Weighted gene co-expression network analysis (WGCNA) to explore genes responsive to Streptococcus oralis biofilm and immune infiltration analysis in human gingival fibroblasts cells

References

• Moraschini V, Poubel LA, Ferreira VF, et al. Evaluation of survival and success rates of dental implants reported in longitudinal studies with a follow-up period of at least 10 years: a systematic review. Int J Oral Maxillofac Surg. 2015;44(3):377–388.
   PubMed Web of Science ®Google Scholar
• Araujo MG, Lindhe J. Peri-implant health. J Clin Periodontol. 2018;45(Suppl 20):S230–S236.
   PubMedGoogle Scholar
• Bumgardner JD, Adatrow P, Haggard WO, et al. Emerging antibacterial biomaterial strategies for the prevention of peri-implant inflammatory diseases. Int J Oral Maxillofac Implants. 2011;26(3):553–560.
   PubMed Web of Science ®Google Scholar
• Dale BA. Fascination with epithelia: architecture, proteins, and functions. J Dent Res. 2003;82(11):866–869.
   PubMed Web of Science ®Google Scholar
• Charalampakis G, Belibasakis GN. Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses. Virulence. 2015;6(3):183–187.
   PubMed Web of Science ®Google Scholar
• Arciola CR, Campoccia D, Montanaro L. Implant infections: adhesion, biofilm formation and immune evasion. Nat Rev Microbiol. 2018;16(7):397–409.
   PubMed Web of Science ®Google Scholar
• Wang Q, Lu H, Zhang L, et al. Peri-implant mucositis sites with suppuration have higher microbial risk than sites without suppuration. J Periodontol. 2020;91(10):1284–1294.
   Web of Science ®Google Scholar
• Furst MM, Salvi GE, Lang NP, et al. Bacterial colonization immediately after installation on oral titanium implants. Clin Oral Implants Res. 2007;18(4):501–508.
   PubMed Web of Science ®Google Scholar
• Ahmed R, Hassall T, Morland B, et al. Viridans streptococcus bacteremia in children on chemotherapy for cancer: an underestimated problem. Pediatr Hematol Oncol. 2003;20(6):439–444.
   PubMed Web of Science ®Google Scholar
• Beighton D, Carr AD, Oppenheim BA. Identification of viridans streptococci associated with bacteraemia in neutropenic cancer patients. J Med Microbiol. 1994;40(3):202–204.
   PubMed Web of Science ®Google Scholar
• De Toledo A, Nagata E, Yoshida Y, et al. Streptococcus oralis coaggregation receptor polysaccharides induce inflammatory responses in human aortic endothelial cells. Mol Oral Microbiol. 2012;27(4):295–307.
   PubMed Web of Science ®Google Scholar
• Ammann TW, Belibasakis GN, Thurnheer T. Impact of early colonizers on in vitro subgingival biofilm formation. PLoS One. 2013;8(12):e83090.
   PubMed Web of Science ®Google Scholar
• Xu H, Sobue T, Thompson A, et al. Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response. Cell Microbiol. 2014;16(2):214–231.
   PubMed Web of Science ®Google Scholar
• Ingendoh-Tsakmakidis A, Eberhard J, Falk CS, et al. In vitro effects of streptococcus oralis biofilm on peri-implant soft tissue cells. Cells. 2020;9.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9(1):559.
   PubMed Web of Science ®Google Scholar
• Yin L, Cai Z, Zhu B, et al. Identification of key pathways and genes in the dynamic progression of HCC based on WGCNA. Genes (Basel). 2018;9.
   Web of Science ®Google Scholar
• Liu Z, Li M, Fang X, et al. Identification of surrogate prognostic biomarkers for allergic asthma in nasal epithelial brushing samples by WGCNA. J Cell Biochem. 2019;120(4):5137–5150.
   PubMed Web of Science ®Google Scholar
• Qian J, Yang J, Liu X, et al. Analysis of lncRNA-mRNA networks after MEK1/2 inhibition based on WGCNA in pancreatic ductal adenocarcinoma. J Cell Physiol. 2020;235(4):3657–3668.
   PubMed Web of Science ®Google Scholar
• Bai K-H, He S-Y, Shu -L-L, et al. Identification of cancer stem cell characteristics in liver hepatocellular carcinoma by WGCNA analysis of transcriptome stemness index. Cancer Med. 2020;9(12):4290–4298.
   PubMed Web of Science ®Google Scholar
• Hoang M, Kim JJ, Kim Y, et al. Alcohol-induced suppression of KDM6B dysregulates the mineralization potential in dental pulp stem cells. Stem Cell Res. 2016;17(1):111–121.
   PubMed Web of Science ®Google Scholar
• Weyant RJ, Burt BA. An assessment of survival rates and within-patient clustering of failures for endosseous oral implants. J Dent Res. 1993;72(1):2–8.
   PubMed Web of Science ®Google Scholar
• Ekfeldt A, Christiansson U, Eriksson T, et al. A retrospective analysis of factors associated with multiple implant failures in maxillae. Clin Oral Implants Res. 2001;12(5):462–467.
