Understanding Competitive Endogenous RNA Network Mechanism in Type 1 Diabetes Mellitus Using Computational and Bioinformatics Approaches

References

• Pozzilli P , Maddaloni E , Buzzetti R . Combination immunotherapies for type 1 diabetes mellitus. Nat Rev Endocrinol . 2015;11(5):289–297. doi:10.1038/nrendo.2015.8 25688000
   PubMed Web of Science ®Google Scholar
• Ni Q , Pham NB , Meng WS , Zhu G , Chen X . Advances in immunotherapy of type I diabetes. Adv Drug Deliv Rev . 2019;139:83–91. doi:10.1016/j.addr.2018.12.003 30528629
   PubMed Web of Science ®Google Scholar
• Cerna M . Epigenetic Regulation in Etiology of Type 1 Diabetes Mellitus. Int J Mol Sci . 2019;21(1):254. doi:10.3390/ijms21010036
   Web of Science ®Google Scholar
• Gastol J , Kapusta P , Polus A , et al. Epigenetic mechanism in search for the pathomechanism of diabetic neuropathy development in diabetes mellitus type 1 (T1DM). Endocrine . 2020;68(1):235–240. doi:10.1007/s12020-019-02172-9 31902112
   PubMed Web of Science ®Google Scholar
• Ilonen J , Lempainen J , Veijola R . The heterogeneous pathogenesis of type 1 diabetes mellitus. Nat Rev Endocrinol . 2019;15(11):635–650. doi:10.1038/s41574-019-0254-y 31534209
   PubMed Web of Science ®Google Scholar
• Paschou SA , Papadopoulou-Marketou N , Chrousos GP , Kanaka-Gantenbein C . On type 1 diabetes mellitus pathogenesis. Endocr Connect . 2018;7(1):R38–R46. doi:10.1530/EC-17-0347 29191919
   PubMed Web of Science ®Google Scholar
• Diaz-Valencia PA , Bougneres P , Valleron AJ . Global epidemiology of type 1 diabetes in young adults and adults: a systematic review. BMC Public Health . 2015;15:255. doi:10.1186/s12889-015-1591-y 25849566
   PubMed Web of Science ®Google Scholar
• Thomas NJ , Jones SE , Weedon MN , Shields BM , Oram RA , Hattersley AT . Frequency and phenotype of type 1 diabetes in the first six decades of life: a cross-sectional, genetically stratified survival analysis from UK Biobank. Lancet Diabetes Endocrinol . 2018;6(2):122–129. doi:10.1016/S2213-8587(17)30362-5 29199115
   PubMed Web of Science ®Google Scholar
• Chiang JL , Kirkman MS , Laffel LM , Peters AL . Type 1 Diabetes Sourcebook A. Type 1 diabetes through the life span: a position statement of the American Diabetes Association. Diabetes Care . 2014;37(7):2034–2054. doi:10.2337/dc14-1140 24935775
   PubMed Web of Science ®Google Scholar
• Patterson CC , Karuranga S , Salpea P , et al. Worldwide estimates of incidence, prevalence and mortality of type 1 diabetes in children and adolescents: results from the International Diabetes Federation Diabetes Atlas, 9th edition. Diabetes Res Clin Pract . 2019;157:107842. doi:10.1016/j.diabres.2019.107842 31518658
   PubMed Web of Science ®Google Scholar
• Liu J , Ren ZH , Qiang H , et al. Trends in the incidence of diabetes mellitus: results from the Global Burden of Disease Study 2017 and implications for diabetes mellitus prevention. BMC Public Health . 2020;20(1):1415. doi:10.1186/s12889-020-09502-x 32943028
   PubMed Web of Science ®Google Scholar
• Tao B , Pietropaolo M , Atkinson M , Schatz D , Taylor D . Estimating the cost of type 1 diabetes in the U.S.: a propensity score matching method. PLoS One . 2010;5(7):e11501. doi:10.1371/journal.pone.0011501 20634976
   PubMed Web of Science ®Google Scholar
• Lapolla A , Amaro F , Bruttomesso D , et al. Diabetic ketoacidosis: a consensus statement of the Italian Association of Medical Diabetologists (AMD), Italian Society of Diabetology (SID), Italian Society of Endocrinology and Pediatric Diabetoloy (SIEDP). Nutr Metab Cardiovasc Dis . 2020;30(10):1633–1644. doi:10.1016/j.numecd.2020.06.006 32771260
