Compositions and methods for t-cell receptor identification
AssigneeRootPath Genomics, Inc.
InventorXi CHEN
Life of this patent
Estimating the term…
Abstract
The present disclosure provides compositions and methods for identifying antigen-reactive T-cell receptors (TCRs). A cancer cell line expressing an endogenous antigen in complex with an exogenous MHC molecule derived from a subject (e.g., a cancer patient) can be used to screen for TCRs recognizing the endogenous antigen in complex with the exogenous MHC molecule.
Claims103
A method for identifying an antigen-reactive cell that recognizes an endogenous antigen of a cancer cell line in complex with an MHC molecule expressed by a subject, comprising:
- (a) providing a cell that is a cancer cell line expressing an endogenous antigen in complex with an exogenous MHC molecule, wherein the exogenous MHC molecule is the MHC molecule expressed by the subject or derived from the subject;
- (b) contacting the cancer cell line with a first plurality of TCR-expressing cells, wherein the first plurality of TCR-expressing cells or a subset of the first plurality of TCR-expressing cells is activated by the endogenous antigen in complex with the exogenous MHC of the cancer cell line;
- and
- (c) subsequent to contacting in (b), identifying the subset of the first plurality of TCR-expressing cells, thereby identifying the antigen-reactive cell that recognizes the endogenous antigen of the cancer cell line.
A composition for identifying an antigen-reactive cell that recognizes an endogenous antigen of a cancer cell line in complex with an MHC molecule expressed by a subject, comprising:
- a cell that is a cancer cell line expressing an endogenous antigen in complex with an exogenous MHC molecule, wherein the exogenous MHC molecule is the MEW molecule expressed by the subject or derived from the subject;
- and
- a T cell expressing a natively paired TCR derived from the subject, wherein a gene expression profile, a transcriptomic profile or a genomic alternation of the cancer cell line resembles that of a cancer cell from the subject.
A method for evaluating an anti-cancer activity of a TCR-expressing cell, comprising:
- (a) providing a plurality of cells, wherein the plurality of cells is derived from a cancer cell line and expresses an endogenous antigen in complex with an exogenous WIC molecule, wherein the exogenous MHC molecule is an WIC molecule expressed by a subject or derived from the subject;
- (b) contacting the plurality of cells with a plurality of TCR-expressing cells expressing a plurality of TCRs derived from the same subject, wherein the plurality of TCRs or a fraction thereof recognizes the endogenous antigen in complex with the exogenous MHC molecule of the plurality of cells or a fraction thereof;
- and
- (c) subsequent to contacting in (b), quantifying (i) the fraction of the plurality of cells that are recognized by the plurality of TCR-expressing cells or a fraction thereof, (ii) the fraction of the plurality of TCR-expressing cells that recognize the plurality of cells or a fraction thereof, and/or (iii) an amount or level of a cytokine secreted by the plurality of TCR-expressing cells or a fraction thereof.
A composition comprising a panel of WIC-engineered cancer cell lines derived from a same cancer type, comprising:
- a first sub-panel comprising at least two MHC-engineered cancer cell lines derived from a same first parental cancer cell line;
- and
- a second sub-panel comprising at least two MHC-engineered cancer cell lines derived from a same second parental cancer cell line;
- and
- wherein the at least two MHC-engineered cancer cell lines of the first sub-panel or the second sub-panel expresses a different exogenous MHC molecule.
A method for identifying an antigen-reactive cell that recognizes an endogenous antigen in complex with an WIC molecule expressed by a subject, the method comprising:
- (a) providing an antigen-presenting cell (APC) expressing an endogenous antigen in complex with an exogenous MHC molecule, wherein the exogenous MHC molecule is the MHC molecule expressed by the subject or derived from the subject;
- (b) contacting the APC with a plurality of TCR-expressing cells derived from the subject, wherein the plurality of TCR-expressing cells or a subset of the plurality of TCR-expressing cells recognizes the endogenous antigen in complex with the exogenous MHC of the APC, and wherein the plurality of TCR-expressing cells or a subset of the plurality of TCR-expressing cells that recognizes the endogenous antigen (i) is attached to a label secreted from the APC or a label transferred by a label-transferring enzyme associated with the APC upon recognizing the endogenous antigen, or (ii) expresses an activation marker upon recognizing the endogenous antigen;
- and
- (c) identifying the subset of the plurality of TCR-expressing cells based on the label or the activation marker, thereby identifying the antigen-reactive cell.
Dependencies are inferred from the claim text.