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
European Journal of Medical Research
Published in: European Journal of Medical Research 1/2014

Open Access 01-12-2014 | Research

RETRACTED ARTICLE: Reanalysis of the gene expression profile in chronic pancreatitis via bioinformatics methods

Authors: Hang Yuan, Bin Wu, Senlin Ma, Xiaoyu Yang, Lei Yin, Aijun Li

Published in: European Journal of Medical Research | Issue 1/2014

Login to get access

Abstract

Background

Diagnosis at an early stage of chronic pancreatitis (CP) is challenging. It has been reported that microRNAs (miRNAs) are increasingly found and applied as targets for the diagnosis and treatment of various cancers. However, to the best of our knowledge, few published papers have described the role of miRNAs in the diagnosis of CP.

Method

We downloaded gene expression profile data from the Gene Expression Omnibus and identified differentially expressed genes (DEGs) between CP and normal samples of Harlan mice and Jackson Laboratory mice. Common DEGs were filtered out, and the semantic similarities of gene classes were calculated using the GOSemSim software package. The gene class with the highest functional consistency was selected, and then the Lists2Networks web-based system was used to analyse regulatory relationships between miRNAs and gene classes. The functional enrichment of the gene classes was assessed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway annotation terms.

Results

A total of 405 common upregulated DEGs and 7 common downregulated DEGs were extracted from the two kinds of mice. Gene cluster D was selected from the common upregulated DEGs because it had the highest semantic similarity. miRNA 124a (miR-124a) was found to have a significant regulatory relationship with cluster D, and DEGs such as CHSY1 and ABCC4 were found to be regulated by miR-124a. The GO term of response to DNA damage stimulus and the pathway of Escherichia coli infection were significantly enriched in cluster D.

