Antigen Epitope Mapping by Sequencing in Complex Biological Samples
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Solution Overview
Problem
Current epitope mapping methods are low-throughput, laborious, and difficult to scale, particularly for identifying antigenic epitopes in complex biological samples, and existing techniques are expensive, sensitive to environmental conditions, or require highly purified antigens and antibodies.
Innovation Solution
A method involving contacting a biological sample with antigens coupled to reporter oligonucleotides, hybridizing these oligonucleotides to capture probes on a substrate, and sequencing to identify and characterize antigen-binding molecules (ABMs) based on their binding affinity to target antigens, using barcode-enabled antigen mapping by sequencing (BEAM-seq).
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If high-resolution epitope mapping methods (electron microscopy, NMR, HDX-MS, X-ray crystallography) are used, then measurement precision is improved, but device complexity and cost increase significantly
Solution Approach 1:
The patent uses barcode-enabled antigens as intermediaries that bridge the antibody-antigen interaction with detectable nucleic acid barcodes. These barcodes serve as mediators to translate the binding event into a sequence that can be read by sequencing, eliminating the need for complex structural analysis methods while maintaining epitope identification capability
Solution Approach 2:
The patent replaces complex mechanical/structural analysis methods (electron microscopy, X-ray crystallography) with a molecular biology-based approach using nucleic acid barcodes and sequencing. This substitution transforms the measurement process from direct structural observation to molecular sequence reading, dramatically simplifying the system
2Measurement precision
If HDX-MS is used for epitope mapping, then measurement precision is improved, but reliability decreases due to sensitivity to pH and temperature fluctuations
Solution Approach 1:
The patent changes the measurement parameter from hydrogen/deuterium exchange (sensitive to pH and temperature) to nucleic acid barcode sequencing (insensitive to environmental conditions). This parameter transformation maintains measurement precision while dramatically improving reliability by using a measurement method that is not affected by physiological fluctuations
3Ease of operation
If competition ELISA is used for epitope mapping, then ease of operation is improved, but productivity decreases due to low throughput
Solution Approach 1:
The patent merges multiple ELISA-like competition measurements into a single parallel sequencing experiment. By using barcode-enabled antigens that can be processed together with standard sequencing workflows, the method combines the ease of operation of ELISA with the high throughput of next-generation sequencing, achieving both interpretability and productivity
4Measurement precision
If residue-level epitope mapping is performed, then measurement precision is improved, but device complexity increases due to difficulty in interpreting protein folding effects
Solution Approach 1:
The patent extracts the epitope identification function from the complex context of protein folding and residue-level structural analysis. By using barcode-enabled antigens, the method isolates the critical binding information into discrete, interpretable barcode sequences, eliminating the need to interpret complex structural data while maintaining residue-level precision
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 high-throughput, reliable, and cost-effective identification and characterization of ABMs, such as antibodies, in complex biological samples, providing residue-level information on antigen-antibody interactions.
Implementation Method 1
hybridizing (i) the first and/or second reporter oligonucleotide to a first capture domain of a first capture probe attached to a first substrate
Data Source
AI summary
The present disclosure relates generally to compositions, methods, and systems for the characterization of antigen-binding molecules (e.g., antibodies) in biological samples. This characterization permits the identification of the ABM that bind to regions of interest, or the mapping of ABMs according to their binding to specific regions of interest, of an antigen. Understanding the binding characteristics of ABMs at a region of interest level may facilitate the identification and production of immunotherapeutic molecules having desired properties.