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Research Articles

Drug target genes and molecular mechanism investigation in isoflurane-induced anesthesia based on WGCNA and machine learning methods

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Pages 319-333 | Received 24 Jul 2023, Accepted 18 Nov 2023, Published online: 06 Dec 2023

References

  • Anastasio N, Ben-Omran T, Teebi A, Ha KC, Lalonde E, Ali R, Almureikhi M, Der Kaloustian VM, Liu J, Rosenblatt DS, et al. 2010. Mutations in SCARF2 are responsible for Van Den Ende–Gupta syndrome. Am J Hum Genet. 87(4):553–559.
  • Bader GH. 2003. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinf. 4(1):1–27.
  • Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. 2014. jvenn: an interactive Venn diagram viewer. BMC Bioinf. 15(1):293. doi: 10.1186/1471-2105-15-293.
  • Baumgart-Schmitt R, Walther C, Wenzel A. 2009. Multi criteria evaluation of sleep and anesthesia by neural networks, fuzzy rules, evolutionary algorithms and support vector machines. World Congress on Medical Physics and Biomedical Engineering, September 7–12, 2009, Munich, Germany.
  • Blaylock M, Engelhardt T, Bissonnette B. 2010. Fundamentals of neuronal apoptosis relevant to pediatric anesthesia. Pediatric Anesthesia. 20(5):383–395. doi: 10.1111/j.1460-9592.2010.03291.x.
  • Bunting KM, Nalloor RI, Vazdarjanova A. 2015. Influence of isoflurane on immediate-early gene expression. Front Behav Neurosci. 9:363. doi: 10.3389/fnbeh.2015.00363.
  • Chinn GA, Duong K, Horovitz TR, Russell J, Sall JW. 2021. Testosterone is sufficient to impart susceptibility to isoflurane neurotoxicity in female neonatal rats. J Neurosurg Anesthesiol. 34(4):429–436. doi: 10.1097/ANA.0000000000000786.
  • Cogill S, Wang L. 2016. Support vector machine model of developmental brain gene expression data for prioritization of Autism risk gene candidates. Bioinformatics. 32(23):3611–3618. doi: 10.1093/bioinformatics/btw498.
  • De Roo M, Klauser P, Briner A, Nikonenko I, Mendez P, Dayer A, Kiss JZ, Muller D, Vutskits L. 2009. Anesthetics rapidly promote synaptogenesis during a critical period of brain development. PLoS One. 4(9):e7043. doi: 10.1371/journal.pone.0007043.
  • Dimitriadou E, Hornik K, Leisch F, Meyer D, Weingessel A. 2011. e1071: misc Functions of the Department of Statistics (e1071).
  • Dweep H, Gretz N. 2015. miRWalk2.0: a comprehensive atlas of microRNA-target interactions. Nat Methods. 12(8):697. doi: 10.1038/nmeth.3485.
  • Esfandyari D, Idrissou BMG, Hennis K, Avramopoulos P, Dueck A, El-Battrawy I, Grüter L, Meier MA, Näger AC, Ramanujam D, et al. 2022. MicroRNA-365 regulates human cardiac action potential duration. Nat Commun. 13(1):220. doi: 10.1038/s41467-021-27856-7.
  • Friedman J, Hastie T, Tibshirani R. 2009. glmnet: lasso and elastic-net regularized generalized linear models. R Package Version. 1(4):1–24.
  • Grider MH, Jessu R, Kabir R. 2023. Physiology, Action Potential. StatPearls. Treasure Island (FL): StatPearls Publishing
  • Harrell FE, Harrell MFE, H D. 2017. Package “rms” Vanderbilt University. 229(Q8).
  • Ito K, Murphy D. 2013. Application of ggplot2 to Pharmacometric Graphics. CPT Pharmacometrics Syst Pharmacol. 2(10):e79. doi: 10.1038/psp.2013.56.
  • Jing Z, Ziwang F, Yinhang W, Yani Z, Jian C, Jingwen W, Shuwen H. 2022. Novel acetylation-related gene signatures for predicting the prognosis of patients with colorectal cancer. Hum Cell. 35(4):1159–1173. doi: 10.1007/s13577-022-00720-6.
  • Johnston D, Magee J, Colbert C, Cristie B. 1996. Active properties of neuronal dendrites. Ann Rev Neurosci. 19:165–186. doi: 10.1146/annurev.ne.19.030196.001121.
