Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth
Oncogenic KRAS mutations occur in approximately 30% of human lung adenocarcinoma. Despite tremendous effort over the past several decades, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the positive and negative regulators of RAS signaling is incomplete. To uncover and corroborate the functional impact of diverse KRAS-interacting proteins on lung cancer growth in vivo, we integrate somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumor barcoding and high-throughput barcode sequencing (Tuba-seq). Through a series of in vivo CRISPR/Cas9 screens, we identified HRAS and NRAS as key suppressors of KRASG12D-driven lung tumor growth in vivo and confirmed these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, we find that these RAS paralogs interact with oncogenic KRASG12D, suppress KRASG12D-KRASG12D interaction, and reduce downstream ERK signaling. Patient-derived mutations HRAST50M and HRASR123C partially abolished this effect. Comparison of the tumor-suppressive effects of HRAS and NRAS in KRASG12D- and BRAFV600E-driven lung cancer models confirmed that these RAS paralogs are specific suppressors of oncogenic KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to specifically uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner and highlights the role of RAS paralog imbalance in oncogenic KRAS-driven cancers.