In-Vitro Identification and In-Vivo Confirmation of DNA Methylation Biomarkers for Urothelial Cancer
Christina U. Köhler,
Michael Walter,
Kerstin Lang,
Sabine Plöttner,
Florian Roghmann,
Joachim Noldus,
Andrea Tannapfel,
Yu Chun Tam,
Heiko U. Käfferlein,
Thomas Brüning
Affiliations
Christina U. Köhler
Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany
Michael Walter
C.ATG Core Facility for NGS and Microarrays, University of Tübingen, Calwerstr. 7, 72076 Tübingen, Germany
Kerstin Lang
Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany
Sabine Plöttner
Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany
Florian Roghmann
Department of Urology, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Hölkeskampring 40, 44625 Herne, Germany
Joachim Noldus
Department of Urology, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Hölkeskampring 40, 44625 Herne, Germany
Andrea Tannapfel
Institute of Pathology, Georgius Agricola Foundation Ruhr, Ruhr University Bochum, Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany
Yu Chun Tam
Institute of Pathology, Georgius Agricola Foundation Ruhr, Ruhr University Bochum, Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany
Heiko U. Käfferlein
Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany
Thomas Brüning
Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bürkle-de-la-Camp Platz 1, 44789 Bochum, Germany
We identified DNA methylation targets specific for urothelial cancer (UC) by genome-wide methylation difference analysis of human urothelial (RT4, J82, 5637), prostate (LNCAP, DU-145, PC3) and renal (RCC-KP, CAKI-2, CAL-54) cancer cell lines with their respective primary epithelial cells. A large overlap of differentially methylated targets between all organs was observed and 40 Cytosine-phosphate-Guanine motifs (CpGs) were only specific for UC cells. Of those sites, two also showed high methylation differences (≥47%) in vivo when we further compared our data to those previously obtained in our array-based analyses of urine samples in 12 UC patients and 12 controls. Using mass spectrometry, we finally assessed seven CpG sites in this “bladder-specific” region of interest in urine samples of patients with urothelial (n = 293), prostate (n = 75) and renal (n = 23) cancer, and 143 controls. DNA methylation was significantly increased in UC compared to non-UC individuals. The differences were more pronounced for males rather than females. Male UC cases could be distinguished from non-UC individuals with >30% sensitivity at 95% specificity (Area under the curve (AUC) 0.85). In summary, methylation sites highly specific in UC cell lines were also specific in urine samples of UC patients showing that in-vitro data can be successfully used to identify biomarker candidates of in-vivo relevance.