Spatially Encoded Biological Assays for High-Multiplex Tissue Mapping
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Solution Overview
Problem
Existing methods fail to provide high-resolution, simultaneous analysis of spatial expression patterns of large numbers of genes, proteins, or other biologically active molecules in tissues, lacking reproducibility and scalability.
Innovation Solution
An assay system with spatially encoded probes delivered in defined patterns, allowing interaction with biological targets, followed by separation and sequencing to determine target abundance or activity at multiple sites, utilizing instrumentation for controlled reagent delivery and digital readout.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If conventional methods like in situ hybridization or microarrays are used, then spatial information can be obtained, but the number of genes or molecules that can be analyzed simultaneously is limited
Solution Approach 1:
The assay system segments the analysis by using multiple independent assay regions on a single substrate, where each region can independently analyze different genes or molecules. This segmentation allows simultaneous analysis of many targets without requiring a single complex assay design, thereby increasing the quantity of substances analyzed while managing system complexity through modular organization
Solution Approach 2:
The assay system employs universal reagents and detection methods that can be applied across multiple assay regions and different target molecules. By using universal probes, enzymes, and detection protocols that work across diverse targets, the system achieves high multiplexing capability without proportionally increasing operational complexity, resolving the contradiction between analyzing many genes simultaneously and maintaining manageable system complexity
2Measurement precision
If laser capture microdissection is used to analyze genes at specific locations, then spatial resolution is improved, but the method becomes expensive and laborious
Solution Approach 1:
The assay system maintains spatial information intrinsically through the spatial arrangement of assay regions on the substrate, eliminating the need for complex physical manipulation or capture steps. The spatial pattern is self-preserving throughout the assay process, allowing high spatial resolution to be achieved without the laborious and expensive laser capture microdissection steps
Solution Approach 2:
The invention replaces mechanical physical manipulation methods like laser capture microdissection with a chemical/biochemical assay system that preserves spatial information through fixed assay regions. Instead of physically cutting and transferring tissue, the system uses spatially patterned probes and reactions that occur in situ, substituting complex mechanical operations with simpler biochemical processes that achieve the same spatial resolution goal
3Stability of the object's composition
If physical transference of tissue into wells is used to preserve spatial information, then spatial patterns are maintained, but spatial resolution decreases and random access is prevented
Solution Approach 1:
The assay system transitions from three-dimensional tissue manipulation to a two-dimensional planar substrate where spatial information is encoded in the x-y positioning of assay regions. This dimensional reduction allows precise spatial addressing and random access to any location on the substrate without the physical constraints of well-based systems, maintaining spatial information while improving resolution and accessibility
Solution Approach 2:
The invention changes the physical parameters of the assay system by using a solid substrate with fixed spatial coordinates rather than removable wells. This parameter change enables direct spatial addressing and random access to any location on the substrate, improving both spatial resolution and operational flexibility while maintaining spatial information through the fixed spatial arrangement of assay regions
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 high-resolution, multiplexed analysis of biological targets across multiple sites, providing spatial maps with high-throughput digital sequencing, enabling detailed cellular function and regulation analysis.
Implementation Method 1
a) providing a sample affixed to a support; b) delivering encoded oligonucleotide probes for multiple nucleic acid targets to the multiple sites in the sample in a known spatial pattern
Data Source
AI summary
The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.