Genomic Target Identification via Gain-in-Function Screening
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Solution Overview
Problem
Current methods for identifying druggable targets linked to disease biology are inefficient and often focus on highly expressed cellular targets, which may not be biologically relevant, and lack effective tools for investigating and manipulating cellular pathways involved in disease phenotypes.
Innovation Solution
A method called Transposon Activated Genomewide Screening (TAGS) that involves providing a population of cells phenotypically negative to a test stimulus, modifying them with a gain-in-function construct, contacting them with the stimulus, and screening for phenotypically positive cells to identify genomic targets through next-generation sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If random insertion of gain-in-function constructs is used to identify genomic targets, then biologically relevant targets can be identified, but the complexity of the screening process increases
Solution Approach 1:
The screening process is divided into distinct modules: (1) random insertion of gain-in-function constructs into the genome, (2) high-throughput sequencing to identify insertion sites, (3) phenotypic screening to identify positive cells, and (4) bioinformatics analysis to map insertions to genes. This segmentation allows each module to be optimized independently while maintaining overall system effectiveness.
Solution Approach 2:
The patent introduces several intermediary elements to manage complexity: (1) gain-in-function constructs serve as intermediaries to activate target genes, (2) high-throughput sequencing acts as an intermediary to bridge phenotypic observation and genotypic identification, and (3) computational pipelines serve as intermediaries to process raw sequencing data into actionable target lists.
2Ease of operation
If traditional gene knock-out methods are used for screening, then the process is simpler to perform, but the ability to identify biologically relevant druggable targets is limited
Solution Approach 1:
Instead of using gene knock-out methods (removing function) as in traditional screening, the patent employs gain-in-function constructs that randomly activate gene expression. This inversion of the traditional approach allows identification of genes whose activation produces the desired phenotypic response, providing a more reliable indication of biologically relevant targets while maintaining systematic screening capabilities.
3Productivity
If focus is placed on highly expressed cellular targets, then screening efficiency is improved, but biological relevance of identified targets decreases
Solution Approach 1:
The patent performs preliminary random activation of genes across the entire genome before applying selection pressure. This preliminary action ensures that all genes, regardless of their baseline expression levels, have the opportunity to be activated and tested. The subsequent phenotypic screening then identifies which of these pre-activated genes are biologically relevant, decoupling the screening efficiency from the initial expression levels of target genes.
Data Source
AI summary
The invention relates to a method of identifying a genomic target for a test stimulus that is capable of modulating a cell phenotype, comprising: a) providing a population of cells that are phenotypically negative in response to the test stimulus; b) modifying the population of cells by random insertion into the cell genome of a gain-in-function construct; c) contacting the modified cell population with the test stimulus; d) screening the exposed modified cell population to identify modified cells that are phenotypically positive in response to the test stimulus; and e) identify a gene or genes associated with said positive phenotype thereby identifying the genomic target of the test stimulus.