mNFE: microbiome network flow entropy for detecting pre-disease states of type 1 diabetes

References

• Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She J-X. et al. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018;562(7728):589–17. doi:10.1038/s41586-018-0620-2.
   PubMed Web of Science ®Google Scholar
• Zhou H, Zhao X, Sun L, Liu YJ, Lv Y, Gang XK, Wang G. Gut microbiota profile in patients with type 1 diabetes based on 16S rRNA gene sequencing: a systematic review. Dis Markers. 2020;2020:1–11. doi:10.1155/2020/3936247.
   Web of Science ®Google Scholar
• Catarino D, Silva D, Guiomar J, Ribeiro C, Ruas L, Cardoso L, Paiva I. Non-immune-mediated versus immune-mediated type 1 diabetes: diagnosis and long-term differences—retrospective analysis. Diabetol Metab Syndr. 2020;12(1):56. doi:10.1186/s13098-020-00563-x.
   PubMed Web of Science ®Google Scholar
• Islam ST, Srinivasan S, Craig ME. Environmental determinants of type 1 diabetes: a role for overweight and insulin resistance. J Paediatr Child Health. 2014;50(11):874–879. doi:10.1111/jpc.12616.
   PubMed Web of Science ®Google Scholar
• Liu R, Aihara K, Chen LN. Dynamical network biomarkers for identifying critical transitions and their driving networks of biologic processes. Quant Biol. 2013;1(2):105–114. doi:10.1007/s40484-013-0008-0.
   Google Scholar
• Liu R, Wang XD, Aihara K, Chen LN. Early diagnosis of complex diseases by molecular biomarkers. Network biomarkers, and dynamical network biomarker. Med Res Rev. 2013;34(3):455–478. doi:10.1002/med.21293.
   PubMed Web of Science ®Google Scholar
• Liu XP, Liu R, Zhao XM, Chen LN. Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers. BMC Med Genomics. 2013;2(Suppl 2):S8. doi:10.1186/1755-8794-6-S2-S8.
   Google Scholar
• Chen LN, Liu R, Liu ZP, Li MY, Aihara K. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Sci Rep. 2012;2(1):342. doi:10.1038/srep00342.
   PubMedGoogle Scholar
• Chen P, Zhong JY, Yang K, Zhang XH, Chen YQ, Liu R. TPD: a web tool for tipping-point detection based on dynamic network biomarker. Brief Bioinform. 2022;23(5):bbac399. doi:10.1093/bib/bbac399.
   PubMed Web of Science ®Google Scholar
• Gao R, Yan JL, Li PL, Chen LN. Detecting the critical states during disease development based on temporal network flow entropy. Brief Bioinform. 2022;23(5):bbac164. doi:10.1093/bib/bbac164.
   PubMed Web of Science ®Google Scholar
• Hu CY, Wong FS, Wen L. Type 1 diabetes and gut microbiota: friend or foe? Pharmacol Res. 2015;98:9–15. doi:10.1016/j.phrs.2015.02.006.
   PubMed Web of Science ®Google Scholar
• Wu HJ, Wu E. The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes. 2012;3(1):4–14. doi:10.4161/gmic.19320.
   PubMed Web of Science ®Google Scholar
• Longman RS, Yang Y, Diehl GE, Kim SV, Littman DR. Microbiota: host interactions in mucosal homeostasis and systemic autoimmunity. Cold Spring Harb Symp Quant Biol. 2014;78(0):193–201. doi:10.1101/sqb.2013.78.020081.
   Google Scholar
• Chervonsky AV. Microbiota and autoimmunity. Cold Spring Harb Perspect Biol. 2013;5(3):a007294. doi:10.1101/cshperspect.a007294.
   PubMed Web of Science ®Google Scholar
• Atarashi K, Honda K. Microbiota in autoimmunity and tolerance. Curr Opin Immunol. 2011;23(6):761–768. doi:10.1016/j.coi.2011.11.002.
