Construction of ceRNA Network to Reveal Potential Biomarkers in Crohn’s Disease and Validation in a TNBS Induced Mice Model

References

• Ramos GP, Papadakis KA. Mechanisms of disease: inflammatory bowel diseases. Mayo Clin Proc. 2019;94(1):155–165. doi:10.1016/j.mayocp.2018.09.013
   PubMed Web of Science ®Google Scholar
• Feuerstein JD, Cheifetz AS. Crohn disease: epidemiology, diagnosis, and management. Mayo Clin Proc. 2017;92(7):1088–1103. doi:10.1016/j.mayocp.2017.04.010
   PubMed Web of Science ®Google Scholar
• Roda G, Chien NS, 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
• Torres J, Mehandru S, Colombel JF, Peyrin-Biroulet L. Crohn’s disease. Lancet. 2017;389(10080):1741–1755. doi:10.1016/S0140-6736(16)31711-1
   PubMed Web of Science ®Google Scholar
• Roda G, Jharap B, Neeraj N, Colombel JF. Loss of Response to Anti-TNFs: definition, Epidemiology, and Management. Clin Transl Gastroenterol. 2016;7:e135. doi:10.1038/ctg.2015.63
   PubMed Web of Science ®Google Scholar
• Axelrad JE, Lichtiger S, Yajnik V. Inflammatory bowel disease and cancer: the role of inflammation, immunosuppression, and cancer treatment. World J Gastroenterol. 2016;22(20):4794–4801. doi:10.3748/wjg.v22.i20.4794
   PubMed Web of Science ®Google Scholar
• Ng SC, Shi HY, Hamidi N, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet. 2017;390(10114):2769–2778. doi:10.1016/S0140-6736(17)32448-0
   PubMed Web of Science ®Google Scholar
• Rogler G, Singh A, Kavanaugh A, Rubin DT. Extraintestinal Manifestations of Inflammatory Bowel Disease: current Concepts, Treatment, and Implications for Disease Management. Gastroenterology. 2021;161(4):1118–1132. doi:10.1053/j.gastro.2021.07.042
   PubMed Web of Science ®Google Scholar
• Cushing K, Higgins PDR. Management of Crohn Disease: a Review. JAMA. 2021;325(1):69–80. doi:10.1001/jama.2020.18936
   PubMed Web of Science ®Google Scholar
• Li Y, Chen B, Gao X, et al. Current diagnosis and management of Crohn’s disease in China: results from a multicenter prospective disease registry. BMC Gastroenterol. 2019;19(1):145. doi:10.1186/s12876-019-1057-2
   PubMed Web of Science ®Google Scholar
• Gomollon F, Dignass A, Annese V, et al. 3rd European Evidence-based Consensus on the Diagnosis and Management of Crohn’s Disease 2016: part 1: diagnosis and Medical Management. J Crohns Colitis. 2017;11(1):3–25. doi:10.1093/ecco-jcc/jjw168
   PubMed Web of Science ®Google Scholar
• Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505(7483):344–352. doi:10.1038/nature12986
   PubMed Web of Science ®Google Scholar
• Chan JJ, Tay Y. Noncoding RNA:RNA Regulatory Networks in Cancer. Int J Mol Sci. 2018;19:5. doi:10.3390/ijms19051310
   Web of Science ®Google Scholar
• Du Z, Sun T, Hacisuleyman E, et al. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nat Commun. 2016;7:10982. doi:10.1038/ncomms10982
   PubMed Web of Science ®Google Scholar
• Zhang X, Zhou Y, Chen S, Li W, Chen W, Gu W. LncRNA MACC1-AS1 sponges multiple miRNAs and RNA-binding protein PTBP1. Oncogenesis. 2019;8(12):73. doi:10.1038/s41389-019-0182-7
   PubMedGoogle Scholar
• Cheng W, Li XW, Xiao YQ, Duan SB. Non-coding RNA-Associated ceRNA Networks in a New Contrast-Induced Acute Kidney Injury Rat Model. Mol Ther Nucleic Acids. 2019;17:102–112. doi:10.1016/j.omtn.2019.05.011
   PubMedGoogle Scholar
• Zhang S, Zhu D, Li H, Li H, Feng C, Zhang W. Characterization of circRNA-Associated-ceRNA Networks in a Senescence-Accelerated Mouse Prone 8 Brain. Mol Ther. 2017;25(9):2053–2061. doi:10.1016/j.ymthe.2017.06.009
   PubMed Web of Science ®Google Scholar
• Liang H, Su X, Wu Q, et al. LncRNA 2810403D21Rik/Mirf promotes ischemic myocardial injury by regulating autophagy through targeting Mir26a. Autophagy. 2020;16(6):1077–1091. doi:10.1080/15548627.2019.1659610
   PubMed Web of Science ®Google Scholar
• Nie J, Zhao Q. Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4(+) T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease. Front Immunol. 2020;11:852. doi:10.3389/fimmu.2020.00852
   PubMed Web of Science ®Google Scholar
• Liu H, Li T, Zhong S, Yu M, Huang W. Intestinal epithelial cells related lncRNA and mRNA expression profiles in dextran sulphate sodium-induced colitis. J Cell Mol Med. 2021;25(2):1060–1073. doi:10.1111/jcmm.16174
   PubMed Web of Science ®Google Scholar
• Mirza AH, Berthelsen CH, Seemann SE, et al. Transcriptomic landscape of lncRNAs in inflammatory bowel disease. Genome Med. 2015;7(1):39. doi:10.1186/s13073-015-0162-2
