Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.
ADVANCED SEARCH
Log in
Top
Molecular Cancer
Published in: Molecular Cancer 1/2015

Open Access 01-12-2015 | Research

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

Authors: Sören Müller, Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann, Carsten Jäger, Anna Melissa Schlitter, Bo Kong, Ivonne Regel, W Kurt Roth, Björn Rotter, Klaus Hoffmeier, Günter Kahl, Ina Koch, Fabian J Theis, Jörg Kleeff, Peter Winter, Christoph W Michalski

Published in: Molecular Cancer | Issue 1/2015

Login to get access

Abstract

Background

Previous 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.

Results

Besides 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.

Conclusions

Here, 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.
Appendix
Available only for authorised users
Literature
1.
2.
Logsdon CD, Simeone DM, Binkley C, Arumugam T, Greenson JK, Giordano TJ, et al. Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer. Cancer Res. 2003;63(10):2649–57.PubMed
3.
Costello E, Greenhalf W, Neoptolemos JP. New biomarkers and targets in pancreatic cancer and their application to treatment. Nat Rev Gastroenterol Hepatol. 2012;9(8):435–44. doi:10.1038/nrgastro.2012.119.CrossRefPubMed
4.
Rosty C, Ueki T, Argani P, Jansen M, Yeo CJ, Cameron JL. Overexpression of S100A4 in pancreatic ductal adenocarcinomas is associated with poor differentiation and DNA hypomethylation. Am J Pathol. 2002;160(1):45–50. doi:10.1016/s0002-9440(10)64347-7.PubMedCentralCrossRefPubMed
5.
Wang L, Tsutsumi S, Kawaguchi T, Nagasaki K, Tatsuno K, Yamamoto S, et al. Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency. Genome Res. 2012;22(2):208–19. doi:10.1101/gr.123109.111.PubMedCentralCrossRefPubMed
6.
Yu M, Ting DT, Stott SL, Wittner BS, Ozsolak F, Paul S, et al. RNA sequencing of pancreatic circulating tumour cells implicates Wnt signalling in metastasis. Nature. 2012;487(7408):510–3. doi:10.1038/nature11217.
7.
Bauer AS, Keller A, Costello E, Greenhalf W, Bier M, Borries A, et al. Diagnosis of pancreatic ductal adenocarcinoma and chronic pancreatitis by measurement of microRNA abundance in blood and tissue. PLoS One. 2012;7(4):e34151. doi:10.1371/journal.pone.0034151.PubMedCentralCrossRefPubMed
8.
Jamieson NB, Morran DC, Morton JP, Ali A, Dickson EJ, Carter CR, et al. MicroRNA molecular profiles associated with diagnosis, clinicopathologic criteria, and overall survival in patients with resectable pancreatic ductal adenocarcinoma. Clin Cancer Res. 2012;18(2):534–45. doi:10.1158/1078-0432.ccr-11-0679.CrossRefPubMed
9.
Munding JB, Adai AT, Maghnouj A, Urbanik A, Zollner H, Liffers ST, et al. Global microRNA expression profiling of microdissected tissues identifies miR-135b as a novel biomarker for pancreatic ductal adenocarcinoma. Int J Canc. 2012;131(2):E86–95. doi:10.1002/ijc.26466.CrossRef
10.
Piepoli A, Tavano F, Copetti M, Mazza T, Palumbo O, Panza A, et al. Mirna expression profiles identify drivers in colorectal and pancreatic cancers. PLoS One. 2012;7(3):e33663. doi:10.1371/journal.pone.0033663.PubMedCentralCrossRefPubMed
11.
Szafranska AE, Davison TS, John J, Cannon T, Sipos B, Maghnouj A, et al. MicroRNA expression alterations are linked to tumorigenesis and non-neoplastic processes in pancreatic ductal adenocarcinoma. Oncogene. 2007;26(30):4442–52. doi:10.1038/sj.onc.1210228.CrossRefPubMed
12.
Zhang Y, Li M, Wang H, Fisher WE, Lin PH, Yao Q, et al. Profiling of 95 microRNAs in pancreatic cancer cell lines and surgical specimens by real-time PCR analysis. World J Surg. 2009;33(4):698–709. doi:10.1007/s00268-008-9833-0.PubMedCentralCrossRefPubMed
13.
Djuranovic S, Nahvi A, Green R. MiRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science (New York, NY). 2012;336(6078):237–40. doi:10.1126/science.1215691.CrossRef
