Spatial Barcoded Capture Probes for Exogenous Nucleic Acid Detection
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Solution Overview
Problem
Current methods fail to provide sensitive detection and characterization of exogenously delivered nucleic acids and cellular responses in complex biological samples, such as solid tissue and FFPE samples, lacking the ability to determine the spatial location and abundance of analytes like proteins, DNA, or RNA with high resolution.
Innovation Solution
The method involves hybridizing probe oligonucleotides to exogenous nucleic acids, generating connected probes, and aligning the biological sample with a substrate array containing capture probes with spatial barcodes, allowing for the release and hybridization of these probes to determine their location and abundance, utilizing RNA-templated ligation and analyte capture agents for spatial analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional detection methods are used for exogenous nucleic acids, then the detection process is simple, but the sensitivity and ability to determine spatial location and abundance are insufficient
Solution Approach 1:
The detection system is segmented into multiple functional components: probe oligonucleotides for target recognition, capture probes with spatial barcodes for location identification, and substrate arrays for organized detection. This segmentation enables high sensitivity and spatial resolution while maintaining manageable system complexity through modular design.
Solution Approach 2:
Probe oligonucleotides serve as intermediaries that hybridize to exogenous nucleic acids and connect them to capture probes. The capture probes with spatial barcodes act as mediators between the target nucleic acids and the detection system, enabling precise spatial localization and abundance determination without requiring direct complex interaction between all system components.
2Loss of information
If spatial analysis techniques are applied to intact tissue, then spatial location information is obtained, but the number of analytes that can be detected is limited to a handful
Solution Approach 1:
The substrate array is designed with universal capture probes that can detect multiple different analytes simultaneously. Each capture probe contains a spatial barcode and a capture domain, allowing the same array structure to detect various exogenous nucleic acids and cellular responses across the entire tissue section, thereby increasing the number of detectable analytes while preserving spatial information.
Solution Approach 2:
The system uses diverse probe oligonucleotide sequences with different complementarities to target specific exogenous nucleic acids. By varying the sequence parameters of the probes while maintaining the same spatial barcode structure, the system can detect multiple analyte types simultaneously without losing spatial resolution, thus increasing analyte quantity detection capability.
3Quantity of substance
If single cell analysis is performed, then significant analyte data is obtained, but the position information of cells in the original tissue is lost
Solution Approach 1:
The capture probes with spatial barcodes serve as intermediaries that link single-cell analyte data to their original spatial positions in the tissue. When probe oligonucleotides hybridize to exogenous nucleic acids in individual cells and are captured by spatially-barcoded probes on the substrate array, the spatial barcode preserves the location information while the analyte data is quantified, thus recovering both quantity and position information simultaneously.
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
This approach enables precise spatial analysis and detection of exogenous nucleic acids and cellular responses, maintaining native spatial context, and is applicable to various biological samples, including FFPE and fresh frozen tissues, enhancing the understanding of disease models and therapeutic efficacy.
Implementation Method 1
hybridizing a first exogenous probe oligonucleotide and a second exogenous probe oligonucleotide to an exogenous nucleic acid
Implementation Method 2
utilizing RNA-templated ligation
Data Source
AI summary
Provided herein are methods for capturing an exogenous probe and/or a capture handle sequence to a capture domain of a capture probe. Compositions, systems, and kits also are disclosed. In some instances, the methods include detecting an exogenous nucleic acid in a biological sample by hybridizing a first exogenous probe oligonucleotide and a second exogenous probe oligonucleotide to an exogenous nucleic acid in a biological sample on a first substrate, coupling the exogenous probe oligonucleotides, and capturing the coupled exogenous probe on a spatial array.