   PubMed Web of Science ®Google Scholar
• Feloutzis A, Lang NP, Tonetti MS, et al. IL-1 gene polymorphism and smoking as risk factors for peri-implant bone loss in a well-maintained population. Clin Oral Implants Res. 2003;14(1):10–17.
   PubMed Web of Science ®Google Scholar
• Wilson TG Jr., Nunn M. The relationship between the interleukin-1 periodontal genotype and implant loss. Initial data. J Periodontol. 1999;70(7):724–729.
   PubMed Web of Science ®Google Scholar
• Jacobi-Gresser E, Huesker K, Schutt S. Genetic and immunological markers predict titanium implant failure: a retrospective study. Int J Oral Maxillofac Surg. 2013;42(4):537–543.
   PubMed Web of Science ®Google Scholar
• Campos MI, dos Santos MC, Trevilatto PC, et al. Early failure of dental implants and TNF-alpha (G-308A) gene polymorphism. Implant Dent. 2004;13(1):95–101.
   PubMedGoogle Scholar
• Petkovic AB, Matic SM, Stamatovic NV, et al. Proinflammatory cytokines (IL-1beta and TNF-alpha) and chemokines (IL-8 and MIP-1alpha) as markers of peri-implant tissue condition. Int J Oral Maxillofac Surg. 2010;39(5):478–485.
   PubMed Web of Science ®Google Scholar
• Belibasakis GN, Bao K, Bostanci N. Transcriptional profiling of human gingival fibroblasts in response to multi-species in vitro subgingival biofilms. Mol Oral Microbiol. 2014;29(4):174–183.
   PubMed Web of Science ®Google Scholar
• Ingendoh-Tsakmakidis A, Mikolai C, Winkel A, et al. Commensal and pathogenic biofilms differently modulate peri-implant oral mucosa in an organotypic model. Cell Microbiol. 2019;21(10):e13078.
   PubMed Web of Science ®Google Scholar
• Yang M, Pan Y, Zhou Y. miR-96 promotes osteogenic differentiation by suppressing HBEGF-EGFR signaling in osteoblastic cells. FEBS Lett. 2014;588(24):4761–4768.
   PubMed Web of Science ®Google Scholar
• Severino VO, Beghini M, de Araujo MF, et al. Expression of IL-6, IL-10, IL-17 and IL-33 in the peri-implant crevicular fluid of patients with peri-implant mucositis and peri-implantitis. Arch Oral Biol. 2016;72:194–199.
   PubMed Web of Science ®Google Scholar
• Ghassib I, Chen Z, Zhu J, et al. Use of IL-1 beta, IL-6, TNF-alpha, and MMP-8 biomarkers to distinguish peri-implant diseases: a systematic review and meta-analysis. Clin Implant Dent Relat Res. 2019;21(1):190–207.
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhang Y, Sculean A, et al. Macrophage behavior and interplay with gingival fibroblasts cultured on six commercially available titanium, zirconium, and titanium-zirconium dental implants. Clin Oral Investig. 2019;23(8):3219–3227.
   PubMed Web of Science ®Google Scholar
• Lin HY, Bumgardner JD. Changes in the surface oxide composition of Co-Cr-Mo implant alloy by macrophage cells and their released reactive chemical species. Biomaterials. 2004;25(7–8):1233–1238.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Cheng X, Jansen JA, et al. Titanium surfaces characteristics modulate macrophage polarization. Mater Sci Eng C Mater Biol Appl. 2019;95:143–151.
   PubMed Web of Science ®Google Scholar
• Okahashi N, Okinaga T, Sakurai A, et al. Streptococcus sanguinis induces foam cell formation and cell death of macrophages in association with production of reactive oxygen species. FEMS Microbiol Lett. 2011;323(2):164–170.
   PubMed Web of Science ®Google Scholar
• He W, Qu T, Yu Q, et al. LPS induces IL-8 expression through TLR4, MyD88, NF-kappaB and MAPK pathways in human dental pulp stem cells. Int Endod J. 2013;46(2):128–136.
   PubMed Web of Science ®Google Scholar
• Baus-Dominguez M, Gomez-Diaz R, Corcuera-Flores JR, et al. Using genetics in periodontal disease to justify implant failure in down syndrome patients. J Clin Med. 2020;9(8.
   Google Scholar
• Xu X, Jeong L, Han J, et al. Developmental expression of Smad1-7 suggests critical function of TGF-beta/BMP signaling in regulating epithelial-mesenchymal interaction during tooth morphogenesis. Int J Dev Biol. 2003;47(1):31–39.
   PubMed Web of Science ®Google Scholar
• Takemura Y, Moriyama Y, Ayukawa Y, et al. Mechanical loading induced osteocyte apoptosis and connexin 43 expression in three-dimensional cell culture and dental implant model. J Biomed Mater Res A. 2019;107(4):815–827.
   PubMed Web of Science ®Google Scholar