   PubMedGoogle Scholar
• Verstockt S, De Hertogh G, Van der Goten J, et al. Gene and Mirna Regulatory Networks During Different Stages of Crohn’s Disease. J Crohns Colitis. 2019;13(7):916–930. doi:10.1093/ecco-jcc/jjz007
   PubMed Web of Science ®Google Scholar
• Vancamelbeke M, Vanuytsel T, Farre 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
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9:559. doi:10.1186/1471-2105-9-559
   PubMed Web of Science ®Google Scholar
• Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523. doi:10.1038/s41467-019-09234-6
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Nastou KC, et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 2021;49(D1):D605–D612. doi:10.1093/nar/gkaa1074
   PubMed Web of Science ®Google Scholar
• Sticht C, De La Torre C, Parveen A, Gretz N. miRWalk: an online resource for prediction of microRNA binding sites. PLoS One. 2018;13(10):e0206239. doi:10.1371/journal.pone.0206239
   PubMed Web of Science ®Google Scholar
• Karagkouni D, Paraskevopoulou MD, Tastsoglou S, et al. DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. Nucleic Acids Res. 2020;48(D1):D101–D110. doi:10.1093/nar/gkz1036
   PubMed Web of Science ®Google Scholar
• Miao YR, Zhang Q, Lei Q, et al. ImmuCellAI: a Unique Method for Comprehensive T-Cell Subsets Abundance Prediction and its Application in Cancer Immunotherapy. Adv Sci. 2020;7(7):1902880. doi:10.1002/advs.201902880
   Web of Science ®Google Scholar
• Antoniou E, Margonis GA, Angelou A, et al. The TNBS-induced colitis animal model: an overview. Ann Med Surg. 2016;11:9–15. doi:10.1016/j.amsu.2016.07.019
   PubMed Web of Science ®Google Scholar
• Ye Y, Zhang L, Hu T, et al. CircRNA_103765 acts as a proinflammatory factor via sponging miR-30 family in Crohn’s disease. Sci Rep. 2021;11(1):565. doi:10.1038/s41598-020-80663-w
   PubMed Web of Science ®Google Scholar
• Li Y, Soendergaard C, Bergenheim FH, et al. COX-2-PGE2 Signaling Impairs Intestinal Epithelial Regeneration and Associates with TNF Inhibitor Responsiveness in Ulcerative Colitis. EBioMedicine. 2018;36:497–507. doi:10.1016/j.ebiom.2018.08.040
   PubMed Web of Science ®Google Scholar
• Singer II, Kawka DW, Schloemann S, Tessner T, Riehl T, Stenson WF. Cyclooxygenase 2 is induced in colonic epithelial cells in inflammatory bowel disease. Gastroenterology. 1998;115(2):297–306. doi:10.1016/s0016-5085(98)70196-9
   PubMed Web of Science ®Google Scholar
• O’Connor PM, Lapointe TK, Beck PL, Buret AG. Mechanisms by which inflammation may increase intestinal cancer risk in inflammatory bowel disease. Inflamm Bowel Dis. 2010;16(8):1411–1420. doi:10.1002/ibd.21217
   PubMed Web of Science ®Google Scholar
• Le Loupp AG, Bach-Ngohou K, Bourreille A, et al. Activation of the prostaglandin D2 metabolic pathway in Crohn’s disease: involvement of the enteric nervous system. BMC Gastroenterol. 2015;15:112. doi:10.1186/s12876-015-0338-7
   PubMed Web of Science ®Google Scholar
• Zundler S, Becker E, Schulze LL, Neurath MF. Immune cell trafficking and retention in inflammatory bowel disease: mechanistic insights and therapeutic advances. Gut. 2019;68(9):1688–1700. doi:10.1136/gutjnl-2018-317977
   PubMed Web of Science ®Google Scholar
• Smids C, Horjus Talabur Horje CS, Drylewicz J, et al. Intestinal T Cell Profiling in Inflammatory Bowel Disease: linking T Cell Subsets to Disease Activity and Disease Course. J Crohns Colitis. 2018;12(4):465–475. doi:10.1093/ecco-jcc/jjx160
   PubMed Web of Science ®Google Scholar
• Noble A, Durant L, Hoyles L, et al. Deficient Resident Memory T Cell and CD8 T Cell Response to Commensals in Inflammatory Bowel Disease. J Crohns Colitis. 2020;14(4):525–537. doi:10.1093/ecco-jcc/jjz175
   PubMed Web of Science ®Google Scholar
• Hadjicharalambous MR, Roux BT, Feghali-Bostwick CA, Murray LA, Clarke DL, Lindsay MA. Long Non-coding RNAs Are Central Regulators of the IL-1beta-Induced Inflammatory Response in Normal and Idiopathic Pulmonary Lung Fibroblasts. Front Immunol. 2018;9:2906. doi:10.3389/fimmu.2018.02906
   PubMed Web of Science ®Google Scholar
• Mo JS, Alam KJ, Kim HS, Lee YM, Yun KJ, Chae SC. MicroRNA 429 Regulates Mucin Gene Expression and Secretion in Murine Model of Colitis. J Crohns Colitis. 2016;10(7):837–849. doi:10.1093/ecco-jcc/jjw033
   PubMed Web of Science ®Google Scholar