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International Journal of Molecular Medicine
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Article Open Access

Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology

  • Authors:
    • Min Qi
    • Xiaoyuan Huang
    • Lei Zhou
    • Jianglin Zhang
  • View Affiliations / Copyright

    Affiliations: Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China, Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
    Copyright: © Qi et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY_NC 3.0].
  • Pages: 1117-1121
    |
    Published online on: February 25, 2014
       https://doi.org/10.3892/ijmm.2014.1668
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Abstract

In this study, we investigated differentially expressed microRNAs (miRNAs or miRs) and their functions in metastatic melanoma using next-generation sequencing technology. The GSE36236 data set was downloaded from the Gene Expression Omnibus (GEO) database and 4 primary cutaneous melanoma samples (used as controls) and 3 metastatic melanoma samples were selected from 31 samples for further analysis. Firstly, the differentially expressed miRNAs were screened by limma package in R language. Secondly, the target genes of the miRNAs were retrieved with TargetScanHuman 6.2, and the interactions among these genes were identified by String and an interaction network was established. Finally, functional and pathway analyses were performed for the genes in the network using Expression Analysis Systematic Explorer (EASE). A total of 4 differentially expressed miRNAs (hsa-miR-146, hsa-miR-27, hsa-miR-877 and hsa-miR-186) were obtained between the metastatic melanoma and primary cutaneous melanoma samples. We predicted 101 high-confidence target genes of hsa-miR-27 and obtained a network with 41 interactions. Finally, functional and pathway analyses revealed that the genes in the network were significantly enriched at the transcriptional level. Differentially expressed miRNAs were identified in the metastatic melanoma compared with the primary cutaneous melanoma samples and the target genes of hsa-miR-27 were found to be significantly enriched at the transcriptional level. The results presented in our study may prove helpful in the diagnosis and treatment of metastatic melanoma.
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1 

Hernandez BY, Green MD, Cassel KD, Pobutsky AM, Vu V and Wilkens LR: Preview of Hawaii cancer facts and figures 2010. Hawaii Med J. 69:223–224. 2010.PubMed/NCBI

2 

Gray-Schopfer V, Wellbrock C and Marais R: Melanoma biology and new targeted therapy. Nature. 445:851–857. 2007. View Article : Google Scholar : PubMed/NCBI

3 

Hatfield S and Ruohola-Baker H: microRNA and stem cell function. Cell Tissue Res. 331:57–66. 2008. View Article : Google Scholar

4 

Agarwala SS: Current systemic therapy for metastatic melanoma. Expert Rev Anticancer Ther. 9:587–595. 2009. View Article : Google Scholar : PubMed/NCBI

5 

Calin GA and Croce CM: MicroRNA-cancer connection: the beginning of a new tale. Cancer Res. 66:7390–7394. 2006. View Article : Google Scholar : PubMed/NCBI

6 

Iorio MV, Ferracin M, Liu CG, et al: MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 65:7065–7070. 2005. View Article : Google Scholar : PubMed/NCBI

7 

Ma L, Teruya-Feldstein J and Weinberg RA: Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature. 449:682–688. 2007. View Article : Google Scholar : PubMed/NCBI

8 

Yanaihara N, Caplen N, Bowman E, et al: Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell. 9:189–198. 2006. View Article : Google Scholar : PubMed/NCBI

9 

Zhou J, Yu L, Gao X, et al: Plasma microRNA panel to diagnose hepatitis B virus-related hepatocellular carcinoma. J Clin Oncol. 29:4781–4788. 2011. View Article : Google Scholar : PubMed/NCBI

10 

Chen CZ: MicroRNAs as oncogenes and tumor suppressors. N Engl J Med. 353:1768–1771. 2005. View Article : Google Scholar : PubMed/NCBI

11 

Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW and Ruohola-Baker H: Stem cell division is regulated by the microRNA pathway. Nature. 435:974–978. 2005. View Article : Google Scholar : PubMed/NCBI

