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Long Non-Coding RNA SNHG6 as a Potential Biomarker for Hepatocellular Carcinoma

  • Original Article
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Pathology & Oncology Research

Abstract

Long Non-coding RNAs (lncRNAs) refer to all non-protein coding transcripts longer than 200 nucleotides. Their critical roles in different biological pathways have been already well established. Altered expression of lncRNAs can be involved in the cancer initiation and/or progression. Since patients with hepatocellular carcinoma (HCC) are usually diagnosed in late stages, developing diagnostic methods seems to be essential. In this study, the expression levels of different lncRNAs were systematically analysed in different genomic and transcriptome datasets. The analyses showed that SNHG6 is among the lncRNAs with distinctive dysregulation of expression and copy number variation in HCC tumors compared with normal tissues. The results also suggest that the dysregulation of SNHG6 is highly cancer type specific. Through co-occurrence analyses, we found that SNHG6 and its related co-expressed genes on 8q are involved in the structural integrity of ribosome and translation. This comprehensive in silico analysis, provides a resource for investigating SNHG6 in hepatocellular carcinoma and lays the groundwork for design of next researches.

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References

  1. Wang C-H, Wey K-C, Mo L-R, Chang K-K, Lin R-C, Kuo J-J (2014) Current trends and recent advances in diagnosis, therapy, and prevention of hepatocellular carcinoma. Asian Pac J Cancer Prev 16:3595–3604

    Article  Google Scholar 

  2. Mazzocca A, Tahmasebi Birgani M, Sabbà C, Carloni V (2014) Tetraspanin-enriched Microdomains and hepatocellular carcinoma progression. Cancer Lett 351(1):23–29

    Article  CAS  PubMed  Google Scholar 

  3. Su C-H, Lin Y, Cai L (2013) Genetic factors, viral infection, other factors and liver cancer: an update on current progress. Asian Pac J Cancer Prev 14:4953–4960

    Article  PubMed  Google Scholar 

  4. de Oliveria Andrade LJ, D'Oliveira A, Melo RC, De Souza EC, Costa Silva CA, Parana R (2009) Association between hepatitis C and hepatocellular carcinoma. J Glob Infect Dis 1:33–37

    Article  PubMed  PubMed Central  Google Scholar 

  5. El-Serag HB (2012) Epidemiology of viral hepatitis and hepatocellular carcinoma. Gastroenterology 142(1264–1273):e1261

    Google Scholar 

  6. Zhu K, Dai Z, Zhou J (2013) Biomarkers for hepatocellular carcinoma: progression in early diagnosis, prognosis, and personalized therapy. Biomarker research 1:10

    Article  PubMed  PubMed Central  Google Scholar 

  7. Hajjari M, Khoshnevisan A, Shin YK (2014) Molecular function and regulation of long non-coding RNAs: paradigms with potential roles in cancer. Tumor Biol 35:10645–10663

    Article  CAS  Google Scholar 

  8. Yarmishyn AA, Kurochkin IV (2015) Long noncoding RNAs: a potential novel class of cancer biomarkers. Front Genet 6:1–10

  9. Ayers D (2013) Long non-coding RNAs: novel emergent biomarkers for cancer diagnostics. Nature 1:31–35

    Google Scholar 

  10. Hajjari M, Behmanesh M, Sadeghizadeh M, Zeinoddini M (2013) Up-regulation of HOTAIR long non-coding RNA in human gastric adenocarcinoma tissues. Med Oncol 30:1–4

    Google Scholar 

  11. Hajjari M, Khoshnevisan A (2013) Potential long non-coding RNAs to be considered as biomarkers or therapeutic targets in gastric cancer. Front Genet 4:1–3

  12. Hajjari M, Khoshnevisan A, Shin YK (2013) Long non-coding RNAs in hematologic malignancies: road to translational research. Front Genet 4:1–2

  13. Shibata C, Otsuka M, Kishikawa T, Ohno M, Yoshikawa T, Takata A, Koike K (2015) Diagnostic and therapeutic application of noncoding RNAs for hepatocellular carcinoma. World J Hepatol 7:1–6

    Article  PubMed  PubMed Central  Google Scholar 

  14. Fang T-T, Sun X-J, Chen J, Zhao Y, Sun R-X, Ren N, Liu B-B (2014) Long non-coding RNAs are differentially expressed in hepatocellular carcinoma cell lines with differing metastatic potential. Asian Pac J Cancer Prev 15:10513–10524

    Article  PubMed  Google Scholar 

  15. Goossens N, Nakagawa S, Sun X and Hoshida Y(2015) Cancer biomarker discovery and validation. Transl Cancer Res 4(3):256–269

