Antibody Barcoded Beads Multiplexed Protein Mapping
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Solution Overview
Problem
Current genomic mapping methods are time-consuming, costly, and labor-intensive, limiting the generation of comprehensive cell-type specific genomic maps, especially for rare cell types or patient samples, due to their inability to efficiently detect and map interactions between nucleic acid molecules and proteins of interest in a multiplexed manner.
Innovation Solution
The development of barcoded detection particles, which comprise antigen-binding proteins associated with immunoglobulin-binding moieties and multivalent binding agents, allowing for the generation of barcoded detection particles that can interact with nucleic acid molecules and proteins, enabling multiplexed detection through split-and-pool barcoding techniques to generate combinatorial barcodes for sequencing analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current genomic mapping methods (ChIP, CLIP, RAP) are used to map protein-nucleic acid interactions, then genome-wide maps can be generated, but the process is time-consuming, costly, and labor-intensive, limiting comprehensive mapping especially for rare cell types
Solution Approach 1:
The invention segments the mapping process by assigning unique barcodes to individual particles (beads) that capture protein-nucleic acid complexes. Each particle acts as an independent reaction unit, allowing parallel processing of multiple samples. This segmentation enables high-throughput mapping by distributing the workload across thousands of particles simultaneously, rather than processing samples sequentially
Solution Approach 2:
The barcoded particle system serves multiple functions: it captures protein-nucleic acid interactions, provides unique identification through barcodes, enables multiplexed detection of multiple targets simultaneously, and facilitates downstream sequencing analysis. This universal platform can map various protein-DNA, protein-RNA, and RNA-RNA interactions using the same core methodology, greatly increasing productivity
2Adaptability or versatility
If current methods are applied to rare cell types or patient samples, then cell-type specific genomic maps can be obtained, but the time and cost requirements make this infeasible for individual labs
Solution Approach 1:
The invention performs preliminary barcoding of particles before they are used in mapping experiments. Barcoded particles are prepared in advance and can be stored for future use, eliminating the need to perform time-consuming mapping experiments whenever new cell types need to be studied. This preliminary preparation allows rapid adaptation to study rare cell types or patient samples without repeating the entire mapping process
Solution Approach 2:
The method merges multiple mapping experiments into a single pooled experiment by combining barcoded particles from different targets and samples. Multiple cell types or conditions can be analyzed simultaneously in one experiment, dramatically reducing the total time required compared to performing separate experiments for each cell type
3Quantity of substance
If comprehensive genomic maps are generated for multiple cell types, then complete reference datasets can be created, but the labor and resource requirements exceed the capacity of individual laboratories
Solution Approach 1:
The invention uses barcoded particles as copies that can be replicated and distributed. Each barcode serves as a digital copy of the target identity, allowing information about protein-nucleic acid interactions to be copied and stored in sequence data without requiring physical replication of the entire experimental system. This reduces complexity by replacing complex physical handling with simpler information copying
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 enables efficient and cost-effective genome-wide and transcriptome-wide mapping of proteins and ncRNAs, improving cell-type accessibility and handling protein diversity, allowing for the identification of protein-nucleic acid interactions at scale without requiring specialized equipment, thus overcoming the limitations of existing methods.
Implementation Method 1
The plurality of barcoding oligonucleotides are associated with the particle via a multivalent binding agent comprising two or more binding moieties capable of binding the first ligand and/or the second ligand
Data Source
AI summary
Disclosed herein include methods, compositions, and kits suitable for use in generating barcoded detection particles. Each barcoded detection particle can comprise a particle associated with an antigen-binding protein and a plurality of barcoding oligonucleotides. The plurality of barcoding oligonucleotides can comprise a first ligand. The particle can comprise a second ligand. The plurality of barcoding oligonucleotides can be associated with the particle via a multivalent binding agent comprising two or more binding moieties capable of binding the first ligand and/or the second ligand. There are provided, in some embodiments, methods for detecting interactions between nucleic acid molecules and proteins of interest. Methods for detecting interactions between ribonucleic acid molecules and RNA-binding proteins (RBPs) are also provided herein.