miREC: a database of miRNAs involved in the development of endometrial cancer

BMC Research Notes

Björn Olsson¹  Karin Klinga-Levan²  Angelica Lindlöf¹  Sanja Jurcevic²  Benjamin Ulfenborg¹ 

[1] Systems Biology Research Centre – Bioinformatics, University of Skövde, Skövde, 541 28, Sweden;Systems Biology Research Centre – Tumor Biology, University of Skövde, Skövde, 54128, Sweden

关键词: Database;    MicroRNA;    Endometrial cancer;   

Others  :  1145810
DOI  :  10.1186/s13104-015-1052-9

 received in 2014-12-02, accepted in 2015-03-11,  发布年份 2015

【 摘 要 】

Background

Endometrial cancer (EC) is the most frequently diagnosed gynecological malignancy and the fourth most common cancer diagnosis overall among women. As with many other forms of cancer, it has been shown that certain miRNAs are differentially expressed in EC and these miRNAs are believed to play important roles as regulators of processes involved in the development of the disease. With the rapidly growing number of studies of miRNA expression in EC, there is a need to organize the data, combine the findings from experimental studies of EC with information from various miRNA databases, and make the integrated information easily accessible for the EC research community.

Findings

The miREC database is an organized collection of data and information about miRNAs shown to be differentially expressed in EC. The database can be used to map connections between miRNAs and their target genes in order to identify specific miRNAs that are potentially important for the development of EC. The aim of the miREC database is to integrate all available information about miRNAs and target genes involved in the development of endometrial cancer, and to provide a comprehensive, up-to-date, and easily accessible source of knowledge regarding the role of miRNAs in the development of EC. Database URL: http://www.mirecdb.org.

Conclusions

Several databases have been published that store information about all miRNA targets that have been predicted or experimentally verified to date. It would be a time-consuming task to navigate between these different data sources and literature to gather information about a specific disease, such as endometrial cancer. The miREC database is a specialized data repository that, in addition to miRNA target information, keeps track of the differential expression of genes and miRNAs potentially involved in endometrial cancer development. By providing flexible search functions it becomes easy to search for EC-associated genes and miRNAs from different starting points, such as differential expression and genomic loci (based on genomic aberrations).

