Gene expression profiling and bioinformatics analysis of hereditary gingival fibromatosis

Fang,Lei; Wang,Yu; Chen,Xuejun

doi:10.3892/br.2017.1031

Gene expression profiling and bioinformatics analysis of hereditary gingival fibromatosis

Authors:
- Lei Fang
- Yu Wang
- Xuejun Chen
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Affiliations: Department of Pathology and Pathophysiology, Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China, Department of Ultrasound in Medicine, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai Institute of Ultrasound in Medicine, Shanghai 200233, P.R. China
Published online on: December 15, 2017 https://doi.org/10.3892/br.2017.1031
Pages: 133-137

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Abstract

Hereditary gingival fibromatosis (HGF) is a benign, non‑hemorrhagic and fibrous gingival overgrowth that may cover all or part of the teeth. It typically interferes with speech, lip closure and chewing, and can also be a psychological burden that affects the self‑esteem of patients. Owing to high genetic heterogeneity, genetic testing to confirm diagnosis is not justified. It is therefore important to identify key signature genes and to understand the molecular mechanisms underlying HGF. The aim of the present study was to determine HGF‑related genes and to analyze these genes through bioinformatics methods. A total of 249 differentially expressed genes (DEGs), consisting of 65 upregulated and 184 downregulated genes, were identified in the GSE4250 dataset of Gene Expression Omnibus (GEO) when comparing with the gums of HGF patients with those of healthy controls using the affy and limma packages in R. Subsequently, 28 enriched gene ontology terms were obtained from the Database for Annotation, Visualization and Integrated Discovery, and a protein‑protein interaction (PPI) network was constructed and analyzed using STRING and Cytoscape. There were 99 nodes and 118 edges in the PPI network of these DEGs obtained through STRING. Among these nodes, 12 core genes were identified, of which the highest degree node was the gene for POTE ankyrin domain family member I. Collectively the results indicate that bioinformatics methods may provide effective strategies for predicting HGF‑related genes and for understanding the molecular mechanisms of HGF.

