Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells.

Marco Mina,Giuseppe Jurman,Mariko Okada-Hatakeyama,Erik Arner,Alistair R R Forrest,Shigeyuki Magi,Masayoshi Itoh,Carsten O Daub,Timo Lassmann,Yoshihide Hayashizaki,Piero Carninci,Hideya Kawaji,Cesare Furlanello

doi:10.1038/srep11999

Abstract

The analysis of CAGE (Cap Analysis of Gene Expression) time-course has been proposed by the FANTOM5 Consortium to extend the understanding of the sequence of events facilitating cell state transition at the level of promoter regulation. To identify the most prominent transcriptional regulations induced by growth factors in human breast cancer, we apply here the Complexity Invariant Dynamic Time Warping motif EnRichment (CIDER) analysis approach to the CAGE time-course datasets of MCF-7 cells stimulated by epidermal growth factor (EGF) or heregulin (HRG). We identify a multi-level cascade of regulations rooted by the Serum Response Factor (SRF) transcription factor, connecting the MAPK-mediated transduction of the HRG stimulus to the negative regulation of the MAPK pathway by the members of the DUSP family phosphatases. The finding confirms the known primary role of FOS and FOSL1, members of AP-1 family, in shaping gene expression in response to HRG induction. Moreover, we identify a new potential regulation of DUSP5 and RARA (known to antagonize the transcriptional regulation induced by the estrogen receptors) by the activity of the AP-1 complex, specific to HRG response. The results indicate that a divergence in AP-1 regulation determines cellular changes of breast cancer cells stimulated by ErbB receptors.

Highlights

The analysis of CAGE (Cap Analysis of Gene Expression) time-course has been proposed by the FANTOM5 Consortium to extend the understanding of the sequence of events facilitating cell state transition at the level of promoter regulation
To confirm the series of biochemical events initiated by HRG and epidermal growth factor (EGF), we first examined by Western blot analysis the activation of the MAPK and Akt signaling pathways in MCF-7 cells at 0 min, 15 min, 30 min, 45 min, 60 min, 80 min, 100 min, 2 hr, 2.5 hr, 3 hr, 3.5 hr, 4 hr, 5 hr, 6 hr, 7 hr and 8 hr after EGF or HRG stimulation (Fig. 1)
The CAGE expression time courses produced by the FANTOM5 consortium provide a rich description of the response of MCF-7 cells to HRG and EGF stimulation up to 8 hours after induction

Summary

Introduction

The analysis of CAGE (Cap Analysis of Gene Expression) time-course has been proposed by the FANTOM5 Consortium to extend the understanding of the sequence of events facilitating cell state transition at the level of promoter regulation. To identify the most prominent transcriptional regulations induced by growth factors in human breast cancer, we apply here the Complexity Invariant Dynamic Time Warping motif EnRichment (CIDER) analysis approach to the CAGE timecourse datasets of MCF-7 cells stimulated by epidermal growth factor (EGF) or heregulin (HRG). We applied the Complexity Invariant Dynamic Time Warping motif EnRichment (CIDER) method[11] to the whole MCF-7 CAGE time-course data to infer the prominent regulatory mechanisms and the respective driving TFs. Our analysis allows reconstructing the regulatory chain induced by ErbB pathway activation through the induction of SRF, moving from the action of immediate early genes to the effect of late TFs on late time-points. The results largely confirm the observations from previous works, elucidate some mechanisms not completely observed before, and propose new putative regulations

Methods

Results

Conclusion