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Tumor Biology
Published in: Tumor Biology 12/2016

01-12-2016 | Original Article

Transcriptomic characterization of differential gene expression in oral squamous cell carcinoma: a meta-analysis of publicly available microarray data sets

Authors: Yang Sun, Zhijian Sang, Qian Jiang, Xiaojun Ding, Youcheng Yu

Published in: Tumor Biology | Issue 12/2016

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Abstract

Oral squamous cell carcinoma (OSCC) is a highly prevalent cancer worldwide, and OSCC often goes undiagnosed until advanced disease is present, which contributes to a low survival rate for OSCC patients. The identification of biomarkers for the early detection OSCC and novel therapeutic targets for OSCC treatment is an important research objective. We performed bioinformatics analyses of the gene expression profile of OSCC using microarray data to identify genes that contribute to the development of OSCC. We also predicted the transcription factors involved in the regulation of differential gene expression in OSCC. Our results showed that PI3K, EGFR, STAT1, and CPBP are important contributors to the changes in cellular physiology that occur during the development of OSCC. Therefore, these genes represent potential diagnostic biomarkers and therapeutic targets for OSCC.
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Literature
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.CrossRefPubMed
2.
3.
Lingen MW, Kalmar JR, Karrison T, Speight PM. Critical evaluation of diagnostic aids for the detection of oral cancer. Oral Oncol. 2008;44:10–22.CrossRefPubMed
4.
Boyle P, Levin B. World cancer report 2008. IARC Press, International Agency for Research on Cancer; 2008.
5.
Cheang MC, Chia SK, Voduc D, Gao D, Leung S, Snider J, et al. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst. 2009;101:736–50.CrossRefPubMedPubMedCentral
6.
Mazumder TH, Nath S, Nath N, Kumar M. Head and neck squamous cell carcinoma: prognosis using molecular approach. Central European Journal of Biology. 2014;9:593–613.
7.
Brooks YS, Ostano P, Jo SH, Dai J, Getsios S, Dziunycz P, et al. Multifactorial ERbeta and NOTCH1 control of squamous differentiation and cancer. J Clin Invest. 2014;124:2260–76.CrossRefPubMedPubMedCentral
8.
Islam M, Datta J, Lang JC, Teknos TN. Down regulation of RhoC by microRNA-138 results in de-activation of FAK, Src and Erk1/2 signaling pathway in head and neck squamous cell carcinoma. Oral Oncol. 2014;50:448–56.CrossRefPubMedPubMedCentral
9.
Biswas NK, Das S, Maitra A, Sarin R, Majumder PP. Somatic mutations in arachidonic acid metabolism pathway genes enhance oral cancer post-treatment disease-free survival. Nat Commun. 2014;5:5835.CrossRefPubMed
10.
Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, et al. Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov. 2013;3:770–81.CrossRefPubMed
11.
Yong-Deok K, Eun-Hyoung J, Yeon-Sun K, Kang-Mi P, Jin-Yong L, Sung-Hwan C, et al. Molecular genetic study of novel biomarkers for early diagnosis of oral squamous cell carcinoma. Med Oral Patol Oral Cir Bucal. 2015;20:e167–79.CrossRefPubMed
12.
Chang JT, Wang HM, Chang KW, Chen WH, Wen MC, Hsu YM, et al. Identification of differentially expressed genes in oral squamous cell carcinoma (OSCC): overexpression of NPM, CDK1 and NDRG1 and underexpression of CHES1. Int J Cancer. 2005;114:942–9.CrossRefPubMed
13.
Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJ, Marra MA. Sequence biases in large scale gene expression profiling data. Nucleic Acids Res. 2006;34:e83.CrossRefPubMedPubMedCentral
14.
15.
Rung J, Brazma A. Reuse of public genome-wide gene expression data. Nat Rev Genet. 2013;14:89–99.CrossRefPubMed
16.