   PubMed Web of Science ®Google Scholar
• Bosi E, Molteni L, Radaelli MG, Folini L, Fermo I, Bazzigaluppi E, Piemonti L, Pastore MR, Paroni R. Increased intestinal permeability precedes clinical onset of type 1 diabetes. Diabetologia. 2006;49(12):2824–2827. doi:10.1007/s00125-006-0465-3.
   PubMed Web of Science ®Google Scholar
• Westerholm-Ormio M, Vaarala O, Pihkala P, Ilonen J, Savilahti E. Immunologic activity in the small intestinal mucosa of pediatric patients with type 1 diabetes. Diabetes. 2003;52(9):2287–95. doi:10.2337/diabetes.52.9.2287.
   PubMed Web of Science ®Google Scholar
• Bendtsen KM, Fisker L, Hansen A, Hansen HF, Nielsen DS. The influence of the young microbiome on inflammatory diseases—lessons from animal studies. Birth Defects Res Part C. 2015;105(4):278–295. doi:10.1002/bdrc.21116.
   PubMedGoogle Scholar
• Brown EM, Kenny DJ, Xavier RJ. Gut microbiota regulation of T cells during inflammation and autoimmunity. Annu Rev Immunol. 2019;37(1):599–624. doi:10.1146/annurev-immunol-042718-041841.
   PubMed Web of Science ®Google Scholar
• de Goffau MC, Fuentes S, den Bogert BV, Honkanen H, de Vos WM, Welling GW, Hyöty H, Harmsen HJM. Aberrant gut microbiota composition at the onset of type 1 diabetes in young children. Diabetologia. 2014;57(8):1569–1577. doi:10.1007/s00125-014-3274-0.
   PubMed Web of Science ®Google Scholar
• Mejía‐León ME, Barca AM. Diet, microbiota and immune system in type 1 diabetes development and evolution. Nutrients. 2015;7(11):9171‐9184. doi:10.3390/nu7115461.
   PubMed Web of Science ®Google Scholar
• Liu XP, Liu R, Zhao XM, Chen LN. Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers. BMC Med Genomics. 2013;6(Suppl 2):S8. doi:10.1186/1755-8794-6-S2-S8.
   PubMedGoogle Scholar
• Li MY, Zeng T, Liu R, Chen LN. Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis. Brief Bioinform. 2013;15(2):229–243. doi:10.1093/bib/bbt027.
   PubMed Web of Science ®Google Scholar
• Yang YK, Tian ZH, Song MY, Ma CX, Ge ZY, Li PL. Detecting the critical states of type 2 diabetes mellitus based on degree matrix network entropy by Cross-Tissue Analysis. Entropy. 2022;24(9):1249. doi:10.3390/e24091249.
   PubMed Web of Science ®Google Scholar
• Liu R, Chen P, Chen LN, Cowen L. Single-sample landscape entropy reveals the imminent phase transition during disease progression. Bioinformatics. 2020;36(5):1522–1532. doi:10.1093/bioinformatics/btz758.
   PubMed Web of Science ®Google Scholar
• Chen P, Li YJ, Liu XP, Liu R, Chen LN. Detecting the tipping points in a three-state model of complex diseases by temporal differential networks. J Transl Med. 2017;15(1):217. doi:10.1186/s12967-017-1320-7.
   PubMedGoogle Scholar
• Liu R, Zhong JY, Yu XT, Li YJ, Chen P. Identifying critical state of complex diseases by single-sample-based hidden Markov model. Front Genet. 2019;10:285. doi:10.3389/fgene.2019.00285.
   PubMed Web of Science ®Google Scholar
• Srinivasan B. A guide to the Michaelis–menten equation: steady state and beyond. FEBS J. 2022;289(20):6086–6098. doi:10.1111/febs.16124.
   PubMed Web of Science ®Google Scholar
• Singh A, Malik P. Bifurcations in a modified Leslie–Gower predator–prey discrete model with Michaelis–menten prey harvesting. J Appl Math Comput. 2021;67(1–2):143–174. doi:10.1007/s12190-020-01491-9.