12 

Giles KM, Barker A, Zhang PM, Epis MR and Leedman PJ: MicroRNA regulation of growth factor receptor signaling in human cancer cells. Methods Mol Biol. 676:147–163. 2011. View Article : Google Scholar : PubMed/NCBI

13 

Jiang S, Zhang HW, Lu MH, et al: MicroRNA-155 functions as an OncomiR in breast cancer by targeting the suppressor of cytokine signaling 1 gene. Cancer Res. 70:3119–3127. 2010. View Article : Google Scholar : PubMed/NCBI

14 

Shumway M, Cochrane G and Sugawara H: Archiving next generation sequencing data. Nucleic Acids Res. 38:D870–D871. 2010. View Article : Google Scholar : PubMed/NCBI

15 

Cock PJ, Fields CJ, Goto N, Heuer ML and Rice PM: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 38:1767–1771. 2010. View Article : Google Scholar : PubMed/NCBI

16 

Kaminuma E, Mashima J, Kodama Y, et al: DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res. 38:D33–D38. 2010. View Article : Google Scholar : PubMed/NCBI

17 

Langmead B, Trapnell C, Pop M and Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R252009. View Article : Google Scholar : PubMed/NCBI

18 

Trapnell C and Salzberg SL: How to map billions of short reads onto genomes. Nat Biotechnol. 27:455–457. 2009. View Article : Google Scholar : PubMed/NCBI

19 

Friedlander MR, Chen W, Adamidi C, et al: Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol. 26:407–415. 2008. View Article : Google Scholar : PubMed/NCBI

20 

Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT and ‘t Hoen PA: New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 11:7162010. View Article : Google Scholar : PubMed/NCBI

21 

Smyth GK: Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor. Gentleman R, Carey V, Dudoit S, Irizarry R and Huber W: Springer; New York: pp. 397–420. 2005, View Article : Google Scholar

22 

Lewis BP, Burge CB and Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 120:15–20. 2005. View Article : Google Scholar : PubMed/NCBI

23 

Friedman RC, Farh KK, Burge CB and Bartel DP: Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19:92–105. 2009. View Article : Google Scholar : PubMed/NCBI

24 

Tong AH, Drees B, Nardelli G, et al: A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 295:321–324. 2002. View Article : Google Scholar : PubMed/NCBI

25 

Szklarczyk D, Franceschini A, Kuhn M, et al: The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39:D561–D568. 2011. View Article : Google Scholar : PubMed/NCBI

26 

Hosack DA, Dennis G Jr, Sherman BT, Lane HC and Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol. 4:R702003. View Article : Google Scholar : PubMed/NCBI

27 

Steeg PS: Tumor metastasis: mechanistic insights and clinical challenges. Nat Med. 12:895–904. 2006. View Article : Google Scholar : PubMed/NCBI

28 

Rabinowits G, Gercel-Taylor C, Day JM, Taylor DD and Kloecker GH: Exosomal microRNA: a diagnostic marker for lung cancer. Clin Lung Cancer. 10:42–46. 2009. View Article : Google Scholar : PubMed/NCBI

29 

Katakowski M, Zheng X, Jiang F, Rogers T, Szalad A and Chopp M: MiR-146b-5p suppresses EGFR expression and reduces in vitro migration and invasion of glioma. Cancer Invest. 28:1024–1030. 2010. View Article : Google Scholar : PubMed/NCBI

30 

Mertens-Talcott SU, Chintharlapalli S, Li X and Safe S: The oncogenic microRNA-27a targets genes that regulate specificity protein transcription factors and the G2-M checkpoint in MDA-MB-231 breast cancer cells. Cancer Res. 67:11001–11011. 2007. View Article : Google Scholar

31 

Scott GK, Mattie MD, Berger CE, Benz SC and Benz CC: Rapid alteration of microRNA levels by histone deacetylase inhibition. Cancer Res. 66:1277–1281. 2006. View Article : Google Scholar : PubMed/NCBI

32 

Gottardo F, Liu CG, Ferracin M, et al: Micro-RNA profiling in kidney and bladder cancers. Urol Oncol. 25:387–392. 2007. View Article : Google Scholar : PubMed/NCBI