  16. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2:401–404

    Article  PubMed  Google Scholar 

  17. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E (2013) Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 6:l1

    Article  Google Scholar 

  18. Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM-P, Jupp S, Koskinen S (2015) Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res 44(D1):D746–D752

  19. Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A (2014) Expression atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res 42:D926–D932

    Article  CAS  PubMed  Google Scholar 

  20. Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A (2012) Gene expression atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res 40:D1077–D1081

    Article  CAS  PubMed  Google Scholar 

  21. Cline MS, Craft B, Swatloski T, Goldman M, Ma S, Haussler D, Zhu J (2013) Exploring TCGA pan-cancer data at the UCSC cancer genomics browser. Sci Rep 3:2652

    Article  PubMed  PubMed Central  Google Scholar 

  22. Lopez B, Cline M, Broom B, Margolin A, Omberg L, Weinstein J, Axton M (2013) Thread 4: data discovery, transparency and visualization. Nat Genet 45. doi:10.1038/ng.2789

  23. Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J (2013) The UCSC cancer genomics browser: update 2013. Nucleic Acids Res 41:D949–D954

    Article  CAS  PubMed  Google Scholar 

  24. Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J (2011) The UCSC cancer genomics browser: update 2011. Nucleic Acids Res 39:D951–D959

    Article  CAS  PubMed  Google Scholar 

  25. Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM (2010) Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 26:i237–i245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, Karolchik D, Archie J, Lenburg ME, Esserman LJ, Kent WJ, Haussler D, Wang T (2009) The UCSC cancer genomics browser. Nat Methods 6:239–240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wurmbach E, Yb C, Khitrov G, Zhang W, Roayaie S, Schwartz M, Fiel I, Thung S, Mazzaferro V, Bruix J (2007) Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatology 45:938–947

    Article  CAS  PubMed  Google Scholar 

  28. Cao C, Zhang T, Zhang D, Xie L, Zou X, Lei L, Wu D, Liu L (2016) The long non-coding RNA, SNHG6–003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma. Oncogene 36:1112–1122

  29. Kim JH, You KR, Kim IH, Cho BH, Kim CY, Kim DG (2004) Over-expression of the ribosomal protein L36a gene is associated with cellular proliferation in hepatocellular carcinoma. Hepatology 39:129–138

    Article  CAS  PubMed  Google Scholar 

  30. Wong QW-L, Li J, Ng SR, Lim SG, Yang H, Vardy LA (2014) RPL39L is an example of a recently evolved ribosomal protein paralog that shows highly specific tissue expression patterns and is upregulated in ESCs and HCC tumors. RNA Biol 11:33–41

    Article  CAS  PubMed  Google Scholar 

  31. Weber RG, Pietsch T, von Schweinitz D, Lichter P (2000) Characterization of genomic alterations in hepatoblastomas: a role for gains on chromosomes 8q and 20 as predictors of poor outcome. Am J Pathol 157:571–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Xiang J-F, Yin Q-F, Chen T, Zhang Y, Zhang X-O, Wu Z, Zhang S, Wang H-B, Ge J, Lu X (2014) Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 24:513–531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This study was affiliated to Ahvaz Jundishapur University of Medical Sciences and Shahid Chamran University of Ahvaz, Iran.

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Author notes

  1. Maryam Tahmasebi Birgani, Mohammadreza Hajjari and Arman Shahrisa contributed equally to this work.

Authors and Affiliations

  1. Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran

    Maryam Tahmasebi Birgani & Zahra Shoja

  2. Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran

    Mohammadreza Hajjari & Atefeh Khoshnevisan

  3. Department of Molecular Genetics, Faculty of Biosciences, Tarbiat Modares University, Tehran, Iran

    Arman Shahrisa

  4. Department of Biotechnology, Iranian Research Organization Science & Technology, Tehran, Iran

    Paria Motahari

  5. Cancer Research Center, Tehran University of Medical Sciences, Tehran, Iran

    Baharak Farhangi

Authors
  1. Maryam Tahmasebi Birgani
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  2. Mohammadreza Hajjari
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  3. Arman Shahrisa
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Corresponding authors

Correspondence to Maryam Tahmasebi Birgani or Mohammadreza Hajjari.

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Birgani, M.T., Hajjari, M., Shahrisa, A. et al. Long Non-Coding RNA SNHG6 as a Potential Biomarker for Hepatocellular Carcinoma. Pathol. Oncol. Res. 24, 329–337 (2018). https://doi.org/10.1007/s12253-017-0241-3

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  • DOI: https://doi.org/10.1007/s12253-017-0241-3

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