Universal donor cells

Abstract

Genetically modified cells that are compatible with multiple subjects, e.g., universal donor cells, and methods of generating said genetic modified cells are provided herein. The universal donor cells comprise at least one genetic modification within or near at least one gene that encodes a survival factor, wherein the genetic modification comprises an insertion of a polynucleotide encoding a tolerogenic factor. The universal donor cells may further comprise at least one genetic modification within or near a gene that encodes one or more MHC-I or MHC-II human leukocyte antigens or a component or a transcriptional regulator of a MHC-I or MHC-II complex, wherein said genetic modification comprises an insertion of a polynucleotide encoding a second tolerogenic factor.

1 . An in vitro method for generating a universal donor cell, the method comprising delivering to a stem cell:
 (a) a first ribonucleoprotein (RNP) complex comprising an RNA-guided nuclease and a guide RNA (gRNA) targeting a target site in a beta-2 microglobulin (B2M) gene locus;   (b) a first vector comprising a nucleic acid, the nucleic acid comprising: (i) a nucleotide sequence encoding programmed death-ligand 1 (PD-L1); (ii) a nucleotide sequence having sequence homology with a genomic region located left of the target site in the B2M gene locus; and (iii) a nucleotide sequence having sequence homology with a genomic region located right of the target site in the B2M gene locus, wherein (i) is flanked by (ii) and (iii); wherein the B2M gene locus is cleaved at the target site and the nucleic acid encoding PD-L1 is inserted into the B2M gene locus, thereby disrupting the B2M gene locus;   (c) a second RNP complex comprising an RNA-guided nuclease and a gRNA targeting a target site in a thioredoxin interacting protein (TXNIP) gene locus; and   (d) a second vector comprising a nucleic acid, the nucleic acid comprising: (i) a nucleotide sequence encoding HLA class I histocompatibility antigen, alpha chain E (HLA-E); (ii) a nucleotide sequence having sequence homology with a genomic region located left of the target site in the TXNIP gene locus; and (iii) a nucleotide sequence having sequence homology with a genomic region located right of the target site in the TXNIP gene locus, wherein (i) is flanked by (ii) and (iii); wherein the TXNIP gene locus is cleaved at the target site and the nucleotide sequence encoding HLA-E is inserted into the TXNIP gene locus, thereby disrupting the TXNIP gene locus and generating a universal donor cell,   wherein the universal donor cell has increased immune evasion and/or cell survival compared to a control cell.   
     
     
         2 . The in vitro method of  claim 1 , wherein the stem cell is an embryonic stem cell, an adult stem cell, an induced pluripotent stem cell, or a hematopoietic stem cell. 
     
     
         3 . The in vitro method of  claim 1 , wherein the stem cell is a human stem cell. 
     
     
         4 . The in vitro method of  claim 1 , wherein the RNA-guided nuclease of each the first RNP complex and the second RNP complex is a Cas9 nuclease. 
     
     
         5 . The in vitro method of  claim 4 , wherein the Cas9 nuclease is linked to at least one nuclear localization signal. 
     
     
         6 . The in vitro method of  claim 1 , wherein the gRNA of the first RNP complex comprises a spacer sequence corresponding to a sequence consisting of any one of SEQ ID NO: 1-3 or 35-44. 
     
     
         7 . The in vitro method of  claim 1 , wherein the gRNA of the first RNP complex comprises a spacer sequence corresponding to a sequence consisting of SEQ ID NO: 2. 
     
     
         8 . The in vitro method of  claim 1 , wherein the nucleotide sequence encoding PD-L1 consists essentially of SEQ ID NO: 11. 
     
     
         9 . The in vitro method of  claim 1 , wherein the nucleotide sequence encoding PD-L1-E is operably linked to an exogenous promoter. 
     
     
         10 . The in vitro method of  claim 9 , wherein the exogenous promoter is a CAG promoter comprising a CMV enhancer, a β-actin promoter, and a chimeric intron. 
     
     
         11 . The in vitro method of  claim 1 , wherein the nucleotide sequence having sequence homology with the genomic region located left of the target site in the B2M gene locus consists essentially of SEQ ID NO: 7. 
     
