title: Quantitative promoter methylation analysis of multiple cancer-related genes in renal cell tumors.
abstract: BACKGROUND
  Aberrant promoter hypermethylation of cancer-associated genes occurs frequently during carcinogenesis and may serve as a cancer biomarker. In this study we aimed at defining a quantitative gene promoter methylation panel that might identify the most prevalent types of renal cell tumors.
  
  
  METHODS
  A panel of 18 gene promoters was assessed by quantitative methylation-specific PCR (QMSP) in 85 primarily resected renal tumors representing the four major histologic subtypes (52 clear cell (ccRCC), 13 papillary (pRCC), 10 chromophobe (chRCC), and 10 oncocytomas) and 62 paired normal tissue samples. After genomic DNA isolation and sodium bisulfite modification, methylation levels were determined and correlated with standard clinicopathological parameters.
  
  
  RESULTS
  Significant differences in methylation levels among the four subtypes of renal tumors were found for CDH1 (p = 0.0007), PTGS2 (p = 0.002), and RASSF1A (p = 0.0001). CDH1 hypermethylation levels were significantly higher in ccRCC compared to chRCC and oncocytoma (p = 0.00016 and p = 0.0034, respectively), whereas PTGS2 methylation levels were significantly higher in ccRCC compared to pRCC (p = 0.004). RASSF1A methylation levels were significantly higher in pRCC than in normal tissue (p = 0.035). In pRCC, CDH1 and RASSF1A methylation levels were inversely correlated with tumor stage (p = 0.031) and nuclear grade (p = 0.022), respectively.
  
  
  CONCLUSIONS
  The major subtypes of renal epithelial neoplasms display differential aberrant CDH1, PTGS2, and RASSF1A promoter methylation levels. This gene panel might contribute to a more accurate discrimination among common renal tumors, improving preoperative assessment and therapeutic decision-making in patients harboring suspicious renal masses.
authors.affiliation: Department of Genetics, Portuguese Oncology Institute, Porto, Portugal. veralmcosta@gmail.com <veralmcosta@gmail.com>
authors.forename: Vera L
authors.initials: VL
authors.lastname: Costa
authors.forename: Rui
authors.initials: R
authors.lastname: Henrique
authors.forename: Franclim R
authors.initials: FR
authors.lastname: Ribeiro
authors.forename: Mafalda
authors.initials: M
authors.lastname: Pinto
authors.forename: Jorge
authors.initials: J
authors.lastname: Oliveira
authors.forename: Francisco
authors.initials: F
authors.lastname: Lobo
authors.forename: Manuel R
authors.initials: MR
authors.lastname: Teixeira
authors.forename: Carmen
authors.initials: C
authors.lastname: Jerónimo
mesh_terms: D018262:Adenocarcinoma, Clear Cell / Q000175:diagnosis / Q000235:genetics*; D018249:Adenoma, Oxyphilic / Q000175:diagnosis / Q000235:genetics*; D015703:Antigens, CD; D014408:Biomarkers, Tumor / Q000302:isolation & purification / Q000378:metabolism*; D015820:Cadherins / Q000302:isolation & purification / Q000378:metabolism; D002291:Carcinoma, Papillary / Q000175:diagnosis / Q000235:genetics*; D002292:Carcinoma, Renal Cell / Q000175:diagnosis / Q000235:genetics*; D051546:Cyclooxygenase 2 / Q000302:isolation & purification / Q000378:metabolism; D019175:DNA Methylation; D003937:Diagnosis, Differential; D006801:Humans; D007680:Kidney Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D008565:Membrane Proteins / Q000302:isolation & purification / Q000378:metabolism; D009363:Neoplasm Proteins / Q000302:isolation & purification / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D025521:Tumor Suppressor Proteins / Q000302:isolation & purification / Q000378:metabolism
chemical_list: D015703:Antigens, CD; D014408:Biomarkers, Tumor; C513384:CDH1 protein, human; D015820:Cadherins; D008565:Membrane Proteins; D009363:Neoplasm Proteins; C411762:RASSF1 protein, human; D025521:Tumor Suppressor Proteins; D051546:Cyclooxygenase 2; C496540:PTGS2 protein, human