nach oben

Erschienen in:

15.05.2017 | Original Article

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

verfasst von: Maryam Tahmasebi Birgani, Mohammadreza Hajjari, Arman Shahrisa, Atefeh Khoshnevisan, Zahra Shoja, Paria Motahari, Baharak Farhangi

Erschienen in: Pathology & Oncology Research | Ausgabe 2/2018

Einloggen, um Zugang zu erhalten

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.

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 16:3595–3604CrossRef

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

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 14:4953–4960CrossRefPubMed

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 1:33–37CrossRefPubMedPubMedCentral

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

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

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

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

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

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

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 7:1–6CrossRefPubMedPubMedCentral

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 15:10513–10524CrossRefPubMed

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 2:401–404CrossRefPubMed

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:l1CrossRef

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–D932CrossRefPubMed

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–D1081CrossRefPubMed

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 3:2652CrossRefPubMedPubMedCentral

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–D954CrossRefPubMed

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–D959CrossRefPubMed

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–i245CrossRefPubMedPubMedCentral

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 6:239–240CrossRefPubMedPubMedCentral

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 45:938–947CrossRefPubMed

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 39:129–138CrossRefPubMed

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 11:33–41CrossRefPubMed

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 157:571–578CrossRefPubMedPubMedCentral

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 24:513–531CrossRefPubMedPubMedCentral

Titel: Long Non-Coding RNA SNHG6 as a Potential Biomarker for Hepatocellular Carcinoma
verfasst von: Maryam Tahmasebi Birgani
Mohammadreza Hajjari
Arman Shahrisa
Atefeh Khoshnevisan
Zahra Shoja
Paria Motahari
Baharak Farhangi
Publikationsdatum: 15.05.2017
Verlag: Springer Netherlands
Erschienen in: Pathology & Oncology Research / Ausgabe 2/2018
Print ISSN: 1219-4956
Elektronische ISSN: 1532-2807
DOI: https://doi.org/10.1007/s12253-017-0241-3

Neu im Fachgebiet Onkologie

Umsetzung der POMGAT-Leitlinie läuft

03.05.2024 DCK 2024 Kongressbericht

Seit November 2023 gibt es evidenzbasierte Empfehlungen zum perioperativen Management bei gastrointestinalen Tumoren (POMGAT) auf S3-Niveau. Vieles wird schon entsprechend der Empfehlungen durchgeführt. Wo es im Alltag noch hapert, zeigt eine Umfrage in einem Klinikverbund.

Springer Medizin

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

Abstract

Neu im Fachgebiet Onkologie

Umsetzung der POMGAT-Leitlinie läuft

CUP-Syndrom: Künstliche Intelligenz kann Primärtumor finden

Sind Frauen die fähigeren Ärzte?

Adjuvante Immuntherapie verlängert Leben bei RCC

Update Onkologie

Springer Medizin

Abstract

Bitte loggen Sie sich ein, um Zugang zu diesem Inhalt zu erhalten

Weitere Artikel der Ausgabe 2/2018

Ki-67 and Cell Cycle Regulators p53, p63 and cyclinD1 as Prognostic Markers for Recurrence/ Progression of Bladder Urothelial Carcinoma

Expression of Hypoxia-Associated Protein HIF-1α in Follicular Thyroid Cancer is Associated with Distant Metastasis

Efficacy and Tolerability of a 2-Year Rituximab Maintenance Therapy in Patients with Advanced Follicular Lymphoma after Induction of Response with Rituximab-Containing First Line-Regimens (HUSOM Study)

TFF3 Expression as Stratification Marker in Borderline Epithelial Tumors of the Ovary

Gemcitabine/Cisplatin Treatment Induces Concomitant SERTAD1, CDKN2B and GADD45A Modulation and Cellular Changes in Bladder Cancer Cells Regardless of the Site of TP53 Mutation

Histopathologic Features are more Important Prognostic Factors than Primary Tumour Location in Gastro-oesophageal Adenocarcinoma Treated with Preoperative Chemoradiation and Surgery

Neu im Fachgebiet Onkologie

Umsetzung der POMGAT-Leitlinie läuft

CUP-Syndrom: Künstliche Intelligenz kann Primärtumor finden

Sind Frauen die fähigeren Ärzte?

Adjuvante Immuntherapie verlängert Leben bei RCC

Update Onkologie