Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Abstract

BackgroundBone morphogenetic protein 4 (BMP4) plays an important role in cancer pathogenesis. In breast cancer, it reduces proliferation and increases migration in a cell line-dependent manner. To characterize the transcriptional mediators of these phenotypes, we performed RNA-seq and DNase-seq analyses after BMP4 treatment in MDA-MB-231 and T-47D breast cancer cells that respond to BMP4 with enhanced migration and decreased cell growth, respectively.ResultsThe RNA-seq data revealed gene expression changes that were consistent with the in vitro phenotypes of the cell lines, particularly in MDA-MB-231, where migration-related processes were enriched. These results were confirmed when enrichment of BMP4-induced open chromatin regions was analyzed. Interestingly, the chromatin in transcription start sites of differentially expressed genes was already open in unstimulated cells, thus enabling rapid recruitment of transcription factors to the promoters as a response to stimulation. Further analysis and functional validation identified MBD2, CBFB, and HIF1A as downstream regulators of BMP4 signaling. Silencing of these transcription factors revealed that MBD2 was a consistent activator of target genes in both cell lines, CBFB an activator in cells with reduced proliferation phenotype, and HIF1A a repressor in cells with induced migration phenotype.ConclusionsIntegrating RNA-seq and DNase-seq data showed that the phenotypic responses to BMP4 in breast cancer cell lines are reflected in transcriptomic and chromatin levels. We identified and experimentally validated downstream regulators of BMP4 signaling that relate to the different in vitro phenotypes and thus demonstrate that the downstream BMP4 response is regulated in a cell type-specific manner.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3428-1) contains supplementary material, which is available to authorized users.

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

“…While associations between different molecular levels (e.g., RNA on protein expression, chromatin accessibility on RNA expression) were generally strongest at the same time point, we identified long-lasting effects across and within regulatory layers, which seem to prepare the cell for differentiation processes already at the exit from pluripotency. It further revealed that chromatin accessibility at gene promoters is necessary but not sufficient for productive gene expression, which has been reported in other systems such as response to BMP4 signaling in cancer (Ampuja et al, 2017). This could indicate that developmental gene promoters are already primed by pluripotency factors before developmental TFs bind them.…”

Classification of early and late stage Liver Hepatocellular Carcinoma patients from their genomics and epigenomics profiles

“…They are significantly upregulated in late stage of HCC. One of the studies reveals the role of RP3-375P9.2 in breast cancer [63].…”

Transcription factors—Intricate players of the bone morphogenetic protein signaling pathway

“…A number of studies have examined TFs in the context of BMP signaling but lack direct evidence of interaction with SMAD proteins. [41][42][43][44] For example, HOX, SOX, FOX, bHLH, POU, and NR3C1 TFs were implicated as master regulators of the specificity of the BMP signaling response at different stages of hair follicle development. 44 In breast cancer cells, MDB2…”

“…was implicated as a common transcriptional activator of BMP4 specific target genes. 42 Interestingly, CBFB functioned as a transcriptional activator in breast cancer cells where BMP4 treatment induces proliferation whereas HIF1A was a transcriptional repressor in cells with induced migration phenotype. 42 Here we focus on those TFs that have been experimentally validated to interact with SMADs upon stimulation of the BMP pathway.…”

“…For example, HOX, SOX, FOX, bHLH, POU, and NR3C1 TFs were implicated as master regulators of the specificity of the BMP signaling response at different stages of hair follicle development . In breast cancer cells, MDB2 was implicated as a common transcriptional activator of BMP4 specific target genes . Interestingly, CBFB functioned as a transcriptional activator in breast cancer cells where BMP4 treatment induces proliferation whereas HIF1A was a transcriptional repressor in cells with induced migration phenotype …”