   PubMed Web of Science ®Google Scholar
• Williams SM , Eleftheriadou A , Alam U , Cuthbertson DJ , Jph W . Cardiac Autonomic Neuropathy in Obesity, the Metabolic Syndrome and Prediabetes: a Narrative Review. Diabetes Ther . 2019;10(6):1995–2021. doi:10.1007/s13300-019-00693-0 31552598
   PubMed Web of Science ®Google Scholar
• Sousa GR , Pober D , Galderisi A , et al. Glycemic Control, Cardiac Autoimmunity, and Long-Term Risk of Cardiovascular Disease in Type 1 Diabetes Mellitus. Circulation . 2019;139(6):730–743. doi:10.1161/CIRCULATIONAHA.118.036068 30586738
   PubMed Web of Science ®Google Scholar
• Gillard P , Schnell O , Groop PH . The nephrological perspective on SGLT-2 inhibitors in type 1 diabetes. Diabetes Res Clin Pract . 2020;170:108462. doi:10.1016/j.diabres.2020.108462 32971152
   PubMed Web of Science ®Google Scholar
• Skyler JS , Bakris GL , Bonifacio E , et al. Differentiation of Diabetes by Pathophysiology, Natural History, and Prognosis. Diabetes . 2017;66(2):241–255. doi:10.2337/db16-0806 27980006
   PubMed Web of Science ®Google Scholar
• Crossen S , Xing G , Hoch JS . Changing costs of type 1 diabetes care among US children and adolescents. Pediatr Diabetes . 2020;21(4):644–648. doi:10.1111/pedi.12996 32061049
   PubMed Web of Science ®Google Scholar
• Zou Q , Qu K , Luo Y , Yin D , Ju Y , Tang H . Predicting Diabetes Mellitus With Machine Learning Techniques. Front Genet . 2018;9:515. doi:10.3389/fgene.2018.00515 30459809
   PubMed Web of Science ®Google Scholar
• Taheri M , Eghtedarian R , Dinger ME , Ghafouri-Fard S . Emerging roles of non-coding RNAs in the pathogenesis of type 1 diabetes mellitus. Biomed Pharmacother . 2020;129:110509. doi:10.1016/j.biopha.2020.110509 32768981
   PubMed Web of Science ®Google Scholar
• Geng G , Zhang Z , Cheng L . Identification of a Multi-Long Noncoding RNA Signature for the Diagnosis of Type 1 Diabetes Mellitus. Front Bioeng Biotechnol . 2020;8:553. doi:10.3389/fbioe.2020.00553 32719778
   PubMed Web of Science ®Google Scholar
• Li Y , Zhou Y , Zhao M , et al. Differential Profile of Plasma Circular RNAs in Type 1 Diabetes Mellitus. Diabetes Metab J . 2020;44(6):854–865. doi:10.4093/dmj.2019.0151 32662258
   PubMed Web of Science ®Google Scholar
• Gonzalez-Moro I , Olazagoitia-Garmendia A , Colli ML , et al. The T1D-associated lncRNA Lnc13 modulates human pancreatic beta cell inflammation by allele-specific stabilization of STAT1 mRNA. Proc Natl Acad Sci U S A . 2020;117(16):9022–9031. doi:10.1073/pnas.1914353117 32284404
   PubMed Web of Science ®Google Scholar
• Ding H , Wang F , Shi X , et al. LncRNA MALAT1 induces the dysfunction of beta cells via reducing the histone acetylation of the PDX-1 promoter in type 1 diabetes. Exp Mol Pathol . 2020;114:104432. doi:10.1016/j.yexmp.2020.104432 32243891
   PubMed Web of Science ®Google Scholar
• Zhang C , Han X , Yang L , et al. Circular RNA circPPM1F modulates M1 macrophage activation and pancreatic islet inflammation in type 1 diabetes mellitus. Theranostics . 2020;10(24):10908–10924. doi:10.7150/thno.48264 33042261
   PubMed Web of Science ®Google Scholar
• Hansen TB , Jensen TI , Clausen BH , et al. Natural RNA circles function as efficient microRNA sponges. Nature . 2013;495(7441):384–388. doi:10.1038/nature11993 23446346
   PubMed Web of Science ®Google Scholar
