Cell Fate Prediction via Multi-Pathway Gene Expression Analysis
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Solution Overview
Problem
Current methods for predicting cell fate in response to stimuli and stresses are limited by their inability to simultaneously monitor multiple pathways, often requiring multiple experiments, providing incomplete information, and taking too long to detect cell responses, making them unreliable and time-consuming.
Innovation Solution
An in vitro or ex vivo method that collects a cellular sample, selects a set of known genes involved in cell signaling pathways, exposes the sample to a stressor, and performs gene expression analysis using an algorithm to calculate fold change values, predicting cell fate through autophagy, apoptosis, pyroptosis, and survival scores.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If current methods are used to predict cell fate, then cell response can be detected, but the prediction is incomplete and ambiguous because multiple pathways cannot be monitored simultaneously
Solution Approach 1:
The patent combines multiple single-pathway prediction methods into a single integrated multi-pathway prediction system. The method simultaneously monitors apoptotic, necrotic, and autophagic pathways by analyzing co-expression patterns of multiple gene sets, thereby obtaining complete cell fate prediction information without requiring separate experiments for each pathway.
Solution Approach 2:
The patent creates a universal prediction system that can determine multiple types of cell fate (apoptosis, necrosis, autophagy) using a single experimental approach. The method analyzes the co-expression of multiple gene sets to provide comprehensive predictions across different cell death pathways simultaneously, making the system multi-functional rather than pathway-specific.
2Loss of information
If multiple separate experiments are performed to monitor different pathways, then complete pathway information can be obtained, but the time required increases significantly
Solution Approach 1:
The patent merges multiple pathway monitoring experiments into a single integrated analysis. By simultaneously analyzing the co-expression patterns of gene sets associated with different pathways (apoptotic, necrotic, autophagic genes), the method obtains complete pathway information from one experiment rather than requiring separate experiments for each pathway.
Solution Approach 2:
The patent enables continuous monitoring of multiple pathways simultaneously through a unified analytical approach. The method continuously evaluates the co-expression patterns of multiple gene sets to determine cell fate predictions for different pathways in parallel, eliminating the sequential time loss associated with performing separate experiments.
3Reliability
If traditional methods are used for cell fate prediction, then some pathway information is obtained, but the results are ambiguous and require multiple experiments to clarify
Solution Approach 1:
The patent combines multiple pathway analyses into a single integrated framework that evaluates co-expression patterns across apoptotic, necrotic, and autophagic gene sets simultaneously. This merging approach provides clear, unambiguous cell fate predictions by considering the relative expression levels of multiple pathway-specific genes together, eliminating the need for multiple separate experiments to clarify ambiguous results.
Data Source
Figure 1
AI summary
Is disclosed an in vitro method for the prediction of cell fate and/or death in response to stimuli and/or stresses based on gene expression analysis on a specific set of genes and elaboration of the data obtained by means of an algorithm comprising the steps of collecting a cellular sample, selecting a set of known genes involved in cell signalling pathways, exposing to a stressor element, gene expression analysis and analysing the data by an algorithm, and its use in lab and clinical research, is disclosed.