Biological and metabolomic insights into RACGAP1-mediated growth and progression of clear cell renal cell carcinoma

Rac-GTPase-activating protein 1 (RACGAP1) is a member of the Rho GTPase-activating protein (GAP) family, which is involved in the process of cytokinesis. But its precise function in clear cell renal cell carcinoma (ccRCC) has not been extensively investigated. In this study, we found that RACGAP1 was regulated by centrosomal protein CEP55 and markedly facilitated the growth and progression of ccRCC in vitro and in vivo. In addition, RACGAP1 knockdown induces G1 phase arrest, resulting in mitotic disorder and subsequent apoptosis. These findings indicated that RACGAP1, a cell cycle-related gene, is crucial for the survival and growth of ccRCC. Furthermore, renal cancer is closely associated with metabolic processes. As demonstrated by our serum-targeted metabolomics study, RACGAP1 dysfunction altered the levels of multiple amino acids/amino acid derivatives, acylcarnitines, fatty acids/acyls, nucleotides, and their metabolites. Spatial metabolomics data further confirmed that downregulation of RACGAP1 expression could inhibit ccRCC growth not only by reprogramming fatty acid and nucleotide metabolism but also by interfering with lipid metabolism. More importantly, we detected higher levels of glutamine, acylcarnitines, and lipids in the tumor margin region, suggesting intratumor metabolic heterogeneity in ccRCC. In conclusion, this study elucidated the biological function of RACGAP1 in promoting ccRCC progression and revealed the regulatory mechanism of RACGAP1 in interfering with metabolic pathways from the perspective of multidimensional metabolomics. These findings will provide new targets and a theoretical basis for the treatment of RCC.<b>NEW & NOTEWORTHY</b> We have demonstrated for the first time that CEP55 directly regulated RACGAP1 expression, and downregulation of RACGAP1 blocked ccRCC mitotic division at the G1 phase and induced apoptosis. Targeted and spatial metabolomics analyses showed that RACGAP1 disruption altered levels of multiple metabolites and inhibited ccRCC growth by reprogramming fatty acid, nucleotide, and lipid metabolism. Importantly, spatial imaging of metabolites uncovered intratumor metabolic heterogeneity in ccRCC, providing novel insights into the metabolic landscape of this malignancy.