Conclusion

DNA damage and E. coli infection might play important roles in CP pathogenesis. In addition, miR-124a might be a potential target for the diagnosis and treatment of CP.
Appendix
Available only for authorised users
Literature
1.
2.
Coté GA, Yadav D, Slivka A, Hawes RH, Anderson MA, Burton FR, Brand RE, Banks PA, Lewis MD, Disario JA, Gardner TB, Gelrud A, Amann ST, Baillie J, Money ME, O’Connell M, Whitcomb DC, Sherman S, North American Pancreatitis Study Group: Alcohol and smoking as risk factors in an epidemiology study of patients with chronic pancreatitis. Clin Gastroenterol Hepatol 2011, 9: 266–273. 10.1016/j.cgh.2010.10.015PubMedCentralCrossRefPubMed
3.
Bloomston M, Frankel WL, Petrocca F, Volinia S, Alder H, Hagan JP, Liu CG, Bhatt D, Taccioli C, Croce CM: MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA 2007, 297: 1901–1908. 10.1001/jama.297.17.1901CrossRefPubMed
4.
Lee EJ, Gusev Y, Jiang J, Nuovo GJ, Lerner MR, Frankel WL, Morgan DL, Postier RG, Brackett DJ, Schmittgen TD: Expression profiling identifies microRNA signature in pancreatic cancer. Int J Canc 2007, 120: 1046–1054.CrossRef
5.
Luzi E, D’Asta F, Brandi ML: MicroRNAs and pancreatic-endocrine system. Noncoding RNA Endocrinol 2013, 1: 9–15. doi:10.2478/micrnado-2013–0003
6.
Nana‒Sinkam SP, Fabbri M, Croce CM: MicroRNAs in cancer: personalizing diagnosis and therapy. Ann N Y Acad Sci 2010, 1210: 25–33. 10.1111/j.1749-6632.2010.05822.xCrossRef
7.
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ: miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, 34(Database issue):D140-D144.PubMedCentralCrossRefPubMed
8.
Szafranska AE, Doleshal M, Edmunds HS, Gordon S, Luttges J, Munding JB, Barth RJ Jr, Gutmann EJ, Suriawinata AA, Pipas JM, Tannapfel A, Korc M, Hahn SA, Labourier E, Tsongalis GJ: Analysis of microRNAs in pancreatic fine-needle aspirates can classify benign and malignant tissues. Clin Chem 2008, 54: 1716–1724. 10.1373/clinchem.2008.109603PubMedCentralCrossRefPubMed
9.
Szafranska A, Davison TS, John J, Cannon T, Sipos B, Maghnouj A, Labourier E, Hahn SA: MicroRNA expression alterations are linked to tumorigenesis and non-neoplastic processes in pancreatic ductal adenocarcinoma. Oncogene 2007, 26: 4442–4452. 10.1038/sj.onc.1210228CrossRefPubMed
10.
Ulmasov B, Oshima K, Rodriguez MG, Cox RD, Neuschwander-Tetri BA: Differences in the degree of cerulein-induced chronic pancreatitis in C57BL/6 mouse substrains lead to new insights in identification of potential risk factors in the development of chronic pancreatitis. Am J Pathol 2013, 183: 692–708. 10.1016/j.ajpath.2013.05.020PubMedCentralCrossRefPubMed
11.
Gharaibeh RZ, Fodor AA, Gibas CJ: Background correction using dinucleotide affinities improves the performance of GCRMA. BMC Bioinforma 2008, 9: 452. 10.1186/1471-2105-9-452CrossRef
12.
Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98: 5116–5121. A published erratum appears in Proc Natl Acad Sci U S A 2001, 98:10515 10.1073/pnas.091062498PubMedCentralCrossRefPubMed
13.
Benesty J, Chen J, Huang Y, Cohen I: Pearson correlation coefficient. Springer Topics in Signal Processing Volume 2. In Noise Reduction in Speech Processing. Edited by: Cohen I, Huang Y, Chen J, Benesty J. Berlin: Springer; 2009:1–4.
14.
Ramoni MF, Sebastiani P, Kohane IS: Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A 2002, 99: 9121–9126. 10.1073/pnas.132656399PubMedCentralCrossRefPubMed
15.
Herrero J, Valencia A, Dopazo J: A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 2001, 17: 126–136. 10.1093/bioinformatics/17.2.126CrossRefPubMed
16.
Tárraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcárate S, Goetz S, Escobar P, Garcia-Garcia F, Conesa A, Montaner D, Dopazo J: GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res 2008, 36(Web Server issue):W308-W314.PubMedCentralCrossRefPubMed
