226
Views
0
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Establishment of Risk Model and Analysis of Immunoinfiltration Based on Mitophagy-Related Associated Genes in Atrial Fibrillation

, , ORCID Icon, , , , & show all
Pages 2561-2583 | Received 21 Apr 2023, Accepted 13 Jun 2023, Published online: 16 Jun 2023

References

  • Lippi G, Sanchis-Gomar F, Cervellin G. Global epidemiology of atrial fibrillation: an increasing epidemic and public health challenge. Int J Stroke. 2021;16(2):217–221. doi:10.1177/1747493019897870
  • Guzel T, Aktan A, Kilic R, et al. Oral anticoagulant use and long-term follow-up results in patients with non-valvular atrial fibrillation in Turkey AFTER-2 study. Anatol J Cardiol. 2022;26(7):567–576. doi:10.5152/AnatolJCardiol.2022.1597
  • Aktan A, Güzel T, Aslan B, et al. Comparison of the real-life clinical outcomes of warfarin with effective time in therapeutic range and non-vitamin K antagonist oral anticoagulants: insight from the AFTER-2 trial. Kardiol Pol. 2023;81(2):132–140. doi:10.33963/KP.a2022.0287
  • Orhan AL, Çınar T, Hayıroğlu Mİ, et al. Atrial fibrillation as a preoperative risk factor predicts long-term mortality in elderly patients without heart failure and undergoing hip fracture surgery. Rev Assoc Med Bras. 2021;67(11):1633–1638. doi:10.1590/1806-9282.20210686
  • Chung MK, Refaat M, Shen WK, et al. Atrial fibrillation: JACC council perspectives. J Am Coll Cardiol. 2020;75(14):1689–1713.
  • Hu YF, Chen YJ, Lin YJ, Chen SA. Inflammation and the pathogenesis of atrial fibrillation. Nat Rev Cardiol. 2015;12(4):230–243.
  • Jalife J, Kaur K. Atrial remodeling, fibrosis, and atrial fibrillation. Trends Cardiovasc Med. 2015;25(6):475–484.
  • Saylik F, Çınar T, Akbulut T, et al. Comparison of catheter ablation and medical therapy for atrial fibrillation in heart failure patients: a meta-analysis of randomized controlled trials. Heart Lung. 2023;57:69–74. doi:10.1016/j.hrtlng.2022.08.012
  • Wiersma M, Meijering RA, Qi XY, et al. Endoplasmic reticulum stress is associated with autophagy and cardiomyocyte remodeling in experimental and human atrial fibrillation. J Am Heart Assoc. 2017;6(10):e006458.
  • Nunnari J, Suomalainen A. Mitochondria: in sickness and in health. Cell. 2012;148(6):1145–1159.
  • Galluzzi L, Baehrecke EH, Ballabio A, et al. Molecular definitions of autophagy and related processes. EMBO J. 2017;36(13):1811–1836.
  • Zhou H, He L, Xu G, Chen L. Mitophagy in cardiovascular disease. Clin Chim Acta. 2020;507:210–218.
  • He L, Zhou Q, Huang Z, et al. PINK1/Parkin-mediated mitophagy promotes apelin-13-induced vascular smooth muscle cell proliferation by AMPKα and exacerbates atherosclerotic lesions. J Cell Physiol. 2019;234(6):8668–8682. doi:10.1002/jcp.27527
  • Xin T, Lu C. Irisin activates Opa1-induced mitophagy to protect cardiomyocytes against apoptosis following myocardial infarction. Aging. 2020;12(5):4474–4488.
  • Liao C-H, Akazawa H, Tamagawa M, et al. Cardiac mast cells cause atrial fibrillation through PDGF-A–mediated fibrosis in pressure-overloaded mouse hearts. J Clin Invest. 2010;120(1):242–253. doi:10.1172/JCI39942
  • Zhang Y-L, Cao H-J, Han X, et al. Chemokine receptor CXCR-2 initiates atrial fibrillation by triggering monocyte mobilization in mice. Hypertension. 2020;76(2):381–392. doi:10.1161/HYPERTENSIONAHA.120.14698
  • Hohmann C, Pfister R, Mollenhauer M, et al. Inflammatory cell infiltration in left atrial appendageal tissues of patients with atrial fibrillation and sinus rhythm. Sci Rep. 2020;10(1):1685.
