Genetic identification of the RAS proteostatic machinery and its failure to regulate oncogenic variants

Abstract

The regulation of cellular homeostasis, differentiation, and proliferation is safeguarded by proteostatic mechanisms, which are crucial for maintaining cellular function. We used endogenously affinity-tagged KRAS cells in a fluorescence-activated cell sorting (FACS)-based CRISPR knockout screen to map genome-wide genetic requirements for proteostatic KRAS regulation. Three regulatory modules emerged, specifically cullin E3 ligase activity (CUL3, NAE1, UBE2M, CAND1, and UBE2L3), LZTR1 protein function (LZTR1, NUDCD3, and ZRSR2), and RAS GTPase modulation and processing (NRAS, HRAS, FNTB, RCE1, ICMT, and GOLGA7), all critical for regulating KRAS abundance. This expands our knowledge on the machinery controlling ubiquitin-meditated RAS family member regulation. Combining endogenous affinity tagging with genetic variant introduction, we found that the oncogenic KRAS G12D mutant exhibits reduced regulation by CRL3LZTR1, potentially contributing to oncogenic transformation and proliferation. In summary, our study genetically defines the machinery regulating RAS GTPase protein abundance, providing a foundation for a deeper molecular understanding and potential therapeutic exploitation of CRL3LZTR1-RAS GTPase regulation in human disease.