Analysis of BMP4 and BMP7 signaling in breast cancer cells unveils time-dependent transcription patterns and highlights a common synexpression group of genes

Abstract

BackgroundBone morphogenetic proteins (BMPs) are members of the TGF-beta superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP4 and BMP7, in particular, have been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We explored the effects of BMP4 and BMP7 treatment on global gene transcription in seven breast cancer cell lines during a 6-point time series, using a whole-genome oligo microarray. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data.ResultsBoth ligands had a strong effect on gene expression, although the response to BMP4 treatment was more pronounced. The cellular functions most strongly affected by BMP signaling were regulation of transcription and development. The observed transcriptional response, as well as its functional outcome, followed a temporal sequence, with regulation of gene expression and signal transduction leading to changes in metabolism and cell proliferation. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMPs, but also highlighted a synexpression group of genes for both ligands. Interestingly, the majority of the genes within these synexpression groups were shared by the two ligands, probably representing the core molecular responses common to BMP4 and BMP7 signaling pathways.ConclusionsAll in all, we show that BMP signaling has a remarkable effect on gene transcription in breast cancer cells and that the functions affected follow a logical temporal pattern. Our results also uncover components of the common cellular transcriptional response to BMP4 and BMP7. Most importantly, this study provides a list of potential novel BMP target genes relevant in breast cancer.

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

“…While categories associated with signaling were observed in both cell lines, in MDA-MB-231 those related to migration were enriched. These data extend our previous results showing enrichment of differentially expressed genes in GO categories that were associated with the BMP4-induced decrease in proliferation [14]. Taken together, the different responses of the cell lines to BMP4 are reflected both at the transcriptional and chromatin levels.…”

“…We have previously characterized transcriptional responses of breast cancer cell lines to BMP4 by using microarray technology [14]. However, in that study we focused only on cells that respond to BMP4 by reduced proliferation.…”

“…For RNA-seq and DNase-seq, one sample per cell line and treatment was used. Samples were collected 3 h after the treatment, based on our previous results showing SMAD1/5/9 protein phosphorylation [9] and gene expression changes by microarray analyses at this time point [14]. For qRT-PCR, samples representing three biological replicates were collected at indicated time points and pooled.…”

“…We have previously searched for BMP4 target genes in a set of breast cancer cell lines that predominantly respond to BMP4 treatment by reduction of proliferation [14]. Here, we used next-generation sequencing (NGS) technologies (RNA-seq and DNase-seq) to uncover BMP4-mediated transcriptional events with a specific focus on comparing cells in which BMP4 has opposing effects, namely antiproliferative and promigratory.…”

DLX1 and MMP3 contribute to oral clefts with and without positive family history of cancer

“…[13][14][15] In recent years, evidence has accumulated of BMPs' important functions in tumour development. 16,17 DLX genes constitute a family of homeobox transcription factors involved in control of cell differentiation and morphogenesis. The mouse and human DLX gene system is formed by three bi-gene clusters: DLX1 and DLX2; DLX3 and DLX4; DLX5 and DLX6.…”