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1	Gawron K, Łazarz-Bartyzel K, Potempa J and Chomyszyn-Gajewska M: Gingival fibromatosis: Clinical, molecular and therapeutic issues. Orphanet J Rare Dis. 11:92016. View Article : Google Scholar
2	Jayachandran M, Kapoor S and Mahesh R: Idiopathic gingival fibromatosis rehabilitation: A case report with two-year followup. Case Rep Dent. 2013:5131532013.
3	Mohan RP, Verma S, Agarwal N and Singh U: Non-syndromic hereditary gingival fibromatosis. BMJ Case Rep. 2013:pii: bcr2012008542. 2013. View Article : Google Scholar
4	Tripathi AK, Dete G, Saimbi CS and Kumar V: Management of hereditary gingival fibromatosis: A 2 years follow-up case report. J Indian Soc Periodontol. 19:342–344. 2015. View Article : Google Scholar
5	Zhou M, Xu L and Meng HX: Diagnosis and treatment of a hereditary gingival fibromatosis case. Chin J Dent Res. 14:155–158. 2011.
6	Häkkinen L and Csiszar A: Hereditary gingival fibromatosis: Characteristics and novel putative pathogenic mechanisms. J Dent Res. 86:25–34. 2007. View Article : Google Scholar
7	Takagi M, Yamamoto H, Mega H, Hsieh KJ, Shioda S and Enomoto S: Heterogeneity in the gingival fibromatoses. Cancer. 68:2202–2212. 1991. View Article : Google Scholar
8	Majumder P, Nair V, Mukherjee M, Ghosh S and Dey SK: The autosomal recessive inheritance of hereditary gingival fibromatosis. Case Rep Dent. 2013:4328642013.
9	Odessey EA, Cohn AB, Casper F and Schechter LS: Hereditary gingival fibromatosis: Aggressive 2-stage surgical resection in lieu of traditional therapy. Ann Plast Surg. 57:557–560. 2006. View Article : Google Scholar
10	Hart TC, Zhang Y, Gorry MC, Hart PS, Cooper M, Marazita ML, Marks JM, Cortelli JR and Pallos D: A mutation in the SOS1 gene causes hereditary gingival fibromatosis type 1. Am J Hum Genet. 70:943–954. 2002. View Article : Google Scholar
11	Harrison M, Odell EW, Agrawal M, Saravanamuttu R and Longhurst P: Gingival fibromatosis with prune-belly syndrome. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 86:304–307. 1998. View Article : Google Scholar
12	Ye X, Shi L, Yin W, Meng L, Wang QK and Bian Z: Further evidence of genetic heterogeneity segregating with hereditary gingival fibromatosis. J Clin Periodontol. 36:627–633. 2009. View Article : Google Scholar
13	Clough E and Barrett T: The Gene Expression Omnibus Database. Methods Mol Biol. 1418:93–110. 2016. View Article : Google Scholar
14	Zhu Y, Zhang W, Huo Z, Zhang Y, Xia Y, Li B, Kong X and Hu L: A novel locus for maternally inherited human gingival fibromatosis at chromosome 11p15. Hum Genet. 121:113–123. 2007. View Article : Google Scholar
15	Team RDC: R: A Language and Environment for Statistical. Computing. 14:12–21. 2011.
16	Gautier L, Cope L, Bolstad BM and Irizarry RA: affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 20:307–315. 2004. View Article : Google Scholar
17	Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W and Smyth GK: limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43:e472015. View Article : Google Scholar
18	Huang W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar
19	Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, et al: STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43:(D1). D447–D452. 2015. View Article : Google Scholar
20	Su G, Morris JH, Demchak B and Bader GD: Biological network exploration with Cytoscape 3. Curr Protoc Bioinformatics. 47:1–24. 2014.
21	Armitage GC: Development of a classification system for periodontal diseases and conditions. Ann Periodontol. 4:1–6. 1999. View Article : Google Scholar
22	Coletta RD and Graner E: Hereditary gingival fibromatosis: A systematic review. J Periodontol. 77:753–764. 2006. View Article : Google Scholar
23	Tipton DA, Howell KJ and Dabbous MK: Increased proliferation, collagen, and fibronectin production by hereditary gingival fibromatosis fibroblasts. J Periodontol. 68:524–530. 1997. View Article : Google Scholar
24	Ramer M, Marrone J, Stahl B and Burakoff R: Hereditary gingival fibromatosis: identification, treatment, control. Journal of the American Dental Association. 127:493–495. 1996. View Article : Google Scholar : PubMed/NCBI
25	Laband PF, Habib G and Humphreys GS: Hereditary gingival fibromatosis. report of an affected family with associated splenomegaly and skeletal and soft-tissue abnormalities. Oral Surg Oral Med Oral Pathol. 17:339–351. 1964. View Article : Google Scholar : PubMed/NCBI
26	Araujo CS, Graner E, Almeida OP, Sauk JJ and Coletta RD: Histomorphometric characteristics and expression of epidermal growth factor and its receptor by epithelial cells of normal gingiva and hereditary gingival fibromatosis. J Periodontal Res. 38:237–241. 2003. View Article : Google Scholar : PubMed/NCBI
27	Karikari TK: Bioinformatics in Africa: The Rise of Ghana? PLOS Comput Biol. 11:e10043082015. View Article : Google Scholar : PubMed/NCBI
28	Kitazawa S, Kitazawa R, Obayashi C and Yamamoto T: Desmoid tumor with ossification in chest wall: possible involvement of BAMBI promoter hypermethylation in metaplastic bone formation. J Bone Miner Res. 20:1472–1477. 2005. View Article : Google Scholar : PubMed/NCBI
29	Straka M, Danisovic L, Bzduch V, Polak S and Varga I: The significance of electron microscopic examination of gingiva in cases of Hunter syndrome and hereditary gingival fibromatosis. Neuro Endocrinol Lett. 37:353–360. 2016.PubMed/NCBI
30	Barak S, Wang Z and Miettinen M: Immunoreactivity for calretinin and keratins in desmoid fibromatosis and other myofibroblastic tumors: A diagnostic pitfall. Am J Surg Pathol. 36:1404–1409. 2012. View Article : Google Scholar : PubMed/NCBI
31	Ornitz DM and Itoh N: The Fibroblast Growth Factor signaling pathway. Wiley Interdiscip Rev Dev Biol. 4:215–266. 2015. View Article : Google Scholar : PubMed/NCBI
32	Lee CH, Marekov LN, Kim S, Brahim JS, Park MH and Steinert PM: Small proline-rich protein 1 is the major component of the cell envelope of normal human oral keratinocytes. FEBS Lett. 477:268–272. 2000. View Article : Google Scholar : PubMed/NCBI
33	Torre K, Larsen A, Kristjansson A and Murphy M: Basal cell carcinoma, arising within a granular cell-type fibrous papule. J Cutan Pathol. 43:1245–1247. 2016. View Article : Google Scholar : PubMed/NCBI
34	Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J and Trajanoski Z: Bioinformatics for cancer immunology and immunotherapy. Cancer Immunol Immunother. 61:1885–1903. 2012. View Article : Google Scholar : PubMed/NCBI