Single-Cell Spatial Transcriptomics via Stimulated Linker Cleavage
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Solution Overview
Problem
Current methods for analyzing biological tissues fail to effectively associate position information of cells with the type and amount of constituents, such as mRNA, at a single-cell resolution, limiting detailed tissue analysis.
Innovation Solution
An analysis method involving imaging, association, cleavage, and binding steps using a surface with molecules having a linker cleavable by stimulation, a barcode sequence, and a target capture portion, allowing for the linkage of cell position information with constituent analysis via sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If spatial transcriptomics method is used with probe containing cleavage site and barcode sequence, then position information of cell can be associated with mRNA information, but the method cannot achieve single-cell resolution analysis
Solution Approach 1:
The invention divides the tissue sample into individual cell units for analysis. By using imaging to identify and isolate individual cells, then selectively cleaving linkers at specific cell positions, the method achieves single-cell resolution by segmenting the tissue analysis into discrete cellular units rather than analyzing bulk tissue together
Solution Approach 2:
The invention applies different properties to different spatial locations on the analysis surface. Each position on the surface has molecules with specific barcode sequences and linkers that are selectively cleaved based on the local cell position, enabling position-specific molecular capture and analysis at single-cell resolution
2Measurement precision
If tissue sectioning is performed to analyze cell constituents, then detailed tissue analysis can be conducted, but position information of cells is lost
Solution Approach 1:
The invention creates a positional map or copy of the tissue architecture through imaging before analysis. The imaging step captures the spatial arrangement of cells, and this positional information is stored and used to guide subsequent selective cleavage and molecular capture, preserving position information without requiring physical tissue sectioning
Solution Approach 2:
The invention performs imaging to record position information before any cleavage or molecular capture steps. By capturing the spatial arrangement of cells in advance, the method ensures that position information is preserved and can be associated with the molecular analysis results that follow
3Measurement precision
If selective stimulation is applied to cleave linker at cell position, then position-specific molecular capture is achieved, but the process complexity increases
Solution Approach 1:
The invention replaces complex mechanical positioning systems with a chemical stimulation approach. Instead of mechanically moving probes or probes to cells, the method uses selective chemical or optical stimulation to trigger linker cleavage at specific positions, simplifying the overall system architecture while maintaining position-specific capture precision
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 analysis of cell constituents at single-cell resolution, associating position information with mRNA or protein data without tissue sectioning, facilitating detailed biological tissue analysis.
Implementation Method 1
a cleavage step of selectively stimulating the position of the cell to cleave the linker of the molecule at the position
Implementation Method 2
a binding step of binding the molecule released from the surface by the cleavage with a constituent of the cell via the target capture portion of the molecule
Data Source
AI summary
An object is to provide a method capable of associating position information of a cell with a cell constituent at a single-cell resolution. That is, the present technology provides an analysis method including: an imaging step of imaging a specimen in a state in which the specimen is being overlapped with a surface to which a molecule having a linker cleavable by stimulation, a barcode sequence, and a target capture portion is immobilized via the linker; an association step of associating a position of a cell with the barcode sequence of the molecule at the position by using a specimen image obtained by the imaging; a cleavage step of selectively stimulating the position of the cell to cleave the linker of the molecule at the position; and a binding step of binding the molecule released from the surface by the cleavage with a constituent of the cell via the target capture portion of the molecule.