High Throughput TCR Target Identification via Segmented Screening
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods are inadequate for determining the antigen specificity of large numbers of T-cell receptors (TCRs) derived from high-throughput single-cell analysis, which is crucial for understanding immune responses and developing targeted therapies.
Innovation Solution
A method involving high-throughput parallel single-cell sequencing to identify natively paired TCR chains, expressing these chains in engineered cells, and contacting them with engineered antigen-presenting cells (APCs) to determine reactive APCs, thereby identifying target antigens.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If high-throughput parallel single-cell sequencing is used to identify TCR chains, then the quantity of TCRs that can be analyzed increases, but the complexity of determining antigen specificity for each TCR increases
Solution Approach 1:
The method segments the antigen specificity determination process into distinct components: TCR chain identification through sequencing, TCR expression in engineered cells, and APC reactivity screening. This segmentation allows high-throughput sequencing to handle TCR identification at scale while the downstream assays systematically evaluate antigen specificity, resolving the contradiction between throughput and complexity.
Solution Approach 2:
Engineered antigen-presenting cells (APCs) serve as intermediaries between the TCRs and the antigens. These engineered APCs are designed to present specific antigens in a controlled manner, enabling systematic screening of TCR-antigen interactions. This intermediary approach allows the complex antigen specificity determination to be managed through standardized, high-throughput assays.
2Productivity
If multiple TCR chains are analyzed simultaneously, then the productivity of the screening process increases, but the precision of determining native TCR pairings decreases
Solution Approach 1:
The method performs preliminary action by identifying and characterizing TCR chains through high-throughput sequencing before expressing them in engineered cells. Single-cell sequencing data is analyzed to identify potential TCR chain pairings, and only those with sufficient native pairing confidence are selected for downstream expression and screening. This preliminary filtering maintains pairing accuracy while enabling high-throughput analysis of multiple TCRs.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables the robust determination of antigen specificity for multiple TCRs, facilitating the discovery of therapeutically relevant TCRs against disease targets and improving our understanding of immune responses.
Implementation Method 1
identifying a plurality of natively paired TCR chains from a biological sample from a subject using high-throughput parallel single-cell sequencing
Implementation Method 2
expressing a TCR polypeptide in one or more engineered cells, wherein the TCR polypeptide comprises at least one pair of the natively paired TCR chains
Implementation Method 3
contacting the one or more engineered cells to one or more of a plurality of engineered antigen presenting cells (APCs), wherein each engineered APC of the plurality of engineered APCs comprises a different antigen polypeptide; identifying a reactive engineered APC of the plurality of engineered APCs
Data Source
AI summary
Provided herein are methods and composition for high-throughput T-cell receptor target identification of natively paired T-cell receptor sequences.