33 

Liu T, Tang H, Lang Y, Liu M and Li X: MicroRNA-27a functions as an oncogene in gastric adenocarcinoma by targeting prohibitin. Cancer Lett. 273:233–242. 2009. View Article : Google Scholar : PubMed/NCBI

34 

Guttilla IK and White BA: Coordinate regulation of FOXO1 by miR-27a, miR-96, and miR-182 in breast cancer cells. J Biol Chem. 284:23204–23216. 2009. View Article : Google Scholar : PubMed/NCBI

35 

Hiroki E, Akahira J, Suzuki F, et al: Changes in microRNA expression levels correlate with clinicopathological features and prognoses in endometrial serous adenocarcinomas. Cancer Sci. 101:241–249. 2010. View Article : Google Scholar : PubMed/NCBI

36 

Rhodes LV, Tilghman SL, Boue SM, et al: Glyceollins as novel targeted therapeutic for the treatment of triple-negative breast cancer. Oncol Lett. 3:163–171. 2012.PubMed/NCBI

37 

Baffa R, Fassan M, Volinia S, et al: MicroRNA expression profiling of human metastatic cancers identifies cancer gene targets. J Pathol. 219:214–221. 2009. View Article : Google Scholar : PubMed/NCBI

38 

Leidinger P, Keller A, Borries A, et al: High-throughput miRNA profiling of human melanoma blood samples. BMC Cancer. 10:2622010. View Article : Google Scholar : PubMed/NCBI

39 

Li X, Nishida T, Noguchi A, et al: Decreased nuclear expression and increased cytoplasmic expression of ING5 may be linked to tumorigenesis and progression in human head and neck squamous cell carcinoma. J Cancer Res Clin Oncol. 136:1573–1583. 2010. View Article : Google Scholar : PubMed/NCBI

40 

Bohm M, Locke WJ, Sutherland RL, Kench JG and Henshall SM: A role for GATA-2 in transition to an aggressive phenotype in prostate cancer through modulation of key androgen-regulated genes. Oncogene. 28:3847–3856. 2009. View Article : Google Scholar : PubMed/NCBI

41 

Wang J, Cai Y, Ren C and Ittmann M: Expression of variant TMPRSS2/ERG fusion messenger RNAs is associated with aggressive prostate cancer. Cancer Res. 66:8347–8351. 2006. View Article : Google Scholar : PubMed/NCBI

42 

Carver BS, Tran J, Gopalan A, et al: Aberrant ERG expression cooperates with loss of PTEN to promote cancer progression in the prostate. Nat Genet. 41:619–624. 2009. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Qi M, Huang X, Zhou L and Zhang J: Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology. Int J Mol Med 33: 1117-1121, 2014.
APA
Qi, M., Huang, X., Zhou, L., & Zhang, J. (2014). Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology. International Journal of Molecular Medicine, 33, 1117-1121. https://doi.org/10.3892/ijmm.2014.1668
MLA
Qi, M., Huang, X., Zhou, L., Zhang, J."Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology". International Journal of Molecular Medicine 33.5 (2014): 1117-1121.
Chicago
Qi, M., Huang, X., Zhou, L., Zhang, J."Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology". International Journal of Molecular Medicine 33, no. 5 (2014): 1117-1121. https://doi.org/10.3892/ijmm.2014.1668
Copy and paste a formatted citation
x
Spandidos Publications style
Qi M, Huang X, Zhou L and Zhang J: Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology. Int J Mol Med 33: 1117-1121, 2014.
APA
Qi, M., Huang, X., Zhou, L., & Zhang, J. (2014). Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology. International Journal of Molecular Medicine, 33, 1117-1121. https://doi.org/10.3892/ijmm.2014.1668
MLA
Qi, M., Huang, X., Zhou, L., Zhang, J."Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology". International Journal of Molecular Medicine 33.5 (2014): 1117-1121.
Chicago
Qi, M., Huang, X., Zhou, L., Zhang, J."Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology". International Journal of Molecular Medicine 33, no. 5 (2014): 1117-1121. https://doi.org/10.3892/ijmm.2014.1668
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