   Web of Science ®Google Scholar
• Khanin R, Vinciotti V, Mersinias V, Smith CP, Wit E. Statistical reconstruction of transcription factor activity using Michaelis–menten kinetics. Biometrics. 2007;63(3):816–823. doi:10.1111/j.1541-0420.2007.00757.x.
   PubMed Web of Science ®Google Scholar
• Ronen M, Rosenberg R, Shraiman BI, Uri A. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA. 2002;99(16):10555–10560. doi:10.1073/pnas.152046799.
   PubMed Web of Science ®Google Scholar
• Chen LN, Wang RQ, Li CG, Aihara K. Modeling biomolecular networks in cells: structures and dynamics. Net Cells: Struct Dyn. 2010. doi:10.1007/978-1-84996-214-8.
   Google Scholar
• Aleksandar DK, Gevers D, Siljander H, Tommi V, Tuulia H, Anu MH, Peet A, Tillmann V, Pöhö P, Mattila I, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17(2):260–273. doi:10.1016/j.chom.2015.01.001.
   PubMed Web of Science ®Google Scholar
• Sun RX, Huang WJ, Xiao Y, Wang DD, Mu GH, Nan H, Ni B-R, Huang X-Q, Wang H-C, Liu Y-F. et al. Shenlian (SL) decoction, a Traditional Chinese Medicine Compound, May ameliorate blood glucose via mediating the gut microbiota in db/db mice. J Diabetes Res. 2022;2022:1–20. doi:10.1155/2022/7802107.
   Web of Science ®Google Scholar
• Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31(9):814–821. doi:10.1038/nbt.2676.
   PubMed Web of Science ®Google Scholar
• Guasch-Ferré M, Santos JL, Martínez-González MA, Clish CB, Razquin C, Wang D, Liang L, Li J, Dennis C, Corella D. et al. Glycolysis/gluconeogenesis- and tricarboxylic acid cycle–related metabolites, Mediterranean diet, and type 2 diabetes. Am J Clin Nutr. 2020;111(4):835–844. doi:10.1093/ajcn/nqaa016.
   PubMed Web of Science ®Google Scholar
• Jin HY, Zhu BJ, Liu X, Jin J, Zou HD. Metabolic characterization of diabetic retinopathy: an 1H-NMR-based metabolomic approach using human aqueous humor. J Pharm Biomed Anal. 2019;174:414–421. doi:10.1016/j.jpba.2019.06.013.
   PubMed Web of Science ®Google Scholar
• Srinuanchai W, Nooin R, Pitchakarn P, Karinchai J, Suttisansanee U, Chansriniyom C, Jarussophon S, Temviriyanukul P, Nuchuchua O. Inhibitory effects of gymnema inodorum (Lour.) decne leaf extracts and its triterpene saponin on carbohydrate digestion and intestinal glucose absorption. J Ethnopharmacol. 2021;266:113398. doi:10.1016/j.jep.2020.113398.
   PubMed Web of Science ®Google Scholar
• Tilg H, Moschen AR. Adipocytokines: mediators linking adipose tissue, inflammation and immunity. Nat Rev Immunol. 2006;6(10):772–783. doi:10.1038/nri1937.
   PubMed Web of Science ®Google Scholar
• Samraj PI, Raj BS, Jeffrey S. Therapeutic benefits of alpha-lipoic acid supplementation in diabetes mellitus: a narrative review. J Diet Suppl. 2022;19(4):566–586. doi:10.1080/19390211.2021.2020387.
   PubMed Web of Science ®Google Scholar
• Xi Y, Xu PF. Diabetes and gut microbiota. World J Diabetes. 2021;12(10):1693–1703. doi:10.4239/wjd.v12.i10.1693.
