DNA hypermethylation in papillary renal cell carcinoma.
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.
Ellinger
Jörg
J
Klinik und Poliklinik für Urologie,Universitätsklinikum Bonn, Bonn, Germany. joerg.ellinger@ukb.uni-bonn.de
Holl
Daniel
D
Nuhn
Philipp
P
Kahl
Philip
P
Haseke
Nicolas
N
Staehler
Michael
M
Siegert
Sabine
S
Hauser
Stefan
S
Stief
Christian G
CG
Müller
Stefan C
SC
Bastian
Patrick J
PJ
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
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