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Supplementary Table 5 from Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities

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posted on 2023-04-03, 22:20 authored by Marcus R. Kelly, Kaja Kostyrko, Kyuho Han, Nancie A. Mooney, Edwin E. Jeng, Kaitlyn Spees, Phuong T. Dinh, Keene L. Abbott, Dana M. Gwinn, E. Alejandro Sweet-Cordero, Michael C. Bassik, Peter K. Jackson

Results from the first pairwise sgRNA screen in A549-Cas9 and H23-Cas9 cells. Columns are as in the previous table, except that they refer to Gene A or Gene B as indicated, where the symbol for GeneA comes alphabetically before the symbol of Gene B. Test statistics reflect comparisons with inferred expected phenotypes from Gene A/safe or Gene B/safe sgRNA pairs (see Methods).

Funding

National Cancer Institute

NIH

NIH Director's New Innovator Award Program

SNSF Postdoc Mobility Grants

History

ARTICLE ABSTRACT

Activating mutations in RAS GTPases drive many cancers, but limited understanding of less-studied RAS interactors, and of the specific roles of different RAS interactor paralogs, continues to limit target discovery. We developed a multistage discovery and screening process to systematically identify genes conferring RAS-related susceptibilities in lung adenocarcinoma. Using affinity purification mass spectrometry, we generated a protein–protein interaction map of RAS interactors and pathway components containing hundreds of interactions. From this network, we constructed a CRISPR dual knockout library targeting 119 RAS-related genes that we screened for KRAS-dependent genetic interactions (GI). This approach identified new RAS effectors, including the adhesion controller RADIL and the endocytosis regulator RIN1, and >250 synthetic lethal GIs, including a potent KRAS-dependent interaction between RAP1GDS1 and RHOA. Many GIs link specific paralogs within and between gene families. These findings illustrate the power of multiomic approaches to uncover synthetic lethal combinations specific for hitherto untreatable cancer genotypes. We establish a deep network of protein–protein and genetic interactions in the RAS pathway. Many interactions validated here demonstrate important specificities and redundancies among paralogous RAS regulators and effectors. By comparing synthetic lethal interactions across KRAS-dependent and KRAS-independent cell lines, we identify several new combination therapy targets for RAS-driven cancers.This article is highlighted in the In This Issue feature, p. 1775