1H NMR metabolomics analysis of renal cell carcinoma cells: Effect of VHL inactivation on metabolism

Von Hippel‐Lindau (VHL) is an onco‐suppressor involved in oxygen and energy‐dependent promotion of protein ubiquitination and proteosomal degradation. Loss of function mutations of VHL (VHL‐cells) result in organ specific cancers with the best studied example in renal cell carcinomas. VHL has a well‐established role in deactivation of hypoxia‐inducible factor (HIF‐1) and in regulation of PI3K/AKT/mTOR activity. Cell culture metabolomics analysis was utilized to determined effect of VHL and HIF‐1α or HIF‐2α on metabolism of renal cell carcinomas (RCC). RCC cells were stably transfected with VHL or shRNA designed to silence HIF‐1α or HIF‐2α genes. Obtained metabolic data was analysed qualitatively, searching for overall effects on metabolism as well as quantitatively, using methods developed in our group in order to determine specific metabolic changes. Analysis of the effect of VHL and HIF silencing on cellular metabolic footprints and fingerprints provided information about the metabolic pathways affected by VHL through HIF function as well as independently of HIF. Through correlation network analysis as well as statistical analysis of significant metabolic changes we have determined effects of VHL and HIF on energy production, amino acid metabolism, choline metabolism as well as cell regulation and signaling. VHL was shown to influence cellular metabolism through its effect on HIF proteins as well as by affecting activity of other factors. What's new? Mutations in the von Hippel‐Lindau (VHL) gene are major drivers of kidney carcinogenesis. Here the authors performed NMR metabolomics analysis to identify metabolic changes in renal cell carcinomas associated with VHL and its downstream targets, hypoxia‐inducing factors HIF‐1alpha and HIF‐2alpha. They find characteristic effects of VHL on choline and amino acids metabolism, many of them independent from HIF proteins. These metabolic changes provide new molecular insight into VHL‐mutant and ‐wild‐type cancer cells and could help develop new biomarkers for renal cell carcinomas in the future.