Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Oncology Letters
      • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Biomedical Reports
      • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • Information for Authors
    • Information for Reviewers
    • Information for Librarians
    • Information for Advertisers
    • Conferences
  • Language Editing
Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • For Authors
    • For Reviewers
    • For Librarians
    • For Advertisers
    • Conferences
  • Language Editing
Login Register Submit
  • This site uses cookies
  • You can change your cookie settings at any time by following the instructions in our Cookie Policy. To find out more, you may read our Privacy Policy.

    I agree
Search articles by DOI, keyword, author or affiliation
Search
Advanced Search
presentation
Molecular Medicine Reports
Join Editorial Board Propose a Special Issue
Print ISSN: 1791-2997 Online ISSN: 1791-3004
Journal Cover
August-2015 Volume 12 Issue 2

Full Size Image

Sign up for eToc alerts
Recommend to Library

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

Medicine International

An International Open Access Journal Devoted to General Medicine.

Journal Cover
August-2015 Volume 12 Issue 2

Full Size Image

Sign up for eToc alerts
Recommend to Library

  • Article
  • Citations
    • Cite This Article
    • Download Citation
    • Create Citation Alert
    • Remove Citation Alert
    • Cited By
  • Similar Articles
    • Related Articles (in Spandidos Publications)
    • Similar Articles (Google Scholar)
    • Similar Articles (PubMed)
  • Download PDF
  • Download XML
  • View XML
Article Open Access

Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma

  • Authors:
    • Guo‑Fang Guan
    • Ying Zheng
    • Lian‑Ji Wen
    • De‑Jun Zhang
    • Duo‑Jiao Yu
    • Yan‑Qing Lu
    • Yan Zhao
    • Hui Zhang
  • View Affiliations / Copyright

    Affiliations: Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China, Department of Otolaryngology, Head and Neck Surgery, Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
    Copyright: © Guan et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY_NC 3.0].
  • Pages: 2457-2464
    |
    Published online on: April 29, 2015
       https://doi.org/10.3892/mmr.2015.3701
  • Expand metrics +
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )
Cited By (CrossRef): 0 citations Loading Articles...

This article is mentioned in:



Abstract

The present study aimed to identify key genes and relevant microRNAs (miRNAs) involved in laryngeal squamous cell carcinoma (LSCC). The gene expression profiles of LSCC tissue samples were analyzed with various bioinformatics tools. A gene expression data set (GSE51985), including ten laryngeal squamous cell carcinoma (LSCC) tissue samples and ten adjacent non‑neoplastic tissue samples, was downloaded from the Gene Expression Omnibus. Differential analysis was performed using software package limma of R. Functional enrichment analysis was applied to the differentially expressed genes (DEGs) using the Database for Annotation, Visualization and Integrated Discovery. Protein‑protein interaction (PPI) networks were constructed for the protein products using information from the Search Tool for the Retrieval of Interacting Genes/Proteins. Module analysis was performed using ClusterONE (a software plugin from Cytoscape). MicroRNAs (miRNAs) regulating the DEGs were predicted using WebGestalt. A total of 461 DEGs were identified in LSCC, 297 of which were upregulated and 164 of which were downregulated. Cell cycle, proteasome and DNA replication were significantly over‑represented in the upregulated genes, while the ribosome was significantly over‑represented in the downregulated genes. Two PPI networks were constructed for the up‑ and downregulated genes. One module from the upregulated gene network was associated with protein kinase. Numerous miRNAs associated with LSCC were predicted, including miRNA (miR)‑25, miR‑32, miR‑92 and miR‑29. In conclusion, numerous key genes and pathways involved in LSCC were revealed, which may aid the advancement of current knowledge regarding the pathogenesis of LSCC. In addition, relevant miRNAs were also identified, which may represent potential biomarkers for use in the diagnosis or treatment of the disease.
View Figures

Figure 1

Figure 2

Figure 3

View References

1 

Schorn VJ and Miles BA: Laryngeal squamous cell carcinoma. ENT Board Prep. Lin F and Patel Z: Springer; New York: pp. 227–233. 2014, View Article : Google Scholar

2 

Almadori G, Bussu F, Cadoni G, Galli J, Paludetti G and Maurizi M: Molecular markers in laryngeal squamous cell carcinoma: towards an integrated clinicobiological approach. Eur J Cancer. 41:683–693. 2005. View Article : Google Scholar : PubMed/NCBI

3 

Järvinen AK, Autio R, Haapa-Paananen S, et al: Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene. 25:6997–7008. 2006. View Article : Google Scholar : PubMed/NCBI

4 

Gajecka M, Rydzanicz M, Jaskula-Sztul R, Kujawski M, Szyfter W and Szyfter K: CYP1A1, CYP2D6, CYP2E1, NAT2, GSTM1 and GSTT1 polymorphisms or their combinations are associated with the increased risk of the laryngeal squamous cell carcinoma. Mutat Res. 574:112–123. 2005. View Article : Google Scholar : PubMed/NCBI

