Cell Barcode Probes for Single-Cell Multi-Omic Multiplexing
Find Innovative SolutionsGenerate Solutions
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 multiplexing these molecules, especially in the context of heterogeneous cell populations.
Innovation Solution
A method involving cell barcode probes (CBPs) with a common genome binding element and a cell barcode is used to barcode macromolecules in individual cells, allowing for multiplexing DNA, RNA, and protein molecules, which includes permeabilizing cells, binding CBPs to genomic DNA, amplifying cell barcodes, and attaching them to macromolecules for high-throughput analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional single cell analysis methods (fluorescent in situ hybridization, 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 serves multiple functions simultaneously: it binds to genomic DNA via the genome binding element for cell identification, and the attached cell barcode can be used to tag and identify all macromolecules (DNA, RNA, protein) from that specific cell across multiple omic analyses, making a single probe design universal for multi-omic applications
Solution Approach 2:
The invention merges previously separate single-cell analysis workflows for genomics, transcriptomics, and proteomics into a unified approach by using a common cell barcode probe system that can identify and tag all three types of macromolecules from the same cell, enabling comprehensive multi-omic analysis
2Measurement precision
If cell barcode probes with common genome binding element are used to bind to genomic DNA, then cell-specific barcoding is achieved, but the complexity of the protocol increases
Solution Approach 1:
The cell barcode probe is designed with a pre-attached cell barcode and genome binding element before the experiment begins. The probe is delivered to cells and binds to genomic DNA in advance of the actual multi-omic analysis, performing the cell identification step preliminarily so that subsequent analyses can directly use the pre-established cell barcode for tagging macromolecules
Solution Approach 2:
The cell barcode probe acts as an intermediary that bridges cell identification and macromolecule tagging. It contains a genome binding element that mediates specific binding to cellular DNA, while simultaneously carrying a cell barcode that can be transferred to or associated with macromolecules, thus mediating between the cell and its molecular contents
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 comprehensive single-cell multi-omic analysis, including genomic, transcriptomic, and proteomic analysis, allowing for the characterization of cellular heterogeneity and discovery of new cell subtypes, particularly in adherent cells from fluid biopsies, with improved diagnostic and prognostic information on cancer 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.