• Khorkova O , Hsiao J , Wahlestedt C . Basic biology and therapeutic implications of lncRNA. Adv Drug Deliv Rev . 2015;87:15–24. doi:10.1016/j.addr.2015.05.012 26024979
   PubMed Web of Science ®Google Scholar
• 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 21802130
   PubMed Web of Science ®Google Scholar
• Yang F , Chen Y , Xue Z , et al. High-Throughput Sequencing and Exploration of the lncRNA-circRNA-miRNA-mRNA Network in Type 2 Diabetes Mellitus. Biomed Res Int . 2020;2020:8162524. doi:10.1155/2020/8162524 32596376
   PubMed Web of Science ®Google Scholar
• Hu W , Ding Y , Wang S , Xu L , Yu H . The Construction and Analysis of the Aberrant lncRNA-miRNA-mRNA Network in Adipose Tissue from Type 2 Diabetes Individuals with Obesity. J Diabetes Res . 2020;2020:3980742. doi:10.1155/2020/3980742 32337289
   PubMed Web of Science ®Google Scholar
• Lin Z , Li X , Zhan X , et al. Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in type 2 diabetes mellitus. J Cell Mol Med . 2017;21(12):3204–3213. doi:10.1111/jcmm.13224 28643459
   PubMed Web of Science ®Google Scholar
• Kong X , Liu CX , Wang GD , et al. LncRNA LEGLTBC Functions as a ceRNA to Antagonize the Effects of miR-34a on the Downregulation of SIRT1 in Glucolipotoxicity-Induced INS-1 Beta Cell Oxidative Stress and Apoptosis. Oxid Med Cell Longev . 2019;2019:4010764. doi:10.1155/2019/4010764 31737170
   PubMed Web of Science ®Google Scholar
• Luo S , Deng M , Xie Z , Li X , Huang G , Zhou Z . Circulating circular RNAs profiles associated with type 1 diabetes. Diabetes Metab Res Rev . 2021;37(3):e3394. doi:10.1002/dmrr.3394 32798322
   PubMed Web of Science ®Google Scholar
• Shi Q , Yao H . Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis. BMC Med Genomics . 2021;14(1):133. doi:10.1186/s12920-021-00931-0 34006268
   PubMed Web of Science ®Google Scholar
• Edgar R , Domrachev M , Lash AE . Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res . 2002;30(1):207–210. doi:10.1093/nar/30.1.207 11752295
   PubMed Web of Science ®Google Scholar
• Yang L , Han X , Zhang C , et al. Hsa_circ_0060450 Negatively Regulates Type I Interferon-Induced Inflammation by Serving as miR-199a-5p Sponge in Type 1 Diabetes Mellitus. Front Immunol . 2020;11:576903. doi:10.3389/fimmu.2020.576903 33133095
   PubMed Web of Science ®Google Scholar
• Gautier L , Cope L , Bolstad BM , Irizarry RA . affy–analysis of Affymetrix GeneChip data at the probe level. Bioinformatics . 2004;20(3):307–315. doi:10.1093/bioinformatics/btg405 14960456
   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 25605792
   PubMed Web of Science ®Google Scholar
• Yu G , Wang LG , Han Y , He QY . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS . 2012;16(5):284–287. doi:10.1089/omi.2011.0118 22455463
   PubMed Web of Science ®Google Scholar
• Ashburner M , Ball CA , Blake JA , et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet . 2000;25(1):25–29. doi:10.1038/75556 10802651
   PubMed Web of Science ®Google Scholar
• Kanehisa M , Goto S , Furumichi M , Tanabe M , Hirakawa M . KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res . 2010;38(Database issue):D355–360. doi:10.1093/nar/gkp896 19880382
   PubMed Web of Science ®Google Scholar
• Shannon P , Markiel A , Ozier O , et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res . 2003;13(11):2498–2504. doi:10.1101/gr.1239303 14597658
   PubMed Web of Science ®Google Scholar
• Vandesompele J , De Preter K , Pattyn F , et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol . 2002;3(7):RESEARCH0034. doi:10.1186/gb-2002-3-7-research0034 12184808