  • Parahuleva MS, Kockskämper J, Heger J, et al. Structural, pro-inflammatory and calcium handling remodeling underlies spontaneous onset of paroxysmal atrial fibrillation in JDP2-overexpressing mice. Int J Mol Sci. 2020;21(23):9095. doi:10.3390/ijms21239095
  • Xiao S, Zhou Y, Liu A, et al. Uncovering potential novel biomarkers and immune infiltration characteristics in persistent atrial fibrillation using integrated bioinformatics analysis. Math Biosci Eng. 2021;18(4):4696–4712.
  • Wang Y, Liu Z, Du Y, et al. Comprehensive analysis of pertinent genes and pathways in atrial fibrillation. Comput Math Methods Med. 2021;2021:4530180. doi:10.1155/2021/4530180
  • Yu S-D, Yu J-Y, Guo Y, et al. Bioinformatic analysis for the identification of potential gene interactions and therapeutic targets in atrial fibrillation. Eur Rev Med Pharmacol Sci. 2021;25(5):2281–2290. doi:10.26355/eurrev_202103_25260
  • Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics. 2007;23(14):1846–1847. doi:10.1093/bioinformatics/btm254
  • Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res. 2007;35(Database):D760–D765. doi:10.1093/nar/gkl887
  • Tsai F-C, Lin Y-C, Chang S-H, et al. Differential left-to-right atria gene expression ratio in human sinus rhythm and atrial fibrillation: implications for arrhythmogenesis and thrombogenesis. Int J Cardiol. 2016;222:104–112. doi:10.1016/j.ijcard.2016.07.103
  • Cubukcuoglu DG, Durdu S, Doğan Y, et al. Molecular signatures of human chronic atrial fibrillation in primary mitral regurgitation. Cardiovasc Ther. 2021;2021:5516185. doi:10.1155/2021/5516185
  • 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
  • Zhuo Z, Lin H, Liang J, et al. Mitophagy-related gene signature for prediction prognosis, immune scenery, mutation, and chemotherapy response in pancreatic cancer. Front Cell Dev Biol. 2022;9:802528. doi:10.3389/fcell.2021.802528
  • 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 L-G, 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
  • Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013;14(1):7. doi:10.1186/1471-2105-14-7
  • 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 U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
  • 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
  • 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
  • Chin CH, Chen S-H, Wu -H-H, et al. CytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8 Suppl 4:S11. doi:10.1186/1752-0509-8-S4-S11
  • Sticht C, De La Torre C, Parveen A, et al. miRWalk: an online resource for prediction of microRNA binding sites. PLoS One. 2018;13(10):e0206239. doi:10.1371/journal.pone.0206239
  • Han H, Cho J-W, Lee S, et al. TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Res. 2018;46(D1):D380–D386. doi:10.1093/nar/gkx1013
  • Nahm FS. Receiver operating characteristic curve: overview and practical use for clinicians. Korean J Anesthesiol. 2022;75(1):25–36. doi:10.4097/kja.21209
  • Charoentong P, Finotello F, Angelova M, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18(1):248–262. doi:10.1016/j.celrep.2016.12.019
  • Yu G, Li F, Qin Y, et al. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010;26(7):976–978. doi:10.1093/bioinformatics/btq064
  • Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–1573. doi:10.1093/bioinformatics/btq170
  • Andrade JG, Wells GA, Deyell MW, et al. Cryoablation or drug therapy for initial treatment of atrial fibrillation. N Engl J Med. 2021;384(4):305–315. doi:10.1056/NEJMoa2029980
  • Aventaggiato M, Vernucci E, Barreca F, et al. Sirtuins’ control of autophagy and mitophagy in cancer. Pharmacol Ther. 2021;221:107748. doi:10.1016/j.pharmthera.2020.107748
  • Katayama H, Hama H, Nagasawa K, et al. Visualizing and modulating mitophagy for therapeutic studies of neurodegeneration. Cell. 2020;181(5):1176–1187.e16. doi:10.1016/j.cell.2020.04.025
