Discovery of synthetic lethal and tumor suppressive paralog pairs in the human genome

CRISPR knockout screens have accelerated the discovery of important cancer genetic dependencies. However, traditional CRISPR-Cas9 screens are limited in their ability to assay the function of redundant or duplicated genes. Paralogs in multi-gene families constitute two-thirds of the protein-coding genome, so this blind spot is the rule, not the exception. To overcome the limitations of single gene CRISPR knockout screens, we developedpairedguide RNAs forParalog gENetic interaction mapping (pgPEN), a pooled CRISPR/Cas9 approach which targets over a thousand duplicated human paralogs in single knockout and double knockout configurations. We applied pgPEN to two cell lineages and discovered that over 10% of human paralogs exhibit synthetic lethality in at least one cellular context. We recovered known synthetic lethal paralogs such asMAP2K1/MAP2K2, important drug targets such asCDK4/CDK6, and numerous other synthetic lethal pairs such asCCNL1/CCNL2.In addition, we identified ten tumor suppressive paralog pairs whose compound loss promotes cell growth. These findings identify a large number of previously unidentified essential gene families and nominate new druggable targets for oncology drug discovery.HighlightsComprehensive genetic interaction mapping of 1,030 human duplicated paralogs using a dual targeting CRISPR/Cas9 approachDuplicated paralogs are highly enriched for genetic interactionsSynthetic lethal paralogs includeCCNL1/CCNL2, CDK4/CDK6, andGSK3A/GSK3BTumor suppressor paralog pairs includeCDKN2A/CDKN2BandFBXO25/FBXO32