Human breast cancer cell lines: vehicle vs. BMP4 incubation. Homo sapiens

Bone morphogenetic proteins (BMPs) are members of the TGF-β 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, in particular, has been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We therefore explored the effects of BMP4 treatment on global gene transcription in five breast cancer cell lines during a 6-point time series. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data. BMP4 had a strong effect on gene expression. The cellular functions most strongly affected 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 BMP4, but also highlighted a synexpression group of genes. Finally, this study provides a list of potential novel BMP target genes relevant in breast cancer. Overall design: Two-condition experiment, vehicle-treated vs. BMP4-treated. Five cell lines were tested at six time points each, what makes a total of 30 samples. RNA samples from three biological replicates were pooled before hybridization.

骨形态发生蛋白（Bone morphogenetic proteins, BMPs）属于转化生长因子-β（Transforming growth factor-β, TGF-β）超家族生长因子成员。该类蛋白以调控骨生成与发育过程的功能著称，近年来越来越多研究证据证实其在肿瘤生物学中发挥关键作用。其中，骨形态发生蛋白4（Bone morphogenetic protein 4, BMP4）已被证实与乳腺癌密切相关。
然而，目前针对肿瘤背景下BMP靶基因的研究仍较为匮乏。为此，本研究针对5株乳腺癌细胞系开展6个时间点的时序实验，探究BMP4处理对其全基因组转录水平的影响。数据分析涵盖差异表达基因层级聚类、基因本体（Gene Ontology, GO）富集分析以及基于模型的时序数据聚类分析。结果显示，BMP4对基因表达具有显著调控作用，受影响最显著的细胞功能包括转录调控与发育过程。
观测到的转录应答及其功能结局呈现明确的时序性变化：基因表达调控与信号转导过程率先发生，随后引发代谢状态与细胞增殖能力的改变。层级聚类分析揭示，各细胞系对BMP4的应答存在显著个体差异，同时也鉴定出一组协同表达基因组。最后，本研究筛选得到一批与乳腺癌相关的潜在新型BMP靶基因。
实验设计：本实验为双处理组对照实验，设置溶剂载体处理组与BMP4处理组。5株细胞系各设置6个时间点进行检测，总计获得30个样本。杂交前，将3次生物学重复的RNA样本混合后用于杂交实验。