In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers

Year 2025, Volume: 59 Issue: 1, 12 - 18, 29.01.2025

Azizeh Asadzadeh , Fatemeh Shams Moattar , Azam Moshfegh

https://doi.org/10.26650/eor.20241393951

Abstract

Purpose: Pulpitis is one of the most common oral inflammatory diseases. There are many limitations in the traditional methods of diagnosing pulpitis. By replacing new diagnostic ways based on biomarkers, it is possible to quickly and accurately identify this disease. Biological indicators have greatly helped not only in the screening of infectious diseases but also in early and appropriate treatment. In this research, differentially expressed genes (DEGs) related to pulpitis were analyzed, and prognostic biomarkers were introduced.

Materials and methods: In this in silico study, we applied the GSE77459 dataset as the gene expression profile of pulpitis. Web tool, GEO2R was used to separate up-regulated and down-regulated DEGs. |logFC|>2 and adjusted p-value < 0.05 was set as the cut off criterion. For the pathway enrichment study of obtained genes, EnrichR was implemented. After constructing a protein-protein interaction (PPI) network, hub genes that are involved in pulpitis were selected. Finally, functionally grouped networks by ClueGO software (v2.5.10) were generated.

Results: GEO2R analysis of the GSE77459 dataset showed 672 up-regulated genes and 239 down-regulated genes with GB_ACC code. Based on Cytoscape results, the 15 top hubba nodes were ranked including PTPRC, ITGAM, CCL2, ICAM1, MMP9, CXCL8, TLR2, CD86, CXCR4, IL1A, CD44, CCL3, ITGAX, CXCL10, and CCR7. Functionally grouped networks determined that these genes were mainly enriched in chemokine-mediated signaling pathway, morphogenesis of endothelium, and neuroinflammatory response.

Conclusion: In our research, 15 genes were introduced as diagnostic biomarkers in pulpitis and their functionally grouped networks were constructed. However, the obtained results need to be validated using in vitro and in vivo methods.

