Identification and Validation of Signature Genes and Potential Therapy Targets of Inflammatory Bowel Disease and Periodontitis

References

• Kobayashi T, Siegmund B, Le Berre C, et al. Ulcerative colitis. Nat Rev Dis Primers. 2020;6(1):74. doi:10.1038/s41572-020-0205-x
   PubMed Web of Science ®Google Scholar
• Roda G, Chien Ng S, Kotze PG, et al. Crohn’s disease. Nat Rev Dis Primers. 2020;6(1):22. doi:10.1038/s41572-020-0156-2
   PubMed Web of Science ®Google Scholar
• Vavricka SR, Schoepfer A, Scharl M, Lakatos PL, Navarini A, Rogler G. Extraintestinal Manifestations of Inflammatory Bowel Disease. Inflamm Bowel Dis. 2015;21(8):1982–1992. doi:10.1097/MIB.0000000000000392
   PubMed Web of Science ®Google Scholar
• Lankarani KB, Sivandzadeh GR, Hassanpour S. Oral manifestation in inflammatory bowel disease: a review. World J Gastroenterol. 2013;19(46):8571–8579. doi:10.3748/wjg.v19.i46.8571
   PubMed Web of Science ®Google Scholar
• Graves D. Cytokines that promote periodontal tissue destruction. J Periodontol. 2008;79(8 Suppl):1585–1591. doi:10.1902/jop.2008.080183
   PubMed Web of Science ®Google Scholar
• Madsen GR, Bertl K, Pandis N, Stavropoulos A, Burisch J. The Impact of Periodontitis on Inflammatory Bowel Disease Activity. Inflamm Bowel Dis. 2023;29(3):396–404. doi:10.1093/ibd/izac090
   PubMed Web of Science ®Google Scholar
• Genco RJ, Borgnakke WS. Risk factors for periodontal disease. Periodontol 2000. 2013;62(1):59–94. doi:10.1111/j.1600-0757.2012.00457.x
   PubMedGoogle Scholar
• Zeng Y, Cao S, Chen M. Integrated analysis and exploration of potential shared gene signatures between carotid atherosclerosis and periodontitis. BMC Med Genomics. 2022;15(1):227. doi:10.1186/s12920-022-01373-y
   PubMed Web of Science ®Google Scholar
• Zhang Y, Qiao D, Chen R, Zhu F, Gong J, Yan F. The Association between Periodontitis and Inflammatory Bowel Disease: a Systematic Review and Meta-analysis. Biomed Res Int. 2021;2021:6692420. doi:10.1155/2021/6692420
   PubMed Web of Science ®Google Scholar
• Bertl K, Burisch J, Pandis N, Bruckmann C, Klinge B, Stavropoulos A. Periodontitis prevalence in patients with ulcerative colitis and Crohn’s disease - PPCC: a case-control study. J Clin Periodontol. 2022;49(12):1262–1274. doi:10.1111/jcpe.13615
   PubMed Web of Science ®Google Scholar
• Vavricka SR, Manser CN, Hediger S, et al. Periodontitis and gingivitis in inflammatory bowel disease: a case-control study. Inflamm Bowel Dis. 2013;19(13):2768–2777. doi:10.1097/01.MIB.0000438356.84263.3b
   PubMed Web of Science ®Google Scholar
• Wang Z, Li S, Tan D, et al. Association between inflammatory bowel disease and periodontitis: a bidirectional two-sample Mendelian randomization study. J Clin Periodontol. 2023;50(6):736–743. doi:10.1111/jcpe.13782
   PubMedGoogle Scholar
• Pietropaoli D, Del Pinto R, Corridoni D, et al. Occurrence of spontaneous periodontal disease in the SAMP1/YitFc murine model of Crohn disease. J Periodontol. 2014;85(12):1799–1805. doi:10.1902/jop.2014.140316
   PubMed Web of Science ®Google Scholar
• Imai J, Ichikawa H, Kitamoto S, et al. A potential pathogenic association between periodontal disease and Crohn’s disease. JCI Insight. 2021;6(23). doi:10.1172/jci.insight.148543
   Web of Science ®Google Scholar
• Liu Y, Huang W, Dai K, et al. Inflammatory response of gut, spleen, and liver in mice induced by orally administered Porphyromonas gingivalis. J Oral Microbiol. 2022;14(1):2088936. doi:10.1080/20002297.2022.2088936
   PubMed Web of Science ®Google Scholar
• Settem RP, El-Hassan AT, Honma K, Stafford GP, Sharma A. Fusobacterium nucleatum and Tannerella forsythia induce synergistic alveolar bone loss in a mouse periodontitis model. Infect Immun. 2012;80(7):2436–2443. doi:10.1128/IAI.06276-11
   PubMed Web of Science ®Google Scholar
