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ORIGINAL RESEARCH

LncRNA-miRNA-mRNA Network Analysis Reveals the Potential Biomarkers in Crohn's Disease Rats Treated with Herb-Partitioned Moxibustion

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Pages 1699-1716 | Published online: 05 Mar 2022

References

  • 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
  • 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
  • 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
  • Kaser A, Zeissig S, Blumberg RS. Inflammatory bowel disease. Annu Rev Immunol. 2010;28:573–621. doi:10.1146/annurev-immunol-030409-101225
  • Zhang YZ, Li YY. Inflammatory bowel disease: pathogenesis. World J Gastroenterol. 2014;20(1):91–99. doi:10.3748/wjg.v20.i1.91
  • Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet. 2020;21(2):102–117. doi:10.1038/s41576-019-0184-5
  • Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet. 2016;17(1):47–62. doi:10.1038/nrg.2015.10
  • Michalik KM, You X, Manavski Y, et al. Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth. Circ Res. 2014;114(9):1389–1397. doi:10.1161/circresaha.114.303265
  • Huang MD, Chen WM, Qi FZ, et al. Long non-coding RNA ANRIL is upregulated in hepatocellular carcinoma and regulates cell proliferation by epigenetic silencing of KLF2. J Hematol Oncol. 2015;8(1):57. doi:10.1186/s13045-015-0153-1
  • Li Z, Chao TC, Chang KY, et al. The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A. 2014;111(3):1002–1007. doi:10.1073/pnas.1313768111
  • Cesana M, Cacchiarelli D, Legnini I, et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011;147(2):358–369. doi:10.1016/j.cell.2011.09.028
  • Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146(3):353–358. doi:10.1016/j.cell.2011.07.014
  • Wang J, Yan S, Yang J, Lu H, Xu D, Wang Z. Non-coding RNAs in Rheumatoid Arthritis: from Bench to Bedside. Front Immunol. 2019;10:3129. doi:10.3389/fimmu.2019.03129
  • Li Y, Zhang S, Zhang C, Wang M. LncRNA MEG3 inhibits the inflammatory response of ankylosing spondylitis by targeting miR-146a. Mol Cell Biochem. 2020;466(1–2):17–24. doi:10.1007/s11010-019-03681-x
  • Tian F, Wang J, Zhang Z, Yang J. LncRNA SNHG7/miR-34a-5p/SYVN1 axis plays a vital role in proliferation, apoptosis and autophagy in osteoarthritis. Biol Res. 2020;53(1):9. doi:10.1186/s40659-020-00275-6
  • Ghafouri-Fard S, Eghtedarian R, Taheri M. The crucial role of non-coding RNAs in the pathophysiology of inflammatory bowel disease. Biomed Pharmacother. 2020;129:110507. doi:10.1016/j.biopha.2020.110507
  • Qiao YQ, Huang ML, Xu AT, Zhao D, Ran ZH, Shen J. LncRNA DQ786243 affects Treg related CREB and Foxp3 expression in Crohn’s disease. J Biomed Sci. 2013;20(1):87. doi:10.1186/1423-0127-20-87
  • Haberman Y, BenShoshan M, Di Segni A, et al. Long ncRNA Landscape in the Ileum of Treatment-Naive Early-Onset Crohn Disease. Inflamm Bowel Dis. 2018;24(2):346–360. doi:10.1093/ibd/izx013
  • Li Y, Zhu L, Chen P, et al. MALAT1 maintains the intestinal mucosal homeostasis in Crohn’s disease via the miR-146b-5p-CLDN11/NUMB pathway. J Crohns Colitis. 2021. doi:10.1093/ecco-jcc/jjab040
  • Bao CH, Wu LY, Shi Y, et al. Moxibustion down-regulates colonic epithelial cell apoptosis and repairs tight junctions in rats with Crohn’s disease. World J Gastroenterol. 2011;17(45):4960–4970. doi:10.3748/wjg.v17.i45.4960
  • Zhou J, Wu LY, Chen L, et al. Herbs-partitioned moxibustion alleviates aberrant intestinal epithelial cell apoptosis by upregulating A20 expression in a mouse model of Crohn’s disease. World J Gastroenterol. 2019;25(17):2071–2085. doi:10.3748/wjg.v25.i17.2071
