100
Views
0
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Predicting Diagnostic Biomarkers Associated with Pyroptosis in Neuropathic Pain Based on Machine Learning and Experimental Validation

ORCID Icon, ORCID Icon, & ORCID Icon
Pages 1121-1145 | Received 03 Nov 2023, Accepted 13 Feb 2024, Published online: 20 Feb 2024

References

  • Finnerup NB, Kuner R, Jensen TS. Neuropathic pain: from mechanisms to treatment. Physiol Rev. 2021;101(1):259–301. doi:10.1152/physrev.00045.2019
  • Bouhassira D. Neuropathic pain: definition, assessment and epidemiology. Rev Neurol. 2019;175(1–2):16–25. doi:10.1016/j.neurol.2018.09.016
  • Hall GC, Morant SV, Carroll D, et al. An observational descriptive study of the epidemiology and treatment of neuropathic pain in a UK general population. BMC Fam Pract. 2013;14(1):28. doi:10.1186/1471-2296-14-28
  • van Hecke O, Austin SK, Khan RA, et al. Neuropathic pain in the general population: a systematic review of epidemiological studies. Pain. 2014;155(4):654–662. doi:10.1016/j.pain.2013.11.013
  • Baldo BA. Toxicities of opioid analgesics: respiratory depression, histamine release, hemodynamic changes, hypersensitivity, serotonin toxicity. Arch Toxicol. 2021;95(8):2627–2642. doi:10.1007/s00204-021-03068-2
  • Colloca L, Ludman T, Bouhassira D, et al. Neuropathic pain. Nat Rev Dis Primers. 2017;3(1):17002. doi:10.1038/nrdp.2017.2
  • Bedoui S, Herold MJ, Strasser A. Emerging connectivity of programmed cell death pathways and its physiological implications. Nat Rev Mol Cell Biol. 2020;21(11):678–695. doi:10.1038/s41580-020-0270-8
  • McKenzie BA, Mamik MK, Saito LB, et al. Caspase-1 inhibition prevents glial inflammasome activation and pyroptosis in models of multiple sclerosis. Proc Natl Acad Sci USA. 2018;115(26):E6065–E6074. doi:10.1073/pnas.1722041115
  • Sborgi L, Rühl S, Mulvihill E, et al. GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death. EMBO J. 2016;35(16):1766–1778. doi:10.15252/embj.201694696
  • McKenzie BA, Dixit VM, Power C. Fiery cell death: pyroptosis in the central nervous system. Trends Neurosci. 2020;43(1):55–73. doi:10.1016/j.tins.2019.11.005
  • Thacker MA, Clark AK, Marchand F, et al. Pathophysiology of peripheral neuropathic pain: immune cells and molecules. Anesth Analg. 2007;105(3):838–847. doi:10.1213/01.ane.0000275190.42912.37
  • Carranza-Aguilar CJ, Hernández-Mendoza A, Mejias-Aponte C, et al. Morphine and fentanyl repeated administration induces different levels of NLRP3-dependent pyroptosis in the dorsal raphe nucleus of male rats via cell-specific activation of TLR4 and opioid receptors. Cell Mol Neurobiol. 2022;42(3):677–694. doi:10.1007/s10571-020-00957-5
  • Hua T, Yang M, Song H, et al. Huc-MSCs-derived exosomes attenuate inflammatory pain by regulating microglia pyroptosis and autophagy via the miR-146a-5p/TRAF6 axis. J Nanobiotechnology. 2022;20(1):324. doi:10.1186/s12951-022-01522-6
  • Zhang Y, Jiang S, Liao F, et al. A transcriptomic analysis of neuropathic pain in the anterior cingulate cortex after nerve injury. Bioengineered. 2022;13(2):2058–2075. doi:10.1080/21655979.2021.2021710
  • Cui CY, Liu X, Peng MH, et al. Identification of key candidate genes and biological pathways in neuropathic pain. Comput Biol Med. 2022;150:106135. doi:10.1016/j.compbiomed.2022.106135
  • Verma-Gandhu M, Herbert TA, Barrett L, et al. T-cell infiltration and signaling in the adult dorsal spinal cord is a major contributor to neuropathic pain-like hypersensitivity. J Neurosci. 2009;29(46):14415–14422. doi:10.1523/JNEUROSCI.4569-09.2009
  • Yu X, Liu H, Hamel KA, et al. Dorsal root ganglion macrophages contribute to both the initiation and persistence of neuropathic pain. Nat Commun. 2020;11(1):264. doi:10.1038/s41467-019-13839-2
  • Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and bioconductor. Bioinformatics. 2007;14(14):1846–1847. doi:10.1093/bioinformatics/btm254