14.
15.
Su H, Xu T, Ganapathy S, Shadfan M, Long M, Huang TH, et al. Elevated snoRNA biogenesis is essential in breast cancer. Oncogene. 2014;33(11):1348–58. doi:10.1038/onc.2013.89.CrossRefPubMed
16.
Martens-Uzunova ES, Olvedy M, Jenster G. Beyond microRNA–novel RNAs derived from small non-coding RNA and their implication in cancer. Cancer Lett. 2013;340(2):201–11. doi:10.1016/j.canlet.2012.11.058.CrossRefPubMed
17.
Cheng J, Deng H, Xiao B, Zhou H, Zhou F, Shen Z. piR-823, a novel non-coding small RNA, demonstrates in vitro and in vivo tumor suppressive activity in human gastric cancer cells. Cancer Lett. 2012;315(1):12–7. doi:10.1016/j.canlet.2011.10.004.CrossRefPubMed
18.
Tahira AC, Kubrusly MS, Faria MF, Dazzani B, Fonseca RS, Maracaja-Coutinho V, et al. Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Mol Cancer. 2011;10:141. doi:10.1186/1476-4598-10-141.PubMedCentralCrossRefPubMed
19.
20.
21.
Xia T, Liao Q, Jiang X, Shao Y, Xiao B, Xi Y, et al. Long noncoding RNA associated-competing endogenous RNAs in gastric cancer. Sci Rep. 2014;4:6088. doi:10.1038/srep06088.PubMedCentralPubMed
22.
Tsai MC, Spitale RC, Chang HY. Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res. 2011;71(1):3–7. doi:10.1158/0008-5472.can-10-2483.PubMedCentralCrossRefPubMed
23.
Dayem Ullah AZ, Cutts RJ, Ghetia M, Gadaleta E, Hahn SA, Crnogorac-Jurcevic T, et al. The pancreatic expression database: recent extensions and updates. Nucleic Acids Res. 2014;42(Database issue):D944–9. doi:10.1093/nar/gkt959.PubMedCentralCrossRefPubMed
24.
Cao WJ, Wu HL, He BS, Zhang YS, Zhang ZY. Analysis of long non-coding RNA expression profiles in gastric cancer. World J Gastroenterol. 2013;19(23):3658–64. doi:10.3748/wjg.v19.i23.3658.PubMedCentralCrossRefPubMed
25.
Wu W, Bhagat TD, Yang X, Song JH, Cheng Y, Agarwal R, et al. Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett’s esophagus and esophageal adenocarcinoma. Gastroenterology. 2013;144(5):956–66. doi:10.1053/j.gastro.2013.01.019. 5.PubMedCentralCrossRefPubMed
26.
Yang X, Song JH, Cheng Y, Wu W, Bhagat T, Yu Y, et al. Long non-coding RNA HNF1A-AS1 regulates proliferation and migration in oesophageal adenocarcinoma cells. Gut. 2014;63(6):881–90. doi:10.1136/gutjnl-2013-305266.PubMedCentralCrossRefPubMed
27.
Muller S, Rycak L, Winter P, Kahl G, Koch I, Rotter B. OmiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Bioinformatics (Oxford, England). 2013;29(20):2651–2. doi:10.1093/bioinformatics/btt457.CrossRef
28.
Li JH, Liu S, Zhou H, Qu LH, Yang JH. StarBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(Database issue):D92–7. doi:10.1093/nar/gkt1248.PubMedCentralCrossRefPubMed
29.
Wang J, Paris PL, Chen J, Ngo V, Yao H, Frazier ML. Next generation sequencing of pancreatic cyst fluid microRNAs from low grade-benign and high grade-invasive lesions. Cancer Lett. 2015;356(2 Pt B):404–9. doi:10.1016/j.canlet.2014.09.029.CrossRefPubMed
30.
Badea L, Herlea V, Dima SO, Dumitrascu T, Popescu I. Combined gene expression analysis of whole-tissue and microdissected pancreatic ductal adenocarcinoma identifies genes specifically overexpressed in tumor epithelia. Hepato-Gastroenterology. 2008;55(88):2016–27.PubMed
31.
Prevot PP, Augereau C, Simion A, Van den Steen G, Dauguet N, Lemaigre FP, et al. Let-7b and miR-495 stimulate differentiation and prevent metaplasia of pancreatic acinar cells by repressing HNF6. Gastroenterology. 2013;145(3):668–78. doi:10.1053/j.gastro.2013.05.016. 3.CrossRefPubMed
32.
Kopp JL, von Figura G, Mayes E, Liu FF, Dubois CL, Morris JP, et al. Identification of Sox9-dependent acinar-to-ductal reprogramming as the principal mechanism for initiation of pancreatic ductal adenocarcinoma. Cancer Cell. 2012;22(6):737–50. doi:10.1016/j.ccr.2012.10.025.PubMedCentralCrossRefPubMed