   PubMed Web of Science ®Google Scholar
• Andersen CL , Jensen JL , Orntoft TF . Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res . 2004;64(15):5245–5250. doi:10.1158/0008-5472.CAN-04-0496 15289330
   PubMed Web of Science ®Google Scholar
• Zhou M , Gao M , Luo Y , Gui R , Ji H . Long non-coding RNA metallothionein 1 pseudogene 3 promotes p2y12 expression by sponging miR-126 to activate platelet in diabetic animal model. Platelets . 2019;30(4):452–459. doi:10.1080/09537104.2018.1457781 29617185
   PubMed Web of Science ®Google Scholar
• Chen W , Peng R , Sun Y , et al. The topological key lncRNA H2k2 from the ceRNA network promotes mesangial cell proliferation in diabetic nephropathy via the miR-449a/b/Trim11/Mek signaling pathway. FASEB J . 2019;33(10):11492–11506. doi:10.1096/fj.201900522R 31336052
   PubMed Web of Science ®Google Scholar
• Zhou B , Yu JW . A novel identified circular RNA, circRNA_010567, promotes myocardial fibrosis via suppressing miR-141 by targeting TGF-beta1. Biochem Biophys Res Commun . 2017;487(4):769–775. doi:10.1016/j.bbrc.2017.04.044 28412345
   PubMed Web of Science ®Google Scholar
• Li C , Wei B , Zhao J . Competing endogenous RNA network analysis explores the key lncRNAs, miRNAs, and mRNAs in type 1 diabetes. BMC Med Genomics . 2021;14(1):35. doi:10.1186/s12920-021-00877-3 33526014
   PubMed Web of Science ®Google Scholar
• Xie C , Chen B , Wu B , Guo J , Shi Y , Cao Y . CircSAMD4A regulates cell progression and epithelialmesenchymal transition by sponging miR3423p via the regulation of FZD7 expression in osteosarcoma. Int J Mol Med . 2020;46(1):107–118. doi:10.3892/ijmm.2020.4585 32319545
   PubMed Web of Science ®Google Scholar
• Liu Y , Liu H , Li Y , et al. Circular RNA SAMD4A controls adipogenesis in obesity through the miR-138-5p/EZH2 axis. Theranostics . 2020;10(10):4705–4719. doi:10.7150/thno.42417 32292524
   PubMed Web of Science ®Google Scholar
• Hu X , Ma R , Cao J , Du X , Cai X , Fan Y . CircSAMD4A aggravates H/R-induced cardiomyocyte apoptosis and inflammatory response by sponging miR-138-5p. J Cell Mol Med . 2020. doi:10.1111/jcmm.16093
   Web of Science ®Google Scholar
• Zurawek M , Dzikiewicz-Krawczyk A , Izykowska K , et al. miR-487a-3p upregulated in type 1 diabetes targets CTLA4 and FOXO3. Diabetes Res Clin Pract . 2018;142:146–153. doi:10.1016/j.diabres.2018.05.044 29859273
   PubMed Web of Science ®Google Scholar
• Azhir Z , Dehghanian F , Hojati Z . Increased expression of microRNAs, miR-20a and miR-326 in PBMCs of patients with type 1 diabetes. Mol Biol Rep . 2018;45(6):1973–1980. doi:10.1007/s11033-018-4352-z 30194557
   PubMed Web of Science ®Google Scholar
• Sebastiani G , Grieco FA , Spagnuolo I , Galleri L , Cataldo D , Dotta F . Increased expression of microRNA miR-326 in type 1 diabetic patients with ongoing islet autoimmunity. Diabetes Metab Res Rev . 2011;27(8):862–866. doi:10.1002/dmrr.1262 22069274
   PubMed Web of Science ®Google Scholar
• Garcia-Diaz DF , Pizarro C , Camacho-Guillen P , Codner E , Soto N , Perez-Bravo F . Expression of miR-155, miR-146a, and miR-326 in T1D patients from Chile: relationship with autoimmunity and inflammatory markers. Arch Endocrinol Metab . 2018;62(1):34–40. doi:10.20945/2359-3997000000006 29694627
   PubMed Web of Science ®Google Scholar