  • Gu Y, Qiu Z, Cheng N, et al. Identification of potential mechanism and hub genes for neuropathic pain by expression-based genome-wide association study. J Cell Biochem. 2019;120(4):4912–4923. doi:10.1002/jcb.27766
  • von Schack D, Agostino MJ, Murray BS, et al. Dynamic changes in the microRNA expression profile reveal multiple regulatory mechanisms in the spinal nerve ligation model of neuropathic pain. PLoS One. 2011;6(3):e17670. doi:10.1371/journal.pone.0017670
  • Jeong H, Na YJ, Lee K, et al. High-resolution transcriptome analysis reveals neuropathic pain gene-expression signatures in spinal microglia after nerve injury. Pain. 2016;157(4):964–976. doi:10.1097/j.pain.0000000000000470
  • Stelzer G, Rosen N, Plaschkes I, et al. The genecards suite: from gene data mining to disease genome sequence analyses. Curr Protoc Bioinformat. 2016;54(1):1.30.1–1.30.33. doi:10.1002/cpbi.5
  • Dong Z, Bian L, Wang M, et al. Identification of a pyroptosis-related gene signature for prediction of overall survival in lung adenocarcinoma. J Oncol. 2021;2021:6365459. doi:10.1155/2021/6365459
  • Wu J, Zhu Y, Luo M, et al. Comprehensive analysis of pyroptosis-related genes and tumor microenvironment infiltration characterization in breast cancer. Front Immunol. 2021;12:748221. doi:10.3389/fimmu.2021.748221
  • Liberzon A, Birger C, Thorvaldsdóttir H, et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–425. doi:10.1016/j.cels.2015.12.004
  • 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
  • Tian S, Wu L, Zheng H, et al. Identification of autophagy-related genes in neuropathic pain through bioinformatic analysis. Hereditas. 2023;160(1):8. doi:10.1186/s41065-023-00269-w
  • Deng YX, He WG, Cai HJ, et al. Analysis and validation of hub genes in blood monocytes of postmenopausal osteoporosis patients. Front Endocrinol. 2022;12:815245. doi:10.3389/fendo.2021.815245
  • Yu G. Gene ontology semantic similarity analysis using Gosemsim. Methods Mol Biol. 2020;2117:207–215.
  • Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30. doi:10.1093/nar/28.1.27
  • Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
  • Gruber HE, Hoelscher GL, Ingram JA, et al. Genome-wide analysis of pain-, nerve- and neurotrophin -related gene expression in the degenerating human annulus. Mol Pain. 2012;8:63. doi:10.1186/1744-8069-8-63
  • Liu Y, Zhao H. Variable importance-weighted random forests. Quant Biol. 2017;5(4):338–351. doi:10.1007/s40484-017-0121-6
  • Engebretsen S, Bohlin J. Statistical predictions with glmnet. Clin Clin Epigenet. 2019;11(1):123. doi:10.1186/s13148-019-0730-1
  • Cai W, van der Laan M. Nonparametric bootstrap inference for the targeted highly adaptive least absolute shrinkage and selection operator (LASSO) estimator. Int J Biostat. 2020;3:10.
  • Park SY. Nomogram: an analogue tool to deliver digital knowledge. J Thorac Cardiovasc Surg. 2018;155(4):1793. doi:10.1016/j.jtcvs.2017.12.107
  • Mandrekar JN. Receiver operating characteristic curve in diagnostic test assessment. J Thorac Oncol. 2010;5(9):1315–1316. doi:10.1097/JTO.0b013e3181ec173d
  • Franz M, Rodriguez H, Lopes C, et al. GeneMANIA update 2018. Nucleic Acids Res. 2018;46(W1):W60–W64. doi:10.1093/nar/gky311
  • Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48(D1):D127–D131. doi:10.1093/nar/gkz757
  • Zhou KR, Liu S, Sun WJ, et al. ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res. 2017;45(D1):D43–D50. doi:10.1093/nar/gkw965
  • Zhang Q, Liu W, Zhang HM, et al. hTFtarget: a comprehensive database for regulations of human transcription factors and their targets. Genomics Proteomics Bioinf. 2020;18(2):120–128. doi:10.1016/j.gpb.2019.09.006
  • Davis AP, Grondin CJ, Johnson RJ, et al. Comparative Toxicogenomics Database (CTD): update 2021. Nucleic Acids Res. 2021;49(D1):D1138–D1143. doi:10.1093/nar/gkaa891
  • Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457. doi:10.1038/nmeth.3337
  • Chen B, Khodadoust MS, Liu CL, et al. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol Biol. 2018;1711:243–259.
