EMBO Molecular Medicine cross-journal focus EMT Epithelial-Mesenchymal Transition cross-journal focus EMT Epithelial-Mesenchymal Transition EDITORS David del Alamo Editor [email protected] | T +49 6221 8891 309 David received his PhD. from the Madrid’s Autónoma University where he studied proximal-distal patterning in Drosophila with Fernando Díaz-Benjumea. As a postdoc, he continued working with Drosophila, first in Marek Mlodzik’s lab (Mount Sinai School of Medicine, New York) on the mechanisms of epithelial planar cell polarity generation, and then with François Schweisguth (Institut Pasteur, Paris) where he focused on the modulation of Notch signalling in lateral inhibition. David joined The EMBO Journal in 2011. Nonia Pariente Senior Editor [email protected] | T +49 6221 8891 305 Nonia joined EMBO Reports in August 2007. She studied biochemistry and molecular biology in Madrid’s Autónoma University, where she also gained her PhD on the generation of new antiviral strategies against RNA viruses. She did a four-year post-doc at UCLA focusing on the development of new strategies for gene therapy. Roberto Buccione Editor [email protected] | T +49 6221 8891 310 Roberto Buccione completed his PhD at the University of l’Aquila, Italy studying the process of oogenesis in mammals. After continuing these studies as a post-doctoral researcher at the EMBO Jackson Laboratory, Bar Harbor ME, USA, he joined the Mario Negri Sud research institute in S. Molecular Maria Imbaro, Italy, where he lead a research group focused on the cell biology of tumour cell Medicine invasion. He joined EMBO Molecular Medicine as a Scientific Editor in October 2012. Maria Polychronidou Editor [email protected] | T +49 6221 8891 410 Maria received her PhD from the University of Heidelberg, where she studied the role of nuclear membrane proteins in development and aging. During her post-doctoral work, she focused on the analysis of tissue-specific regulatory functions of Hox transcription factors using a combination of computational and genome-wide methods. emboj.embopress.org | embor.embopress.org | embomolmed.embopress.org | msb.embopress.org full articles The EMBO Journal Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion. Bracken CP, Li X, Wright JA, Lawrence DM, Pillman KA, Salmanidis M, Anderson MA, Dredge BK, Gregory PA, Tsykin A, Neilsen C, Thomson DW, Bert AG, Leerberg JM, Yap AS, Jensen KB, Khew-Goodall Y, Goodall GJ. DOI: 10.15252/embj.201488641 | Published 28.07.2014 MiR-133 promotes cardiac reprogramming by directly repressing Snai1 and silencing fibroblast signatures. Muraoka N, Yamakawa H, Miyamoto K, Sadahiro T, Umei T, Isomi M, Nakashima H, Akiyama M, Wada R, Inagawa K, Nishiyama T, Kaneda R, Fukuda T, Takeda S, Tohyama S, Hashimoto H, Kawamura Y, Goshima N, Aeba R, Yamagishi H, Fukuda K, Ieda M. DOI: 10.15252/embj.201387605 | Published 11.06.2014 EMBO Reports Review Dedifferentiation and reprogramming: origins of cancer stem cells. Friedmann-Morvinski D, Verma IM. DOI: 10.1002/embr.201338254 | Published 14.02.2014 Article E2F1 induces miR-224/452 expression to drive EMT through TXNIP downregulation. Knoll S, Fürst K, Kowtharapu B, Schmitz U, Marquardt S, Wolkenhauer O, Martin H, Pützer BM. DOI: 10.15252/embr.201439392 | Published 23.10.2014 EMBO Molecular Medicine Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients. Tan TZ, Miow QH, Miki Y, Noda T, Mori S, Huang RY, Thiery JP. DOI: 10.15252/emmm.201404208 | Published 11.09.2014 Molecular Systems Biology A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration. Yizhak K, Le Dévédec SE, Rogkoti VM, Baenke F, de Boer VC, Frezza C, Schulze A, van de Water B, Ruppin E. DOI: 10.15252/msb.20134993 | Published 01.08.2014 For further reading please see inside back cover Article Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion Cameron P Bracken1,2, Xiaochun Li1, Josephine A Wright1, David M Lawrence1, Katherine A Pillman1, Marika Salmanidis1, Matthew A Anderson1, B Kate Dredge3, Philip A Gregory1,2, Anna Tsykin1, Corine Neilsen1, Daniel W Thomson1, Andrew G Bert1, Joanne M Leerberg4, Alpha S Yap4, Kirk B Jensen3, Yeesim Khew-Goodall1,3,*,† & Gregory J Goodall1,2,3,**,† Abstract Introduction The microRNAs of the miR-200 family maintain the central charac- MicroRNAs and their targets are important components in the regu- teristics of epithelia and inhibit tumor cell motility and invasive- latory networks that maintain cell phenotype and control cell differ- ness. Using the Ago-HITS-CLIP technology for transcriptome-wide entiation. Although microRNAs typically act as mild modulators of identification of direct microRNA targets in living cells, along gene expression, exerting only a modest inhibitory effect on individ- with extensive validation to verify the reliability of the approach, ual targets, conceivably they can broadly refine gene expression we have identified