Characterization and therapeutic suppression of KEAP1-NRF2-driven resistance to KRAS inhibitors in pancreatic and lung cancer

ABSTRACT The recent approval of KRAS inhibitors supports the therapeutic value of targeting mutant KRAS cancers. However, clinical efficacy is hindered by both primary and treatment-associated acquired resistance. We applied a CRISPR-Cas9 loss-of-function screen and identified loss of KEAP1 as a resistance mechanism to the KRASG12D-selective inhibitor MRTX1133 and the RAS(ON) multi-selective inhibitor RMC-7977 in pancreatic cancer models. RNA-sequencing analyses revealed a KEAP1KO transcriptome that is distinct from the ERK-, MYC-, and YAP/TAZ-TEAD-dependent transcriptional programs that drive KRAS inhibitor resistance, demonstrating a distinct mechanism of resistance. We then established a PDAC KEAP1-deficient (PKD) gene signature that was enriched in patients and preclinical models insensitive to KRAS inhibitor treatment. Finally, we observed that KEAP1-deficient cells exhibited elevated glutamine metabolism, and combination treatment with the glutamine antagonist DRP-104 (sirpiglenastat) enhanced KRAS inhibitor suppression of pancreatic and lung tumors. SIGNIFICANCE KEAP1 loss is associated with reduced response to KRAS inhibitor therapy. We demonstrate that KEAP1 loss-associated resistance can be overcome by pharmacologic inhibition of the KEAP1 loss-induced glutamine dependency, establishing a combination to enhance RAS inhibitor clinical efficacy. Competing Interest Statement C. A. Stalnecker has received consulting fees from Reactive Biosciences. K.L. Bryant has received research funding support from SpringWorks Therapeutics. A.D. Cox has consulted for Eli Lilly and Mirati Therapeutics, Inc., a Bristol Myers Squibb company. T. Papagiannakopoulos received funding from Pfizer Medical Education Group, Dracen Pharmaceuticals, Kymera Therapeutics, Bristol Myers Squibb, and Agios Pharmaceuticals not related to the submitted work. C.J. Der is a consultant/advisory board member for AskY Therapeutics, Cullgen, Deciphera Pharmaceuticals, Kestrel Therapeutics, Mirati Therapeutics, Reactive Biosciences, Revolution Medicines, and SHY Therapeutics. C.J. Der has received research funding support from Deciphera Pharmaceuticals, Mirati Therapeutics, Reactive Biosciences, Revolution Medicines, and SpringWorks Therapeutics. B.M. Wolpin has consulted for Agenus, BMS/Mirati, EcoR1 Capital, GRAIL, Harbinger Health, Ipsen, Lustgarten Foundation, Revolution Medicines, Tango Therapeutics, and Third Rock Ventures. B.M. Wolpin has received research funding from BMS/Celgene, BreakThrough Cancer, Eli Lilly, Harbinger Health, Lustgarten Foundation, NIH/NCI, Novartis, Pancreatic Cancer Action Network, Revolution Medicines, Servier/Agios, and Stand Up to Cancer. A.J. Aguirre. has consulted for Affini-T Therapeutics, AstraZeneca, Blueprint Medicines, Boehringer Ingelheim, Curie.Bio, Incyte, Kestrel Therapeutics, Merck & Co., Inc., Mirati Therapeutics Inc., Nimbus Therapeutics, Oncorus, Inc., Plexium, Quanta Therapeutics, Reactive Biosciences, Revolution Medicines, Riva Therapeutics, Servier Pharmaceuticals, Syros Pharmaceuticals, Taiho Pharmaceuticals, T-knife Therapeutics, Third Rock Ventures, and Ventus Therapeutics; holds equity in Riva Therapeutics and Kestrel Therapeutics. A.J. Aguirre. has research funding from Amgen, AstraZeneca, Boehringer Ingelheim, Bristol Myers Squibb, Deerfield, Inc., Eli Lilly, Mirati Therapeutics Inc., Novartis, Novo Ventures, Revolution Medicines. K.-K. Wong has consulted for and/or has received Grant/Research support from: Tango Therapeutics, Janssen Pharmaceuticals, Pfizer, Bristol Myers Squibb, Zentalis Pharmaceuticals, Blueprint Medicines, Takeda Pharmaceuticals, Mirati Therapeutics, Novartis, Genentech, Merus, Bridgebio Pharma, Xilio Therapeutics, Allerion Therapeutics, Boehringer Ingelheim, Cogent Therapeutics, Revolution Medicines and AstraZeneca. Other authors declare no competing interests.