33.
Charrier A, Chen R, Chen L, Kemper S, Hattori T, Takigawa M, et al. Connective tissue growth factor (CCN2) and microRNA-21 are components of a positive feedback loop in pancreatic stellate cells (PSC) during chronic pancreatitis and are exported in PSC-derived exosomes. J Cell Commun Signal. 2014;8(2):147–56. doi:10.1007/s12079-014-0220-3.PubMedCentralCrossRefPubMed
34.
Cao ZQ, Shen Z, Huang WY. MicroRNA-802 promotes osteosarcoma cell proliferation by targeting p27. Asian Pac J Cancer Prev. 2013;14(12):7081–4.CrossRefPubMed
35.
Wang LQ, Chen G, Liu XY, Liu FY, Jiang SY, Wang Z. microRNA802 promotes lung carcinoma proliferation by targeting the tumor suppressor menin. Mol Med Rep. 2014;10(3):1537–42. doi:10.3892/mmr.2014.2361.PubMed
36.
Wang C, Ren R, Hu H, Tan C, Han M, Wang X, et al. MiR-182 is up-regulated and targeting Cebpa in hepatocellular carcinoma. Chin J Cancer Res. 2014;26(1):17–29. doi:10.3978/j.issn.1000-9604.2014.01.01.PubMedCentralPubMed
37.
Lan F, Yue X, Han L, Shi Z, Yang Y, Pu P, et al. Genome-wide identification of TCF7L2/TCF4 target miRNAs reveals a role for miR-21 in Wnt-driven epithelial cancer. Int J Oncol. 2012;40(2):519–26. doi:10.3892/ijo.2011.1215.PubMed
38.
Ji J, Yamashita T, Wang XW. Wnt/beta-catenin signaling activates microRNA-181 expression in hepatocellular carcinoma. Cell & Bioscience. 2011;1(1):4. doi:10.1186/2045-3701-1-4.CrossRef
39.
Liu J, Xu D, Wang Q, Zheng D, Jiang X, Xu L. LPS induced miR-181a promotes pancreatic cancer cell migration via targeting PTEN and MAP2K4. Dig Dis Sci. 2014;59(7):1452–60. doi:10.1007/s10620-014-3049-y.CrossRefPubMed
40.
Sicard F, Gayral M, Lulka H, Buscail L, Cordelier P. Targeting miR-21 for the therapy of pancreatic cancer. Mol Ther. 2013;21(5):986–94. doi:10.1038/mt.2013.35.PubMedCentralCrossRefPubMed
41.
Sanchez-Tillo E, de Barrios O, Siles L, Cuatrecasas M, Castells A, Postigo A. Beta-catenin/TCF4 complex induces the epithelial-to-mesenchymal transition (EMT)-activator ZEB1 to regulate tumor invasiveness. Proc Natl Acad Sci U S A. 2011;108(48):19204–9. doi:10.1073/pnas.1108977108.PubMedCentralCrossRefPubMed
42.
Wellner U, Schubert J, Burk UC, Schmalhofer O, Zhu F, Sonntag A, et al. The EMT-activator ZEB1 promotes tumorigenicity by repressing stemness-inhibiting microRNAs. Nat Cell Biol. 2009;11(12):1487–95. doi:10.1038/ncb1998.CrossRefPubMed
43.
Zhao G, Zhang JG, Shi Y, Qin Q, Liu Y, Wang B, et al. MiR-130b is a prognostic marker and inhibits cell proliferation and invasion in pancreatic cancer through targeting STAT3. PLoS One. 2013;8(9):e73803. 10.1371/journal.pone.0073803.PubMedCentralCrossRefPubMed
44.
Cao Y, Hoeppner LH, Bach S, E G, Guo Y, Wang E. Neuropilin-2 promotes extravasation and metastasis by interacting with endothelial alpha5 integrin. Cancer Res. 2013;73(14):4579–90. doi:10.1158/0008-5472.can-13-0529.PubMedCentralCrossRefPubMed
45.
Li C, Wu JJ, Hynes M, Dosch J, Sarkar B, Welling TH, et al. c-Met is a marker of pancreatic cancer stem cells and therapeutic target. Gastroenterology. 2011;141(6):2218–27. doi:10.1053/j.gastro.2011.08.009. 6.CrossRefPubMed
46.
Chen Q, Zhao X, Zhang H, Yuan H, Zhu M, Sun Q, et al. MiR-130b suppresses prostate cancer metastasis through down-regulation of MMP2. Molecular carcinogenesis. 2014. doi:10.1002/mc.22204
47.
48.
Serviss JT, Johnsson P, Grander D. An emerging role for long non-coding RNAs in cancer metastasis. Front Genet. 2014;5:234. doi:10.3389/fgene.2014.00234.PubMedCentralCrossRefPubMed
49.
Liu JH, Chen G, Dang YW, Li CJ, Luo DZ. Expression and prognostic significance of lncRNA MALAT1 in pancreatic cancer tissues. Asian Pac J Cancer Prev. 2014;15(7):2971–7.CrossRefPubMed
