Integrated Metabolomic and Transcriptomic Analysis of Modified Nucleosides for Biomarker Discovery in Clear Cell Renal Cell Carcinoma
Daniel A. Mohl,
Simon Lagies,
Kyra Zodel,
Matthias Zumkeller,
Asin Peighambari,
Athina Ganner,
Dietmar A. Plattner,
Elke Neumann-Haefelin,
Mojca Adlesic,
Ian J. Frew,
Bernd Kammerer
Affiliations
Daniel A. Mohl
Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
Simon Lagies
Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
Kyra Zodel
Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre—University of Freiburg, 79106 Freiburg, Germany
Matthias Zumkeller
Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre—University of Freiburg, 79106 Freiburg, Germany
Asin Peighambari
Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre—University of Freiburg, 79106 Freiburg, Germany
Athina Ganner
Renal Division, Department of Medicine, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
Dietmar A. Plattner
Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
Elke Neumann-Haefelin
Renal Division, Department of Medicine, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
Mojca Adlesic
Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre—University of Freiburg, 79106 Freiburg, Germany
Ian J. Frew
Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre—University of Freiburg, 79106 Freiburg, Germany
Bernd Kammerer
Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers. The biallelic inactivation of the von Hippel–Lindau tumor suppressor gene (VHL) is the truncal driver mutation of most cases of ccRCC. Cancer cells are metabolically reprogrammed and excrete modified nucleosides in larger amounts due to their increased RNA turnover. Modified nucleosides occur in RNAs and cannot be recycled by salvage pathways. Their potential as biomarkers has been demonstrated for breast or pancreatic cancer. To assess their suitability as biomarkers in ccRCC, we used an established murine ccRCC model, harboring Vhl, Trp53 and Rb1 (VPR) knockouts. Cell culture media of this ccRCC model and primary murine proximal tubular epithelial cells (PECs) were investigated by HPLC coupled to triple-quadrupole mass spectrometry using multiple-reaction monitoring. VPR cell lines were significantly distinguishable from PEC cell lines and excreted higher amounts of modified nucleosides such as pseudouridine, 5-methylcytidine or 2′-O-methylcytidine. The method’s reliability was confirmed in serum-starved VPR cells. RNA-sequencing revealed the upregulation of specific enzymes responsible for the formation of those modified nucleosides in the ccRCC model. These enzymes included Nsun2, Nsun5, Pus1, Pus7, Naf1 and Fbl. In this study, we identified potential biomarkers for ccRCC for validation in clinical trials.
