An integrative oncogene-dependency map identifies unique vulnerabilities of oncogenic EGFR, KRAS, and RIT1 in lung cancer

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>Advances in precision oncology have transformed cancer therapy from broadly-applied cytotoxic therapy to personalized treatments based on each tumor’s unique molecular alterations. Here we investigate the oncogene-specific dependencies conferred by lung cancer driver variants of <jats:italic>KRAS, EGFR</jats:italic>, and <jats:italic>RIT1</jats:italic>. Integrative analysis of genome-wide CRISPR screens in isogenic cell lines identified shared and unique vulnerabilities of each oncogene. The non-identical landscape of dependencies underscores the importance of genotype-guided therapies to maximize tumor responses. Combining genetic screening data with small molecule sensitivity profiling, we identify a unique vulnerability of <jats:italic>RIT1</jats:italic>-mutant cells to loss of spindle assembly checkpoint regulators. This sensitivity may be related to a novel role of RIT1 in mitosis; we find that oncogenic RIT1<jats:sup>M90I</jats:sup> alters mitotic timing via weakening of the spindle assembly checkpoint. In addition, we uncovered a specific cooperation of mutant <jats:italic>RIT1</jats:italic> with loss of Hippo pathway genes. In human lung cancer, <jats:italic>RIT1</jats:italic> mutations and amplifications frequently co-occur with loss of Hippo pathway gene expression. These results provide the first genome-wide atlas of oncogenic <jats:italic>RIT1</jats:italic>-cooperating factors and genetic dependencies and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in <jats:italic>RIT1</jats:italic>-mutant lung cancer.</jats:p>

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

“…Like other groups (Dandage and Landry, 2019;Dede et al, 2020;Wang et al, 2015), we noticed that paralogous genes are less likely to be essential for cell growth than non-paralogous "singleton" genes in CRISPR knockout screening data ( Fig. 1B) (Vichas et al, 2020). Given the utility of targeting cancer-essential genes for therapy, we reasoned that this paralog blind spot may prevent detection of important druggable cancer dependencies.…”

“…Data was re-analyzed from a larger drug screen in (Berger et al, 2016). (E) Rank plot of CRISPR scores from an erlotinib sensitization screen in PC9-Cas9-EGFR T790M/L858R cells (Vichas et al, 2020). MAP2K1 (encodes MEK1) or MAP2K2 (encodes MEK2) single gene knockout does not result in significantly decreased cell growth.…”

“…To determine whether known therapeutic vulnerabilities are missed in CRISPR knockout screens, we compared our previous drug sensitivity profiling of PC9-EGFR L858R/T790M cells (Berger et al, 2016) to recent genetic vulnerabilities identified in the same system (Vichas et al, 2020). These cells exhibit resistance to the EGFR tyrosine kinase inhibitor, erlotinib, which can be reversed by treatment with trametinib, a kinase inhibitor of MEK1 and MEK2 -protein kinases encoded by the paralogous genes MAP2K1 and MAP2K2, which are part of the Ras/MAPK pathway (Fig.…”

“…To map genetic interactions between paralogs, we applied the pgPEN library to PC9 lung adenocarcinoma cells previously engineered to constitutively express Cas9 (Thomas et al, 2020;Vichas et al, 2020) using standard pooled CRISPR screening methodology in triplicate ( Fig. 2A).…”

“…PC9 single-gene CRISPR knockout screen and drug sensitivity profiling data PC9-Cas9 and PC9-Cas9-EGFR T790M/L858R single-gene CRISPR knockout screen data (Vichas et al, 2020) and erlotinib/trametinib drug sensitivity data (Berger et al, 2016) were re-analyzed from previously published data. The relative essentiality of singletons versus paralogs in the PC9-Cas9 CRISPR knockout screen using the Brunello library (Doench et al, 2016) was assessed via a two-tailed Kolmogorov-Smirnov test (Fig.…”