Lee YH, Nath SK. Systemic lupus erythematosus susceptibility loci defined by genome scan meta-analysis. Hum Genet. 2005;118:434–43.CrossRefPubMed
17.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.CrossRefPubMedPubMedCentral
18.
Du J, Yuan Z, Ma Z, Song J, Xie X, Chen Y. KEGG-PATH: Kyoto encyclopedia of genes and genomes-based pathway analysis using a path analysis model. Mol BioSyst. 2014;10:2441–7.CrossRefPubMed
19.
Xia J, Fjell CD, Mayer ML, Pena OM, Wishart DS, Hancock RE. INMEX—a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res. 2013;41:W63–70.CrossRefPubMedPubMedCentral
20.
Lee YH, Song GG. Meta-analysis of differentially expressed genes in ankylosing spondylitis. Genet Mol Res. 2015;14:5161–70.CrossRefPubMed
21.
Toro-Domínguez D, Carmona-Sáez P, Alarcón-Riquelme ME. Shared signatures between rheumatoid arthritis, systemic lupus erythematosus and Sjögren’s syndrome uncovered through gene expression meta-analysis. Arthritis Research & Therapy. 2014;16:489.CrossRef
22.
Santiago JA, Potashkin JA. Network-based metaanalysis identifies HNF4A and PTBP1 as longitudinally dynamic biomarkers for Parkinson’s disease. Proc Natl Acad Sci U S A. 2015;112:2257–62.CrossRefPubMedPubMedCentral
23.
Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19:185–93.CrossRefPubMed
24.
Song GG, Kim JH, Seo YH, Choi SJ, Ji JD, Lee YH. Meta-analysis of differentially expressed genes in primary Sjogren’s syndrome by using microarray. Hum Immunol. 2014;75:98–104.CrossRefPubMed
25.
Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, et al. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol. 2007;25:663–8.CrossRefPubMed
26.
Zhou XL, JH W, Wang XJ, Guo FJ. Integrated microRNA-mRNA analysis revealing the potential roles of microRNAs in tongue squamous cell cancer. Mol Med Rep. 2015;12:885–94.PubMedPubMedCentral
27.
28.
Wang F, Hu S, Liu W, Qiao Z, Gao Y, Bu Z. Deep-sequencing analysis of the mouse transcriptome response to infection with Brucella melitensis strains of differing virulence. PLoS One. 2011;6:e28485.CrossRefPubMedPubMedCentral
29.
Wei Z, Li HA. Markov random field model for network-based analysis of genomic data. Bioinformatics. 2007;23:1537–44.CrossRefPubMed
30.
Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, Pelletier D, et al. Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Hum Mol Genet. 2009;18:2078–90.CrossRefPubMedPubMedCentral
31.
Kong X, Ding X, Yang Q. Identification of multi-target effects of Huaier aqueous extract via microarray profiling in triple-negative breast cancer cells. Int J Oncol. 2015;46:2047–56.PubMed
32.
van Breda SG, Claessen SM, Lo K, van Herwijnen M, Brauers KJ, Lisanti S et al. Epigenetic mechanisms underlying arsenic-associated lung carcinogenesis. Arch Toxicol. 2014.
33.
Prieto C, Risueno A, Fontanillo C. De las Rivas J. Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One. 2008;3:e3911.CrossRefPubMedPubMedCentral
34.
Vermeirssen V, Barrasa MI, Hidalgo CA, Babon JA, Sequerra R, Doucette-Stamm L, et al. Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res. 2007;17:1061–71.CrossRefPubMedPubMedCentral
35.
Wang J, Ni Z, Duan Z, Wang G, Li F. Altered expression of hypoxia-inducible factor-1alpha (HIF-1alpha) and its regulatory genes in gastric cancer tissues. PLoS One. 2014;9:e99835.CrossRefPubMedPubMedCentral
36.
Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 2003;4:R28.CrossRefPubMedPubMedCentral
37.
38.
Carvalho AL, Nishimoto IN, Califano JA, Kowalski LP. Trends in incidence and prognosis for head and neck cancer in the United States: a site-specific analysis of the SEER database. Int J Cancer. 2005;114:806–16.CrossRefPubMed
39.
Heaton CM, Durr ML, Tetsu O, van Zante A. Wang SJ. TP53 and CDKN2a mutations in never-smoker oral tongue squamous cell carcinoma. Laryngoscope. 2014;124:E267–73.CrossRefPubMed
