Flow-Based Oligonucleotide Encoding for Spatial Single-Cell Multi-Omics
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Solution Overview
Problem
Current biological sample processing systems for spatial multi-omics face inefficiencies and resource wastage, particularly in single-cell analysis, which lack high throughput and fail to provide detailed spatial organization and interactions between cells.
Innovation Solution
The use of oligonucleotides with flow-based encoding schemes, allowing for multiplexed measurements by generating unique flowgrams through flow-based sequencing, combined with primer binding sites and target-related domains, to analyze multiple targets simultaneously.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If bulk assays are used to detect DNA, RNA, and proteins, then throughput is improved, but spatial organization and single-cell resolution are lost
Solution Approach 1:
The invention segments the tissue sample into individual cell units by capturing single cells on wells of a substrate. Each well contains capture oligonucleotides that specifically bind to mRNA from a single cell, physically separating cells while maintaining spatial context. This segmentation enables simultaneous analysis of multiple cells (high throughput) while preserving individual cell identity and spatial information.
Solution Approach 2:
The invention introduces capture oligonucleotides as intermediary molecules that bridge the gap between bulk detection and single-cell analysis. These oligonucleotides are attached to the substrate and serve as mediators to capture and isolate mRNA from individual cells. The capture oligonucleotides enable selective binding of cell-specific mRNA, allowing throughput processing while maintaining single-cell resolution through the intermediary capture step.
2Measurement precision
If single-cell analysis techniques are used, then spatial organization is preserved, but throughput and efficiency decrease
Solution Approach 1:
The invention merges the advantages of single-cell analysis with high-throughput processing by combining multiple single-cell capture events on a single substrate. Multiple wells on the substrate each capture a single cell, allowing parallel processing of many cells simultaneously. This merging approach maintains spatial organization at the single-cell level while achieving bulk-level throughput by processing numerous cells in parallel on the same platform.
Solution Approach 2:
The invention transitions from analyzing cells in a single dimension (one cell at a time) to analyzing cells across multiple spatial dimensions simultaneously. The substrate provides a two-dimensional array of wells, each capable of capturing and analyzing a single cell. This dimensional expansion allows throughput processing by distributing single-cell analysis across many spatial locations on the substrate, effectively parallelizing the analysis across the third dimension of time through simultaneous processing.
3Adaptability or versatility
If flow-based encoding with multiple oligonucleotides is used, then multiplexing capability is improved, but sequence determination complexity increases
Solution Approach 1:
The invention applies preliminary action by pre-encoding oligonucleotides with flow-based codes before the actual analysis. Each oligonucleotide is assigned a unique flow-based sequence pattern that can be rapidly read during sequencing. This preliminary encoding step simplifies the overall process because the identity of each oligonucleotide is already determined by its flow pattern, eliminating the need for complex de novo sequence determination during the analysis phase and enabling straightforward multiplexing.
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
Enhances the efficiency and throughput of spatial multi-omics by enabling high-resolution, multiplexed analysis of RNA, proteins, and genomic DNA, providing detailed spatial information on cell phenotypes and interactions.
Implementation Method 1
oligonucleotide hybridization to an RNA transcript
Data Source
AI summary
Despite the advance of screening technology, omic-based studies with spatial resolution still requires laborious efforts, hampering the analysis of biology and disease. The present disclosure provides methods, systems, probes, and platforms that may be based on the use of flow-based sequencing to increase the throughput of analyte screening with spatial resolution.