Spatial Nucleic Acid Capture Using Transposome-Barcoded Arrays
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Solution Overview
Problem
Existing spatial analysis methods fail to provide comprehensive data on the position of single cells within a tissue sample and require excessive experimental testing for tissue-specific permeabilization conditions, leading to resource wastage and inefficiency.
Innovation Solution
A method involving in situ reverse transcription, tagmentation, and capture of fragmented products on a spatial array, utilizing transposome complexes and capture probes with spatial barcodes to determine the location of target nucleic acids across various tissue types without the need for optimization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional spatial analysis methods are used, then tissue-specific permeabilization optimization is required, but this leads to excessive experimental testing and resource wastage
Solution Approach 1:
The patent applies universality by developing a standardized permeabilization protocol using protease XIV that works across multiple tissue types (breast, lung, liver, kidney, spleen) without requiring tissue-specific optimization. This single protocol performs the function of permeabilizing diverse tissue types uniformly, eliminating the need for separate optimization experiments for each tissue type while maintaining reliable spatial analysis results
2Measurement precision
If tissue-specific permeabilization optimization is performed, then analysis accuracy may be improved, but reagent and sequencing costs increase
Solution Approach 1:
The standardized protease XIV-based permeabilization protocol serves multiple tissue types simultaneously, reducing the total quantity of reagents needed compared to performing separate optimization experiments for each tissue type. The universal protocol eliminates redundant reagent consumption from repeated testing while maintaining detection precision across different tissues
3Reliability
If multiple permeabilization conditions are tested, then optimal conditions may be found, but the complexity of the process increases
Solution Approach 1:
The patent replaces complex tissue-specific optimization procedures with a single universal permeabilization protocol using protease XIV. This standardized approach simplifies the experimental workflow by eliminating multiple condition-testing steps while maintaining reliable spatial analysis results across diverse tissue types through the consistent application of the same protocol
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-resolution spatial analysis of target nucleic acids in biological samples, retaining native spatial context and reducing the need for tissue-specific permeabilization optimization, thereby improving efficiency and reducing experimental costs.
Implementation Method 1
hybridizing a primer to the target RNA in the biological sample
Implementation Method 2
extending the primer using the target RNA as a template to provide a cDNA hybridized to the target RNA
Implementation Method 3
contacting a transposome complex with the biological sample to insert a second adapter into the extended cDNA:RNA duplex
Implementation Method 4
hybridizing the first adapter of the 5′ cDNA molecule to a capture domain of a capture probe in an array
Data Source
AI summary
Provided herein are methods, compositions, and kits for the transposome-mediated capture of analytes on a substrate including spatially barcoded capture probes.