mRNA expression profiles of methylated APAF-1 and DAPK-1 tumor suppressor genes uncover clear cell renal cell carcinomas with aggressive phenotype

Purpose: We determined the relation between promoter methylation and mRNA expression of the p53 target genes APAF-1 and DAPK-1 in 55 consecutive tumor and corresponding normal tissue samples. Materials and Methods: Tissue was taken from nonmetastatic clear cell renal cell carcinoma at a median followup of 75 months. Quantitative methylation specific real-time polymerase chain reaction and quantitative real-time reverse transcriptase-polymerase chain reaction were used. Results: The mRNA expression levels of APAF-1 and DAPK-1 were significantly higher in tumor vs nontumor tissue from the same kidney (p = 0.003 and 0.0001, respectively). Expression levels of the 2 genes did not correlate with tumor stage but they were significantly lower in high grade (G3) tumors (p = 0.018 and 0.05, respectively). In patients with positive lymph node staging mRNA expression of APAF-1 and DAPK-1 was significantly lower. On matched pair analysis of tumor tissue the methylation level of the APAF-1 gene correlated inversely with the mRNA expression level (p = 0.02). In tumor and normal kidney tissue from patients with lesions 4 cm or greater mRNA expression levels of DAPK-1 were significantly lower in those who later had metastatic disease (p = 0.04 and 0.02, respectively). Conclusions: These data demonstrate decreased tumor suppressor gene expression in more aggressive subtypes of clear cell renal cell carcinoma. The lower mRNA level of the DAPK-1 gene in tumor and normal tissue from patients with an unfavorable clinical outcome suggests the organ specific loss of tumor suppressor gene expression, predisposing to metastatic tumor disease and shorter overall survival.