• Sohn J, Li L, Zhang L, et al. Periodontal disease is associated with increased gut colonization of pathogenic Haemophilusparainfluenzae in patients with Crohn’s disease. Cell Rep. 2023;42(2):112120. doi:10.1016/j.celrep.2023.112120
   PubMed Web of Science ®Google Scholar
• Qian J, Lu J, Huang Y, et al. Periodontitis Salivary Microbiota Worsens Colitis. J Dent Res. 2022;101(5):559–568. doi:10.1177/00220345211049781
   PubMed Web of Science ®Google Scholar
• Kitamoto S, Nagao-Kitamoto H, Jiao Y, et al. The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis. Cell. 2020;182(2):447–462.e414. doi:10.1016/j.cell.2020.05.048
   PubMed Web of Science ®Google Scholar
• Rutgeerts P, Sandborn WJ, Feagan BG, et al. Infliximab for induction and maintenance therapy for ulcerative colitis. N Engl J Med. 2005;353(23):2462–2476. doi:10.1056/NEJMoa050516
   PubMed Web of Science ®Google Scholar
• Wong U, Cross RK. Primary and secondary nonresponse to infliximab: mechanisms and countermeasures. Expert Opin Drug Metab Toxicol. 2017;13(10):1039–1046. doi:10.1080/17425255.2017.1377180
   PubMed Web of Science ®Google Scholar
• Vancamelbeke M, Vanuytsel T, Farré R, et al. Genetic and Transcriptomic Bases of Intestinal Epithelial Barrier Dysfunction in Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017;23(10):1718–1729. doi:10.1097/MIB.0000000000001246
   PubMed Web of Science ®Google Scholar
• Vanhove W, Peeters PM, Staelens D, et al. Strong Upregulation of AIM2 and IFI16 Inflammasomes in the Mucosa of Patients with Active Inflammatory Bowel Disease. Inflamm Bowel Dis. 2015;21(11):2673–2682. doi:10.1097/MIB.0000000000000535
   PubMed Web of Science ®Google Scholar
• Papapanou PN, Behle JH, Kebschull M, et al. Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. BMC Microbiol. 2009;9:221. doi:10.1186/1471-2180-9-221
   PubMed Web of Science ®Google Scholar
• Demmer RT, Behle JH, Wolf DL, et al. Transcriptomes in healthy and diseased gingival tissues. J Periodontol. 2008;79(11):2112–2124. doi:10.1902/jop.2008.080139
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Walter W, Sánchez-Cabo F, Ricote M. GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics. 2015;31(17):2912–2914. doi:10.1093/bioinformatics/btv300
   PubMed Web of Science ®Google Scholar
• Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011;12(1):77. doi:10.1186/1471-2105-12-77
   PubMed Web of Science ®Google Scholar
• Arijs I, Li K, Toedter G, et al. Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis. Gut. 2009;58(12):1612–1619. doi:10.1136/gut.2009.178665
   PubMed Web of Science ®Google Scholar
• Bain CC, Schridde A. Origin, Differentiation, and Function of Intestinal Macrophages. Front Immunol. 2018;9:2733. doi:10.3389/fimmu.2018.02733
   PubMed Web of Science ®Google Scholar
• Cheng WC, Hughes FJ, Taams LS. The presence, function and regulation of IL-17 and Th17 cells in periodontitis. J Clin Periodontol. 2014;41(6):541–549. doi:10.1111/jcpe.12238
   PubMed Web of Science ®Google Scholar
• Liu H, Hong XL, Sun TT, Huang XW, Wang JL, Xiong H. Fusobacterium nucleatum exacerbates colitis by damaging epithelial barriers and inducing aberrant inflammation. J Dig Dis. 2020;21(7):385–398. doi:10.1111/1751-2980.12909
   PubMed Web of Science ®Google Scholar
• Figueredo CM, Martins AP, Lira-Junior R, et al. Activity of inflammatory bowel disease influences the expression of cytokines in gingival tissue. Cytokine. 2017;95:1–6. doi:10.1016/j.cyto.2017.01.016
   PubMed Web of Science ®Google Scholar
• Jia L, Wu R, Han N, et al. Porphyromonas gingivalis and Lactobacillus rhamnosus GG regulate the Th17/Treg balance in colitis via TLR4 and TLR2. Clin Transl Immunol. 2020;9(11):e1213. doi:10.1002/cti2.1213
   PubMed Web of Science ®Google Scholar
• Yuan X, Zhou F, Wang H, et al. Systemic antibiotics increase microbiota pathogenicity and oral bone loss. Int J Oral Sci. 2023;15(1):4. doi:10.1038/s41368-022-00212-1
