DNA methylation analysis of the HIF-1α prolyl hydroxylase domain genes PHD1, PHD2, PHD3 and the factor inhibiting HIF gene FIH in invasive breast carcinomas

Aims: Hypoxia-inducible factor-1 (HIF-1) activity is regulated by prolyl hydroxylase (PHD1, PHD2, PHD3) and factor inhibiting HIF-1 (FIH) that target the alpha subunit of HIF-1 (HIF-1 alpha) for proteosomal degradation. We hypothesised that the elevated HIF-1 alpha level is due in some tumours to epigenetic silencing by DNA hypermethylation of the promoter region of one or more of the PHDs and FIH genes. The aims were to define the presence or absence of promoter methylation of PHDs and FIH in cell lines of various sources and breast carcinomas and, if present, determine its effect on mRNA and protein expression. Methods and results: Tumour cell lines (n = 20) and primary invasive breast carcinomas (n = 168) were examined for promoter region DNA methylation using methylation-sensitive high-resolution melting. There was evidence of PHD3 but not of PHD1, PHD2 or FIH DNA methylation in breast cancer (SkBr3) and leukaemic (HL60 and CCRF-CEM) cell lines, but there was no evidence of methylation in any of 168 breast cancers. Only the high-level PHD3 methylation seen in leukaemic cell lines correlated with absent mRNA and protein expression. Conclusions: Methylation-induced epigenetic silencing of PHD1, PHD2, PHD3 and FIH is unlikely to underlie up-regulated HIF-1 alpha expression in human breast cancer but may play a role in other tumour types.