50.
Chelala C, Hahn SA, Whiteman HJ, Barry S, Hariharan D, Radon TP, et al. Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets. BMC Genomics. 2007;8:439. doi:10.1186/1471-2164-8-439.PubMedCentralCrossRefPubMed
51.
Kim K, Jutooru I, Chadalapaka G, Johnson G, Frank J, Burghardt R, et al. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene. 2013;32(13):1616–25. doi:10.1038/onc.2012.193.PubMedCentralCrossRefPubMed
52.
You L, Chang D, Du HZ, Zhao YP. Genome-wide screen identifies PVT1 as a regulator of Gemcitabine sensitivity in human pancreatic cancer cells. Biochem Biophys Res Commun. 2011;407(1):1–6. doi:10.1016/j.bbrc.2011.02.027.CrossRefPubMed
53.
Pang Q, Ge J, Shao Y, Sun W, Song H, Xia T, et al. Increased expression of long intergenic non-coding RNA LINC00152 in gastric cancer and its clinical significance. Tumour Biol. 2014;35(6):5441–7. doi:10.1007/s13277-014-1709-3.CrossRefPubMed
54.
Dong XY, Rodriguez C, Guo P, Sun X, Talbot JT, Zhou W, et al. SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum Mol Genet. 2008;17(7):1031–42. doi:10.1093/hmg/ddm375.PubMedCentralCrossRefPubMed
55.
Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res. 2011;39(2):675–86. doi:10.1093/nar/gkq776.PubMedCentralCrossRefPubMed
56.
Cheng J, Guo JM, Xiao BX, Miao Y, Jiang Z, Zhou H. PiRNA, the new non-coding RNA, is aberrantly expressed in human cancer cells. Clin Chim Acta. 2011;412(17–18):1621–5. doi:10.1016/j.cca.2011.05.015.CrossRefPubMed
57.
Müller S, Rycak L, Afonso-Grunz F, Winter P, Zawada AM, Damrath E, et al. APADB: a database for alternative polyadenylation and microRNA regulation events. Database. 2014; bau076.
58.
59.
Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics (Oxford, England). 1998;14(8):656–64.CrossRef
60.
Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007;35(Web Server issue):W169–75. doi:10.1093/nar/gkm415.PubMedCentralCrossRefPubMed
61.
Zhang HM, Chen H, Liu W, Liu H, Gong J, Wang H, et al. AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res. 2012;40(Database issue):D144–9. doi:10.1093/nar/gkr965.PubMedCentralCrossRefPubMed
62.
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011;39(Database issue):D561–8. doi:10.1093/nar/gkq973.PubMedCentralCrossRefPubMed
Metadata
Title
Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Authors
Sören Müller
Susanne Raulefs
Philipp Bruns
Fabian Afonso-Grunz
Anne Plötner
Rolf Thermann
Carsten Jäger
Anna Melissa Schlitter
Bo Kong
Ivonne Regel
W Kurt Roth
Björn Rotter
Klaus Hoffmeier
Günter Kahl
Ina Koch
Fabian J Theis
Jörg Kleeff
Peter Winter
Christoph W Michalski
Publication date
01-12-2015
Publisher
BioMed Central
Published in
Molecular Cancer / Issue 1/2015
Electronic ISSN: 1476-4598
DOI
https://doi.org/10.1186/s12943-015-0358-5

Other articles of this Issue 1/2015

Molecular Cancer 1/2015 Go to the issue

Research

Stromal ING1 expression induces a secretory phenotype and correlates with breast cancer patient survival

Review

p66Shc as a switch in bringing about contrasting responses in cell growth: implications on cell proliferation and apoptosis

Research

Targeting of YAP1 by microRNA-15a and microRNA-16-1 exerts tumor suppressor function in gastric adenocarcinoma

Research

Impaired autophagy in mouse embryonic fibroblasts null for Krüppel-like Factor 4 promotes DNA damage and increases apoptosis upon serum starvation

Research

Long non-coding RNA TUG1 is up-regulated in hepatocellular carcinoma and promotes cell growth and apoptosis by epigenetically silencing of KLF2

Research

A20 suppresses hepatocellular carcinoma proliferation and metastasis through inhibition of Twist1 expression
Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras
Prof. Fabrice Barlesi
Developed by: Springer Medicine
Image Credits