  • Shi Y, Guo Y, Zhou J, et al. Herbs-partitioned moxibustion improves intestinal epithelial tight junctions by upregulating A20 expression in a mouse model of Crohn’s disease. Biomed Pharmacother. 2019;118:109149. doi:10.1016/j.biopha.2019.109149
  • Bao CH, Wu LY, Wu HG, et al. Moxibustion inhibits apoptosis and tumor necrosis factor-alpha/tumor necrosis factor receptor 1 in the colonic epithelium of Crohn’s disease model rats. Dig Dis Sci. 2012;57(9):2286–2295. doi:10.1007/s10620-012-2161-0
  • Zhao JM, Liu YN, Zheng HD, et al. Effect of Herb-Partitioned Moxibustion on Autophagy and Immune-Associated Gene Expression Profiles in a Rat Model of Crohn’s Disease. Evid Based Complement Alternat Med. 2019;2019:3405146. doi:10.1155/2019/3405146
  • Morris GP, Beck PL, Herridge MS, Depew WT, Szewczuk MR, Wallace JL. Hapten-induced model of chronic inflammation and ulceration in the rat colon. Gastroenterology. 1989;96(3):795–803.
  • Okayasu I, Hatakeyama S, Yamada M, Ohkusa T, Inagaki Y, Nakaya R. A novel method in the induction of reliable experimental acute and chronic ulcerative colitis in mice. Gastroenterology. 1990;98(3):694–702. doi:10.1016/0016-5085(90)90290-h
  • Wallace JL, Keenan CM, Gale D, Shoupe TS. Exacerbation of experimental colitis by nonsteroidal anti-inflammatory drugs is not related to elevated leukotriene B4 synthesis. Gastroenterology. 1992;102(1):18–27. doi:10.1016/0016-5085(92)91779-4
  • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290–295. doi:10.1038/nbt.3122
  • Finn RD, Mistry J, Schuster-Böckler B, et al. Pfam: clans, web tools and services. Nucleic Acids Res. 2006;34(Databaseissue):D247–251. doi:10.1093/nar/gkj149
  • Li A, Zhang J, Zhou Z. PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. BMC Bioinform. 2014;15(1):311. doi:10.1186/1471-2105-15-311
  • Sun L, Liu H, Zhang L, Meng J. lncRScan-SVM: a Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine. PLoS One. 2015;10(10):e0139654. doi:10.1371/journal.pone.0139654
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–410. doi:10.1016/s0022-2836(05)80360-2
  • Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31(1):439–441. doi:10.1093/nar/gkg006
  • Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008;36(Databaseissue):D154–158. doi:10.1093/nar/gkm952
  • Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012;40(1):37–52. doi:10.1093/nar/gkr688
  • Guo L, Yu J, Liang T, Zou Q. miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels. Sci Rep. 2016;6:23700. doi:10.1038/srep23700
  • Tino P. Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays. BMC Bioinform. 2009;10:310. doi:10.1186/1471-2105-10-310
  • Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–d613. doi:10.1093/nar/gky1131
  • Li N, Shi R. Expression alteration of long non-coding RNAs and their target genes in the intestinal mucosa of patients with Crohn’s disease. Clin Chim Acta. 2019;494:14–21. doi:10.1016/j.cca.2019.02.031
  • Rankin CR, Theodorou E, Man Law IK, et al. Identification of novel mRNAs and lncRNAs associated with mouse experimental colitis and human inflammatory bowel disease. Am J Physiol Gastrointest Liver Physiol. 2018;315(5):G722–g733. doi:10.1152/ajpgi.00077.2018
  • 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
  • Qi Q, Im H, Li KS, et al. Influence of herb-partitioned moxibustion at Qihai (CV6) and bilateral Tianshu (ST25) and Shangjuxu (ST37) acupoints on toll-like receptors 4 signaling pathways in patients with ulcerative coliti. J Tradit Chin Med. 2021;41(3):479–485. doi:10.19852/j.cnki.jtcm.20210310.001
  • Liu Y, Sun J, Wang X, Shi L, Yan Y. Effect of herb-partitioned moxibustion for primary dysmenorrhea: a randomized clinical trial. J Tradit Chin Med. 2019;39(2):237–245.
