title: DNA hypermethylation in papillary renal cell carcinoma.
abstract: OBJECTIVE
  To investigate the pattern of DNA CpG island hypermethylation in papillary renal cell carcinoma (pRCC).
  
  
  METHODS
  DNA from pRCC (n= 32) and adjacent normal tissue (n= 15) was isolated. A quantitative methylation-specific PCR was performed to analyse the methylation pattern at APC (actin beta), CDH1 (E-cadherin), GSTP1 (glutathione S-transferase pi 1), RASSF1A (Ras association domain family member 1A) and TIMP3 (TIMP metallopeptidase inhibitor 3); a sequence of ACTB without CpG was used to normalize for DNA input and to calculate the relative amount of methylated DNA (normalized index of methylation, NIM).
  
  
  RESULTS
  RASSF1A hypermethylation was observed in most pRCC and normal samples (100 vs 94.4%), but the median NIM was significantly higher in pRCC samples (2.11 vs 0.61; P < 0.001). RASSF1A hypermethylation allowed discrimination of pRCC and normal tissue with a sensitivity of 87.5% and a specificity of 73.3% as determined via receiver operator characteristic analysis (area under curve = 0.814). Hypermethylation at APC (3.0 vs 6.7%), CDH1 (15.6 vs 0%), GSTP1 (21.9 vs 6.7%) and TIMP3 (6.3 vs 0%) was infrequent in pRCC and normal tissue. CDH1 was significantly correlated with pathological stage (P= 0.015), and patients with methylated CDH1 methylation showed a trend towards shorter recurrence-free survival (log-rank P= 0.057). The number of methylated gene sites was correlated with pathological stage (P= 0.007) and lymph node metastasis (P= 0.008).
  
  
  CONCLUSIONS
  DNA hypermethylation at RASSF1A is common in pRCC tissue irrespective of the histological subtype, but also frequently seen at lower levels in normal adjacent tissue. Aberrant hypermethylation could be a prognostic marker for pRCC.
authors.affiliation: Klinik und Poliklinik für Urologie,Universitätsklinikum Bonn, Bonn, Germany. joerg.ellinger@ukb.uni-bonn.de
authors.forename: Jörg
authors.initials: J
authors.lastname: Ellinger
authors.forename: Daniel
authors.initials: D
authors.lastname: Holl
authors.forename: Philipp
authors.initials: P
authors.lastname: Nuhn
authors.forename: Philip
authors.initials: P
authors.lastname: Kahl
authors.forename: Nicolas
authors.initials: N
authors.lastname: Haseke
authors.forename: Michael
authors.initials: M
authors.lastname: Staehler
authors.forename: Sabine
authors.initials: S
authors.lastname: Siegert
authors.forename: Stefan
authors.initials: S
authors.lastname: Hauser
authors.forename: Christian G
authors.initials: CG
authors.lastname: Stief
authors.forename: Stefan C
authors.initials: SC
authors.lastname: Müller
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Bastian
mesh_terms: D015703:Antigens, CD; D015820:Cadherins / Q000235:genetics; D002292:Carcinoma, Renal Cell / Q000473:pathology* / Q000601:surgery; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D017491:Genes, APC; D051549:Glutathione S-Transferase pi / Q000235:genetics; D006801:Humans; D007680:Kidney Neoplasms / Q000473:pathology* / Q000601:surgery; D009392:Nephrectomy; D016133:Polymerase Chain Reaction; D019717:Tissue Inhibitor of Metalloproteinase-3 / Q000235:genetics; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D015703:Antigens, CD; C513384:CDH1 protein, human; D015820:Cadherins; C411762:RASSF1 protein, human; C088390:TIMP3 protein, human; D019717:Tissue Inhibitor of Metalloproteinase-3; D025521:Tumor Suppressor Proteins; C496556:GSTP1 protein, human; D051549:Glutathione S-Transferase pi