Single-Cell Multi-Omics Co-Encapsulation for RNA-DNA Linkage
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Solution Overview
Problem
Existing technologies face challenges in scaling parallel analysis of RNA and DNA from the same cell, integrating high-content live-cell imaging, and simultaneously profiling RNA, DNA, and proteins with single-cell resolution, particularly in cancer research where therapeutic challenges arise from genetic and phenotypic heterogeneity.
Innovation Solution
A microfluidic device co-encapsulates individual cells with two barcoded beads, one for mRNA capture and the other for genomic DNA, using photocleavable linkers to release barcodes, enabling scalable linkage of scRNA-seq and scDNA-seq, and integrating live-cell imaging.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If scRNA-seq is used for scalable mutation detection, then scalability is improved, but the ability to resolve copy number alterations and detect lowly expressed genes deteriorates
Solution Approach 1:
The invention separates DNA and RNA analysis into distinct bead types (DNA barcoding beads and RNA capture beads) that are co-encapsulated with individual cells in microwells. This segmentation allows each bead type to be optimized for its specific nucleic acid while maintaining single-cell resolution and scalability through parallel processing.
Solution Approach 2:
The invention uses microwell arrays as an intermediary platform that enables simultaneous co-encapsulation of cells with both DNA and RNA barcoding beads. This intermediary system allows parallel processing of multiple nucleic acid types from the same cell while maintaining scalability through automated fluid handling and imaging.
2Measurement precision
If multiple nucleic acid types are analyzed from the same cell, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The microwell array system serves multiple functions: it co-encapsulates cells with different bead types, performs lysis, enables barcode release through photocleavage, and facilitates imaging. This multi-functionality reduces the need for separate systems for each analysis type while maintaining single-cell resolution.
Solution Approach 2:
The invention merges DNA barcoding and RNA capture functionalities into a single microwell system where both bead types co-exist with individual cells. This combining approach enables simultaneous multi-omic analysis from the same cell while using a unified platform rather than separate systems.
3Ease of manufacture
If barcoded beads are randomly deposited in microwells, then ease of manufacture is improved, but measurement precision deteriorates due to inability to link scRNA-seq with live cell imaging
Solution Approach 1:
The invention uses optical barcodes (fluorescent signals) on the beads that can be read by sequential fluorescence hybridization in the device on a fluorescence microscope. This optical encoding system enables precise identification and linkage of cell identity without affecting the random deposition manufacturing process.
Solution Approach 2:
The invention uses optical barcodes as a copyable identifier system that can be read optically without physically moving or repositioning the beads. This allows the cell identity information to be copied and linked to imaging data while maintaining the simplicity of random bead deposition during manufacturing.
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 simultaneous, scalable genome-wide analysis of RNA and DNA from thousands of individual cells, linking phenotypic and genotypic data for improved cancer research and therapeutic strategies.
Implementation Method 1
using photocleavable linkers to release barcodes
Data Source
AI summary
Single-cell multi-omics by co-encapsulating a single cell with two beads, the first an RNA barcoding bead having barcoded mRNA capture primer oligonucleotides attached on the bead surface; and the second a DNA barcoding bead having two types of oligonucleotides releasably attached to the surface: (1) barcoded adapter oligonucleotides that are complementary to oligonucleotides bound to the transposase that are eventually incorporated into gDNA fragments and (2) polyadenylated barcoded oligonucleotides containing the same barcode sequence as the adapters. In addition, integrated analysis of RNA and protein, including intracellular protein, from individual cells using similar co-encapsulation of a single cell, an RNA barcoding bead, and with/without a specific or non-specific protein binding bead in a microwell, to avoid protein fixation by first lysing the cell to liberate intracellular contents, and then capturing protein either on a solid surface or in solution with barcoded affinity reagents.