DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors [RNA-seq]. Homo sapiens

Using genome-wide approaches, we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at transcription start site (TSS) and shore regions. Approximately 60% of them exhibited a methylation-dependent expression level and 20% of them were also dependent on the methyl-CpG-binding protein domain 2. Thus, these specific DNA methylation patterns were linked to an epigenetic control of their expression, upon CAF-secreted factors. We have therefore identified some molecular events defining the responsiveness of groups of genes to stromal cell contents in human breast tumors. Overall design: RNAseq of untreated SKBR3 cells and AU565 cells, CAF-conditionned medium treated cells, DAC treated cells, siMBD2 treated cells, siCtrl, in duplicates or in quadriplicates for untreated SKBR3 cells