5 

Ogino T, Shigyo H, Ishii H, et al: HLA class I antigen down-regulation in primary laryngeal squamous cell carcinoma lesions as a poor prognostic marker. Cancer Res. 66:9281–9289. 2006. View Article : Google Scholar : PubMed/NCBI

6 

Celetti A, Testa D, Staibano S, et al: Overexpression of the cytokine osteopontin identifies aggressive laryngeal squamous cell carcinomas and enhances carcinoma cell proliferation and invasiveness. Clin Cancer Res. 11:8019–8027. 2005. View Article : Google Scholar : PubMed/NCBI

7 

Zimmerman AL and Wu S: MicroRNAs, cancer and cancer stem cells. Cancer Lett. 300:10–19. 2011. View Article : Google Scholar

8 

Liu M, Wu H, Liu T, et al: Regulation of the cell cycle gene, BTG2, by miR-21 in human laryngeal carcinoma. Cell Res. 19:828–837. 2009. View Article : Google Scholar : PubMed/NCBI

9 

Bian K, Fan J, Zhang X, et al: MicroRNA-203 leads to G1 phase cell cycle arrest in laryngeal carcinoma cells by directly targeting survivin. FEBS Lett. 586:804–809. 2012. View Article : Google Scholar : PubMed/NCBI

10 

Long XB, Sun GB, Hu S, et al: Let-7a microRNA functions as a potential tumor suppressor in human laryngeal cancer. Oncol Rep. 22:1189–1195. 2009.PubMed/NCBI

11 

Wu H, Liu T, Wang R, et al: MicroRNA-16 targets zyxin and promotes cell motility in human laryngeal carcinoma cell line HEp-2. IUBMB Life. 63:101–108. 2011.PubMed/NCBI

12 

Cai KM, Bao XL, Kong XH, et al: Hsa-miR-34c suppresses growth and invasion of human laryngeal carcinoma cells via targeting c-Met. Int J Mol Med. 25:565–571. 2010. View Article : Google Scholar : PubMed/NCBI

13 

Lian M, Fang J, Han D, et al: Microarray gene expression analysis of tumorigenesis and regional lymph node metastasis in laryngeal squamous cell carcinoma. PLoS One. 8:e848542013. View Article : Google Scholar

14 

Diboun I, Wernisch L, Orengo CA and Koltzenburg M: Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics. 7:2522006. View Article : Google Scholar : PubMed/NCBI

15 

Huang DW, Sherman BT, Tan Q, et al: The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8:R1832007. View Article : Google Scholar : PubMed/NCBI

16 

Aoki-Kinoshita KF and Kanehisa M: Gene annotation and pathway mapping in KEGG. Methods Mol Biol. 396:71–91. 2007.PubMed/NCBI

17 

Hunter S, Jones P, Mitchell A, et al: InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40:D306–D312. 2012. View Article : Google Scholar :

18 

von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P and Snel B: STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31:258–261. 2003. View Article : Google Scholar : PubMed/NCBI

19 

Shannon P, Markiel A, Ozier O, et al: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498–2504. 2003. View Article : Google Scholar : PubMed/NCBI

20 

Nepusz T, Yu H and Paccanaro A: Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods. 9:471–472. 2012. View Article : Google Scholar : PubMed/NCBI

21 

Zhang B, Kirov S and Snoddy J: WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 33:W741–W748. 2005. View Article : Google Scholar : PubMed/NCBI

22 

Evan GI and Vousden KH: Proliferation, cell cycle and apoptosis in cancer. Nature. 411:342–348. 2001. View Article : Google Scholar : PubMed/NCBI

23 

Kastan MB and Bartek J: Cell-cycle checkpoints and cancer. Nature. 432:316–323. 2004. View Article : Google Scholar : PubMed/NCBI

24 

Cai K, Luo Y and Li L: Expression of MCM2 protein and its biological characteristic in human laryngeal squamous cell carcinoma. J Acta Academiae Medicinae Jiangxi. 3:58–60. 2008.

25 

Sherr CJ: G1 phase progression: cycling on cue. J Cell. 79:551–555. 1994. View Article : Google Scholar

26 

Dong Y, Sui L, Sugimoto K, Tai Y and Tokuda M: Cyclin D1. CDK4 complex, a possible critical factor for cell proliferation and prognosis in laryngeal squamous cell carcinomas. Int J Cancer. 95:209–215. 2001. View Article : Google Scholar : PubMed/NCBI

27 

Freeman A, Morris LS, Mills AD, et al: Minichromosome maintenance proteins as biological markers of dysplasia and malignancy. Clin Cancer Res. 5:2121–2132. 1999.PubMed/NCBI

28 

Chatrath P, Scott IS, Morris LS, et al: Aberrant expression of minichromosome maintenance protein-2 and Ki67 in laryngeal squamous epithelial lesions. Br J Cancer. 89:1048–1054. 2003. View Article : Google Scholar : PubMed/NCBI

29 

Torres-Rendon A, Roy S, Craig G and Speight P: Expression of Mcm2, geminin and Ki67 in normal oral mucosa, oral epithelial dysplasias and their corresponding squamous-cell carcinomas. Br J Cancer. 100:1128–1134. 2009. View Article : Google Scholar : PubMed/NCBI

