid substitution is located at a position in the amino acid sequence selected from position 9, 31, 56, 62, 63, 66, 73, 77, 80, 81, 95, 97, 99, 114, 116, 150, 152, 156, 171, or combinations thereof. 
     
     
         3 . The variant HLA protein of  claim 2 , wherein the HLA-A is selected from A*02:01, A*03:01, and A*29:01. 
     
     
         4 . The variant HLA protein of  claim 3 , wherein the amino acid sequence of the HLA-A is selected from SEQ ID NOs: 1, 2, or 3. 
     
     
         5 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-B and the at least one amino acid substitution is located at a position in the amino acid sequence selected from position 9, 24, 33, 45, 46, 52, 59, 62, 66, 70, 73, 77, 81, 95, 97, 99, 114, 116, 143, 147, 152, 156, 163, 167, 171, 178, or combinations thereof. 
     
     
         6 . The variant HLA protein of  claim 5 , wherein the HLA-B 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. 
     
     
         7 . The variant HLA protein of  claim 6 , wherein the amino acid sequence of the HLA-B is selected from SEQ ID NOs: 4-13. 
     
     
         8 . The variant HLA protein of  claim 7 , wherein the position is 59 or 116, and the at least one amino acid substituted is histidine. 
     
     
         9 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-C and the at least one amino acid substitution is located at a position in the amino acid sequence selected from position 4, 24, 30, 33, 45, 52, 59, 62, 63, 66, 67, 70, 73, 74, 77, 80, 81, 95, 97, 99, 114, 116, 143, 147, 152, 167, 171, or combinations thereof. 
     
     
         10 . The variant HLA protein of  claim 9 , wherein the HLA-C is selected from C*06:02 and C*18:01. 
     
     
         11 . The variant HLA protein of  claim 10 , wherein the amino acid sequence of the HLA-C is selected from SEQ ID NOs: 14 or 15. 
     
     
         12 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-DQA1 and the at least one amino acid substitution is located at a position in the amino acid sequence selected from position 34, 44, 61, 64, 69, 76, 80, or combinations thereof. 
     
     
         13 . The variant HLA protein of  claim 12 , wherein the HLA-DQA1 is selected from DQA1*01:01, DQA1*01:02, DQA1*02:01, DQA1*03:01, DQA1*05:01 and DQA1*05:05. 
     
     
         14 . The variant HLA protein of  claim 13 , wherein the amino acid sequence of the HLA-DQA1 is selected from SEQ ID NOs: 19-23. 
     
     
         15 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-DQB1 and the at least one amino acid substitution is located at a position in the amino acid sequence selected from position 9, 26, 28, 30, 37, 38, 47, 53, 57, 67, 70, 71, 74, 86, 87, 90, or combinations thereof. 
     
     
         16 . The variant HLA protein of  claim 15 , wherein the HLA-DQB1 is selected from DQB1*02:01, DQB1*03:01, DQB1*03:02, DQB1*05:01, DQB1*06:01 and DQB1*06:02. 
     
     
         17 . The variant HLA protein of  claim 16 , wherein the amino acid sequence of the HLA-DQB1 is selected from SEQ ID NOs: 24-29. 
     
     
         18 . A variant HLA protein of  claim 17 , wherein the position is 57 or 71, and the at least one amino acid substituted is aspartic acid, glutamic acid, or tyrosine. 
     
     
         19 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-DPA1 and the at least one amino acid substitution is located at a position in the amino acid sequence selected from position 11, 28, 31, 72, 73, 96, or combinations thereof. 
     
     
         20 . The variant HLA protein of  claim 19 , wherein the HLA-DPA1 is DPA1*02:01. 
     
     
         21 . The variant HLA protein of  claim 20 , wherein the amino acid sequence of the HLA-DPA1 is SEQ ID NO: 16. 
     
     
         22 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-DPB1 and the at least one amino acid substitution is located at a position in the amino acid sequence selected position 9, 11, 33, 35, 36, 55, 56, 65, 69, 72, 76, 84, 87, 91, or combinations thereof. 
     
     
         23 . The variant HLA protein of  claim 22 , wherein the HLA-DPB1 is DPB*13:01. 
     
     
         24 . The variant HLA protein of  claim 23 , wherein the amino acid sequence of the HLA-DPB1 is SEQ ID NO: 17. 
     
     
         25 . The variant HLA protein of  claim 1 , wherein the amino acid sequence is at least 95% identical to HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5 and the at least one amino acid substitution is located at a position in the amino acid sequence selected from position 9, 11, 13, 26, 28, 30, 32, 33, 37, 38, 40, 47, 57, 58, 67, 71, 74, 78, 85, 86, or combinations thereof. 
     
     
         26 . The variant HLA protein of  claim 25 , wherein the HLA-DRB 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. 
     
     
         27 . The variant HLA protein of  claim 26 , wherein the amino acid sequence of the HLA-DRB is selected from SEQ ID NOs: 30-58. 
     
     
         28 . A variant HLA protein of  claim 27 , wherein the position is 47, 67, 70, 71, 74, 85, 86, or 71, and the at least one amino acid substituted is isoleucine, aspartic acid, alanine, valine, leucine, methionine, tyrosine, arginine, or phenylalanine. 
     
     
         29 . An engineered hematopoietic cell comprising the variant HLA protein of  claim 27 . 
     
     
         30 . An engineered hematopoietic cell comprising the variant HLA protein of  claim 4 .