Immune Repertoire Sequencing for Clone-Level Vaccine Response Tracking
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Solution Overview
Problem
Current methods are inadequate for characterizing the dynamics of B cell and T cell repertoires in response to infections and vaccinations, particularly in determining the breadth of the immune response and the formation of immunological memory, and in understanding how the human immune system responds to these events.
Innovation Solution
A method involving high-throughput sequencing of rearranged CDR3 regions of TCR and Ig loci from multiple biological samples taken before, during, and after vaccination or infection, combined with bioinformatics analysis, to identify and track vaccine- or infection-induced T and B cell clones, including their recruitment to memory populations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional methods are used to characterize immune response, then the process is simpler, but the measurement precision and ability to track individual clones is insufficient
Solution Approach 1:
The patent segments the immune repertoire analysis into distinct temporal stages (pre-vaccination, acute response at day 14, and memory formation at day 90). By analyzing CDR3 regions at these segmented time points, the method achieves clone-level resolution of immune responses while managing complexity through structured temporal segmentation rather than continuous monitoring.
Solution Approach 2:
The patent performs preliminary sequencing of the T cell repertoire before vaccination to establish a baseline of pre-existing clones. This preliminary action enables subsequent identification of vaccine-induced clones by comparing against the baseline, achieving precise measurement of immune response without requiring complex real-time monitoring during the actual immune activation process.
2Loss of information
If high-throughput sequencing is performed at multiple time points to track immune dynamics, then the characterization detail is improved, but the time and resource investment increases
Solution Approach 1:
The patent employs periodic sampling at three strategically selected time points (pre-vaccination, day 14 acute response, and day 90 memory formation) rather than continuous monitoring. This periodic action captures the essential dynamics of immune response and memory formation while minimizing time loss and resource investment compared to continuous or more frequent sampling approaches.
Solution Approach 2:
The patent performs sequencing on a subset of individuals (n=9) at multiple time points, which represents a partial action approach. This allows comprehensive characterization of immune dynamics in a manageable cohort, balancing the need for detailed temporal information with practical constraints of time and resources. The partial sampling of the population provides sufficient information to understand immune response patterns without requiring exhaustive analysis of all potential subjects.
3Difficulty of detecting and measuring
If enrichment steps are added to isolate responsive clones, then the detection sensitivity is improved, but the procedure complexity and potential bias increase
Solution Approach 1:
The patent extracts and sequences the CDR3 regions directly from total T cell populations without performing enrichment steps. By taking out only the specific CDR3 nucleic acid sequences for sequencing while leaving the rest of the immune population unmanipulated, the method achieves adequate detection sensitivity for vaccine-induced clones while avoiding the complexity and potential bias introduced by enrichment procedures such as tetramer staining or flow sorting.
Solution Approach 2:
The high-throughput sequencing methodology itself provides the necessary detection sensitivity through deep sequencing coverage, making the system self-sufficient without requiring additional enrichment steps. The sequencing depth and analytical methods are designed to detect rare vaccine-induced clones directly in the unpurified T cell population, allowing the system to serve its own detection needs without external enrichment assistance.
Data Source
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AI summary
Methods of monitoring and measuring dynamic adaptive immune cell responses are provided. High-throughput sequencing of T cell receptor and immunoglobulin loci is used to characterize the breadth of an effector cell response to a stimulus, such as a vaccine or infection. Unique responding effector cell clones and abundance thereof can be determined. Additionally, methods for determining the contribution of responding effector cells to the immunological memory compartment are provided.