DNA methylation profiling in doxorubicin treated primary locally advanced breast tumours identifies novel genes associated with survival and treatment response

Abstract

BackgroundBreast cancer is the most frequent cancer in women and consists of a heterogeneous collection of diseases with distinct histopathological, genetic and epigenetic characteristics. In this study, we aimed to identify DNA methylation based biomarkers to distinguish patients with locally advanced breast cancer who may benefit from neoadjuvant doxorubicin treatment.ResultsWe investigated quantitatively the methylation patterns in the promoter regions of 14 genes (ABCB1, ATM, BRCA1, CDH3, CDKN2A, CXCR4, ESR1, FBXW7, FOXC1, GSTP1, IGF2, HMLH1, PPP2R2B, and PTEN) in 75 well-described pre-treatment samples from locally advanced breast cancer and correlated the results to the available clinical and molecular parameters. Six normal breast tissues were used as controls and 163 unselected breast cancer cases were used to validate associations with histopathological and clinical parameters.Aberrant methylation was detected in 9 out of the 14 genes including the discovery of methylation at the FOXC1 promoter. Absence of methylation at the ABCB1 promoter correlated with progressive disease during doxorubicin treatment. Most importantly, the DNA methylation status at the promoters of GSTP1, FOXC1 and ABCB1 correlated with survival, whereby the combination of methylated genes improved the subdivision with respect to the survival of the patients. In multivariate analysis GSTP1 and FOXC1 methylation status proved to be independent prognostic markers associated with survival.ConclusionsQuantitative DNA methylation profiling is a powerful tool to identify molecular changes associated with specific phenotypes. Methylation at the ABCB1 or GSTP1 promoter improved overall survival probably due to prolonged availability and activity of the drug in the cell while FOXC1 methylation might be a protective factor against tumour invasiveness. FOXC1 proved to be general prognostic factor, while ABCB1 and GSTP1 might be predictive factors for the response to and efficacy of doxorubicin treatment. Pharmacoepigenetic effects such as the reported associations in this study provide molecular explanations for differential responses to chemotherapy and it might prove valuable to take the methylation status of selected genes into account for patient management and treatment decisions.

Transcriptional analysis of CXCR4, DNMT3A, DNMT3B and DNMT1 gene expression in primary advanced uterine cervical carcinoma

“…Chick and Szyf (41) and Ateeq et al (42) demonstrated that the demethylating agent 5'-aza-2'-deoxycytidine induced prometastatic CXCR4 gene expression by the demethylation of its promoter in MCF-7 and ZR-75-1 breast cancer cell lines. By contrast, the results presented by Dejeux et al (43) in a group of 6 normal breast tissue samples and 163 unselected samples from locally advanced breast cancer did not demonstrate methylation of CpGs located in the promoter region of the CXCR4 gene either the non-cancer samples nor in the breast cancer samples. Przybylski et al (44) and Sato et al (45) analyzed the methylation status of the CXCR4 gene in pancreatic cell lines.…”

BRCA1 and GATA3 corepress FOXC1 to inhibit the pathogenesis of basal-like breast cancers

“…In breast cancer, FOXC1 expression is strongly associated with the basal-like subtype of breast cancer and postulated to be a marker of poor prognosis (Ray et al, 2010;Taube et al, 2010). FOXC1 expression in breast cancers appears to be controlled at the transcriptional level, and methylation of the FOXC1 promoter was shown to be an independent prognostic marker associated with survival (Dejeux et al, 2010) and CD44-positive (basal-like) breast tumors. Exogenous expression of FOXC1 induced a progenitor-like phenotype in differentiated mammary epithelial cells (Bloushtain-Qimron et al, 2008).…”

Epigenomic Biomarkers for the Advance of Personalized Medicine

“…Hypermethylation of the GSTP1 gene promoter is present in a high frequency of prostate tumors and is being proposed as a candidate complement for the discussed PSA testing (Van Neste et al 2012). In terms of drug prediction, hypermethylation and gene inactivation of GSTP1 has been associated to prolonged survival in breast cancer patients treated with doxorubicin (Dejeux et al 2010). Consistently, promoter hypermethylation of ABCB1-a membranebound transporter that actively effluxes a wide range of compounds from cells, including chemotherapy drugs-was also related to doxorubicin response (Chekhun et al 2006), thus reinforcing the role of this particular mechanism in the treatment of breast cancer patients with doxorubicin.…”