miR-17-5p Regulates Endocytic Trafficking through Targeting TBC1D2/Armus Andrius Serva 1 , Bettina Knapp 1,2 , Yueh-Tso Tsai 1 , Christoph Claas 1 , Tautvydas Lisauskas 1 , Petr Matula 3,4 , Nathalie Harder 3 , Lars Kaderali 1,2 , Karl Rohr 3 , Holger Erfle 1 , Roland Eils 3 , Vania Braga 5 , Vytaute Starkuviene 1 * 1 BioQuant, University of Heidelberg, Heidelberg, Germany, 2 Institute for Medical Informatics and Biometry, University of Technology Dresden, Dresden, Germany, 3 Integrative Bioinformatics and Systems Biology, DKFZ, BioQuant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany, 4 Center for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic, 5 National Heart and Lung Institute, Imperial College London, London, United Kingdom Abstract miRNA cluster miR-17-92 is known as oncomir-1 due to its potent oncogenic function. miR-17-92 is a polycistronic cluster that encodes 6 miRNAs, and can both facilitate and inhibit cell proliferation. Known targets of miRNAs encoded by this cluster are largely regulators of cell cycle progression and apoptosis. Here, we show that miRNAs encoded by this cluster and sharing the seed sequence of miR-17 exert their influence on one of the most essential cellular processes – endocytic trafficking. By mRNA expression analysis we identified that regulation of endocytic trafficking by miR-17 can potentially be achieved by targeting of a number of trafficking regulators. We have thoroughly validated TBC1D2/Armus, a GAP of Rab7 GTPase, as a novel target of miR-17. Our study reveals regulation of endocytic trafficking as a novel function of miR-17, which might act cooperatively with other functions of miR-17 and related miRNAs in health and disease. Citation: Serva A, Knapp B, Tsai Y-T, Claas C, Lisauskas T, et al. (2012) miR-17-5p Regulates Endocytic Trafficking through Targeting TBC1D2/Armus. PLoS ONE 7(12): e52555. doi:10.1371/journal.pone.0052555 Editor: Kalpana Ghoshal, The Ohio State University, United States of America Received August 2, 2012; Accepted November 15, 2012; Published December 20, 2012 Copyright: ß 2012 Serva et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by BMBF FORSYS ViroQuant (#0313923), BMBF SysTec (0315523A) and Baden Wu¨ rttemberg Stiftung (P-LS-Meth/11). AS is supported by LGFG fellowship of Graduate Academy of Heidelberg University. PM is partially supported by the Grant Agency of the Czech Republic (P302/12/ G157). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: vytaute.starkuviene@bioquant.uni-heidelberg.de Introduction MicroRNAs (miRNAs) are short non-coding RNAs (18 to 24 nt in length) regulating gene expression in metazoans. miRNAs bind to target mRNAs in a complementary or partially complementary way, resulting in degradation and/or translational repression of mRNAs [1]. miRNAs are postulated to bind to 39 untranslated regions (39UTRs) of transcripts [2]. Recent experimental evidence demonstrates the existence of a new class of miRNA targets containing miRNA binding sites in both their 59UTR and 39UTR [3], or within a coding region [4,5]. Individual miRNA are able to simultaneously coordinate expression of numerous transcripts [6] and their encoded proteins [7,8]. miRNAs are predicted to regulate expression of more than 60% of protein-coding mam- malian genes [9] and the list of biological processes regulated by miRNAs are rapidly increasing. Roles of miRNAs in the regulation of cell cycle progression, senescence, development and tumour biology are well established [10,11], with numerous miRNAs identified as key regulators. One of the most studied in this context is the miRNA-17-92 cluster, called oncomir-1 and frequently over-expressed in many tumours [12]. It consists of 6 miRNAs: miR-17-5p, miR-18a-5p, miR-19a- 3p, miR-20a-5p, miR-19b-3p, and miR-92a-3p (further named as miR-17, miR-18a, miR-19a, miR-20a, miR-19b and miR-92a, respectively). Series of duplications and subsequent loss of the individual members resulted in the appearance of two other paralogue clusters miR-106b-25 and miR-106a-363. Fifteen miRNAs belonging to one of these clusters can be assigned to four classes according to their seed sequences [13]. miRNAs belonging to the same class might have overlapping targets and, consequently, functions as shown by Ventura et al [14]. The importance of the miR-17-92 cluster in tumour biology is further exemplified by frequent deletion of this cluster in breast and ovarian cancers [15]. Down-regulation of members of this cluster occurs also during aging [16], haematopoietic and lung differen- tiation [17,18] as well as during HIV infection [19]. Recently, miR-17-92 and both paralogue clusters were shown to be up- regulated in early re-programming stages and during induction of pluripotent stem cells [20]. Regulation of cell cycle progression accounts for the majority of these functions; and miR-17-92 was shown to either facilitate [18,21–23] or inhibit cell proliferation depending on different cellular context. Individual members of the miR-17-92 cluster have been characterized to a varying degree and their functions appear to be both cooperative and individual [24]. For instance, miR-19 has been shown to be a key component in promoting c-myc-induced B lymphomagenesis [25,26]. In contrast, miR-92a turned out to be dispensable in inducing lymphoma growth [12], but regulates proliferation of myeloid cells [22]. The majority of known targets of the miR-17-92 cluster have been identified for miR-17 [27], which builds miR-17 seed family with other 5 miRNAs encoded by miR-17-92 (miR-20a) and by paralogues clusters miR-106b-25 (miR-106b-5p and miR-93-5p PLOS ONE | www.plosone.org 1 December 2012 | Volume 7 | Issue 12 | e52555