2. Academic Validation
  3. Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities

Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities

  • Cancer Discov. 2020 Dec;10(12):1950-1967. doi: 10.1158/2159-8290.CD-19-1274.
Marcus R Kelly  # 1 2,  Kaja Kostyrko  # 3,  Kyuho Han  # 4,  Nancie A Mooney 1,  Edwin E Jeng 4,  Kaitlyn Spees 4,  Phuong T Dinh 3,  Keene L Abbott 1,  Dana M Gwinn 3,  E Alejandro Sweet-Cordero 5,  Michael C Bassik 6 7,  Peter K Jackson 8 7 9
Affiliations

Affiliations

  • 1 Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California.
  • 2 Program in Cancer Biology, Stanford University School of Medicine, Stanford, California.
  • 3 Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California.
  • 4 Department of Genetics, Stanford University School of Medicine, Stanford, California.
  • 5 Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California. pjackson@stanford.edu bassik@stanford.edu Alejandro.Sweet-Cordero@ucsf.edu.
  • 6 Department of Genetics, Stanford University School of Medicine, Stanford, California. pjackson@stanford.edu bassik@stanford.edu Alejandro.Sweet-Cordero@ucsf.edu.
  • 7 Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California.
  • 8 Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California. pjackson@stanford.edu bassik@stanford.edu Alejandro.Sweet-Cordero@ucsf.edu.
  • 9 Department of Pathology, Stanford University School of Medicine, Stanford, California.
  • # Contributed equally.
PMID: 32727735 DOI: 10.1158/2159-8290.CD-19-1274
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. SIGNIFICANCE: 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.

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