Optically Readable Barcode Beads for High-Throughput TCR Screening
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Solution Overview
Problem
Current methods for identifying antigen-specific T-cell receptors (TCRs) and antibodies are labor-intensive, time-consuming, and lack high-throughput capabilities, hindering the development of effective cancer therapies and antibody discovery processes.
Innovation Solution
A solid support detection system utilizing optically readable oligonucleotide probes and beads with unique barcoding systems that enable high-throughput analysis of molecular interactions, allowing for the characterization and identification of millions of molecular interactions, including TCR-antigen pairs and antibody-antigen interactions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional bulk population assays are used to identify TCR sequences, then TCR sequences can be identified through indirect determination, but the process becomes complex and time-consuming
Solution Approach 1:
The patent segments the bulk population into individual single cells, allowing parallel analysis of thousands of TCR sequences simultaneously. Each cell is isolated in a separate well or droplet, enabling high-throughput identification without the complexity and time constraints of bulk population methods.
Solution Approach 2:
The patent changes the scale parameter from bulk population level to single-cell level, transforming the analysis from indirect bulk determination to direct single-cell sequencing. This parameter change enables rapid parallel processing while maintaining identification accuracy.
2Productivity
If in silico-based approaches are used for neoantigen prediction, then high-throughput prediction is achieved, but the complexity of TCR structure and interaction makes modeling extremely challenging
Solution Approach 1:
The patent uses experimentally determined TCR sequences from single-cell sequencing as intermediaries to validate and refine in silico predictions. Instead of directly modeling the complex TCR-antigen interaction, the method obtains actual sequence data from functional TCRs and uses this empirical data to improve prediction algorithms.
Solution Approach 2:
The patent implements a feedback loop where in silico predictions are tested against experimentally identified TCR sequences, and the results feed back to improve the prediction model. This iterative process increases throughput while managing complexity through continuous model refinement based on real data.
3Measurement precision
If hybridoma-based screening is used to identify antigen-specific antibodies, then new antigen-specific antibodies can be identified, but the process becomes extremely labor-intensive and time-consuming
Solution Approach 1:
The patent replaces the mechanical, manual processes of hybridoma-based screening (limiting dilution cloning, manual picking, individual cell culture) with automated single-cell sorting and high-throughput sequencing. This substitution dramatically increases productivity while maintaining the ability to identify antigen-specific antibodies through functional screening.
Solution Approach 2:
The patent changes the throughput parameter from low (one cell at a time in hybridoma) to high (thousands of cells in parallel via single-cell sequencing). The method maintains identification accuracy by preserving the functional screening step while parallelizing the analysis across many cells simultaneously.
4Measurement precision
If Next-Generation Sequencing is used to collect tumor genotype information, then accuracy and turnaround time are improved, but obtaining corresponding antigen-specific TCR sequence and assessing T-cell response remains challenging
Solution Approach 1:
The patent merges the TCR sequencing process with the tumor genotype analysis workflow. By performing single-cell TCR sequencing on T cells that have been activated by tumor antigens, the method simultaneously obtains both tumor genotype information and corresponding antigen-specific TCR sequences in a unified assay, greatly simplifying the overall process.
Solution Approach 2:
The patent uses antigen-presenting cells (APCs) or tumor cells as intermediaries to link tumor genotype information with TCR sequence identification. These intermediaries present tumor-derived antigens to T cells, enabling the isolation and sequencing of antigen-specific TCRs in the context of the actual tumor antigens.
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
This approach accelerates and simplifies the screening and characterization of molecular interactions, enabling the rapid identification of antigen-specific TCRs and antibodies, thereby facilitating the development of personalized and efficient cancer therapies and antibody discovery.
Implementation Method 1
Each sequence of the plurality of nucleotide sequences comprises at least 3 distinct fluorescent labels comprising up to 7 unique fluorescent combinations to form a fluorescent word
Data Source
AI summary
A system and method are provided for simplifying and accelerating the screening and characterization of molecular interactions by high-throughput functional screening and sequencing of single cells. More specifically, a platform is provided which combines a solid support and an innovative method for capturing and barcoding of nucleic acids that allows simultaneous phenotyping and genotyping of >100, 000s of cells.