【 授权许可】

   
2015 Ulfenborg et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Ferlay J, Shin HR, Bray F, Forman D, Mathers C, Parkin DM: Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 2010, 127:2893-917.
• [2]Chung TKH, Cheung T-H, Huen N-Y, Wong KWY, Lo KWK, Yim S-F, et al.: Dysregulated microRNAs and their predicted targets associated with endometrioid endometrial adenocarcinoma in Hong Kong women. Int J Cancer 2009, 124:1358-65.
• [3]Boren T, Xiong Y, Hakam A, Wenham R, Apte S, Wei Z, et al.: MicroRNAs and their target messenger RNAs associated with endometrial carcinogenesis. Gynecol Oncol 2008, 110:206-15.
• [4]Cohn D, Fabbri M, Valeri N, Alder H, Ivanov I, Liu C, et al.: Comprehensive miRNA profiling of surgically staged endometrial cancer. Am J Obstet Gynecol 2010, 202:656. e-656.e658
• [5]Wu W, Lin Z, Zhuang Z, Liang X: Expression profile of mammalian microRNAs in endometrioid adenocarcinoma. Eur J Cancer Prev 2009, 18:50-5.
• [6]Ratner ES, Tuck D, Richter C, Nallur S, Patel RM, Schultz V, et al.: MicroRNA signatures differentiate uterine cancer tumor subtypes. Gynecol Oncol 2010, 118:251-7.
• [7]Torres A, Torres K, Pesci A, Ceccaroni M, Paszkowski T, Cassandrini P, et al.: Diagnostic and prognostic significance of miRNA signatures in tissues and plasma of endometrioid endometrial carcinoma patients. Int J Cancer 2013, 132:1633-45.
• [8]Liu X, Xia W, Dai YM, Shao NS, Zhang WY: [Expression of microRNAs in endometrioid adenocarcinoma]. Zhonghua Yi Xue Za Zhi / Chin J Med Genetics 2009, 89:1365-7.
• [9]Lee JW, Park YA, Choi JJ, Lee YY, Kim CJ, Choi C, et al.: The expression of the miRNA-200 family in endometrial endometrioid carcinoma. Gynecol Oncol 2011, 120:56-62.
• [10]Hutvagner G, McLachlan J, Pasquinelli A, Balint E, Tuschl T, Zamore P: A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Sci STKE 2001, 293:834.
• [11]Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, et al.: The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-9.
• [12]Lee Y, Jeon K, Lee J, Kim S, Kim V: MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 2002, 21:4663-70.
• [13]Blenkiron C, Miska E: miRNAs in cancer: approaches, aetiology, diagnostics and therapy. Hum Mol Genet 2007, 16:R106.
• [14]Stahlhut ECE, Slack F: The role of microRNAs in cancer. Yale J Biol Med 2006, 79:131.
• [15]Gottardo F, Liu CG, Ferracin M, Calin GA, Fassan M, Bassi P, et al.: Micro-RNA profiling in kidney and bladder cancers. Urol Oncol 2007, 25:387-92.
• [16]Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, et al.: MicroRNA signatures in human ovarian cancer. Cancer Res 2007, 67:8699.
• [17]Sempere LF, Christensen M, Silahtaroglu A, Bak M, Heath CV, Schwartz G, et al.: Altered MicroRNA expression confined to specific epithelial cell subpopulations in breast cancer. Cancer Res 2007, 67:11612-20.
• [18]Jurcevic S, Olsson B, Klinga-Levan K: MicroRNA expression in human endometrial adenocarcinoma. Cancer Cell Int 2014, 14:88. BioMed Central Full Text
• [19]Park SM, Gaur AB, Lengyel E, Peter ME: The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2. Genes Dev 2008, 22:894-907.
• [20]Myatt SS, Wang J, Monteiro LJ, Christian M, Ho KK, Fusi L, et al.: Definition of microRNAs that repress expression of the tumor suppressor gene FOXO1 in endometrial cancer. Cancer Res 2010, 70:367.
• [21]Wu D, Huang H-j, He C-n, Wang K-y: MicroRNA-199a-3p regulates endometrial cancer cell proliferation by targeting mammalian target of rapamycin (mTOR). Int J Gynecol Cancer 2013, 23:1191-7.
• [22]Tsukamoto O, Miura K, Mishima H, Abe S, Kaneuchi M, Higashijima A, et al.: Identification of endometrioid endometrial carcinoma-associated microRNAs in tissue and plasma. Gynecol Oncol 2014, 132:715-21.
• [23]Zhang X, Dong Y, Ti H, Zhao J, Wang Y, Li T, et al.: Diagnostic and prognostic significance of miRNA signatures in tissues and plasma of endometrioid carcinomas. Hum Pathol 2013, 44:2571-80.
• [24]Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-504.
• [25]Zhou J, Song T, Gong S, Zhong M, Su G: microRNA regulation of the expression of the estrogen receptor in endometrial cancer. Mol Med Report 2010, 3:387-92.
• [26]Chung TK, Lau TS, Cheung TH, Yim SF, Lo KW, Siu NS et al. Dysregulation of microRNA-204 mediates migration and invasion of endometrial cancer by regulating FOXC1. In Book Dysregulation of microRNA-204 mediates migration and invasion of endometrial cancer by regulating FOXC1 (Editor ed.^eds.), 2011/03/15 edition. City; 2011.
• [27]Wong YF, Cheung TH, Lo KW, Yim SF, Siu NS, Chan SC, et al.: Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling. Oncogene 2007, 26:1971-82.
• [28]Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T: miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, 37:D105-10.
• [29]Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG: The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, 37:D155-8.
• [30]Lee SJ, Cicila GT: Functional genomics in rat models of hypertension: using differential expression and congenic strains to identify and evaluate candidate genes. Crit Rev Eukaryot Gene Expr 2002, 12:297-316.
• [31]Hanahan D, Coussens LM: Accessories to the crime: functions of cells recruited to the tumor microenvironment. Cancer Cell 2012, 21:309-22.
• [32]Ruepp A, Kowarsch A, Schmidl D, Buggenthin F, Brauner B, Dunger I, et al.: PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol 2010, 11:R6. BioMed Central Full Text
• [33]Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, et al.: miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 2009, 37:D98-104.
• [34]Tanzer A, Stadler PF: Molecular evolution of a microRNA cluster. J Mol Biol 2004, 339:327-35.
• [35]Sass S, Dietmann S, Burk UC, Brabletz S, Lutter D, Kowarsch A, et al.: MicroRNAs coordinately regulate protein complexes. BMC Syst Biol 2011, 5:136. BioMed Central Full Text
• [36]Ambros V: The evolution of our thinking about microRNAs. Nat Med 2008, 14:1036-40.
• [37]Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell 2011, 144:646-74.
• [38]Li L, Yuan L, Luo J, Gao J, Guo J, Xie X: MiR-34a inhibits proliferation and migration of breast cancer through down-regulation of Bcl-2 and SIRT1. Clin Exp Med 2013, 13:109-17.
• [39]Aranha MM, Santos DM, Solá S, Steer CJ, Rodrigues CMP: miR-34a regulates mouse neural stem cell differentiation. PLoS One 2011, 6:e21396.
• [40]Holland CM, Saidi SA, Evans AL, Sharkey AM, Latimer JA, Crawford RAF, et al.: Transcriptome analysis of endometrial cancer identifies peroxisome proliferator-activated receptors as potential therapeutic targets. Mol Cancer Ther 2004, 3:993-1001.
• [41]Knapp P, Chabowski A, Blachnio-Zabielska A, Jarzabek K, Wolczynski S: Altered peroxisome-proliferator activated receptors expression in human endometrial cancer. PPAR Res 2012, 2012:471524.
• [42]Baskerville S, Bartel DP: Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005, 11:241-7.
• [43]Zhang YF, Zhang R, Su B: Diversity and evolution of MicroRNA gene clusters. Sci China Ser C Life Sci 2009, 52:261-6.
• [44]Kent OA, McCall MN, Cornish TC, Halushka MK: Lessons from miR-143/145: the importance of cell-type localization of miRNAs. Nucleic Acids Res 2014, 42:7528-38.
• [45]Hamta A, Adamovic T, Helou K, Levan G: Cytogenetic aberrations in spontaneous endometrial adenocarcinomas in the BDII rat model as revealed by chromosome banding and comparative genome hybridization. Cancer Genet Cytogenet 2005, 159:123-8.