     
         12 . The in vitro method of  claim 1 , wherein the nucleotide sequence having sequence homology with the genomic region located right of the target site in the B2M gene locus consists essentially of SEQ ID NO: 13. 
     
     
         13 . The in vitro method of  claim 1 , wherein the first vector consists essentially of SEQ ID NO: 33. 
     
     
         14 . The in vitro method of  claim 1 , wherein disrupting the B2M gene locus leads to reduced or eliminated expression of B2M. 
     
     
         15 . The in vitro method of  claim 1 , wherein the gRNA of the second RNP complex comprises a spacer sequence corresponding to a sequence consisting of any one of SEQ ID NO: 16-20. 
     
     
         16 . The in vitro method of  claim 1 , wherein the gRNA of the second RNP complex comprises a spacer sequence corresponding to a sequence consisting of SEQ ID NO: 20. 
     
     
         17 . The in vitro method of  claim 1 , wherein the nucleotide sequence encoding HLA-E consists essentially of SEQ ID NO: 55. 
     
     
         18 . The in vitro method of  claim 17 , wherein SEQ ID NO: 55 comprises a sequence encoding a B2M signal peptide, a sequence encoding an HLA-G presentation peptide, a sequence encoding a B2M membrane protein, and a sequence encoding HLA-E without its signal peptide. 
     
     
         19 . The in vitro method of  claim 1 , wherein the nucleotide sequence encoding HLA-E is operably linked to an exogenous promoter. 
     
     
         20 . The in vitro method of  claim 19 , wherein the exogenous promoter is a CAG promoter comprising a CMV enhancer, a β-actin promoter, and a chimeric intron. 
     
     
         21 . The in vitro method of  claim 1 , wherein the nucleotide sequence having sequence homology with the genomic region located left of the target site in the TXNIP gene locus consists essentially of SEQ ID NO: 25. 
     
     
         22 . The in vitro method of  claim 1 , wherein the nucleotide sequence having sequence homology with the genomic region located right of the target site in the TXNIP gene locus consists essentially of SEQ ID NO: 32. 
     
     
         23 . The in vitro method of  claim 1 , wherein the second vector consists essentially of SEQ ID NO: 34 or SEQ ID NO: 56. 
     
     
         24 . The in vitro method of  claim 1 , wherein disrupting the TXNIP gene locus leads to reduced or eliminated expression of TXNIP. 
     
     
         25 . The in vitro method of  claim 1 , wherein the universal donor expresses PD-L1 and HLA-E and does not express B2M and TXNIP. 
     
     
         26 . The in vitro method of  claim 1 , wherein the control cell is a wild type cell or a cell that does not comprise the nucleotide sequence encoding PDL-1 inserted into the B2M gene locus and the nucleotide sequence encoding HLA-E inserted into the TXNIP gene locus. 
     
     
         27 . The in vitro method of  claim 1 , wherein:
 the gRNA of the first RNP complex comprises a spacer sequence corresponding to a sequence consisting of SEQ ID NO: 20;   the nucleotide sequence encoding PD-L1 consists essentially of SEQ ID NO: 11;   the nucleotide sequence having sequence homology with the genomic region located left of the target site in the B2M gene locus consists essentially of SEQ ID NO: 7;   the nucleotide sequence having sequence homology with the genomic region located right of the target site in the B2M gene locus consists essentially of SEQ ID NO: 13;   the gRNA of the second RNP complex comprises a spacer sequence corresponding to a sequence consisting of SEQ ID NO: 20;   the nucleotide sequence encoding HLA-E consists essentially of SEQ ID NO: 55;   the nucleotide sequence having sequence homology with the genomic region located left of the target site in the TXNIP gene locus consists essentially of SEQ ID NO: 25; and   the nucleotide sequence having sequence homology with the genomic region located right of the target site in the TXNIP gene locus consists essentially of SEQ ID NO: 32.   
     
     
         28 . The in vitro method of  claim 27  wherein SEQ ID NO: 11 is operably linked to an exogenous promoter and SEQ ID NO: 55 is operably linked to an exogenous promoter. 
     
     
         29 . The in vitro method of  claim 28 , wherein the exogenous promoter is a CAG promoter comprising a CMV enhancer, a β-actin promoter, and a chimeric intron.