  • Gui X, Wang H, Wu L, et al. Botulinum toxin type A promotes microglial M2 polarization and suppresses chronic constriction injury-induced neuropathic pain through the P2X7 receptor. Cell Biosci. 2020;10(1):45. doi:10.1186/s13578-020-00405-3
  • Sui P, Watanabe H, Ossipov MH, et al. Proteomics of neuropathic pain: proteins and signaling pathways affected in a rat model. J Proteome Res. 2014;13(9):3957–3965. doi:10.1021/pr500241q
  • LaCroix-Fralish ML, Austin JS, Zheng FY, et al. Patterns of pain: meta-analysis of microarray studies of pain. Pain. 2011;152(8):1888–1898. doi:10.1016/j.pain.2011.04.014
  • Jiang BC, Liu T, Gao YJ. Chemokines in chronic pain: cellular and molecular mechanisms and therapeutic potential. Pharmacol Ther. 2020;212:107581. doi:10.1016/j.pharmthera.2020.107581
  • Baral P, Udit S, Chiu IM. Pain and immunity: implications for host defence. Nat Rev Immunol. 2019;19(7):433–447. doi:10.1038/s41577-019-0147-2
  • Li Y, Yin C, Li X, et al. Electroacupuncture alleviates paclitaxel-induced peripheral neuropathic pain in rats via suppressing TLR4 signaling and TRPV1 upregulation in sensory neurons. Int J Mol Sci. 2019;20(23):5917. doi:10.3390/ijms20235917
  • Iannotta M, Belardo C, Trotta MC, et al. N-palmitoyl-D-glucosamine, a natural monosaccharide-based glycolipid, inhibits TLR4 and prevents LPS-induced inflammation and neuropathic pain in mice. Int J Mol Sci. 2021;22(3):1491. doi:10.3390/ijms22031491
  • Xu S, Wang J, Jiang J, et al. TLR4 promotes microglial pyroptosis via lncRNA-F630028O10Rik by activating PI3K/AKT pathway after spinal cord injury. Cell Death Dis. 2020;11(8):693. doi:10.1038/s41419-020-02824-z
  • Chen K, Shang S, Yu S, et al. Identification and exploration of pharmacological pyroptosis-related biomarkers of ulcerative colitis. Front Immunol. 2022;13:998470. doi:10.3389/fimmu.2022.998470
  • Li T, Liu N, Zhang G, et al. CASP4 and CASP8 as newly defined autophagy-pyroptosis-related genes associated with clinical and prognostic features of renal cell carcinoma. J Cancer Res Ther. 2022;18(7):1952–1960. doi:10.4103/jcrt.jcrt_126_22
  • Sun X, Li X, Zhou Y, et al. Exogenous TIPE2 Inhibit TAK1 to improve inflammation and neuropathic pain induced by sciatic nerve injury through inactivating NF-κB and JNK. Neurochem Res. 2022;47(10):3167–3177. doi:10.1007/s11064-022-03671-4
  • Liu C, Zhang F, Liu H, et al. NF-kB mediated CX3CL1 activation in the dorsal root ganglion contributes to the maintenance of neuropathic pain induced in adult male Sprague Dawley rats1. Acta Cir Bras. 2018;33(7):619–628. doi:10.1590/s0102-865020180070000007
  • Xu M, Cheng Z, Ding Z, et al. Resveratrol enhances IL-4 receptor-mediated anti-inflammatory effects in spinal cord and attenuates neuropathic pain following sciatic nerve injury. Mol Pain. 2018;14:1744806918767549. doi:10.1177/1744806918767549
  • Bian C, Wang ZC, Yang JL, et al. Up-regulation of interleukin-23 induces persistent allodynia via CX3CL1 and interleukin-18 signaling in the rat spinal cord after tetanic sciatic stimulation. Brain Behav Immun. 2014;37:220–230. doi:10.1016/j.bbi.2013.12.011
  • Zheng Q, Lin R, Chen Y, et al. SARS-CoV-2 induces ”cytokine storm” hyperinflammatory responses in RA patients through pyroptosis. Front Immunol. 2022;13:1058884. doi:10.3389/fimmu.2022.1058884
  • Cai D, Zhao Y, Yu F. Puerarin ameliorates acute lung injury by modulating NLRP3 inflammasome-induced pyroptosis. Cell Death Discov. 2022;8(1):368. doi:10.1038/s41420-022-01137-8
  • Sanna MD, Guandalini L, Romanelli MN, et al. The new HDAC1 inhibitor LG325 ameliorates neuropathic pain in a mouse model. Pharmacol Biochem Behav. 2017;160:70–75. doi:10.1016/j.pbb.2017.08.006
  • Chen JX, Zhi JW, Wang YP, et al. LncRNA-PEAK1 promotes neuronal apoptosis after intracerebral hemorrhage by miR-466i-5p/caspase 8 axis. Heliyon. 2023;9(4):e15091. doi:10.1016/j.heliyon.2023.e15091
  • Brown PN, Yin H. PNA-based microRNA inhibitors elicit anti-inflammatory effects in microglia cells. Chem Commun. 2013;49(39):4415–4417. doi:10.1039/C2CC36540E
  • Ferrara G, Benzi A, Sturla L, et al. Sirt6 inhibition delays the onset of experimental autoimmune encephalomyelitis by reducing dendritic cell migration. J Neuroinflammation. 2020;17(1):228. doi:10.1186/s12974-020-01906-1
  • Batchu S. In silico analysis of the immunological landscape of hippocampi in alzheimer’s disease. Dement Geriatr Cognit Disord. 2020;49(3):252–254. doi:10.1159/000508283
  • Chen HR, Chen CW, Kuo YM, et al. Monocytes promote acute neuroinflammation and become pathological microglia in neonatal hypoxic-ischemic brain injury. Theranostics. 2022;12(2):512–529. doi:10.7150/thno.64033
  • Baniahmad A, Birkner K, Görg J, et al. The frequency of follicular T helper cells differs in acute and chronic neuroinflammation. Sci Rep. 2020;10(1):20485. doi:10.1038/s41598-020-77588-9