Methods and systems for antigen screening

Abstract

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and antigen screening. Polynucleotide processing may be useful for a variety of applications. Antigen screening may comprise the use of one or more engineered cells. Engineered cells may be useful for characterizing one or more analytes including, for example, a polypeptide antigen.

1 . A method for screening an antigen, comprising:
 (a) contacting an immune receptor with a plurality of engineered cells to yield an engineered cell bound to said immune receptor, wherein said plurality of engineered cells comprise (i) a complex comprising a polypeptide antigen coupled to a major histocompatibility complex (MHC) molecule; and (ii) a first nucleic acid molecule comprising a sequence encoding for said polypeptide antigen;   (b) generating a plurality of partitions, wherein a partition of said plurality of partitions comprises (i) said engineered cell bound to said immune receptor; and (ii) a plurality of nucleic acid barcode molecules comprising a common barcode sequence; and   (c) generating a second nucleic acid molecule comprising (i) a sequence corresponding to said polypeptide antigen and (ii) a sequence corresponding to said common barcode sequence.   
     
     
         2 . The method of  claim 1 , wherein in (a), said polypeptide antigen is covalently coupled to said WIC molecule. 
     
     
         3 . The method of  claim 1 , wherein in (a), said complex is displayed on the surface of said plurality of engineered cells. 
     
     
         4 . The method of  claim 1 , wherein said plurality of nucleic acid barcode molecules further comprise a capture sequence and wherein said first nucleic acid molecule further comprises a sequence configured to hybridize with said capture sequence. 
     
     
         5 . The method of  claim 4 , wherein (c) comprises hybridizing said first nucleic acid molecule to a nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules and performing a nucleic acid extension reaction to generate said second nucleic acid molecule. 
     
     
         6 . The method of  claim 4 , wherein (c) comprises hybridizing said first nucleic acid molecule to a nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules and performing a ligation reaction to generate said second nucleic acid molecule. 
     
     
         7 . The method of  claim 1 , further comprising sequencing said first nucleic acid molecule or derivative thereof to generate sequencing reads corresponding to said polypeptide antigen and said common barcode sequence. 
     
     
         8 . The method of  claim 1 , wherein said immune receptor is a T cell receptor. 
     
     
         9 . The method of  claim 8 , wherein (a) comprises contacting a cell comprising said immune receptor with said plurality of engineered yeast cells and wherein, in (b), said partition comprises said engineered yeast cell bound to said cell. 
     
     
         10 . The method of  claim 9 , wherein said cell is a T cell. 
     
     
         11 . The method of  claim 9 , wherein said cell comprises a messenger ribonucleic acid (mRNA) molecule encoding for said immune receptor and further comprising, prior to (b), generating a third nucleic acid molecule comprising (i) a sequence corresponding to said immune receptor and (ii) a sequence corresponding to said common barcode sequence. 
     
     
         12 . The method of  claim 11 , wherein said plurality of nucleic acid barcode molecules further comprise a capture sequence and wherein (c) comprises hybridizing said mRNA molecule to a nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules and performing a nucleic acid extension reaction to generate said third nucleic acid molecule. 
     
     
         13 . The method of  claim 11 , wherein said partition further comprises a fourth nucleic acid molecule comprising a poly-T sequence, wherein said plurality of nucleic acid barcode molecules further comprise a template switching oligonucleotide (TSO) sequence, and wherein (c) comprises (i) using said fourth nucleic acid molecule and said mRNA molecule to generate a complementary deoxyribonucleic acid (cDNA) molecule comprising said sequence corresponding to said immune receptor and (ii) performing a template switching reaction using a nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules to generate said third nucleic acid molecule. 
     
     
         14 . The method of  claim 13 , further comprising (i) sequencing said first nucleic acid molecule or derivative thereof to generate sequencing reads corresponding to said polypeptide antigen and said common barcode sequence; and (ii) sequencing said third nucleic acid molecule or derivative thereof to generate sequencing reads corresponding to said immune receptor and said common barcode sequence. 
     
     
         15 . The method of  claim 14 , further comprising using said sequencing reads corresponding to said common barcode sequence to associate said immune receptor and said polypeptide antigen. 
     
     
         16 . The method of  claim 1 , wherein said plurality of nucleic acid barcode molecules are attached to a solid support. 
     
     
         17 . The method of  claim 16 , wherein said solid support is a bead. 
     
     
         18 . The method of  claim 17 , wherein said plurality of nucleic acid barcode molecules is releasably attached to said bead. 
     
     
         19 . The method of  claim 18 , further comprising releasing said plurality of nucleic acid barcode molecules from said bead. 
     
     
         20 . The method of  claim 17 , wherein said bead is a gel bead. 
     
     
         21 - 25 . (canceled)