  • Heijman J, Voigt N, Nattel S, et al. Cellular and molecular electrophysiology of atrial fibrillation initiation, maintenance, and progression. Circ Res. 2014;114(9):1483–1499. doi:10.1161/CIRCRESAHA.114.302226
  • Breda C, Davanzo GG, Basso PJ, et al. Mitochondria as central hub of the immune system. Redox Biol. 2019;26:101255. doi:10.1016/j.redox.2019.101255
  • Najbauer EE, Tekwani Movellan K, Giller K, et al. Structure and gating behavior of the human integral membrane protein VDAC1 in a lipid bilayer. J Am Chem Soc. 2022;144(7):2953–2967. doi:10.1021/jacs.1c09848
  • Yuan M, Gong M, He J, et al. IP3R1/GRP75/VDAC1 complex mediates endoplasmic reticulum stress-mitochondrial oxidative stress in diabetic atrial remodeling. Redox Biol. 2022;52:102289. doi:10.1016/j.redox.2022.102289
  • Hayiroglu Mİ, Altay S. The role of artificial intelligence in coronary artery disease and atrial fibrillation. Balk Med J. 2023;40(3):151–152. doi:10.4274/balkanmedj.galenos.2023.06042023
  • Lu N, Malemud CJ. Extracellular signal-regulated kinase: a regulator of cell growth, inflammation, chondrocyte and bone cell receptor-mediated gene expression. Int J Mol Sci. 2019;20(15):3792. doi:10.3390/ijms20153792
  • Zhang P, Miao Q, Wang X, et al. Identification of a novel 4-gene diagnostic model for atrial fibrillation risk based on integrated analysis across independent data sets. Comb Chem High Throughput Screen. 2022;25(2):229–240. doi:10.2174/1386207324666210121103304
  • Goette A, Staack T, Röcken C, et al. Increased expression of extracellular signal-regulated kinase and angiotensin-converting enzyme in human atria during atrial fibrillation. J Am Coll Cardiol. 2000;35(6):1669–1677. doi:10.1016/S0735-1097(00)00611-2
  • Johnson GL, Lapadat R. Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases. Science. 2002;298(5600):1911–1912. doi:10.1126/science.1072682
  • Aschar-Sobbi R, Izaddoustdar F, Korogyi AS, et al. Increased atrial arrhythmia susceptibility induced by intense endurance exercise in mice requires TNFalpha. Nat Commun. 2015;6(1):6018. doi:10.1038/ncomms7018
  • Park CB, Asin-Cayuela J, Cámara Y, et al. MTERF3 is a negative regulator of mammalian mtDNA transcription. Cell. 2007;130(2):273–285. doi:10.1016/j.cell.2007.05.046
  • Wredenberg A, Lagouge M, Bratic A, et al. MTERF3 regulates mitochondrial ribosome biogenesis in invertebrates and mammals. PLoS Genet. 2013;9(1):e1003178. doi:10.1371/journal.pgen.1003178
  • Zhu S, Xu N, Han Y, et al. MTERF3 contributes to MPP+-induced mitochondrial dysfunction in SH-SY5Y cells. Acta Biochim Biophys Sin. 2022;54(8):1113–1121. doi:10.3724/abbs.2022098
  • Andersson DC, Fauconnier J, Park CB, et al. Enhanced cardiomyocyte Ca 2+ cycling precedes terminal AV-block in mitochondrial cardiomyopathy Mterf3 KO mice. Antioxid Redox Signal. 2011;15(9):2455–2464. doi:10.1089/ars.2011.3915
  • Miyosawa K, Iwata H, Minami-Takano A, et al. Enhanced monocyte migratory activity in the pathogenesis of structural remodeling in atrial fibrillation. PLoS One. 2020;15(10):e0240540. doi:10.1371/journal.pone.0240540
  • Aguiar CM, Gawdat K, Legere S, et al. Fibrosis independent atrial fibrillation in older patients is driven by substrate leukocyte infiltration: diagnostic and prognostic implications to patients undergoing cardiac surgery. J Transl Med. 2019;17(1):413. doi:10.1186/s12967-019-02162-5
  • Smorodinova N, Bláha M, Melenovský V, et al. Analysis of immune cell populations in atrial myocardium of patients with atrial fibrillation or sinus rhythm. PLoS One. 2017;12(2):e0172691. doi:10.1371/journal.pone.0172691
  • Xu Y, Shen J, Ran Z. Emerging views of mitophagy in immunity and autoimmune diseases. Autophagy. 2020;16(1):3–17. doi:10.1080/15548627.2019.1603547
  • Patoli D, Mignotte F, Deckert V, et al. Inhibition of mitophagy drives macrophage activation and antibacterial defense during sepsis. J Clin Invest. 2020;130(11):5858–5874. doi:10.1172/JCI130996