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A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions
Published on: May 27, 2021
Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome
Phoebe C R Parrish1, James D Thomas2, Austin M Gabel3
1Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Abstract:
CRISPR screens have accelerated the discovery of important cancer vulnerabilities. However, single-gene knockout phenotypes can be masked by redundancy among related genes. Paralogs constitute two-thirds of the human protein-coding genome, so existing methods are likely inadequate for assaying a large portion of gene function. Here, we develop paired guide RNAs for paralog genetic interaction mapping (pgPEN), a pooled CRISPR-Cas9 single- and double-knockout approach targeting more than 2,000 human paralogs. We apply pgPEN to two cell types and discover that 12% of human paralogs exhibit synthetic lethality in at least one context. We recover known synthetic lethal paralogs MEK1/MEK2, important drug targets CDK4/CDK6, and other synthetic lethal pairs including CCNL1/CCNL2. Additionally, we identify ten tumor suppressor paralog pairs whose compound loss promotes cell proliferation. These findings nominate drug targets and suggest that paralog genetic interactions could shape the landscape of positive and negative selection in cancer.
Insights
This study introduces pgPEN, a CRISPR screening method to uncover gene functions lost in cancer. It identifies over 2,000 paralogs, revealing crucial synthetic lethal interactions and potential drug targets.
Area of Science:
- Genomics
- Cancer Biology
- CRISPR Technology
Background:
- CRISPR screens identify cancer vulnerabilities, but gene redundancy masks phenotypes.
- Paralogs, comprising two-thirds of the human genome, present challenges for functional analysis.
- Existing methods are insufficient for comprehensive paralog functional screening.
Purpose of the Study:
- To develop and apply a novel CRISPR-based approach for paralog genetic interaction mapping.
- To identify synthetic lethal paralog pairs and their roles in cancer.
- To nominate new therapeutic targets based on paralog interactions.
Main Methods:
- Developed paired guide RNAs for paralog genetic interaction mapping (pgPEN).
- Utilized a pooled CRISPR-Cas9 single- and double-knockout system.
- Targeted over 2,000 human paralogs across two cell types.
Main Results:
- Discovered that 12% of human paralogs exhibit synthetic lethality in at least one context.
- Validated known synthetic lethal paralogs (MEK1/MEK2, CDK4/CDK6) and identified new pairs (CCNL1/CCNL2).
- Identified ten tumor suppressor paralog pairs whose combined loss promotes cell proliferation.
Conclusions:
- pgPEN effectively maps paralog genetic interactions and uncovers functional redundancy.
- Paralog synthetic lethality represents a significant source of cancer vulnerabilities.
- Findings nominate novel drug targets and highlight the importance of paralog interactions in cancer evolution.
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