  • Hu H, Chen L, Jin X, Li R, Fang J. Effect of herb-partitioned moxibustion on pain and quality of life in women with endometriosis: a protocol for a randomized clinical trial. J Tradit Chin Med. 2020;40(2):324–332.
  • Joos S, Brinkhaus B, Maluche C, et al. Acupuncture and moxibustion in the treatment of active Crohn’s disease: a randomized controlled study. Digestion. 2004;69(3):131–139. doi:10.1159/000078151
  • Bao CH, Zhao JM, Liu HR, et al. Randomized controlled trial: moxibustion and acupuncture for the treatment of Crohn’s disease. World J Gastroenterol. 2014;20(31):11000–11011. doi:10.3748/wjg.v20.i31.11000
  • Zhang J, Wang XJ, Wu LJ, et al. Herb-partitioned moxibustion alleviates colonic inflammation in Crohn’s disease rats by inhibiting hyperactivation of the NLRP3 inflammasome via regulation of the P2X7R-Pannexin-1 signaling pathway. PLoS One. 2021;16(5):e0252334. doi:10.1371/journal.pone.0252334
  • Turner JR. Intestinal mucosal barrier function in health and disease. Nat Rev Immunol. 2009;9(11):799–809. doi:10.1038/nri2653
  • Di sabatino A, Ciccocioppo R, Luinetti O, et al. Increased enterocyte apoptosis in inflamed areas of Crohn’s disease. Dis Colon Rectum. 2003;46(11):1498–1507. doi:10.1007/s10350-004-6802-z
  • Ruiz E, Penrose HM, Heller S, et al. Bacterial TLR4 and NOD2 signaling linked to reduced mitochondrial energy function in active inflammatory bowel disease. Gut Microbes. 2020;11(3):350–363. doi:10.1080/19490976.2019.1611152
  • Cheng C, Hua J, Tan J, Qian W, Zhang L, Hou X. Identification of differentially expressed genes, associated functional terms pathways, and candidate diagnostic biomarkers in inflammatory bowel diseases by bioinformatics analysis. Exp Ther Med. 2019;18(1):278–288. doi:10.3892/etm.2019.7541
  • Li H, Li Q, Sun S, Lei P, Cai X, Shen G. Integrated Bioinformatics Analysis Identifies ELAVL1 and APP as Candidate Crucial Genes for Crohn’s Disease. J Immunol Res. 2020;2020:3067273. doi:10.1155/2020/3067273
  • Yin J, Hu T, Xu L, et al. Circular RNA expression profile in peripheral blood mononuclear cells from Crohn disease patients. Medicine. 2019;98(26):e16072. doi:10.1097/md.0000000000016072
  • Tawfik A, Knight P, Duckworth CA, Pritchard DM, Rhodes JM, Campbell BJ. Replication of Crohn’s Disease Mucosal E. coli Isolates inside Macrophages Correlates with Resistance to Superoxide and Is Dependent on Macrophage NF-kappa B Activation. Pathogens. 2019;8(2). doi:10.3390/pathogens8020074
  • Wang X, Lu Y, Wu L, et al. Moxibustion Inhibits the ERK Signaling Pathway and Intestinal Fibrosis in Rats with Crohn’s Disease. Evid Based Complement Alternat Med. 2013;2013:198282. doi:10.1155/2013/198282
  • Mortensen JH, Lindholm M, Langholm LL, et al. The intestinal tissue homeostasis - the role of extracellular matrix remodeling in inflammatory bowel disease. Expert Rev Gastroenterol Hepatol. 2019;13(10):977–993. doi:10.1080/17474124.2019.1673729
  • Lee T, Lee E, Arrollo D, Lucas PC, Parameswaran N. Non-Hematopoietic β-Arrestin1 Confers Protection Against Experimental Colitis. J Cell Physiol. 2016;231(5):992–1000. doi:10.1002/jcp.25216
