Nanoexpression for Antibody Repertoire Interrogation
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Solution Overview
Problem
Current methods for interrogating antibody repertoires are inefficient due to the inability to determine antigen specificity from protein sequences, requiring large-scale testing and being time-consuming and costly, especially when dealing with complex libraries exceeding 10^9 combinations.
Innovation Solution
The use of nanoexpression and antibody display technologies, such as phage display, with fully sequenced and barcoded repertoires to selectively pair heavy and light chain sequences, reducing library complexity by enriching for native pairs and using identification regions to annotate antigen specificity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If combinatorial libraries with random H+L pairing are used, then library diversity is increased, but library complexity exceeds 10^9 combinations making technical challenges arise
Solution Approach 1:
The patent segments the antibody repertoire into individually barcoded heavy and light chain sequences from single cells. Each chain is independently characterized with its own barcode, allowing separate tracking and pairing. This segmentation reduces the effective library complexity from 10^9 random combinations to manageable pairs by using actual single-cell derived sequences rather than random combinatorial libraries.
Solution Approach 2:
The patent creates synthetic single-cell sequences by pairing heavy and light chain sequences that were independently derived from single cells. These synthetic sequences serve as copies of actual functional antibodies, allowing the repertoire to be interrogated without needing to physically produce each antibody. The barcodes act as digital copies that track the origin and characteristics of each antibody pair.
2Reliability
If cherry-picking specific members for expression is done, then functional antibodies can be produced, but the process is time consuming and expensive
Solution Approach 1:
The patent replaces the mechanical process of in-vitro antibody production and testing with a computational approach. By using barcoded DNA sequences that encode antibody chains from single cells, the system can digitally store, retrieve, and analyze antibody information without physically producing each antibody. This substitution of physical experimentation with computational analysis dramatically reduces time and cost.
Solution Approach 2:
The patent performs preliminary characterization of heavy and light chain sequences from single cells before pairing them into functional antibodies. By pre-identifying and barcoding the sequences along with their binding characteristics, the system prepares all necessary information in advance, eliminating the need for time-consuming in-vitro production and testing of each individual antibody.
3Measurement precision
If large numbers of antibodies are tested to ensure coverage, then adequate repertoire coverage is achieved, but the number of antibodies that would need to be tested becomes prohibitively large
Solution Approach 1:
The patent uses barcoded DNA sequences as digital copies of antibody chains to represent the repertoire. Instead of physically testing numerous antibodies, the system sequences and analyzes the barcode information from single-cell derived sequences. This allows comprehensive repertoire coverage to be achieved through computational analysis of sequence data rather than physical testing of large numbers of antibodies.
Solution Approach 2:
The patent substitutes physical antibody testing with computational sequence analysis. By converting antibody chains into barcoded DNA sequences that can be digitally stored and analyzed, the system can interrogate the entire repertoire through sequencing rather than requiring physical production and testing of each antibody, dramatically reducing the quantity needed to be tested.
Data Source
AI summary
Disclosed herein are methods and compositions for using nanoexpression to interrogate antigen specificity within antibody repertoires. Also disclosed herein is an antibody display system composition comprising one or more recombinant nucleic acid sequences comprising a first nucleic acid sequence encoding a heavy chain variable region sequence or fragment thereof operatively linked to a first identification region sequence and a second nucleic acid sequence encoding a light chain variable region sequence or fragment thereof operatively linked to a second identification region sequence.