hundreds of miR-200a and miR-200b targets, patterns because each microRNA may target several hundred different providing insights into general features of miRNA target site mRNAs. Thus, one microRNA can potentially influence a biological selection. Gene ontology analysis revealed a predominant effect process by having a coordinated effect on multiple components of miR-200 targets in widespread coordinate control of actin of a network or pathway. However, due to the uncertainties in cytoskeleton dynamics. Functional characterization of the miR-200 predicting or experimentally identifying the spectrum of targets of targets indicates that they constitute subnetworks that underlie individual miRNAs, there are few confirmed examples of broad the ability of cancer cells to migrate and invade, including coor- network regulation by a miRNA. dinate effects on Rho-ROCK signaling, invadopodia formation, The miR-200 family of microRNAs acts as enforcers of the epithe- MMP activity, and focal adhesions. Thus, the miR-200 family lial phenotype. They are expressed in most, if not all, epithelial cells maintains the central characteristics of the epithelial phenotype and their expression must be turned off for epithelial to mesenchy- by acting on numerous targets at multiple levels, encompassing mal transition (EMT) to occur (Burk et al, 2008; Gregory et al, both cytoskeletal effectors that control actin filament organiza- 2008a; Korpal et al, 2008; Park et al, 2008). EMT involves a tion and dynamics, and upstream signals that locally regulate morphological change whereby immobile epithelial cells acquire the cytoskeleton to maintain cell morphology and prevent cell pro-invasive mesenchymal characteristics that are key to various migration. developmental processes and are drivers of metastatic progression in cancer (Nieto, 2013). Two major targets of miR-200 in controlling Keywords cytoskeleton; HITS-CLIP; invadopodia; microRNA; miR-200 EMT are the transcription repressors, ZEB1 and ZEB2 (formerly Subject Categories Cancer; Cell Adhesion, Polarity & Cytoskeleton; RNA known as SIP1) (Gregory et al, 2008a; Park et al, 2008). Further- Biology more, the ZEB proteins are strong repressors of transcription of the DOI 10.15252/embj.201488641 | Received 2 April 2014 | Revised 6 June 2014 | miR-200 genes, producing a double negative feedback loop that is Accepted 12 June 2014 | Published online 28 July 2014 central to the control of EMT in in vitro models (Bracken et al, The EMBO Journal (2014) 33: 2040–2056 2008; Burk et al, 2008; Parker et al, 2009; Gregory et al, 2011) and has been implicated in contributing to cancer progression through promotion of EMT in various epithelial-derived cancers. However, like all microRNAs, the miR-200 family members are predicted to 1 Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia 2 Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia 3 School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia 4 Division of Molecular Cell Biology, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Qld, Australia *Corresponding author. Tel: +61 8 8222 3410; Fax: +61 8 8232 4092; Email: [email protected] **Corresponding author. Tel: +61 8 8222 3430; Fax +61 8 8232 4092; Email: [email protected] †These authors contributed equally to the work 2040 The EMBO Journal Vol 33 | No 18 | 2014 ª 2014 The Authors Cameron P Bracken et al miR-200 targets a cytoskeletal regulatory network The EMBO Journal The EMBO Journal miR-200 targets a cytoskeletal regulatory network Cameron P Bracken et al A have many other targets. Some of these may also play central roles cancer cell invasion and metastasis. In particular, we show that the Figure 1. Genome-wide identification of miR-200 targets by Ago-HITS- in mediating the epithelial response to miR-200, while others may formation of invadopodia, which relies on rearrangement of the CLIP. provide a more subtle role in the sculpting of phenotype by actin cytoskeleton and provides a site for localized secretion of A Percentages of total reads and read peaks derived from Ago-HITS-CLIP and mapped relative to their genomic locations. miR-200. enzymes to degrade the extracellular matrix, is regulated by miR-200 B, C Histograms displaying read peaks across the CFL2 and MPRIP 30UTRs. The The miR-200 family consists of 5 miRNAs that are closely related at multiple points in the pathway. y-axis shows the number of overlapping unique sequencing reads in sequence, but are predicted to comprise two distinct classes in comprising the peak, and the x-axis indicates the position of the peak terms of their targets, with miR-200a and miR-141 sharing identical within the 30UTR. The locations of potential seed sites (black arrows, seed regions and miR-200b, miR-200c, and miR-429 constituting a Results 8-mers; purple arrows, 7-mers; yellow arrows, 6-mers; asterisk, central- paired) are indicated.