  • Wang Y, de Vallière C, Imenez Silva PH, et al. The Proton-activated Receptor GPR4 Modulates Intestinal Inflammation. J Crohns Colitis. 2018;12(3):355–368. doi:10.1093/ecco-jcc/jjx147
  • Day R, Forbes A. Heparin, cell adhesion, and pathogenesis of inflammatory bowel disease. Lancet. 1999;354(9172):62–65. doi:10.1016/s0140-6736(98)09267-8
  • Su Z, Zhi X, Zhang Q, Yang L, Xu H, Xu Z. LncRNA H19 functions as a competing endogenous RNA to regulate AQP3 expression by sponging miR-874 in the intestinal barrier. FEBS Lett. 2016;590(9):1354–1364. doi:10.1002/1873-3468.12171
  • Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505(7483):344–352. doi:10.1038/nature12986
  • Li H, Zuo J, Tang W. Phosphodiesterase-4 Inhibitors for the Treatment of Inflammatory Diseases. Front Pharmacol. 2018;9:1048. doi:10.3389/fphar.2018.01048
  • Czub E, Nowak JK, Szaflarska-Poplawska A, et al. Comparison of fecal pyruvate kinase isoform M2 and calprotectin in assessment of pediatric inflammatory bowel disease severity and activity. Acta Biochim Pol. 2014;61(1):99–102.
  • Winkelmann P, Unterweger AL, Khullar D, et al. The PI3K pathway as a therapeutic intervention point in inflammatory bowel disease. Immun Inflamm Dis. 2021;9(3):804–818. doi:10.1002/iid3.435
  • Bilski J, Mazur-Bialy A, Wojcik D, et al. Role of Obesity, Mesenteric Adipose Tissue, and Adipokines in Inflammatory Bowel Diseases. Biomolecules. 2019;9:12. doi:10.3390/biom9120780
  • Han X, Benight N, Osuntokun B, Loesch K, Frank SJ, Denson LA. Tumour necrosis factor alpha blockade induces an anti-inflammatory growth hormone signalling pathway in experimental colitis. Gut. 2007;56(1):73–81. doi:10.1136/gut.2006.094490
  • Xie M, Xiong Z, Yin S, et al. Adiponectin Alleviates Intestinal Fibrosis by Enhancing AMP-Activated Protein Kinase Phosphorylation. Dig Dis Sci. 2021. doi:10.1007/s10620-021-07015-0
  • Cheng S, Ma X, Geng S, et al. Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury. mSystems. 2018;3(5). doi:10.1128/mSystems.00137-18
  • Zhou W, Cao Q, Peng Y, et al. FoxO4 inhibits NF-kappaB and protects mice against colonic injury and inflammation. Gastroenterology. 2009;137(4):1403–1414. doi:10.1053/j.gastro.2009.06.049
  • Mo Y, Liu B, Qiu S, et al. Down-regulation of microRNA-34c-5p alleviates neuropathic pain via the SIRT1/STAT3 signaling pathway in rat models of chronic constriction injury of sciatic nerve. J Neurochem. 2020;154(3):301–315. doi:10.1111/jnc.14998
  • Beale EG, Harvey BJ, Forest C. PCK1 and PCK2 as candidate diabetes and obesity genes. Cell Biochem Biophys. 2007;48(2–3):89–95. doi:10.1007/s12013-007-0025-6
  • Ko CW, Counihan D, Wu J, Hatzoglou M, Puchowicz MA, Croniger CM. Macrophages with a deletion of the phosphoenolpyruvate carboxykinase 1 (Pck1) gene have a more proinflammatory phenotype. J Biol Chem. 2018;293(9):3399–3409. doi:10.1074/jbc.M117.819136
  • Guo H, Chi Y, Chi N. Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis. Sci Rep. 2021;11(1):5428. doi:10.1038/s41598-021-83742-8
  • Batistel F, Osorio JS, Ferrari A, Trevisi E, Socha MT, Loor JJ. Immunometabolic Status during the Peripartum Period Is Enhanced with Supplemental Zn, Mn, and Cu from Amino Acid Complexes and Co from Co Glucoheptonate. PLoS One. 2016;11(5):e0155804. doi:10.1371/journal.pone.0155804