3D Spatial Transcriptomics via Probe Migration
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Solution Overview
Problem
Current methods for determining and quantifying the relative locations of specific cellular analytes, including RNAs, within a three-dimensional space are limited and require improvement for accurate analysis.
Innovation Solution
A method involving the migration of spatial probes in three dimensions, where each probe has a targeting domain and a migration barcode sequence, allowing for the identification of target molecules' locations through sequencing analysis, enabling precise three-dimensional analysis of biological samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If microscopy-based technologies are used to determine locations of specific RNAs within a multidimensional space, then spatial information can be obtained, but the measurement precision and quantitative accuracy are limited
Solution Approach 1:
The patent replaces microscopy-based detection with a sequencing-based detection system. Instead of using optical microscopes to visualize and determine RNA locations, the invention uses nucleic acid probes with barcode sequences that are captured and sequenced. This substitution of mechanical/optical detection with biochemical sequencing enables high-precision quantitative measurement of spatial locations while maintaining manageable system complexity through standardized molecular biology techniques.
Solution Approach 2:
The patent changes the detection parameter from optical signal intensity (microscopy) to nucleic acid sequence information (sequencing). By encoding spatial location information in the sequence of barcode regions of captured probes, the system achieves higher measurement precision and quantitative accuracy. The sequencing technology provides digital, countable data that enables precise determination of RNA locations and abundances in three-dimensional space.
2Loss of information
If spatial probes with migration domains are used to achieve three-dimensional separation, then location information is obtained, but the device complexity increases
Solution Approach 1:
The patent segments the spatial probe into distinct functional domains: a targeting domain for specific RNA binding, a migration domain for three-dimensional separation, and a barcode sequence for identification. This segmentation allows each component to perform its specific function efficiently. The migration domain can be selectively cleaved after separation, simplifying the final detection step while preserving the spatial information encoded during the migration process.
Solution Approach 2:
The migration domain acts as an intermediary that temporarily holds spatial information during the separation process. It mediates between the targeting function (binding to RNA) and the detection function (barcode sequencing). After the migration domain fulfills its separation function, it can be cleaved away, leaving only the essential barcode sequence for detection. This intermediary approach enables complex three-dimensional separation without permanently complicating the probe structure.
3Measurement precision
If three populations of spatial probes are migrated in three dimensions, then high-density spatial mapping is achieved, but the loss of time increases
Solution Approach 1:
The patent performs preliminary separation of spatial probes in three dimensions before the actual detection step. By pre-establishing the three-dimensional spatial arrangement through controlled migration of probes with different migration domains, the system prepares the sample in advance. This preliminary action organizes the spatial information in a readable format, allowing rapid subsequent sequencing and analysis. The time-consuming separation step is completed beforehand, enabling faster final measurement and reducing the critical analysis time.
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 method provides a high-density, quantitative three-dimensional map of analyte distribution, enhancing the accuracy and precision of spatial transcriptomics by identifying target molecules' locations within biological samples.
Implementation Method 1
migrating a first population of spatial probes into the biological sample
Data Source
AI summary
In some embodiments described herein are methods for three-dimensional analysis of a biological sample, comprising migrating a population of spatial probes into the biological sample in each of three dimensions, wherein each spatial probe comprises a targeting domain and a migration domain. Also provided are kits and compositions for use according to any of the methods described herein.