Targeting Ubiquitin Signaling vulnerabilities in KEAP1-Inactivated Lung Cancer

Lung cancer cells rely on protein homeostasis regulators, particularly the ubiquitin-proteasome system (UPS), to sustain malignancy. Genetic alterations in UPS components, such as E3 ubiquitin ligases (E3s) and deubiquitinating enzymes (DUBs), are common and create context-dependent therapeutic dependencies. To investigate how these changes drive tumor formation, we conducted CRISPR screens on metabolically stressed murine lung cancer models and identified specific cancer vulnerabilities, including KEAP1. Although KEAP1 is frequently mutated in aggressive non-small cell lung cancers (NSCLC, ~15%), our findings reveal an unexpected proto-oncogenic role for KEAP1 in a genetically defined subset of NSCLC. Mechanistically, Keap1 deletion activated NRF2 and upregulated Aldh3a1. This led to elevated NADH/NAD? ratios, triggered reductive stress, and suppressed tumor growth. Given the poor prognosis of KEAP1-mutated patients, combinatorial CRISPR dropout screens revealed druggable E3s and DUBs as Keap1-dependent co-vulnerabilities. Notably, depleting these co-dependencies such as the E3 ligases Herc2, Ubr4 and Huwe1 ablated the in vivo development of Keap1-inactivated tumors. We demonstrate that targeting the UPS represents an underexplored, promising therapeutic approach for patients with KEAP1-inactivated tumors, especially under metabolic stress. Overall design: Comparative gene expression profiling analysis of RNA-seq data for KPL, KP, and KPP primary murine lung tumor cell lines: KI696 (1µM) treatment vs. vehicle control (DMSO)