CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells

Metabolic reprogramming by oncogenic signals promotes cancer initiation and progression. The oncogene KRAS and tumor suppressor STK11, which encodes the kinase LKB1, regulate metabolism and are frequently mutated in non-small cell lung cancer (NSCLC). Concurrent KRAS mutation and LKB1 loss (KL) specifies aggressive oncological behavior(1,2). We show that KL cells and tumors share metabolomic signatures of perturbed nitrogen handling. KL cells express the urea cycle enzyme carbamoyl phosphate synthetase-1 (CPS1), which produces carbamoyl phosphate (CP) in the mitochondria from ammonia and bicarbonate, initiating nitrogen disposal. CPS1 transcription is suppressed by LKB1 via AMPK, and CPS1 expression anticorrelates with LKB1 in human NSCLC. Silencing CPS1 in KL cells induces cell death and reduces tumor growth. Surprisingly, cell death results from pyrimidine depletion rather than ammonia toxicity, as CPS1 enables an unconventional pathway of nitrogen flow from ammonia into pyrimidines. CPS1 loss reduces the pyrimidine/purine ratio, compromises S-phase progression, and induces DNA polymerase stalling and DNA damage. Exogenous pyrimidines reverse DNA damage and rescue growth. The data indicate that the KL oncogenotype imposes a novel metabolic vulnerability related to exquisite dependence on a cross-compartmental pathway of pyrimidine metabolism in an aggressive subset of NSCLC.