In Situ Transcriptomics Barcoding for Spatial Multi-Target Cell Profiling
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Solution Overview
Problem
Existing single-cell technologies struggle to accurately profile the genome, epigenome, transcriptome, or proteome of individual cells, particularly in resolving spatial gene and protein co-expression patterns and identifying responses to genetically modifying agents.
Innovation Solution
A method involving associating oligonucleotide barcodes with targets within an optically resolved cell volume, sequencing these barcodes, and demultiplexing the signals to detect multiple targets in situ, enabling identification of cells responding to genetically modifying agents.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If existing single-cell technologies are used to profile genome, epigenome, transcriptome, or proteome, then cell composition can be analyzed, but spatial gene and protein co-expression patterns cannot be accurately resolved
Solution Approach 1:
The method segments the detection process into distinct functional modules: oligonucleotide barcodes are associated with specific targets (genes, proteins), each barcode contains embedded spatial information, and multiple targets are detected through sequential or parallel sequencing cycles. This segmentation enables simultaneous preservation of spatial resolution and profiling reliability by treating spatial coordinates and molecular identity as separate but integrated data dimensions.
2Measurement precision
If multiple targets are detected within an optically resolved volume, then spatial co-expression patterns can be resolved, but the complexity of sequencing and demultiplexing signals increases
Solution Approach 1:
Oligonucleotide barcodes serve as intermediary molecules that bridge the gap between target molecules (genes, proteins) and detection systems. Each barcode contains encoded spatial coordinates and target identity information, allowing multiple targets to be detected simultaneously without direct optical interference. The barcodes act as mediators that translate complex spatial-molecular information into sequencable nucleotide sequences, simplifying the demultiplexing process through computational biology rather than complex optical hardware.
3Measurement precision
If oligonucleotide barcodes are associated with each target, then precise detection of multiple targets is enabled, but the quantity of sequencing data and processing requirements increase
Solution Approach 1:
The oligonucleotide barcode design implements universality by creating a multi-functional detection system. Each barcode simultaneously encodes: (1) target identity, (2) spatial coordinates (x, y, z positions), (3) expression quantification information, and (4) enables cross-validation between different molecular layers (genome, transcriptome, proteome). This multi-functionality reduces the total data volume needed compared to separate detection methods for each parameter, as a single barcode sequence provides integrated information that would otherwise require multiple separate measurements.
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 precise detection and quantification of multiple targets within a cell, facilitating understanding of cellular processes and disease spread, such as cancer, through spatial gene and protein co-expression analysis.
Implementation Method 1
associating a different oligonucleotide barcode from a known set of barcodes with each of the plurality of targets
Data Source
AI summary
Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.