• Wischer JL , Oermann MH , Zadvinskis IM , Kinney KC . Effects of iPad Video Education on Patient Knowledge, Satisfaction, and Cardiac Rehabilitation Attendance. Qual Manag Health Care . 2018;27(4):204–208. doi:10.1097/QMH.0000000000000185 30260927
   PubMed Web of Science ®Google Scholar
• Li M , Zhang S , Qiu Y , et al. Upregulation of miR-665 promotes apoptosis and colitis in inflammatory bowel disease by repressing the endoplasmic reticulum stress components XBP1 and ORMDL3. Cell Death Dis . 2017;8(3):e2699. doi:10.1038/cddis.2017.76 28333149
   PubMed Web of Science ®Google Scholar
• Wang G , Yuan J , Cai X , et al. HucMSC-exosomes carrying miR-326 inhibit neddylation to relieve inflammatory bowel disease in mice. Clin Transl Med . 2020;10(2):e113. doi:10.1002/ctm2.113 32564521
   PubMed Web of Science ®Google Scholar
• Olaru AV , Yamanaka S , Vazquez C , et al. MicroRNA-224 negatively regulates p21 expression during late neoplastic progression in inflammatory bowel disease. Inflamm Bowel Dis . 2013;19(3):471–480. doi:10.1097/MIB.0b013e31827e78eb 23399735
   PubMed Web of Science ®Google Scholar
• Bogdani M , Korpos E , Simeonovic CJ , Parish CR , Sorokin L , Wight TN . Extracellular matrix components in the pathogenesis of type 1 diabetes. Curr Diab Rep . 2014;14(12):552. doi:10.1007/s11892-014-0552-7 25344787
   PubMed Web of Science ®Google Scholar
• Marro BS , Legrain S , Ware BC , Oldstone MB . Macrophage IFN-I signaling promotes autoreactive T cell infiltration into islets in type 1 diabetes model. JCI Insight . 2019;4(2):24. doi:10.1172/jci.insight.125067
   Web of Science ®Google Scholar
• Chang TJ , Wang WC , Hsiung CA , et al. Genetic Variation in the Human SORBS1 Gene is Associated With Blood Pressure Regulation and Age at Onset of Hypertension: a SAPPHIRe Cohort Study. Medicine . 2016;95(10):e2970. doi:10.1097/MD.0000000000002970 26962801
   PubMed Web of Science ®Google Scholar
• Germain M , Pezzolesi MG , Sandholm N , et al. SORBS1 gene, a new candidate for diabetic nephropathy: results from a multi-stage genome-wide association study in patients with type 1 diabetes. Diabetologia . 2015;58(3):543–548. doi:10.1007/s00125-014-3459-6 25476525
   PubMed Web of Science ®Google Scholar
• Fu Y , Zhou N , Bai W , et al. Association of the CACNA2D2 gene with schizophrenia in Chinese Han population. PeerJ . 2020;8:e8521. doi:10.7717/peerj.8521 32071821
   PubMed Web of Science ®Google Scholar
• Huang Q , Deng G , Wei R , Wang Q , Zou D , Wei J . Comprehensive Identification of Key Genes Involved in Development of Diabetes Mellitus-Related Atherogenesis Using Weighted Gene Correlation Network Analysis. Front Cardiovasc Med . 2020;7:580573. doi:10.3389/fcvm.2020.580573 33195466
   PubMed Web of Science ®Google Scholar
• Sanders LN , Schoenhard JA , Saleh MA , et al. BMP Antagonist Gremlin 2 Limits Inflammation After Myocardial Infarction. Circ Res . 2016;119(3):434–449. doi:10.1161/CIRCRESAHA.116.308700 27283840
   PubMed Web of Science ®Google Scholar
• Bruinsma IB , de Jager M , Carrano A , et al. Small heat shock proteins induce a cerebral inflammatory reaction. J Neurosci . 2011;31(33):11992–12000. doi:10.1523/JNEUROSCI.0945-11.2011 21849559
   PubMed Web of Science ®Google Scholar
• Chen LL . The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol . 2016;17(4):205–211. doi:10.1038/nrm.2015.32 26908011
   PubMed Web of Science ®Google Scholar
• Engreitz JM , Haines JE , Perez EM , et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature . 2016;539(7629):452–455. doi:10.1038/nature20149 27783602
   PubMed Web of Science ®Google Scholar