Three-Dimensional Spatial Profiling with Migrating Capture Probes
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for studying spatial heterogeneity in tissues fail to provide comprehensive data on the position of single cells within a biological sample, relying on pre-defined markers that introduce selection bias and are costly and laborious.
Innovation Solution
A method involving spatially-programmed capture probes with programmable migration domains, detectable moieties, and capture domains is used to determine the three-dimensional location of nucleic acids in a biological sample by immobilizing the sample in a hydrogel matrix, permeabilizing it, and migrating the probes to bind specifically to nucleic acids, allowing for sequencing and imaging to identify their location.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If pre-defined markers are used to study spatial heterogeneity, then the analysis can be performed with existing methods, but selection bias is introduced and the process becomes costly and laborious
Solution Approach 1:
The patent extracts and removes the limitation of pre-defined markers by using unbiased, genome-wide nucleic acid capture. Instead of being constrained to specific pre-selected markers, the method captures all nucleic acids in the tissue section, eliminating selection bias while maintaining spatial information through the hydrogel matrix embedding and spatial barcode assignment.
Solution Approach 2:
The patent creates a universal method that can analyze any nucleic acid sequence in the tissue without requiring prior knowledge or specific marker selection. The spatially-resolved RNA sequencing approach is applicable to any gene or transcript of interest, making the method universally applicable across different research questions and tissue types.
2Quantity of substance
If single-cell data is obtained with high analyte coverage, then comprehensive gene expression data is achieved, but spatial position information is lost
Solution Approach 1:
The patent embeds tissue sections within a hydrogel matrix, creating a nested structure where the spatial context is preserved within the matrix. The tissue section maintains its three-dimensional architecture while being contained within the hydrogel, allowing subsequent nucleic acid capture and sequencing to be performed while retaining spatial position information through the embedded structure.
Solution Approach 2:
The patent adds the spatial dimension back to single-cell RNA sequencing by performing the analysis within the intact tissue section embedded in hydrogel. Instead of dissociating cells and losing spatial information, the method maintains the three-dimensional tissue architecture and assigns spatial barcodes based on the physical location within the embedded section, effectively adding spatial positioning to comprehensive gene expression data.
3Adaptability or versatility
If comprehensive nucleic acid data is captured across the genome, then unbiased discovery is enabled, but the cost and labor increase significantly
Solution Approach 1:
The patent performs preliminary actions by embedding the tissue section in hydrogel and capturing all nucleic acids in situ before sequencing. The spatial context is established and preserved through the hydrogel embedding and spatial barcode assignment during the capture process, eliminating the need for subsequent complex spatial reconstruction or multiple separate experiments, thereby reducing overall cost and labor despite comprehensive genome-wide coverage.
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
This approach provides high-resolution, unbiased data on nucleic acid distribution in three-dimensional space, retaining the native spatial context of the sample, enabling detailed analysis of gene and protein expression across multiple analytes.
Implementation Method 1
migrating the spatially-programmed capture probe into the hydrogel matrix from a point distal to the hydrogel matrix contacting the array
Implementation Method 2
migrating the spatially-programmed capture probe into the hydrogel matrix from a point distal to the hydrogel matrix contacting the array
Implementation Method 3
detecting the detectable moiety
Data Source
AI summary
This disclosure relates to compositions and methods for three-dimensional spatial profiling of analytes in a biological sample.