Single-Cell Barcode Probes for Multi-Omic Tissue Profiling
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Solution Overview
Problem
Existing methods for analyzing DNA, RNA, and protein molecules at single-cell resolution are limited in their ability to provide comprehensive multiplexing and require improved techniques for barcoding and kits to facilitate high-throughput analysis of cellular heterogeneity and tissue composition.
Innovation Solution
The use of cell barcode probes (CBPs) with a common genome binding element and unique cell barcode for barcoding macromolecules, allowing multiple analytes from each single cell to be barcoded in a single assay, enabling comprehensive profiling of tissues and cells through methods such as single cell multi-omic analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If traditional single cell analysis methods (FISH, flow cytometry, qPCR) are used, then single cell resolution is achieved, but comprehensive multiplexing of DNA, RNA and protein molecules is limited
Solution Approach 1:
The cell barcode probe is designed as a universal tool that can simultaneously detect multiple types of macromolecules (DNA, RNA, and proteins) through a single assay system. The probe contains both a genome binding element for DNA anchoring and barcode sequences that can be read to identify cell origin, enabling one reagent to perform multiple detection functions across different molecular types.
Solution Approach 2:
The invention merges the barcoding function with the genome binding function into a single integrated probe molecule. By combining the genome binding element and cell-specific barcode in one probe structure, the system eliminates the need for separate barcoding and detection steps, achieving comprehensive multiplexing through a unified assay platform.
2Productivity
If high throughput analysis is implemented, then productivity increases, but measurement precision and single cell resolution may be compromised
Solution Approach 1:
The cell barcode probe acts as an intermediary that bridges the gap between high throughput processing and single cell precision. By anchoring barcodes to the genome at specific locations, the probe creates a stable link that maintains single cell identification accuracy even when processing many cells simultaneously through automated workflows.
Solution Approach 2:
The barcoding is performed preliminarily by anchoring cell-specific barcodes to the genome before the actual analysis. This preliminary action establishes permanent cellular identifiers that persist through subsequent high-throughput processing steps, ensuring that single cell resolution is maintained throughout the entire workflow.
3Device complexity
If multiple analytes are barcoded in a single assay, then device complexity is reduced, but the difficulty of detecting and measuring increases
Solution Approach 1:
The detection system is segmented into distinct functional components: the genome binding element for DNA anchoring, the cell barcode sequences for identification, and the readout mechanisms for different analyte types. This segmentation allows each component to be optimized independently while working together to detect multiple omics layers through a unified interface.
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-throughput analysis of DNA, RNA, and protein molecules at single-cell resolution, facilitating the characterization of cellular heterogeneity, profiling of tissue composition, and discovery of new cell subtypes, particularly in adherent cells from fluid biopsies, providing diagnostic and prognostic information on tumor development and progression.
Implementation Method 1
the genome binding element hybridizes to a region in the genomic DNA, thereby forming a nucleic acid duplex between the genome binding element and the region of the genomic DNA
Data Source
AI summary
The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.