   PubMed Web of Science ®Google Scholar
• Kerishnan JP, Mohammad S, Alias MS, et al. Identification of biomarkers for periodontal disease using the immunoproteomics approach. PeerJ. 2016;4:e2327. doi:10.7717/peerj.2327
   PubMed Web of Science ®Google Scholar
• Schmidt M, Hellwig B, Hammad S, et al. A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin κ C as a compatible prognostic marker in human solid tumors. Clin Cancer Res. 2012;18(9):2695–2703. doi:10.1158/1078-0432.CCR-11-2210
   PubMed Web of Science ®Google Scholar
• Schmidt M, Micke P, Gehrmann M, Hengstler JG. Immunoglobulin kappa chain as an immunologic biomarker of prognosis and chemotherapy response in solid tumors. Oncoimmunology. 2012;1(7):1156–1158. doi:10.4161/onci.21653
   PubMed Web of Science ®Google Scholar
• Kalluri R. Basement membranes: structure, assembly and role in tumour angiogenesis. Nat Rev Cancer. 2003;3(6):422–433. doi:10.1038/nrc1094
   PubMed Web of Science ®Google Scholar
• Karsdal MA, Nielsen SH, Leeming DJ, et al. The good and the bad collagens of fibrosis - Their role in signaling and organ function. Adv Drug Deliv Rev. 2017;121:43–56. doi:10.1016/j.addr.2017.07.014
   PubMed Web of Science ®Google Scholar
• Eshelman MA, Harris L, Deiling S, Koltun WA, Jeganathan NA, Yochum GS. Transcriptomic analysis of ileal tissue from Crohn’s disease patients identifies extracellular matrix genes that distinguish individuals by age at diagnosis. Physiol Genomics. 2020;52(10):478–484. doi:10.1152/physiolgenomics.00062.2020
   PubMed Web of Science ®Google Scholar
• Chen S, Puthanveetil P, Feng B, Matkovich SJ, Dorn GW, Chakrabarti S. Cardiac miR-133a overexpression prevents early cardiac fibrosis in diabetes. J Cell Mol Med. 2014;18(3):415–421. doi:10.1111/jcmm.12218
   PubMed Web of Science ®Google Scholar
• Solé C, Moliné T, Vidal M, Ordi-Ros J, Cortés-Hernández J. An Exosomal Urinary miRNA Signature for Early Diagnosis of Renal Fibrosis in Lupus Nephritis. Cells. 2019;8(8):773. doi:10.3390/cells8080773
   PubMed Web of Science ®Google Scholar
• Savin IA, Markov AV, Zenkova MA, Sen’kova AV. Asthma and Post-Asthmatic Fibrosis: a Search for New Promising Molecular Markers of Transition from Acute Inflammation to Pulmonary Fibrosis. Biomedicines. 2022;10(5):1017. doi:10.3390/biomedicines10051017
   PubMed Web of Science ®Google Scholar
• Wang T, Jin H, Hu J, et al. COL4A1 promotes the growth and metastasis of hepatocellular carcinoma cells by activating FAK-Src signaling. J Exp Clin Cancer Res. 2020;39(1):148. doi:10.1186/s13046-020-01650-7
   PubMed Web of Science ®Google Scholar
• Huang R, Gu W, Sun B, Gao L. Identification of COL4A1 as a potential gene conferring trastuzumab resistance in gastric cancer based on bioinformatics analysis. Mol Med Rep. 2018;17(5):6387–6396. doi:10.3892/mmr.2018.8664
   PubMed Web of Science ®Google Scholar
• Li T, Gao X, Han L, Yu J, Li H. Identification of hub genes with prognostic values in gastric cancer by bioinformatics analysis. World J Surg Oncol. 2018;16(1):114. doi:10.1186/s12957-018-1409-3
   PubMed Web of Science ®Google Scholar
• Li F, Wang NN, Chang X, et al. Bioinformatics analysis suggests that COL4A1 may play an important role in gastric carcinoma recurrence. J Dig Dis. 2019;20(8):391–400. doi:10.1111/1751-2980.12758
   PubMed Web of Science ®Google Scholar
• Yang J, Hao R, Zhang Y, Deng H, Teng W, Wang Z. Construction of circRNA-miRNA-mRNA network and identification of novel potential biomarkers for non-small cell lung cancer. Cancer Cell Int. 2021;21(1):611. doi:10.1186/s12935-021-02278-z
   PubMed Web of Science ®Google Scholar
• Ben-Horin S, Kopylov U, Chowers Y. Optimizing anti-TNF treatments in inflammatory bowel disease. Autoimmun Rev. 2014;13(1):24–30. doi:10.1016/j.autrev.2013.06.002
   PubMed Web of Science ®Google Scholar