Abstract
BackgroundPooled 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.ResultsThrough 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.ConclusionsTogether, 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 CRISPR-based loss of function screens.
Highlights
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
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
We looked at gene expression from all cell lines in the Cancer Cell Line Encyclopedia (CCLE) [19] and considered the role of tissue-specific vs. constitutive gene expression
Summary
Pooled library CRISPR/Cas knockout screening across hundreds of cell lines has identified genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. Monogenic pooled library CRISPR-Cas 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]. Even with the CRISPR technology, the number of essential genes detected through these screens is still far less than the number of genes constitutively expressed in a given cell line. This phenomenon was previously observed in systematic gene knockout studies in S. cerevisiae [5, 6], where only 17% of yeast genes were essential for growth in rich medium [6]. A similar study in C. elegans [10] suggested that, at the organismal level, virtually every gene is required for optimal growth in some condition
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
