DNA Methylation Status of Key Cell-Cycle Regulators Such as CDKNA2/p16 and CCNA1 Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors

Abstract

Purpose: To explore alterations in gene promoter methylation as a potential cause of acquired drug resistance to doxorubicin or combined treatment with 5-fluorouracil and mitomycin C in human breast cancers.Experimental Design: Paired tumor samples from locally advanced breast cancer patients treated with doxorubicin and 5-fluorouracil-mitomycin C were used in the genome-wide DNA methylation analysis as discovery cohort. An enlarged cohort from the same two prospective studies as those in the discovery cohort was used as a validation set in pyrosequencing analysis.Results: A total of 469 genes were differentially methylated after treatment with doxorubicin and revealed a significant association with canonical pathways enriched for immune cell response and cell-cycle regulating genes including CDKN2A, CCND2, CCNA1, which were also associated to treatment response. Treatment with FUMI resulted in 343 differentially methylated genes representing canonical pathways such as retinoate biosynthesis, gai signaling, and LXR/RXR activation. Despite the clearly different genes and pathways involved in the metabolism and therapeutic effect of both drugs, 46 genes were differentially methylated before and after treatment with both doxorubicin and FUMI. DNA methylation profiles in genes such as BRCA1, FOXC1, and IGFBP3, and most notably repetitive elements like ALU and LINE1, were associated with TP53 mutations status.Conclusion: We identified and validated key cell-cycle regulators differentially methylated before and after neoadjuvant chemotherapy such as CDKN2A and CCNA1 and reported that methylation patterns of these genes may be potential predictive markers to anthracycline/mitomycine sensitivity. Clin Cancer Res; 20(24); 6357-66. Ó2014 AACR.

DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival

“…Bisulfite conversion and DNA methylation analysis using the Illumina Infinium HumanMethylation27 and HumanMethylation450 beadchip assays was carried out as previously described [32, 33]. Preprocessing and normalization involved steps of probe filtering, color bias correction, background subtraction and subset quantile normalization as previously described [34].…”

The effect of 5-fluorouracil/leucovorin chemotherapy on CpG methylation, or the confounding role of leukocyte heterogeneity: An illustration

“…In a human lung cancer cell line, higher concentrations of 5-FU induced significant DNA hypermethylation 25 . In breast cancer locally advanced tumors, key cell cycle regulator genes were differentially methylated before and after combined treatment with 5-FU and mitomycin D 26 . These data suggest that 5-FU treatment may affect DNA methylation of peripheral blood leukocytes, through direct and indirect mechanisms.…”

The association between methylated <em>CDKN2A</em> and cervical carcinogenesis, and its diagnostic value in cervical cancer: a meta-analysis

“…5-Azacytidine was the first hypomethylating agent to be approved by the US Food and Drug Administration for the treatment of myelodysplastic syndrome,41 and subsequent studies further confirmed its anticancer effectiveness 42,43. Advanced studies have also demonstrated that the methylation status of cell cycle regulators is associated with the sensitivity of chemotherapeutic agents in breast cancer 44. From this perspective, hypomethylation of methylated CDKN2A using a hypomethylating agent might be a whole new approach to cervical cancer therapy.…”