30 

Mishra R: Glycogen synthase kinase 3 beta: can it be a target for oral cancer. Mol Cancer. 9:1442010. View Article : Google Scholar : PubMed/NCBI

31 

Almond JB and Cohen GM: The proteasome: a novel target for cancer chemotherapy. Leukemia. 16:433–443. 2002. View Article : Google Scholar : PubMed/NCBI

32 

Orlowski RZ and Kuhn DJ: Proteasome inhibitors in cancer therapy: lessons from the first decade. Clin Cancer Res. 14:1649–1657. 2008. View Article : Google Scholar : PubMed/NCBI

33 

Rajkumar SV, Richardson PG, Hideshima T and Anderson KC: Proteasome inhibition as a novel therapeutic target in human cancer. J Clin Oncol. 23:630–639. 2005. View Article : Google Scholar : PubMed/NCBI

34 

Lee GY, Haverty PM, Li L, et al: Comparative oncogenomics identifies PSMB4 and SHMT2 as potential cancer driver genes. Cancer Res. 74:3114–3126. 2014. View Article : Google Scholar : PubMed/NCBI

35 

Munkacsy G, Abdul-Ghani R, Mihaly Z, et al: PSMB7 is associated with anthracycline resistance and is a prognostic biomarker in breast cancer. Br J Cancer. 102:361–368. 2010. View Article : Google Scholar :

36 

Dar AA, Goff LW, Majid S, Berlin J and El-Rifai W: Aurora kinase inhibitors-rising stars in cancer therapeutics? Mol Cancer Ther. 9:268–278. 2010. View Article : Google Scholar : PubMed/NCBI

37 

Mehra R, Serebriiskii IG, Burtness B, Astsaturov I and Golemis EA: Aurora kinases in head and neck cancer. Lancet Oncol. 14:e425–e435. 2013. View Article : Google Scholar : PubMed/NCBI

38 

Bonci D, Coppola V, Musumeci M, et al: The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nat Med. 14:1271–1277. 2008. View Article : Google Scholar : PubMed/NCBI

39 

Cimmino A, Calin GA, Fabbri M, et al: miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA. 102:13944–13949. 2005. View Article : Google Scholar : PubMed/NCBI

40 

Zhang H, Zuo Z, Lu X, Wang L, Wang H and Zhu Z: MiR-25 regulates apoptosis by targeting Bim in human ovarian cancer. Oncol Rep. 27:594–598. 2012.

41 

Soon PS, Tacon LJ, Gill AJ, et al: miR-195 and miR-483-5p identified as predictors of poor prognosis in adrenocortical cancer. Clin Cancer Res. 15:7684–7692. 2009. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Guan GF, Zheng Y, Wen LJ, Zhang DJ, Yu DJ, Lu YQ, Zhao Y and Zhang H: Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma. Mol Med Rep 12: 2457-2464, 2015.
APA
Guan, G., Zheng, Y., Wen, L., Zhang, D., Yu, D., Lu, Y. ... Zhang, H. (2015). Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma. Molecular Medicine Reports, 12, 2457-2464. https://doi.org/10.3892/mmr.2015.3701
MLA
Guan, G., Zheng, Y., Wen, L., Zhang, D., Yu, D., Lu, Y., Zhao, Y., Zhang, H."Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma". Molecular Medicine Reports 12.2 (2015): 2457-2464.
Chicago
Guan, G., Zheng, Y., Wen, L., Zhang, D., Yu, D., Lu, Y., Zhao, Y., Zhang, H."Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma". Molecular Medicine Reports 12, no. 2 (2015): 2457-2464. https://doi.org/10.3892/mmr.2015.3701
Copy and paste a formatted citation
x
Spandidos Publications style
Guan GF, Zheng Y, Wen LJ, Zhang DJ, Yu DJ, Lu YQ, Zhao Y and Zhang H: Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma. Mol Med Rep 12: 2457-2464, 2015.
APA
Guan, G., Zheng, Y., Wen, L., Zhang, D., Yu, D., Lu, Y. ... Zhang, H. (2015). Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma. Molecular Medicine Reports, 12, 2457-2464. https://doi.org/10.3892/mmr.2015.3701
MLA
Guan, G., Zheng, Y., Wen, L., Zhang, D., Yu, D., Lu, Y., Zhao, Y., Zhang, H."Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma". Molecular Medicine Reports 12.2 (2015): 2457-2464.
Chicago
Guan, G., Zheng, Y., Wen, L., Zhang, D., Yu, D., Lu, Y., Zhao, Y., Zhang, H."Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma". Molecular Medicine Reports 12, no. 2 (2015): 2457-2464. https://doi.org/10.3892/mmr.2015.3701
Follow us
  • Twitter
  • LinkedIn
  • Facebook
About
  • Spandidos Publications
  • Careers
  • Cookie Policy
  • Privacy Policy
How can we help?
  • Help
  • Live Chat
  • Contact
  • Email to our Support Team