Single-Chain Antibody Libraries for Spatial Target Identification
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Solution Overview
Problem
Current antibody therapeutics discovery workflows are limited by the need for known targets, often using in vitro models that do not reflect the complex tissue environment, and are not suitable for personalized medicine, failing to provide spatial information on single cells within tissues.
Innovation Solution
Development of methods for generating single-chain antigen-binding molecule/nucleic acid conjugate libraries, displayed via ribosomal or mRNA/cDNA techniques, and screened using spatial arrays with capture probes to identify and locate antigens in biological samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If conventional antibody screening workflows are used, then known targets can be screened, but the process is limited by the need for known targets and does not provide spatial information on single cells within tissues
Solution Approach 1:
The invention segments the screening process into multiple stages: (1) displaying antigen-binding molecules on individual cells within intact tissue sections, (2) screening for binding to unknown or known targets, (3) determining the spatial location of bound molecules, and (4) identifying the target antigen. This segmentation allows the system to handle both novel and known targets while providing spatial information, resolving the contradiction between versatility and complexity.
Solution Approach 2:
The invention uses spatial barcodes as intermediaries to link the physical location of cells in the tissue section with their antigen-binding activity. The spatial barcode system mediates between the complex tissue environment and the screening process, enabling identification of targets and spatial information without requiring prior knowledge of targets, thus improving versatility while managing complexity through a systematic intermediary approach.
2Reliability
If in vitro models are used for screening, then the screening process can be simplified, but the models do not accurately reflect the in vivo tissue context
Solution Approach 1:
The invention performs preliminary actions by displaying antigen-binding molecules on individual cells within intact tissue sections before screening. This preliminary display in the native tissue context preserves the in vivo environment and cell-cell interactions, ensuring that the screening accurately reflects biological relevance while maintaining the ability to process and analyze the data systematically.
Solution Approach 2:
The invention adds the spatial dimension to the screening process by determining the location of antigen-binding molecules within the tissue section. This dimensional addition transforms the screening from a two-dimensional or solution-based approach to a three-dimensional spatial analysis, preserving the in vivo context while enabling systematic identification and characterization of targets through computational analysis of spatial patterns.
3Ease of manufacture
If single-chain antibodies are used, then the molecules are smaller and easier to generate libraries, but the screening process requires sophisticated display and detection systems
Solution Approach 1:
The invention merges the display and detection functions into a single integrated system. The spatial array combines the display of single-chain antibodies on individual cells with the detection of their binding activity and spatial location in one platform. This merging simplifies the overall process by eliminating the need for separate display and detection systems, thereby maintaining ease of library generation while reducing the complexity of the complete screening workflow.
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-resolution spatial analysis of antigen-binding molecules, facilitating the discovery of therapeutic antibodies tailored to specific tissue environments and personalized medicine applications.
Implementation Method 1
an mRNA of the plurality of in vitro transcribed mRNAs includes in a 5' to 3' direction: (i) an analyte capture sequence that hybridizes to a capture domain of a capture probe
Implementation Method 2
in vitro translating the plurality of in vitro transcribed mRNAs, thereby generating the antigen-binding molecule/nucleic acid conjugate library
Data Source
Figure 1
Figure 2A~2C
Figure 2D~2E
AI summary
Provided herein are methods, compositions, and kits including single-chain antibody nucleic acid libraries and methods of displaying single-chain antibodies and screening single-chain antibodies on a spatial array.