Compositions and methods for generating and characterizing recombinant antigen binding molecules
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Solution Overview
Problem
Current methods for isolating and characterizing antigen-binding molecules, such as monoclonal antibodies, face challenges including low-throughput analysis, poor RNA quality leading to inefficient amplification of B cell receptor sequences, and the generation of non-humanized antibodies, making it difficult to rapidly screen for cancer-specific antibodies.
Innovation Solution
A method involving spatial profiling to capture and sequence antigen-binding molecules from tissue samples using spatial barcodes, enabling high-throughput analysis and production of recombinant antibodies with desired properties, which are then screened for tumor specificity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If current isolation and characterization methods (hybridoma capture, phage display, yeast display) are used, then antigen-binding molecules can be isolated, but the throughput is low and RNA quality is poor leading to inefficient amplification
Solution Approach 1:
The patent replaces traditional mechanical/isolation-based methods (hybridoma capture, phage display, yeast display) with a spatially-resolved sequencing approach that uses nucleic acid barcoding and high-throughput sequencing to identify and characterize antigen-binding molecules, thereby increasing throughput while preserving RNA quality through in situ analysis
Solution Approach 2:
The patent changes the fundamental parameter of measurement from protein-based isolation to nucleic acid-based sequencing, allowing for high-throughput analysis of B cell receptor sequences while maintaining the ability to work with degraded RNA through spatial barcoding and in situ amplification
2Productivity
If bulk approaches are used for antibody isolation, then large numbers of antibodies can be processed, but heavy-light chain pairing is lost
Solution Approach 1:
The patent segments the antibody isolation process into spatially-resolved single-cell analysis units, where each cell's B cell receptor sequences (heavy and light chains) are captured and barcoded together in situ, preserving the pairing information while enabling high-throughput processing through parallel sequencing of multiple cells
Solution Approach 2:
The patent introduces spatial barcodes as an intermediary that links the physical location of each cell to its sequenced B cell receptor sequences, allowing for the preservation of heavy-light chain pairing information through computational reconstruction of paired sequences from spatially-resolved data
3Productivity
If traditional screening methods are used, then antibody sequences can be obtained, but the ability to screen multiple individuals and combine samples is limited
Solution Approach 1:
The patent creates a universal spatially-resolved sequencing platform that can process multiple individual samples through the same workflow, using standardized spatial barcodes and sequencing protocols to enable combination and comparison of B cell receptor repertoires from multiple patients or conditions
Solution Approach 2:
The patent merges multiple individual samples into a single high-throughput sequencing experiment by processing them through the same spatial barcoding workflow, allowing for the combination of B cell receptor sequences from multiple individuals in a unified analysis framework
4Ease of manufacture
If VDJ mice are used to generate humanized antibodies, then some humanization is achieved, but the antibodies are not fully humanized and require additional humanization steps
Solution Approach 1:
The patent extracts fully human B cell receptor sequences directly from human tumor tissue samples through spatially-resolved sequencing, eliminating the need for VDJ mice and subsequent humanization steps by obtaining native human antibodies directly from the patient's own immune repertoire
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 efficient, high-throughput identification and characterization of tumor-specific antibodies, allowing for precise targeting of cancer cells and potential therapeutic applications.
Implementation Method 1
a first capture probe comprising (i) a spatial barcode sequence and (ii) the capture domain, the capture domain comprising a capture sequence
Data Source
AI summary
The present disclosure relates generally to the field of immunology, and particularly relates to compositions, methods, and systems for the analysis and generation of antigen-binding molecules produced by immune cells obtained from tissue samples (e.g., antibodies produced by B cells in tumor tissue samples or TCRs produced by T cells in tumor tissue samples) using spatial methodologies, and for the production and characterization of recombinant antigen-binding molecules (e.g., antibodies, TCRs) with desired properties.