  • Jurgensen S, Castillo PE. 2015. Selective dysregulation of hippocampal inhibition in the mouse lacking autism candidate gene CNTNAP2. J Neurosci. 35(43):14681–14687. doi: 10.1523/JNEUROSCI.1666-15.2015.
  • Kim C, Kong G, Lee H, Tran Q, Vo TT, Kwon SH, Park J, Kim SH, Park J. 2022. Scavenger receptor class F member 2 (SCARF2) as a novel therapeutic target in glioblastoma. Toxicol Res. 38(2):249–256. doi: 10.1007/s43188-022-00125-5.
  • Krawczyk P, Lonc T, Świstek R, Tyszecki P, Andres J. 2022. Anesthesia for gynecological cancer surgery. Folia Med Cracov. 62(3):19–42.
  • Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 9(1):559. doi: 10.1186/1471-2105-9-559.
  • Li F, Gao W, Li Y, Wang Y, Liu L, Zhang X. 2023. Potential biomarkers and endometrial immune microenvironment in recurrent implantation failure. Biomolecules. 13(3):406. doi: 10.3390/biom13030406.
  • Liaw A, Wiener M. 2002. Classification and regression by randomForest. R News. 2(23):18–22.
  • Liu X, Wang Q. 2015. Screening of feature genes in distinguishing different types of breast cancer using support vector machine. Onco Targets Ther. 8:2311–2317. doi: 10.2147/OTT.S85271.
  • Llevot J. 2020. Predictive medicine, machine learning, and anesthesia. Revista Española de Anestesiología y Reanimación. 67(10):535–537.
  • Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. 2008. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 9 Suppl 1(Suppl 1):S4. doi: 10.1186/gb-2008-9-s1-s4.
  • Moura APS, Galley HF, Webster NR. 2017. Brief isoflurane anaesthesia affects differential gene expression, gene ontology and gene networks in rat brain. Behav Brain Res Int J. 317:453–460.
  • Otasek D, Morris JH, Boucas J, Pico AR, Demchak B. 2019. Cytoscape automation: empowering workflow-based network analysis. Genome Biol. 20(1):185. doi: 10.1186/s13059-019-1758-4.
  • Ou M, Zhao W, Liu J, Liang P, Huang H, Yu H, Zhu T, Zhou C. 2020. The general anesthetic isoflurane bilaterally modulates neuronal excitability. iScience. 23(1):100760. doi: 10.1016/j.isci.2019.100760.
  • Ouyang W, Hemmings HC. 2005. Depression by isoflurane of the action potential and underlying voltage-gated ion currents in isolated rat neurohypophysial nerve terminals. J Pharmacol Exp Ther. 312(2):801–808. doi: 10.1124/jpet.104.074609.
  • Pillai AM, Garcia-Fresco GP, Sousa AD, Dupree JL, Philpot BD, Bhat MA. 2007. No effect of genetic deletion of contactin-associated protein (CASPR) on axonal orientation and synaptic plasticity. J Neurosci Res. 85(11):2318–2331. eng. doi: 10.1002/jnr.21374.
  • Ps A, Tp A, Jp A, Ez A, Ras A, Hk A, Tn B, Pm B, Tk B, Mh B. 2021. Isoflurane affects brain functional connectivity in rats 1 month after exposure. NeuroImage. 234:117987.
  • Purtell K. 2015. Effects of the general anesthetic isoflurane on voltage-gated sodium channels and the presynaptic action potential Dissertations & Theses - Gradworks.
  • Qi T, Wu D, Duan Z, Chen C, Qiu J, Kang J. 2020. Overexpression of fatty acid 2-hydroxylase is associated with an increased sensitivity to cisplatin by ovarian cancer and better prognoses. Genet Test Mol Biomarkers. 24(10):632–640. eng. doi: 10.1089/gtmb.2019.0259.
  • Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. 2015. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43(7):e47-e47. doi: 10.1093/nar/gkv007.
  • Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26(1):139–140. doi: 10.1093/bioinformatics/btp616.
  • Saha P, Das A, Chatterjee N, Chakrabarti D, Sinha D. 2021. Impact of anesthetics on oncogenic signaling network: a review on propofol and isoflurane. Fundamental Clin Pharmacol. 36(1):49–71. doi: 10.1111/fcp.12732.