   PubMed Web of Science ®Google Scholar
• Yang JY, Lee YS, Kim Y, Lee SH, Ryu S, Fukuda S, Hase K, Yang C-S, Lim HS, Kim M-S. et al. Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice. Mucosal Immunol. 2017;10(1):104–116. doi:10.1038/mi.2016.42.
   PubMed Web of Science ®Google Scholar
• Sun Y, Nie Q, Zhang S, He H, Zuo S, Chen C, Yang J, Chen H, Hu J, Li S. et al. Parabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a. Nat Commun. 2023;14(1):7740. doi:10.1038/s41467-023-43622-3.
   PubMed Web of Science ®Google Scholar
• Sousa AP, Cunha DM, Franco C, Teixeira C, Gojon F, Baylina P, Fernandes R. Which role plays 2-hydroxybutyric acid on insulin resistance? Metabolites. 2021;11(12):835. doi:10.3390/metabo11120835.
   PubMed Web of Science ®Google Scholar
• Qian X, Si Q, Lin GP, Zhu MM, Lu JY, Zhang H, Wang G, Chen W. Bifidobacterium adolescentis is effective in relieving type 2 diabetes and May Be related to its dominant core genome and gut microbiota modulation capacity. Nutrients. 2022;14(12):2479. doi:10.3390/nu14122479.
   PubMed Web of Science ®Google Scholar
• Ezeji JC, Sarikonda DK, Hopperton A, Erkkila H, Cohen DE, Martinez SP, Cominelli F, Kuwahara T, Dichosa AEK, Good CE. et al. Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes. 2021;13(1):1922241. doi:10.1080/19490976.2021.1922241.
   PubMed Web of Science ®Google Scholar
• Liu XP, Chang X, Leng SY, Tang H, Aihara K, Chen LN. Detection for disease tipping points by landscape dynamic network biomarkers. Natl Sci Rev. 2019;6(4):775–785. doi:10.1093/nsr/nwy162.
   PubMed Web of Science ®Google Scholar
• Zhong JY, Han CY, Wang YK, Chen P, Liu R, Valencia A. Identifying the critical state of complex biological systems by the directed-network rank score method. Bioinformatics. 2022;38(24):5398–5405. doi:10.1093/bioinformatics/btac707.
   PubMed Web of Science ®Google Scholar
• Peng H, Zhong JY, Chen P, Liu R. Identifying the critical states of complex diseases by the dynamic change of multivariate distribution. Brief Bioinform. 2022;23(5):bbac177. doi:10.1093/bib/bbac177.
   PubMed Web of Science ®Google Scholar
• Sun YC, Zhao HQ, Wu M, Xu JH, Zhu SS, Gao J. Identifying critical states of hepatocellular carcinoma based on landscape dynamic network biomarkers. Comput Biol Chem. 2020;85:107202. doi:10.1016/j.compbiolchem.2020.107202.
   PubMed Web of Science ®Google Scholar
• Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA, von Mering C. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11(5):e1004226. doi:10.1371/journal.pcbi.1004226.
   PubMed Web of Science ®Google Scholar
• Shi JF, Teschendorff AE, Chen WY, Chen LN, Li TJ. Quantifying Waddington’s epigenetic landscape: a comparison of single cell potency measures. Brief Bioinform. 2018;21:248–261.
   Web of Science ®Google Scholar
• Li L, Dai H, Fang ZY, Chen LN. c-CSN: single-cell RNA sequencing data analysis by conditional cell-specific network. Genomics, Proteomics Bioinf. 2021;19(2):319–329. doi:10.1016/j.gpb.2020.05.005.
   PubMed Web of Science ®Google Scholar
• Huang N, Mi TY, Xu SM, Dadd T, Ye X, Chen GQ, Du Y, Santhanam U. Traffic derived air pollution compromises skin barrier function and stratum corneum redox status: a population study. J Cosmet Dermatol. 2019;19(7):1751–1759. doi:10.1111/jocd.13194.
   PubMed Web of Science ®Google Scholar