40.
Judd NP, Winkler AE, Murillo-Sauca O, Brotman JJ, Law JH, JS Jr L, et al. ERK1/2 regulation of CD44 modulates oral cancer aggressiveness. Cancer Res. 2012;72:365–74.CrossRefPubMed
41.
42.
Oliveira-Costa JP, Oliveira LR, Zanetti R, Zanetti JS, da Silveira GG, Chavichiolli Buim ME, et al. BRCA1 and gammaH2AX as independent prognostic markers in oral squamous cell carcinoma. Oncoscience. 2014;1:383–91.CrossRefPubMedPubMedCentral
43.
Yap L, Lee D, Khairuddin A, Pairan M, Puspita B, Siar C et al. The opposing roles of NOTCH signalling in head and neck cancer: a mini review. Oral Dis. 2015.
44.
Vincent-Chong VK, Salahshourifar I, Karen-Ng LP, Siow MY, Kallarakkal TG, Ramanathan A et al. Overexpression of MMP13 is associated with clinical outcomes and poor prognosis in oral squamous cell carcinoma. Scientific World Journal. 2014;2014:897523.
45.
Shieh TM, Lin SC, Liu CJ, Chang SS, TH K, Chang KW. Association of expression aberrances and genetic polymorphisms of lysyl oxidase with areca-associated oral tumorigenesis. Clin Cancer Res. 2007;13:4378–85.CrossRefPubMed
46.
CQ X, Zhu ST, Wang M, Guo SL, Sun XJ, Cheng R, et al. Pathway analysis of differentially expressed genes in human esophageal squamous cell carcinoma. Eur Rev Med Pharmacol Sci. 2015;19:1652–61.
47.
Gotte M, Mohr C, Koo CY, Stock C, Vaske AK, Viola M, et al. miR-145-dependent targeting of junctional adhesion molecule A and modulation of fascin expression are associated with reduced breast cancer cell motility and invasiveness. Oncogene. 2010;29:6569–80.CrossRefPubMed
48.
Guariguata L, Whiting DR, Hambleton I, Beagley J, Linnenkamp U, Shaw JE. Global estimates of diabetes prevalence for 2013 and projections for 2035. Diabetes Res Clin Pract. 2014;103:137–49.CrossRefPubMed
49.
Jalouli J, Jalouli MM, Sapkota D, Ibrahim SO, Larsson PA, Sand L. Human papilloma virus, herpes simplex virus and epstein barr virus in oral squamous cell carcinoma from eight different countries. Anticancer Res. 2012;32:571–80.PubMed
50.
Miller CS, Johnstone BM. Human papillomavirus as a risk factor for oral squamous cell carcinoma: a meta-analysis, 1982–1997. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 2001;91:622–35.CrossRefPubMed
51.
Syrjanen S, Lodi G, von Bultzingslowen I, Aliko A, Arduino P, Campisi G, et al. Human papillomaviruses in oral carcinoma and oral potentially malignant disorders: a systematic review. Oral Dis. 2011;17(Suppl 1):58–72.CrossRefPubMed
52.
Roizman B, Frenkel N. The transcription and state of herpes simplex virus DNA in productive infection and in human cervical cancer tissue. Cancer Res. 1973;33:1402–16.PubMed
53.
Koffa M, Koumantakis E, Ergazaki M, Tsatsanis C, Spandidos DA. Association of herpesvirus infection with the development of genital cancer. Int J Cancer. 1995;63:58–62.CrossRefPubMed
54.
zur Hausen H, Schulte-Holthausen H, Klein G, Henle W, Henle G, Clifford P, et al. EBV DNA in biopsies of Burkitt tumours and anaplastic carcinomas of the nasopharynx. Nature. 1970;228:1056–8.CrossRefPubMed
55.
Wolf H, zur Hausen H, Becker V. EB viral genomes in epithelial nasopharyngeal carcinoma cells. Nat New Biol. 1973;244:245–7.CrossRefPubMed
56.
Jiang X, Wang J, Chen X, Hong Y, Wu T, Chen X, et al. Elevated autocrine chemokine ligand 18 expression promotes oral cancer cell growth and invasion via Akt activation. Oncotarget. 2016;7:16262.PubMedPubMedCentral
57.
Jeon Y, Cho J, Lee S, Choi Y, Park H, Jung S, et al. Esculetin induces apoptosis through EGFR/PI3K/Akt signaling pathway and nucleophosmin relocalization. J Cell Biochem. 2016;117:1210.CrossRefPubMed
58.
