Discovery of a CPS1-deficient HCC subtype with therapeutic potential via integrative genomic and experimental analysis

BACKGROUND AND AIMS Metabolic reprogramming plays an important role in tumorigenesis. However, the metabolic types of different tumors are diverse and lack of in-depth study. Here, through analysis of big databases and clinical samples, we identified Carbamoyl phosphate synthetase I(CPS1)-deficient hepatocellular carcinoma(HCC) subtype, explored tumorigenesis mechanism of this HCC subtype, and aimed to investigate metabolic reprogramming as target for HCC prevention. APPROACH AND RESULTS Pan-cancer study involving differentially expressed metabolic genes of 7,764 tumor samples in 16 cancer types provided by The Cancer Genome Atlas(TCGA) demonstrated that urea cycle(UC) was liver-specific and HCC-downregulated. A large-scale gene expression data analysis including a total of 2,596 HCC cases in 7 HCCDB datasets combined with a total of 17,444 hepatectomy cohort data identified a specific CPS1-deficent HCC subtype with poor clinical prognosis. In vitro and in vivo validation confirmed crucial role of CPS1 in HCC. LC-MS assay and Seahorse analysis revealed that UC dysregulation(UCD) led to the deceleration of the tricarboxylic acid(TCA) cycle, while excess ammonia caused by CPS1 deficiency activated fatty acid β-oxidation(FAO) through p-AMPK. Mechanistically, FAO provided sufficient ATP for cell proliferation and enhanced chemoresistance of HCC cells by activating FOXM1. Subcutaneous xenograft tumor models and patient-derived organoids(PDOs) were employed to identify that blocking FAO by Eto may provide therapeutic benefit to HCC patients with CPS1-deficiency. CONCLUSIONS In conclusion, our results prove a direct link between UCD and cancer stemness in HCC, define a CPS1-deficient HCC subtype through big-data mining, and provide insights for novel therapeutic for this type of HCC through targeting FAO.