title: Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer.
abstract: Bone 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.
  
  
  
  The 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.
  
  
  
  Integrating 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.
authors.affiliation: BioMediTech, University of Tampere, Tampere, Finland. minna.ampuja@uta.fi.|Fimlab Laboratories, Tampere, Finland. minna.ampuja@uta.fi.
authors.forename: M
authors.identifier: 0000-0003-1407-5399
authors.initials: M
authors.lastname: Ampuja
authors.affiliation: BioMediTech, University of Tampere, Tampere, Finland.
authors.forename: T
authors.initials: T
authors.lastname: Rantapero
authors.affiliation: BioMediTech, University of Tampere, Tampere, Finland.|Fimlab Laboratories, Tampere, Finland.
authors.forename: A
authors.initials: A
authors.lastname: Rodriguez-Martinez
authors.affiliation: BioMediTech, University of Tampere, Tampere, Finland.
authors.forename: M
authors.initials: M
authors.lastname: Palmroth
authors.affiliation: BioMediTech, University of Tampere, Tampere, Finland.
authors.forename: E L
authors.initials: EL
authors.lastname: Alarmo
authors.affiliation: BioMediTech, University of Tampere, Tampere, Finland.
authors.forename: M
authors.initials: M
authors.lastname: Nykter
authors.affiliation: BioMediTech, University of Tampere, Tampere, Finland.|Fimlab Laboratories, Tampere, Finland.
authors.forename: A
authors.initials: A
authors.lastname: Kallioniemi
mesh_terms: D055415:Bone Morphogenetic Protein 4 / Q000378:metabolism* / Q000494:pharmacology; D001943:Breast Neoplasms / Q000473:pathology*; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000187:drug effects; D002843:Chromatin / Q000187:drug effects / Q000378:metabolism; D003851:Deoxyribonucleases / Q000378:metabolism*; D006801:Humans; D010641:Phenotype; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000187:drug effects; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D055415:Bone Morphogenetic Protein 4; D002843:Chromatin; D003851:Deoxyribonucleases
keywords: Bone morphogenetic protein; Breast cancer; DNase-seq; NGS; RNA-seq; Transcription factor