17.
Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S: GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 2010, 26: 976–978. 10.1093/bioinformatics/btq064CrossRefPubMed
18.
Allocco DJ, Kohane IS, Butte AJ: Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinforma 2004, 5: 18. 10.1186/1471-2105-5-18CrossRef
19.
Lachmann A, Ma’ayan A: Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinforma 2010, 11: 87. 10.1186/1471-2105-11-87CrossRef
20.
Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T: Identification of tissue-specific microRNAs from mouse. Curr Biol 2002, 12: 735–739.CrossRefPubMed
21.
Nakamachi Y, Kawano S, Takenokuchi M, Nishimura K, Sakai Y, Chin T, Saura R, Kurosaka M, Kumagai S: MicroRNA‒124a is a key regulator of proliferation and monocyte chemoattractant protein 1 secretion in fibroblast‒like synoviocytes from patients with rheumatoid arthritis. Arthritis Rheum 2009, 60: 1294–1304. 10.1002/art.24475CrossRefPubMed
22.
Sanuki R, Onishi A, Koike C, Muramatsu R, Watanabe S, Muranishi Y, Irie S, Uneo S, Koyasu T, Matsui R, Chérasse Y, Urade Y, Watanabe D, Kondo M, Yamashita T, Furukawa T: miR-124a is required for hippocampal axogenesis and retinal cone survival through Lhx2 suppression. Nat Neurosci 2011, 14: 1125–1134. 10.1038/nn.2897CrossRefPubMed
23.
Baroukh N, Ravier MA, Loder MK, Hill EV, Bounacer A, Scharfmann R, Rutter GA, Van Obberghen E: MicroRNA-124a regulates Foxa2 expression and intracellular signaling in pancreatic β-cell lines. J Biol Chem 2007, 282: 19575–19588. 10.1074/jbc.M611841200CrossRefPubMed
24.
Kalathas D, Theocharis DA, Bounias D, Kyriakopoulou D, Papageorgakopoulou N, Stavropoulos MS, Vynios DH: Chondroitin synthases I, II, III and chondroitin sulfate glucuronyltransferase expression in colorectal cancer. Mol Med Rep 2011, 4: 363–368.PubMed
25.
Wilson DG, Phamluong K, Lin WY, Barck K, Carano RA, Diehl L, Peterson AS, Martin F, Solloway MJ: Chondroitin sulfate synthase 1 (Chsy1) is required for bone development and digit patterning. Dev Biol 2012, 363: 413–425. 10.1016/j.ydbio.2012.01.005CrossRefPubMed
26.
Tian J, Ling L, Shboul M, Lee H, O’Connor B, Merriman B, Nelson SF, Cool S, Ababneh OH, Al-Hadidy A, Masri A, Hamamy H, Reversade B: Loss of CHSY1, a secreted FRINGE enzyme, causes syndromic brachydactyly in humans via increased NOTCH signaling. Am J Hum Genet 2010, 87: 768–778. 10.1016/j.ajhg.2010.11.005PubMedCentralCrossRefPubMed
27.
Thornberry NA, Bull HG, Calaycay JR, Chapman KT, Howard AD, Kostura MJ, Miller DK, Molineaux SM, Weidner JR, Aunins J, Elliston KO, Ayala JM, Casano FJ, Chin J, Ding GJF, Egger LA, Gaffney EP, Limjuco G, Palyha OC, Raju SM, Rolando AM, Salley JP, Yamin TT, Lee TD, Shively JE, Maccross M, Mumford RA, Schmidt JA, Tocci MJ: A novel heterodimeric cysteine protease is required for interleukin-1β processing in monocytes. Nature 1992, 356: 768–774. 10.1038/356768a0CrossRefPubMed
28.
Ramadani M, Yang Y, Gansauge F, Gansauge S, Beger HG: Overexpression of caspase-1 (interleukin-1β converting enzyme) in chronic pancreatitis and its participation in apoptosis and proliferation. Pancreas 2001, 22: 383–387. 10.1097/00006676-200105000-00008CrossRefPubMed
29.
Gottesman MM, Ambudkar SV: Overview: ABC transporters and human disease. J Bioenerg Biomembr 2001, 33: 453–458. 10.1023/A:1012866803188CrossRefPubMed
30.
Lage H: An overview of cancer multidrug resistance: a still unsolved problem. Cell Mol Life Sci 2008, 65: 3145–3167. 10.1007/s00018-008-8111-5CrossRefPubMed
31.
El-Sheikh AAK, van den Heuvel JJMW, Koenderink JB, Russel FG: Interaction of nonsteroidal anti-inflammatory drugs with multidrug resistance protein (MRP) 2/ABCC2- and MRP4/ABCC4-mediated methotrexate transport. J Pharmacol Exp Ther 2007, 320: 229–235.CrossRefPubMed
32.
