Integrated Epigenetics of Human Breast Cancer: Synoptic Investigation of Targeted Genes, MicroRNAs and Proteins upon Demethylation Treatment

Abstract

BackgroundThe contribution of aberrant DNA methylation in silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations are reversible, it became of interest to determine the effects of the 5-aza-2′-deoxycytidine (DAC) demethylation therapy in breast cancer at different molecular levels.Methods and FindingsHere we investigate a synoptic model to predict complete DAC treatment effects at the level of genes, microRNAs and proteins for several human breast cancer lines. The present study assessed an effective treatment dosage based on the cell viability, cytotoxicity, apoptosis and methylation assays for the investigated cell lines. A highly aggressive and a non-aggressive cell line were investigated using omics approaches such as MALDI-TOF MS, mRNA- and microRNA expression arrays, 2-D gel electrophoresis and LC-MS-MS. Complete molecular profiles including the biological interaction and possible early and late systematic stable or transient effects of the methylation inhibition were determined. Beside the activation of several epigenetically suppressed TSGs, we also showed significant dysregulation of some important oncogenes, oncomiRs and oncosuppressors miRNAs as well as drug tolerance genes/miRNAs/proteins.ConclusionsIn the present study, the results denote some new molecular DAC targets and pathways based on the chemical modification of DNA methylation in breast cancer. The outlined approach might prove to be useful as an epigenetic treatment model also for other human solid tumors in the management of cancer patients.

SOXC transcription factors in mantle cell lymphoma: the role of promoter methylation in SOX11 expression

“…The decrease in SOX11 mRNA and protein levels in 5-AZA treated Granta519 and Rec1 MCL cell lines and the fact that the SOX11 promoter region is already hypomethylated in MCL (current data and1213) suggest that effect of 5-AZA on SOX11 levels might be indirect. Promoter methylation-independent effects of 5-AZA on certain genes were already reported in MCL15, AML16, colon cancer17 and in breast cancer18. Vegliante et al showed that the histone deacetylase (HDAC) inhibitor SAHA induced SOX11 expression in JVM2 and Raji cell lines.…”

Calcification of vascular smooth muscle cells is induced by secondary calciprotein particles and enhanced by tumor necrosis factor-α

“…Real-time PCR reactions were performed in three replicates. The fold difference for each samples were calculated using the comparative Ct method (2 ÀDDCt ) [21,28].…”

The increasing roles of epigenetics in breast cancer: Implications for pathogenicity, biomarkers, prevention and treatment

“…However, in cancer cells, they have been found hypermethylated, a phenomenon which leads to inappropriate gene silencing . Especially in BC cells, these silenced genes have been identified as proapoptotic genes ( HOXA5, TMS1 ), cell cycle‐inhibitor genes ( p16, RASSF1A ) or DNA repair genes ( BRCA1 ) …”

“…30 Especially in BC cells, these silenced genes have been identified as proapoptotic genes (HOXA5, TMS1), cell cycle-inhibitor genes (p16, RASSF1A) or DNA repair genes (BRCA1). 3,31,32 CpG DNA methylation is carried out by DNA methyltransferases (DNMTs). Two types of DNMTs have been described: the "de novo" DNMTs (DNMT3A and DNMT3B) that establish the pattern of methylation during embryonic development, and the "maintenance" DNMTs (DNMT1) which are highly expressed during the S-phase of the cell cycle and are responsible for maintaining the pattern of methylation through adult development.…”

“…54 As such, miRNAs play a key role in many cellular processes such as cellular growth, differentiation and apoptosis. 32,54 They also contribute to the development and progression of cancer. 32,54,56 Aberrant expression of miRNAs is seen in BC.…”