Spatial Barcoding of Cellular Analytes Before Sequencing
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Solution Overview
Problem
Existing sequencing technologies for genomic, transcriptomic, and proteomic profiling of biological samples do not provide spatial information about analytes, limiting the understanding of cell identity and disease treatment development.
Innovation Solution
A method involving probes with barcodes is used to generate a composite barcode in cells, detect these barcodes in situ, and perform single cell barcoding to determine spatial locations of analytes, followed by sequencing to locate the analytes in a biological sample.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If whole genome amplification and sequencing technologies are used, then genomic, transcriptomic, and proteomic profiling is achieved, but spatial information of analytes is lost
Solution Approach 1:
The method segments the profiling process into two distinct phases: (1) in situ barcoding where spatial information is captured by assigning unique barcodes to analytes at their original locations, and (2) dissociation and sequencing where cells are separated for high-throughput analysis. This segmentation allows both spatial information preservation and comprehensive profiling to be achieved in their respective optimal conditions.
Solution Approach 2:
The patent applies preliminary action by performing barcoding of analytes with spatial identifiers before cell dissociation. The barcodes are attached to analytes while they remain in their native spatial context, ensuring that location information is captured prior to any disruption of tissue architecture.
2Loss of information
If barcodes are detected in situ before dissociation, then spatial information is preserved, but detection complexity increases
Solution Approach 1:
The patent introduces barcodes as intermediary molecules that serve as mediators between the analytes and the detection system. These barcodes can be detected through various modalities (fluorescence, sequencing, etc.) and serve as a bridge that preserves spatial information while enabling subsequent high-throughput analysis after dissociation.
Solution Approach 2:
The method replaces direct mechanical or optical detection of analyte locations with a molecular coding system. Instead of directly measuring spatial positions, the system uses barcode sequences that encode location information, which can then be read through standard molecular biology techniques like sequencing.
3Measurement precision
If multiple probes with different barcodes are used, then analyte identification improves, but probe complexity increases
Solution Approach 1:
The patent employs universal probe designs where probes share common structural elements (such as RNA polymerase binding sites, promoter sequences, or hybridization regions) while varying only the barcode portions. This universality allows a single set of enzymatic reactions and processing protocols to handle multiple different analytes, reducing overall system complexity despite the diversity of targets.
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
Preserves spatial information of analytes, allowing for accurate correlation of sequencing results with their locations, enhancing the understanding of cell identity and disease treatment strategies.
Implementation Method 1
contacting a plurality of cells in the biological sample with a plurality of probes to generate a composite barcode in a cell of the plurality of cells, wherein the probes of the plurality of probes comprise a target binding sequence and a barcode sequence
Data Source
AI summary
The present disclosure relates in some aspects to methods, compositions, and kits of processing or analyzing a sample. A method for processing a sample may comprise providing probes with barcodes to generate a composite barcode, detecting the barcodes to determine a spatial location and hybridizing probes to analytes (e.g., an RNA molecule) and performing sequencing.