  • Sait H, Srivastava S, Pandey M, Ravichandran D, Shukla A, Mandal K, Saxena D, Shambhavi A, Majethia P, Rao LP. 2023. Neurodegeneration with brain iron accumulation: a case series highlighting phenotypic and genotypic diversity in 20 Indian families. Neurogenetics. 24(2):113–127. eng. doi: 10.1007/s10048-023-00712-0.
  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 13(11):2498–2504. doi: 10.1101/gr.1239303.
  • Sigurdsson S, Alexandersson KF, Sulem P, Feenstra B, Gudmundsdottir S, Halldorsson GH, Olafsson S, Sigurdsson A, Rafnar T, Thorgeirsson T, et al. 2017. Sequence variants in ARHGAP15, COLQ and FAM155A associate with diverticular disease and diverticulitis. Nat Commun. 8:15789. eng. doi: 10.1038/ncomms15789.
  • Stenroos P, Pirttimäki T, Paasonen J, Paasonen E, Salo RA, Koivisto H, Natunen T, Mäkinen P, Kuulasmaa T, Hiltunen M, et al. 2021. Isoflurane affects brain functional connectivity in rats 1 month after exposure. Neuroimage. 234:117987. doi: 10.1016/j.neuroimage.2021.117987.
  • Sticht C, De La Torre C, Parveen A, Gretz N. 2018. miRWalk: an online resource for prediction of microRNA binding sites. PLoS One. 13(10):e0206239. doi: 10.1371/journal.pone.0206239.
  • Stuart G, Spruston N, Sakmann B, Häusser M. 1997. Action potential initiation and backpropagation in neurons of the mammalian CNS. Trends Neurosci. 20(3):125–131. doi: 10.1016/s0166-2236(96)10075-8.
  • Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P. 2016. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res. 45:D362–D368. doi: 10.1093/nar/gkw937.
  • Vevera J, Zarrei M, Hartmannová H, Jedličková I, Mušálková D, Přistoupilová A, Oliveriusová P, Trešlová H, Nosková L, Hodaňová K, et al. 2019. Rare copy number variation in extremely impulsively violent males. Genes Brain Behav. 18(6):e12536.
  • Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. J Neurosci. 40(21):4103–4115. doi: 10.1523/JNEUROSCI.2946-19.2020.
  • Wang Y. 2015. Biological processes and pathway changes in isoflurane-induced anesthesia revealed by bioinformatics analysis of gene expression profiles. J Anesthesia. 29(6):912–919. doi: 10.1007/s00540-015-2049-1.
  • Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L. 2021. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. The Innovation. 2(3):100141. doi: 10.1016/j.xinn.2021.100141.
  • Yang D, Yang XJ, Shao C, Yang K. 2021. Isoflurane decreases substantia gelatinosa neuron excitability and synaptic transmission from periphery in the rat spinal dorsal horn. Neuroreport. 32(2):77–81. doi: 10.1097/WNR.0000000000001557.
  • Ye H, Li T, Wang H, Wu J, Yi C, Shi J, Wang P, Song C, Dai L, Jiang G. 2021. TSPAN1, TMPRSS4, SDR16C5, and CTSE as novel panel for pancreatic cancer: a bioinformatics analysis and experiments validation. Front Immunol. 12:649551. doi: 10.3389/fimmu.2021.649551.
  • Yon J-H, Daniel-Johnson J, Carter L, Jevtovic-Todorovic V. 2005. Anesthesia induces neuronal cell death in the developing rat brain via the intrinsic and extrinsic apoptotic pathways. Neuroscience. 135(3):815–827. doi: 10.1016/j.neuroscience.2005.03.064.
  • Zhang F, Chen G, Wang L, Feng Z, Mi W. 2021. LncRNA taurine up-regulated gene 1 participates in isoflurane induced neurotoxicity. Mol Cell Toxicol. 17(3):347–356. doi: 10.1007/s13273-021-00141-w.
  • Zhao H, Wang W, Liu L, Wang J, Yan Q. 2020. Functional modular network identifies the key genes of preoperative inhalation anesthesia and intravenous anesthesia in off-pump coronary artery bypass grafting. Comput Math Methods Med. 2020:4574792.
  • Zheng Y, Ji Q, Xie L, Wang C, Yu CN, Wang YL, Jiang J, Chen F, Li WB. 2021. Ferroptosis-related gene signature as a prognostic marker for lower-grade gliomas. J Cell Mol Med. 25(6):3080–3090. eng. doi: 10.1111/jcmm.16368.

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