Oligonucleotide Antigen Labeling for Spatial Antibody Identification
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Solution Overview
Problem
Current methods are inadequate for efficiently identifying and characterizing drug-reactive antibodies (DRAs) or anti-drug antibodies (ADAs), which can inhibit or prevent the efficacy of antibody-based therapies, posing a significant challenge in clinical trials and drug development.
Innovation Solution
A method involving a reporter oligonucleotide conjugated antigen is used to label antigen-binding molecules (ABMs) in a tissue sample, attaching them to capture probes on an array, generating spatially barcoded polynucleotides, and sequencing these barcodes to determine ABM-antigen interactions, enabling precise identification and quantification of drug-specific antibodies.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional methods are used to identify drug-reactive antibodies, then the process is simpler, but the identification efficiency and precision are insufficient
Solution Approach 1:
The method segments the identification process into distinct functional modules: (1) labeling module with reporter oligonucleotide-conjugated antigens, (2) capture module with spatially barcoded capture probes on arrays, (3) sequencing module for high-throughput analysis. This segmentation enables parallel processing of multiple samples and antigens simultaneously, dramatically improving identification efficiency while maintaining systematic control over the complex workflow
Solution Approach 2:
The patent introduces several intermediary elements to bridge different functional stages: reporter oligonucleotides serve as intermediaries between antigens and detection systems; spatially barcoded capture probes act as intermediaries between labeled antibodies and sequencing platforms; and the array substrate serves as an intermediary platform that organizes and facilitates high-throughput interactions. These intermediaries enable efficient information transfer and processing across the identification workflow
2Loss of information
If comprehensive characterization of drug-reactive antibodies is performed, then the understanding of antibody diversity improves, but the time and resources required increase
Solution Approach 1:
The method performs preliminary actions by pre-conjugating multiple different antigens with reporter oligonucleotides and pre-positioning spatially barcoded capture probes on arrays before sample introduction. This preliminary preparation enables simultaneous parallel processing of multiple antigens and samples, allowing comprehensive antibody repertoire characterization to be completed in a single experimental run rather than requiring sequential analysis, thereby dramatically reducing the time required while maintaining complete information capture
Solution Approach 2:
The patent adds spatial dimensionality through the use of arrays with spatially barcoded capture probes, where each location on the array corresponds to a specific antigen or experimental condition. This spatial organization enables multiplexed analysis of antibody-antigen interactions across multiple dimensions (different antigens, different samples, different conditions) simultaneously, allowing comprehensive characterization without proportional increases in time or resources
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 allows for the accurate detection and quantification of drug-reactive antibodies, guiding drug development and monitoring patient responses to antibody-drug conjugates (ADCs) or antibody therapeutics (AbTXs), assessing pre-existing immune responses to modified versions, and providing insights into antibody diversity.
Implementation Method 1
contacting a tissue sample comprising one or more cells expressing an antigen-binding molecule (ABM) with a reporter oligonucleotide conjugated antigen, wherein the ABM expressed by the ABM-expressing cell binds to the antigen
Implementation Method 2
attaching a first analyte of an ABM-expressing cell of the tissue sample to a first capture domain of a first capture probe of an array of capture probes attached to a substrate
Data Source
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AI summary
Provided herein are methods for identification of antigen binding molecules such as antibodies from a sample by exposing the antigen binding molecules to an antigen conjugated to an oligonucleotide.