Spatial Transcriptomics Barcoding for 2 μm Tissue Profiling
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Solution Overview
Problem
Existing spatial transcriptomics technologies struggle to provide detailed understanding of molecular dynamics in complex tissues like the central nervous system due to limitations in spatial resolution and the risk of cell manipulation biases, failing to correlate single-cell expression with morphological entities effectively.
Innovation Solution
A method involving high-density spatial transcriptomics using spatially barcoded reverse transcription oligonucleotides deposited on a substrate, allowing for 2 μm resolution RNA-sequencing with over a million barcodes, capturing mRNA at precise locations and linking it with spatial barcodes for comprehensive tissue profiling.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If spatially barcoded oligonucleotides are deposited into 100 μm features on a glass slide, then transcriptome measurements can be obtained, but the spatial resolution is insufficient to capture detailed tissue dynamics in complex tissues
Solution Approach 1:
The invention segments the continuous tissue space into discrete 2 μm resolution bins, allowing high-density spatial transcriptomics measurements to be assigned to specific morphological features. This segmentation enables capture of detailed tissue dynamics by dividing the tissue into many small, manageable spatial units that can be individually characterized.
Solution Approach 2:
The invention applies local quality by correlating gene expression profiles with specific local morphological features (such as cell bodies, dendrites, axons) rather than treating the tissue as uniform. This allows different regions to be characterized by their unique morphological properties and associated transcriptomic signatures.
2Productivity
If cells are dissociated for single-cell transcriptomics analysis, then high throughput molecular profiling is achieved, but cell manipulation biases alter the molecular state
Solution Approach 1:
The invention uses self-service by allowing intact cells to remain in situ within the tissue architecture and perform their natural functions while being measured. The cells are not manipulated or dissociated, so they maintain their native molecular states and physiological behaviors, providing unbiased transcriptomic data.
Solution Approach 2:
The invention introduces spatial barcodes as intermediaries that link morphological features to transcriptome measurements without requiring cell manipulation. These barcodes serve as mediators that enable correlation of gene expression with spatial position and morphological identity while cells remain undisturbed in their native environment.
3Measurement precision
If 2 μm resolution spatial transcriptomics is implemented with over a million barcodes, then detailed 2D transcriptome profiling is achieved, but the device complexity increases
Solution Approach 1:
The invention uses copying by creating digital representations (barcodes) of spatial positions rather than requiring complex physical structures at each location. The barcodes are sequence information that can be read and decoded computationally, simplifying the physical device while maintaining high spatial resolution through information encoding.
Solution Approach 2:
The invention replaces complex mechanical positioning systems with a biochemical coding system. Instead of using precise mechanical mechanisms to position probes at 2 μm resolution, the system uses spatially barcoded oligonucleotides whose positions are encoded in their sequence information, allowing computational rather than mechanical determination of spatial coordinates.
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 detailed 2D transcriptome profiling and differential expression analysis, identifying tissue dynamics with high accuracy and resolving cell types based on their spatial and temporal positions, enhancing understanding of complex tissue structures.
Implementation Method 1
capturing material from one or more cells of the plurality of cells with the capture molecule of the spatial barcode, thereby linking the capture material from the one or more cells with the spatial barcode
Data Source
AI summary
The present disclosure relates to systems and method of in-situ tissue profiling. Methods for spatiotemporal processing of a sample, capturing molecules of interest, and correlating cells in the sample to the capture molecules are provided.