Lui VWY, Hedberg ML, Li H, Vangara BS, Pendleton K, Zeng Y, et al. Frequent mutation of the PI3K pathway in head and neck cancer defines predictive biomarkers. Cancer Discovery. 2013;3:761.CrossRefPubMedPubMedCentral
59.
Lin C, Chou Y, Chiou H, Chen M, Yang W, Hsieh M, et al. Pterostilbene suppresses oral cancer cell invasion by inhibiting MMP-2 expression. Expert Opin Ther Targets. 2014;18:1109.CrossRefPubMed
60.
Lin K, Chien C, Tseng C, Chen Y, Chang L, Lin S. Furano-1,2-naphthoquinone inhibits Src and PI3K/Akt signaling pathways in Ca9-22 human oral squamous carcinoma cells. Integrative Cancer Therapies. 2012;13:NP18.CrossRefPubMed
61.
Shin JA, Ryu MH, Kwon KH, Choi B, Cho SD. Down-regulation of Akt by methanol extracts of Impatiens balsamina L. promotes apoptosis in human oral squamous cell carcinoma cell lines. J Oral Pathol Med. 2014.
62.
Li Q, Song X, Ji Y, Jiang H, Xu L. The dual mTORC1 and mTORC2 inhibitor AZD8055 inhibits head and neck squamous cell carcinoma cell growth in vivo and in vitro. Biochem Biophys Res Commun. 2013;440:701.CrossRefPubMed
63.
Molinolo AA, Marsh C, El Dinali M, Gangane N, Jennison K, Hewitt S, et al. mTOR as a molecular target in HPV-associated oral and cervical squamous carcinomas. Clinical Cancer Research: an Official Journal of the American Association for Cancer Research. 2012;18:2558.CrossRef
64.
Yu C, Hung S, Liao H, Lee C, Lin H, Lai H, et al. RAD001 enhances the radiosensitivity of SCC4 oral cancer cells by inducing cell cycle arrest at the G2/M checkpoint. Anticancer Res. 2014;34:2927.PubMed
65.
Yu C-C, Huang H-b, Hung S-K, Liao H-F, Lee C-C, Lin H-Y et al. AZD2014 radiosensitizes oral squamous cell carcinoma by inhibiting AKT/mTOR axis and inducing G1/G2/M cell cycle arrest. PLoS ONE. 2016, 11.
66.
Su Y-C, Yu C-C, Hung S-K, Lin H-Y, Chan MW-Y, Huang H-B et al., editors. Effect of NVP-BEZ235, dual phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor, on radiosensitivity of oral cancer cell line through G2/M phase checkpoint regulation. ASCO Annual Meeting Proceedings; 2014.
67.
Kumar P, Benedict R, Urzua F, Fischbach C, Mooney D, Polverini P. Combination treatment significantly enhances the efficacy of antitumor therapy by preferentially targeting angiogenesis. Laboratory Investigation; a Journal of Technical Methods and Pathology. 2005;85:756.CrossRefPubMed
68.
Wang H, Wu Q, Liu Z, Luo X, Fan Y, Liu Y, et al. Downregulation of FAP suppresses cell proliferation and metastasis through PTEN/PI3K/AKT and Ras-ERK signaling in oral squamous cell carcinoma. Cell Death Dis. 2014;5:e1155.CrossRefPubMed
69.
Qian M, Qian D, Jing H, Li Y, Ma C, Zhou Y. Combined cetuximab and celecoxib treatment exhibits a synergistic anticancer effect on human oral squamous cell carcinoma in vitro and in vivo. Oncol Rep. 2014;32:1681–8.PubMed
70.
TS W, Tan CT, Chang CC, Lin BR, Lai WT, Chen ST, et al. B-cell lymphoma/leukemia 10 promotes oral cancer progression through STAT1/ATF4/S100P signaling pathway. Oncogene. 2015;34:1207–19.CrossRef
71.
Cancer Genome Atlas N. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015;517:576–82.CrossRef
72.
Teixeira MS, Camacho-Vanegas O, Fernandez Y, Narla G, DiFeo A, Lee B, et al. KLF6 allelic loss is associated with tumor recurrence and markedly decreased survival in head and neck squamous cell carcinoma. Int J Cancer. 2007;121:1976–83.CrossRefPubMed
Metadata
Title
Transcriptomic characterization of differential gene expression in oral squamous cell carcinoma: a meta-analysis of publicly available microarray data sets
Authors
Yang Sun
Zhijian Sang
Qian Jiang
Xiaojun Ding
Youcheng Yu
Publication date
01-12-2016
Publisher
Springer Netherlands
Published in
Tumor Biology / Issue 12/2016
Print ISSN: 1010-4283
Electronic ISSN: 1423-0380
DOI
https://doi.org/10.1007/s13277-016-5439-6

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