High throughput process for t cell receptor target identification of natively-paired t cell receptor sequences

Abstract

Provided herein are methods and compositions for high-throughput T-cell receptor target identification of natively paired T-cell receptor sequences.

1 - 119 . (canceled) 
     
     
         120 . A library of T-cell receptor (TCR) polypeptides comprising a first TCR polypeptide and a second TCR polypeptide, wherein the first TCR polypeptide recognizes a first MHC-type expressed by one or more antigen-presenting cells (APCs) of a first plurality of APCs and the second TCR polypeptide recognizes a second MHC-type expressed by one or more APCs of a second plurality of APCs. 
     
     
         121 . The library of  claim 120 , wherein
 (a) the first TCR polypeptide is specific to a complex comprising (i) a first antigen polypeptide presented by one or more APCs of the first plurality of APCs and (ii) an MHC of the first MHC-type, and   (b) the second TCR polypeptide is specific to a complex comprising (i) a second antigen polypeptide presented by one of more APCs of the second plurality of APCs and (ii) an MHC of the second MHC-type.   
     
     
         122 . The library of  claim 120 , wherein the first TCR polypeptide comprises a pair of natively paired TCR chains comprising a TCR-alpha chain and a TCR-beta chain. 
     
     
         123 . The library of  claim 120 , wherein the second TCR polypeptide comprises a pair of natively paired TCR chains comprising a TCR-alpha chain and a TCR-beta chain. 
     
     
         124 . The library of  claim 120 , wherein the first TCR polypeptide comprises a pair of natively paired TCR chains comprising a TCR-gamma chain and a TCR-delta chain. 
     
     
         125 . The library of  claim 120 , wherein the second TCR polypeptide comprises a pair of natively paired TCR chains comprising a TCR-gamma chain and a TCR-delta chain. 
     
     
         126 . The library of  claim 121 , wherein the first antigen polypeptide is associated with a disease, cancer, or viral infection. 
     
     
         127 . The library of  claim 121 , wherein the second antigen polypeptide is associated with a disease, cancer, or viral infection. 
     
     
         128 . A preparation comprising a first plurality of engineered cells from a first subject and a second plurality of engineered cells from a second subject, wherein one or more cells of the first plurality of engineered cells expresses the first TCR polypeptide of the library of  claim 120  and one or more cells of the second plurality of engineered cells expresses the second TCR polypeptide of the library of  claim 120 . 
     
     
         129 . The preparation of  claim 128 , wherein the first MHC-type recognized by the first TCR polypeptide is similar to the MHC type of the first subject. 
     
     
         130 . The preparation of  claim 128 , wherein the second MHC-type recognized by the second TCR polypeptide is similar to the MHC type of the second subject. 
     
     
         131 . The preparation of  claim 128 , wherein the one or more APCs of the first plurality of APCs is engineered to express MHC genes matched to the first subject. 
     
     
         132 . The preparation of  claim 128 , wherein the one or more APCs of the second plurality of APCs is engineered to express MHC genes matched to the second subject. 
     
     
         133 . The preparation of  claim 128 , wherein the one or more APCs of the first plurality of APCs is engineered to not express an endogenous MHC polypeptide of the first subject. 
     
     
         134 . The preparation of  claim 128 , wherein the one or more APCs of the second plurality of engineered APCs is engineered to not express an endogenous MHC polypeptide of the second subject.