Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screen
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RESEARCH
Open Access
Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens Merve Dede1,2†, Megan McLaughlin1,2†, Eiru Kim1 and Traver Hart1,3* * Correspondence: traver@hart-lab. org † Merve Dede and Megan McLaughlin contributed equally to this work. 1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 3 Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA Full list of author information is available at the end of the article
Abstract Background: Pooled library CRISPR/Cas9 knockout screening across hundreds of cell lines has identified genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the number of essential genes detected from these monogenic knockout screens is low compared to the number of constitutively expressed genes in a cell. Results: Through a systematic analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we observe that half of all constitutively expressed genes are never detected in any CRISPR screen and that these never-essentials are highly enriched for paralogs. We investigated functional buffering among approximately 400 candidate paralog pairs using CRISPR/enCas12a dual-gene knockout screening in three cell lines. We observe 24 synthetic lethal paralog pairs that have escaped detection by monogenic knockout screens at stringent thresholds. Nineteen of 24 (79%) synthetic lethal interactions are present in at least two out of three cell lines and 14 of 24 (58%) are present in all three cell lines tested, including alternate subunits of stable protein complexes as well as functionally redundant enzymes. Conclusions: Together, these observations strongly suggest that functionally redundant paralogs represent a targetable set of genetic dependencies that are systematically under-represented among cell-essential genes in monogenic CRISPRbased loss of function screens.
Background The adaptation of CRISPR-Cas9 system to genome-wide knockout screens in mammalian cells has greatly transformed the search for cancer-specific genomic vulnerabilities that can be targeted therapeutically. Monogenic pooled library CRISPR-Cas9 knockout screens revealed that mammalian cells have as much as 3–4 times more essential genes than the previous RNAi technology was able to detect at the same false discovery rate [1]. Moreover, through immense monogenic screening efforts, multiple groups © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the articl
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