Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer

Molecular Cancer

Research

Anna Melissa Schlitter¹  Bo Kong²  Susanne Raulefs²  Ivonne Regel²  Philipp Bruns²  Jörg Kleeff²  Carsten Jäger²  Christoph W Michalski³  Rolf Thermann⁴  W Kurt Roth⁴  Klaus Hoffmeier⁵  Björn Rotter⁵  Anne Plötner⁵  Peter Winter⁵  Fabian J Theis⁶  Günter Kahl⁷  Fabian Afonso-Grunz⁸  Sören Müller⁹  Ina Koch^1,10 

[1] Department of Pathology, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany;Department of Surgery, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany;Department of Surgery, University of Heidelberg, Heidelberg, Germany;GFE Blut mbH, Frankfurt Biotechnology Innovation Center, Frankfurt am Main, Germany;GenXPro GmbH, Frankfurt Biotechnology Innovation Center, Frankfurt am Main, Germany;Institute of Computational Biology, Helmholtz Zentrum Munich, Neuherberg, Germany;Department of Mathematics, TU Munich, Boltzmannstrasse 3, Garching, Germany;Molecular BioSciences, Goethe University, Frankfurt am Main, Germany;Molecular BioSciences, Goethe University, Frankfurt am Main, Germany;GenXPro GmbH, Frankfurt Biotechnology Innovation Center, Frankfurt am Main, Germany;Molecular BioSciences, Goethe University, Frankfurt am Main, Germany;GenXPro GmbH, Frankfurt Biotechnology Innovation Center, Frankfurt am Main, Germany;Molecular Bioinformatics Group, Institute of Computer Science, Cluster of Excellence Frankfurt ‘Macromolecular Complexes’ Faculty of Computer Science and Mathematics, Frankfurt am Main, Germany;Molecular Bioinformatics Group, Institute of Computer Science, Cluster of Excellence Frankfurt ‘Macromolecular Complexes’ Faculty of Computer Science and Mathematics, Frankfurt am Main, Germany;

关键词: Pancreatic cancer;    MACE;    3′UTR;    miRNA;    Long non-coding RNA;    Wnt signalling;    Next-generation sequencing;    ZEB1;    TCF4;   

DOI  :  10.1186/s12943-015-0358-5

 received in 2014-11-11, accepted in 2015-04-06,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundPrevious studies identified microRNAs (miRNAs) and messenger RNAs with significantly different expression between normal pancreas and pancreatic cancer (PDAC) tissues. Due to technological limitations of microarrays and real-time PCR systems these studies focused on a fixed set of targets. Expression of other RNA classes such as long intergenic non-coding RNAs or sno-derived RNAs has rarely been examined in pancreatic cancer. Here, we analysed the coding and non-coding transcriptome of six PDAC and five control tissues using next-generation sequencing.ResultsBesides the confirmation of several deregulated mRNAs and miRNAs, miRNAs without previous implication in PDAC were detected: miR-802, miR-2114 or miR-561. SnoRNA-derived RNAs (e.g. sno-HBII-296B) and piR-017061, a piwi-interacting RNA, were found to be differentially expressed between PDAC and control tissues. In silico target analysis of miR-802 revealed potential binding sites in the 3′ UTR of TCF4, encoding a transcription factor that controls Wnt signalling genes. Overexpression of miR-802 in MiaPaCa pancreatic cancer cells reduced TCF4 protein levels. Using Massive Analysis of cDNA Ends (MACE) we identified differential expression of 43 lincRNAs, long intergenic non-coding RNAs, e.g. LINC00261 and LINC00152 as well as several natural antisense transcripts like HNF1A-AS1 and AFAP1-AS1. Differential expression was confirmed by qPCR on the mRNA/miRNA/lincRNA level and by immunohistochemistry on the protein level.ConclusionsHere, we report a novel lncRNA, sncRNA and mRNA signature of PDAC. In silico prediction of ncRNA targets allowed for assigning potential functions to differentially regulated RNAs.

【 授权许可】

Unknown   
© Müller et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.