Rius M, Hummel-Eisenbeiss J, Keppler D: ATP-dependent transport of leukotrienes B4 and C4 by the multidrug resistance protein ABCC4 (MRP4). J Pharmacol Exp Ther 2008, 324: 86–94.CrossRefPubMed
33.
Bartsch H, Nair J: Chronic inflammation and oxidative stress in the genesis and perpetuation of cancer: role of lipid peroxidation, DNA damage, and repair. Langenbecks Arch Surg 2006, 391: 499–510. 10.1007/s00423-006-0073-1CrossRefPubMed
34.
Sodhi RK, Singh N, Jaggi AS: Poly(ADP-ribose) polymerase-1 (PARP-1) and its therapeutic implications. Vascul Pharmacol 2010, 53: 77–87. 10.1016/j.vph.2010.06.003CrossRefPubMed
35.
Boehler C, Gauthier LR, Mortusewicz O, Biard DS, Saliou JM, Bresson A, Sanglier-Cianferani S, Smith S, Schreiber V, Boussin F, Dantzer F: Poly(ADP-ribose) polymerase 3 (PARP3), a newcomer in cellular response to DNA damage and mitotic progression. Proc Natl Acad Sci U S A 2011, 108: 2783–2788. 10.1073/pnas.1016574108PubMedCentralCrossRefPubMed
36.
Hamby AM, Suh SW, Kauppinen TM, Swanson RA: Use of a poly(ADP-ribose) polymerase inhibitor to suppress inflammation and neuronal death after cerebral ischemia-reperfusion. Stroke 2007, 38(2 Suppl):632–636.CrossRefPubMed
37.
de la Lastra CA, Villegas I, Sánchez-Fidalgo S: Poly(ADP-ribose) polymerase inhibitors: new pharmacological functions and potential clinical implications. Curr Pharm Des 2007, 13: 933–962. 10.2174/138161207780414241CrossRefPubMed
38.
Jagtap P, Szabó C: Poly(ADP-ribose) polymerase and the therapeutic effects of its inhibitors. Nat Rev Drug Discov 2005, 4: 421–440. 10.1038/nrd1718CrossRefPubMed
39.
Kauppinen TM, Suh SW, Berman AE, Hamby AM, Swanson RA: Inhibition of poly(ADP-ribose) polymerase suppresses inflammation and promotes recovery after ischemic injury. J Cereb Blood Flow Metab 2009, 29: 820–829. 10.1038/jcbfm.2009.9CrossRefPubMed
40.
Karmali MA, Steele BT, Petric M, Lim C: Sporadic cases of haemolytic-uraemic syndrome associated with faecal cytotoxin and cytotoxin-producing Escherichia coli in stools. Lancet 1983, 1: 619–620.CrossRefPubMed
41.
Mead PS, Griffin PM: Escherichia coli O157:H7. Lancet 1998, 352: 1207–1212. 10.1016/S0140-6736(98)01267-7CrossRefPubMed
42.
Baradkar VP, Mathur M, Kumar S: Pancreatic abscess secondary to gall stones caused by Escherichia coli. Indian J Pathol Microbiol 2009, 52: 573–574. 10.4103/0377-4929.56162CrossRefPubMed
43.
Issekutz AC, Bhimji S: Role for endotoxin in the leukocyte infiltration accompanying Escherichia coli inflammation. Infect Immun 1982, 36: 558–566.PubMedCentralPubMed
Metadata
Title
RETRACTED ARTICLE: Reanalysis of the gene expression profile in chronic pancreatitis via bioinformatics methods
Authors
Hang Yuan
Bin Wu
Senlin Ma
Xiaoyu Yang
Lei Yin
Aijun Li
Publication date
01-12-2014
Publisher
BioMed Central
Published in
European Journal of Medical Research / Issue 1/2014
Electronic ISSN: 2047-783X
DOI
https://doi.org/10.1186/2047-783X-19-31

Other articles of this Issue 1/2014

European Journal of Medical Research 1/2014 Go to the issue

Research

Downregulation of TES by hypermethylation in glioblastoma reduces cell apoptosis and predicts poor clinical outcome

Research

Low-frequency pulsed electromagnetic fields significantly improve time of closure and proliferation of human tendon fibroblasts

Research

Nasal position of nasotracheal tubes: a retrospective analysis of intraoperatively generated three-dimensional X-rays during maxillofacial surgery

Research

The prevalence of BRCA1/2 mutations of triple-negative breast cancer patients in Xinjiang multiple ethnic region of China

Research

Dynamic change of glomerular filtration rate in the early stage is associated with kidney allograft status: a preliminary report

Research

Treatment of mild and moderate type-2 diabetes: open prospective trial with Hintonia latiflora extract