title: Diagnostic markers of urothelial cancer based on DNA methylation analysis.
abstract: BACKGROUND
  Early detection and risk assessment are crucial for treating urothelial cancer (UC), which is characterized by a high recurrence rate, and necessitates frequent and invasive monitoring. We aimed to establish diagnostic markers for UC based on DNA methylation.
  
  
  METHODS
  In this multi-center study, three independent sample sets were prepared. First, DNA methylation levels at CpG loci were measured in the training sets (tumor samples from 91 UC patients, corresponding normal-appearing tissue from these patients, and 12 normal tissues from age-matched bladder cancer-free patients) using the Illumina Golden Gate methylation assay to identify differentially methylated loci. Next, these methylated loci were validated by quantitative DNA methylation by pyrosequencing, using another cohort of tissue samples (Tissue validation set). Lastly, methylation of these markers was analyzed in the independent urine samples (Urine validation set). ROC analysis was performed to evaluate the diagnostic accuracy of these 12 selected markers.
  
  
  RESULTS
  Of the 1303 CpG sites, 158 were hyper ethylated and 356 were hypo ethylated in tumor tissues compared to normal tissues. In the panel analysis, 12 loci showed remarkable alterations between tumor and normal samples, with 94.3% sensitivity and 97.8% specificity. Similarly, corresponding normal tissue could be distinguished from normal tissues with 76.0% sensitivity and 100% specificity. Furthermore, the diagnostic accuracy for UC of these markers determined in urine samples was high, with 100% sensitivity and 100% specificity.
  
  
  CONCLUSIONS
  Based on these preliminary findings, diagnostic markers based on differential DNA methylation at specific loci can be useful for non-invasive and reliable detection of UC and epigenetic field defect.
authors.affiliation: Department of Molecular Pathology, Nara Medical University, 840, Shijyo-cho, Kashihara, Japan. yychihara@gmail.com
authors.forename: Yoshitomo
authors.initials: Y
authors.lastname: Chihara
authors.forename: Yae
authors.initials: Y
authors.lastname: Kanai
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Fujimoto
authors.forename: Kokichi
authors.initials: K
authors.lastname: Sugano
authors.forename: Kiyotaka
authors.initials: K
authors.lastname: Kawashima
authors.forename: Gangning
authors.initials: G
authors.lastname: Liang
authors.forename: Peter A
authors.initials: PA
authors.lastname: Jones
authors.forename: Kiyohide
authors.initials: K
authors.lastname: Fujimoto
authors.forename: Hiroki
authors.initials: H
authors.lastname: Kuniyasu
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Hirao
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000032:analysis* / Q000235:genetics; D002295:Carcinoma, Transitional Cell / Q000175:diagnosis* / Q000235:genetics* / Q000652:urine; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D055088:Early Detection of Cancer / Q000379:methods; D005260:Female; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D008875:Middle Aged; D012372:ROC Curve; D001749:Urinary Bladder Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000652:urine; D055815:Young Adult
chemical_list: D014408:Biomarkers, Tumor