Photo-Reactive DNA Barcodes for Tissue Spatial Omics
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Solution Overview
Problem
Existing imaging-based analysis and high-throughput screening methods fail to capture comprehensive spatial information, including morphological, genomic, and proteomic data at cellular and subcellular levels, leading to loss of critical cell or subcellular location-specific information.
Innovation Solution
A method involving the use of DNA barcodes with photo-reactive nucleobases to form covalently linked complexes with amplification products, followed by selective radiation and washing steps, allowing for repeated deposition and radiation at varying sequences and locations to generate spatial information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If imaging-based analysis and high-throughput screening are used to select information from tissue samples, then spatial selection capability is improved, but comprehensive capture of spatial information including morphological, genomic, and proteomic data is lost
Solution Approach 1:
The method segments the complex task of capturing multiple types of spatial information into distinct modular steps: (1) imaging-based spatial selection, (2) nucleic acid amplification at selected locations, (3) barcode deposition, (4) crosslinking, and (5) sequencing. Each step handles a specific aspect of information capture, allowing comprehensive data collection without overwhelming system complexity.
Solution Approach 2:
The patent introduces DNA barcodes as intermediary molecules that bridge the gap between spatial information (captured by imaging) and molecular information (genomic/transcriptomic data). The barcodes serve as mediators that can be deposited at specific spatial locations, crosslinked to amplification products, and later sequenced to recover both spatial and molecular information simultaneously.
2Loss of information
If multiple channels of spatial information are collected at cellular and subcellular levels, then information comprehensiveness is improved, but the ability to maintain spatial relationships between features deteriorates
Solution Approach 1:
The method adds a temporal dimension to spatial information capture by using sequential barcode deposition at different locations. By depositing barcodes at multiple discrete locations in sequence and using photo-reactive nucleobases for location-specific crosslinking, the system preserves spatial relationships across multiple dimensions (x, y, z coordinates) while collecting comprehensive molecular information.
Solution Approach 2:
The patent applies local quality by using photo-reactive nucleobases that can be selectively activated at specific spatial locations within the tissue sample. This allows different regions of the sample to have different barcode sequences deposited and crosslinked, preserving the unique spatial identity of each location while enabling comprehensive molecular analysis.
3Reliability
If DNA barcodes with photo-reactive nucleobases are used to form covalently linked complexes, then spatial information preservation is improved, but the number of processing steps increases
Solution Approach 1:
The method uses periodic action by cycling through sequences of barcode deposition, irradiation for crosslinking, and washing steps. This periodic cycle allows multiple different barcode sequences to be deposited at different locations and crosslinked in sequence, preserving spatial information while enabling comprehensive molecular profiling through repeated application of the same reliable crosslinking mechanism.
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 the collection of multi-dimensional cellular and subcellular data, linking morphological and spatial information with transcriptomic, genomic, or proteomic profiles, applicable to diverse sample types, including tissues and cells.
Implementation Method 1
the DNA barcodes comprise a photo-reactive nucleobase capable of crosslinking to another nucleobase; selectively radiating the population of cells to form covalently linked DNA barcode-amplification product complexes
Data Source
AI summary
Provided herein are compositions, kits, and methods for collection, integration, and analysis of spatially based information from tissues at the cellular or subcellular level. Layers of information include, without limitation, gene expression, morphology, nucleic acids, and proteins. In some workflows, light-based technologies are incorporated for selective spatial barcoding of regions. In further steps, such barcoded tags are optionally analyzed by high throughput Next Generation Sequencing.