Pathogen Inactivation for Multiplex Spatial Transcriptomics
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Solution Overview
Problem
Existing methods for detecting analytes in pathogen-comprising samples require DNA or RNA preparation, which limits analysis to high-safety level labs, and are inefficient in multiplex detection.
Innovation Solution
A method that inactivates pathogens within the sample without isolating RNA or DNA, allowing for multiplex spatial transcriptomics analysis outside high-safety level labs, using at least 20 different sets of analyte-specific probes and decoding oligonucleotides for sequential signal-encoding.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If DNA or RNA isolation is performed for spatial transcriptomics analysis, then analysis can be conducted, but the analysis must be performed in high-safety level labs and requires complex preparation steps
Solution Approach 1:
The patent extracts and removes the pathogen from the sample through inactivation and removal steps, separating the pathogen removal function from the analyte detection function. This allows the analyte analysis to proceed without requiring high-safety level laboratory infrastructure, as the pathogen is eliminated before analysis begins
Solution Approach 2:
The patent performs pathogen inactivation and removal as preliminary actions before spatial transcriptomics analysis. By inactivating and removing pathogens in advance (before the main analysis), the sample is prepared in a way that eliminates safety concerns while preserving analyte integrity for subsequent detection
2Productivity
If multiple analytes are detected using traditional methods, then detection is possible, but the process requires multiple separate assays and is time-consuming
Solution Approach 1:
The patent merges multiple analyte detection capabilities into a single spatial transcriptomics assay. By using probe sets with unique identifier sequences that can be detected through the same imaging and analysis pipeline, multiple analytes are detected simultaneously in one experiment rather than requiring separate assays for each analyte
Solution Approach 2:
The patent creates a universal detection platform where a single spatial transcriptomics workflow can detect multiple different analytes. The probe design system allows any number of analytes to be targeted using the same basic detection methodology, making the system multi-functional and highly productive
3Adaptability or versatility
If directly labeled probe sets are used for sequential hybridization, then detection rounds can be performed, but the probe sets must be denatured after every detection round requiring multiple differently tagged probe sets
Solution Approach 1:
The patent introduces an intermediary system using unique identifier sequences on probes that do not require fluorescent labels. These identifier sequences serve as mediators that can be detected through hybridization with decoding oligonucleotides, eliminating the need to denature and re-tag probes between detection rounds. The identifier sequence acts as a stable intermediary that preserves analyte information through multiple detection cycles
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 efficient and flexible detection of multiple analytes in parallel, reducing the need for complex probe sets and signal oligonucleotides, while allowing analysis in lower-safety level labs.
Implementation Method 1
each set of analyte-specific probes specifically hybridizing to a different analyte
Implementation Method 2
contacting the sample with at least one set of decoding oligonucleotides per analyte, wherein in each set of decoding oligonucleotides for an individual analyte each decoding oligonucleotide comprises: (aa) an identifier connector element (t) comprising a nucleotide sequence which is essentially complementary to at least a section of the unique identifier sequence of the identifier element (T)
Implementation Method 3
contacting the sample with at least a set of signal oligonucleotides, each signal oligonucleotide comprising: (aa) a translator connector element (C) comprising a nucleotide sequence which is essentially complementary to at least a section of the nucleotide sequence of a translator element (c) comprised in a decoding oligonucleotide
Data Source
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Figure 3
Figure 3
AI summary
The present disclosure pertains to novel multiplex methods and kits for detecting different analytes in a sample in parallel by sequential signal-encoding of said analytes. In particular, the present disclosure pertains to a method that results in inactivation of pathogens for in-situ spatial transcriptomics (e.g. Molecular Cartography) without the step DNA or RNA preparation prior to analysis.