Keywords

Dental pulp, inflammation, gene ontology, DEGs, PPI, Pulpitis

References

• Arola DD, Gao S, Zhang H, Masri R. The Tooth: Its Structure and Properties. Dent Clin North Am 2017;61:651-68. google scholar
• Mazzoni A, Breschi L, Carrilho M, Nascimento FD, Orsini G, Ruggeri Jr A, et al.. A review of the nature, role, and function of dentin non-collagenous proteins. Part II: enzymes, serum proteins, and growth factors. Endodontic topics 2009;21:19-40. google scholar
• Galler KM, Weber M, Korkmaz Y, Widbiller M, Feuerer M. Inflammatory Response Mechanisms of the Dentine-Pulp Complex and the Periapical Tissues. Int J Mol Sci 2021;22:1480. google scholar
• Donnermeyer D, Dammaschke T, Lipski M, Schafer E. Effectiveness of diagnosing pulpitis: A systematic review. International Endodontic Journal 2023;56:296-325. google scholar
• Kratunova E, Silva D. Pulp therapy for primary and immature permanent teeth: an overview. Gen Dent 2018;66:30-8. google scholar
• Chandra R, Tripathi S, Jain J, Meherotra A, De R, Dixit M. Vital Pulp Therpay. J Adv Med Dent Scie Res 2023;11:62-81. google scholar
• Abu-Tahun I, Rabah'ah A, Khraisat A. A review of the questions and needs in endodontic diagnosis. Odontostomatol Trop 2012;35:11-20. google scholar
• Liu R, Wang X, Aihara K, Chen L. Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers. Med Res Rev 2014;34:455-78. google scholar
• Tappia PS, Ramjiawan B. Biomarkers for Early Detection of Cancer: Molecular Aspects. Int J Mol Sci 2023; 24:5272. google scholar
• Burke HB. Predicting Clinical Outcomes Using Molecular Biomarkers. Biomark Cancer 2016;8:89-99. google scholar
• Kong J, Wang F, Teodoro G, Cooper L, Moreno CS, Kurc T, et al.., editors. High-performance computational analysis of glioblastoma pathology images with database support identifies molecular and survival correlates. EEE Int Conf Bioinformatics Biomed 2013;229-36. google scholar
• Liu X, Liu ZP, Zhao XM, Chen L. Identifying disease genes and module biomarkers by differential interactions. J Am Med Inform Assoc 2012;19:241-8. google scholar
• Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with Cytoscape 3. Curr Protoc Bioinformatics. 2014; 47:8.13.1-24. google scholar
• Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al.. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009;25:1091-3. google scholar
• Zhang D, Zheng C, Zhu T, Yang F, Zhou Y. Identification of key module and hub genes in pulpitis using weighted gene co-expression network analysis. BMC Oral Health 2023;23:2. google scholar
• Jiang Y, He Y, Chen Y, Zeng J, Huang W, Huang L, et al.. Overexpression of MicroRNA-155 aggravates pulpitis by targeting kinesin superfamily Proteins-5C based on illumina high-throughput sequencing. Int Endod J 2023;56:837-53. google scholar
• Huang X, Chen K. Differential Expression of Long Noncoding RNAs in Normal and Inflamed Human Dental Pulp. J Endod 2018;44:62-72. google scholar
• Fouad A. The microbial challenge to pulp regeneration. Adv Dent Res 2011;23:285-9. google scholar
• Yu C, Abbott PV. An overview of the dental pulp: its functions and responses to injury. Aust Dent J 2007;52:S4-S6. google scholar
• Karrar RN, Cushley S, Duncan HF, Lundy FT, Abushouk SA, Clarke M, et al.. Molecular biomarkers for objective assessment of symptomatic pulpitis: A systematic review and meta-analysis. Int Endod J 2023;56:1160-77. google scholar
• Brizuela C, Meza G, Mercade M, Inostroza C, Chaparro A, Bravo I, et al.. Inflammatory biomarkers in dentinal fluid as an approach to molecular diagnostics in pulpitis. Int Endod J 2020;53(9):1181-91. google scholar
• Rechenberg D-K, Galicia JC, Peters OA. Biological markers for pulpal inflammation: a systematic review. PloS one 2016;11:e0167289. google scholar
• Al Barashdi MA, Ali A, McMullin MF, Mills K. Protein tyrosine phosphatase receptor type C (PTPRC or CD45). J Clin Pathol 2021;74:548-52. google scholar
• He R-j, Yu Z-h, Zhang R-y, Zhang Z-y. Protein tyrosine phosphatases as potential therapeutic targets. Acta pharmacologica sinica 2014;35:1227-46. google scholar
• Rheinlander A, Schraven B, Bommhardt U. CD45 in human physiology and clinical medicine. Immunol Lett 2018;196:22-32. google scholar
• Roberts A, Fürnrohr B, Vyse T, Rhodes B. The complement receptor 3 (CD11b/CD18) agonist Leukadherin-1 suppresses human innate inflammatory signalling. Clin Exp Immunol 2016.;185:361-71. google scholar
• Hirsch V, Wolgin M, Mitronin AV, Kielbassa AM. Inflammatory cytokines in normal and irreversibly inflamed pulps: a systematic review Arch Oral Biol 2017;82:38-46. google scholar
• Hubbard AK, Rothlein R. Intercellular adhesion molecule-1 (ICAM-1) expression and cell signaling cascades. Free Radic Biol Med 2000;28:1379-86. google scholar
• Frank PG, Lisanti MP. ICAM-1: role in inflammation and in the regulation of vascular permeability. Am J Physiol Heart Circ Physiol 2008;295:H926-H7. google scholar
• Vandooren J, Van den Steen PE, Opdenakker G. Biochemistry and molecular biology of gelatinase B or matrix metalloproteinase-9 (MMP-9): the next decade. Crit Rev Biochem Mol Biol 2013;48(3):222-72. google scholar
• Sharma R, Kumar V, Logani A, Chawla A, Mir R, Sharma S, et al.. Association between concentration of active MMP-9 in pulpal blood and pulpotomy outcome in permanent mature teeth with irreversible pulpitis-a preliminary study. Int Endod J 2021;54(4):479-89. google scholar
• Karapanou V, Kempuraj D, Theoharides TC. Interleukin-8 is increased in gingival crevicular fluid from patients with acute pulpitis. J Endod 2008;34:148-51. google scholar
• Russo RC, Garcia CC, Teixeira MM, Amaral FA. The CXCL8/IL-8 chemokine family and its receptors in inflammatory diseases. Expert Rev Clin Immunol 2014;10:593-619. google scholar
• Lee PR, Lee J-H, Park JM, Oh SB. Upregulation of toll-like receptor 2 in dental primary afferents following pulp injury. Exp Neurobiol 2021;30:329. google scholar
• Newton S, Ding Y, Chung C-S, Chen Y, Lomas-Neira JL, Ayala A. Sepsis-induced changes in macrophage co-stimulatory molecule expression: CD86 as a regulator of anti-inflammatory IL-10 response. Surg Infect 2004;5:375-83. google scholar
• Chen M, Zeng J, Yang Y, Wu B. Diagnostic biomarker candidates for pulpitis revealed by bioinformatics analysis of merged microarray gene expression datasets. BMC Oral Health 2020;20:1-13. google scholar