comPACT Peptide-MHC Complexes for Barcode-Based T Cell Isolation
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Solution Overview
Problem
Current methods for producing peptide-MHC multimers are laborious, yield low quantities of properly folded complexes, have poor exchange efficiency, and are not suitable for high-throughput isolation of patient-specific TCRs for personalized immunotherapies, especially for neoepitopes with varying MHC haplotypes.
Innovation Solution
A method involving distinct particle sets with unique antigen peptides and barcodes, allowing T cells to bind and be isolated based on antigen specificity, with ratios of barcodes determining the antigen specificity, enabling high-throughput identification and isolation of T cell receptors.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional solid-phase synthesis and refolding methods are used to produce peptide-MHC multimers, then the complexes can be formed, but the production is laborious and yields are low
Solution Approach 1:
The invention segments the peptide-MHC complex production into distinct modular components: a universal MHC scaffold and interchangeable peptide ligands. This allows parallel production of multiple peptide variants by simply changing the peptide component while keeping the MHC scaffold constant, dramatically improving productivity and reducing manufacturing complexity
Solution Approach 2:
The invention creates a universal MHC scaffold that can bind multiple different peptide ligands. This multi-functional scaffold enables a single refolding reaction to produce a library of peptide-MHC complexes, eliminating the need for separate refolding reactions for each peptide and significantly enhancing production efficiency
2Productivity
If commercial peptide synthesis is used, then peptides can be obtained, but the turnaround time is too long for personalized immunotherapies
Solution Approach 1:
The invention performs preliminary action by pre-synthesizing and storing a library of peptide ligands before they are needed for T cell isolation. This allows rapid exchange of peptides onto the MHC scaffold without time-consuming synthesis steps during the actual therapeutic process, enabling fast turnaround for personalized immunotherapies
Solution Approach 2:
The invention uses peptide analogs and mimics that can be rapidly synthesized or exchanged, replacing the need for time-consuming de novo peptide synthesis. This copying approach allows rapid generation of peptide-MHC complexes for screening patient-specific T cell responses
3Measurement precision
If peptide exchange reactions are performed to screen multiple ligands, then T cell specificity can be identified, but exchange efficiency is poor
Solution Approach 1:
The invention changes the chemical parameters of the peptide-MHC interaction by using engineered MHC scaffolds with modified binding interfaces. These parameter changes enable rapid and efficient peptide exchange while maintaining stable T cell recognition, solving the contradiction between identification precision and exchange efficiency
Solution Approach 2:
The invention uses a conditional ligand as an intermediary that facilitates efficient peptide exchange. The conditional ligand binds the MHC scaffold in a reversible manner, allowing rapid displacement by target peptides during exchange reactions, thereby improving exchange efficiency without compromising T cell specificity identification
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
Enhances the efficiency and accuracy of identifying and isolating T cell receptors, facilitating personalized immunotherapies by providing a high-signal-to-noise ratio for T cell screening and enabling rapid production of patient-specific TCRs.
Implementation Method 1
Each TCR recognizes a ligand presented by a major histocompatibility complex (MHC) molecule on target cells
Implementation Method 2
performing an assay to identify one or more barcodes bound to the particle set that is bound to the isolated T cell
Data Source
AI summary
Disclosed herein are antigenic peptide-MHC complexes, termed comPACT polypeptides and comPACT polynucleotides, and methods of producing such complexes. Also discloses herein are methods of producing libraries of comPACT polynucleotides and polypeptides, and their exemplary use in capturing cancer neoepitope-reactive T cells with high accuracy. Dual particle detection approaches for detection of neoantigen specific T cells with improved sensitivity and specificity are provided. Signal to noise ratio analysis of isolated T cells for detection of neoantigen-specific T cells with improved T cells is also provided.