Therapeutic Agent Detection Probes for 3D Cellular Localization
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for detecting therapeutic agents like siRNA and microRNA face challenges in delivery verification, off-target knockdowns, and localization to specific tissues or cells, with bulk RNA sequencing losing small effects in noise and RNA-FISH having low multiplexity and requiring long probes.
Innovation Solution
A method using detection probes to identify anti-sense nucleic acid molecules and target molecules in a three-dimensional biological matrix, generating signals to determine their relative positions and levels, enabling precise localization and co-localization within cells.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If bulk RNA sequencing is used to determine global transcriptional changes, then comprehensive gene expression data is obtained, but small effects are lost in noise and localization to specific tissues or cell-types is impossible
Solution Approach 1:
The patent segments the biological sample into individual cells or spatial locations, transitioning from bulk homogenized analysis to cell-by-cell or location-by-location analysis. This segmentation enables detection of small transcriptional effects in specific cell types while maintaining comprehensive gene expression coverage across the entire sample.
Solution Approach 2:
The patent adds a spatial dimension to gene expression analysis by maintaining the spatial architecture of the tissue sample during sequencing. This allows simultaneous获得 comprehensive gene expression data and precise spatial localization, resolving the contradiction between quantity of data and measurement precision.
2Measurement precision
If RNA-FISH is used to localize transcriptional changes to specific cells, then spatial resolution is improved, but multiplexity is limited and long probes are required
Solution Approach 1:
The patent employs universal sequencing technologies that can simultaneously detect multiple gene targets (high multiplexity) while maintaining spatial resolution. This replaces the limited multiplexity of traditional RNA-FISH with a platform that can analyze hundreds or thousands of genes across multiple cell types in parallel.
Solution Approach 2:
The patent changes the probe length parameter from long probes (250-1,500 bases) required by RNA-FISH to short probes suitable for next-generation sequencing. This parameter change enables detection of small therapeutic molecules (20-50 bases) while maintaining spatial localization capability through the sequencing platform.
3Measurement precision
If RNA-FISH is used to detect transcriptional changes, then localization is achieved, but small therapeutic molecules (20-50 bases) cannot be directly detected due to requirement for long probes
Solution Approach 1:
The patent changes the probe length parameter from long probes (250-1,500 bases) to short probes that can directly hybridize to small therapeutic molecules (20-50 bases). This parameter change enables the detection and localization of small RNA therapeutics while maintaining the spatial resolution advantage of FISH-based methods.
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
Provides precise localization and co-localization of therapeutic agents within cells, overcoming limitations of bulk RNA sequencing and RNA-FISH, allowing for deeper insight into cellular effects and therapeutic efficacy.
Implementation Method 1
using detection probes separate from the anti-sense nucleic acid molecule and the target molecule to detect a first set of signals and a second set of signals from the biological sample
Data Source
AI summary
The present disclosure provides methods and systems for analyzing agents (e.g., therapeutic agents) in a biological sample having a three-dimensional matrix.