Exploration of the Shared Gene Signatures and Molecular Mechanisms Between Ischemic Stroke and Atherosclerosis

References

• 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 issue):D760–5. doi:10.1093/nar/gkl887
   PubMed Web of Science ®Google Scholar
• Hägg DA, Jernås M, Wiklund O, et al. Expression Profiling of Macrophages from Subjects with Atherosclerosis to Identify Novel Susceptibility Genes. IntJ Mol Med. 2008;21(6):697–704.
   PubMed Web of Science ®Google Scholar
• Krug T, Gabriel JP, Taipa R, et al. Ttc7b Emerges as a Novel Risk Factor for Ischemic Stroke through the Convergence of Several Genome-Wide Approaches. J Cereb Blood Flow Metab. 2012;32(6):1061–1072. doi:10.1038/jcbfm.2012.24
   PubMed Web of Science ®Google Scholar
• Barr TL, Conley Y, Ding J, et al. Genomic Biomarkers and Cellular Pathways of Ischemic Stroke by Rna Gene Expression Profiling. Neurology. 2010;75(11):1009–1014. doi:10.1212/WNL.0b013e3181f2b37f
   PubMed Web of Science ®Google Scholar
• O’Connell GC, Treadway MB, Petrone AB, et al. Peripheral Blood Akap7 Expression as an Early Marker for Lymphocyte-Mediated Post-Stroke Blood Brain Barrier Disruption. Sci Rep. 2017;7(1):1172. doi:10.1038/s41598-017-01178-5
   PubMedGoogle Scholar
• O’Connell GC, Petrone AB, Treadway MB, et al. Machine-Learning Approach Identifies a Pattern of Gene Expression in Peripheral Blood That Can Accurately Detect Ischaemic Stroke. NPJ Genomic Med. 2016;1:16038. doi:10.1038/npjgenmed.2016.38
   PubMed Web of Science ®Google Scholar
• Chen R, Mias GI, Li-Pook-Than J, et al. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes. Cell. 2012;148(6):1293–1307. doi:10.1016/j.cell.2012.02.009
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. Wgcna: an R Package for Weighted Correlation Network Analysis. BMC Bioinf. 2008;9:559. doi:10.1186/1471-2105-9-559
   PubMed Web of Science ®Google Scholar
• Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. Jvenn: an Interactive Venn Diagram Viewer. BMC Bioinf. 2014;15(1):293. doi:10.1186/1471-2105-15-293
   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
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Nastou KC, et al. The String Database in 2021: customizable Protein-Protein Networks, and Functional Characterization of User-Uploaded Gene/Measurement Sets. Nucleic Acids Res. 2021;49(D1):D605–d12. doi:10.1093/nar/gkaa1074
   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
   PubMed Web of Science ®Google Scholar
• Bindea G, Mlecnik B, Hackl H, et al. Cluego: a Cytoscape Plug-in to Decipher Functionally Grouped Gene Ontology and Pathway Annotation Networks. Bioinformatics. 2009;25(8):1091–1093. doi:10.1093/bioinformatics/btp101
   PubMed Web of Science ®Google Scholar
• Ehsani Ardakani MJ, Safaei A, Arefi Oskouie A, et al. Evaluation of Liver Cirrhosis and Hepatocellular Carcinoma Using Protein-Protein Interaction Networks. Gastroenterol Hepatol Bed Bench. 2016;9(Suppl1):S14–s22.
   PubMedGoogle Scholar
• Huang Z, Shi J, Gao Y, et al. Hmdd V3.0: a Database for Experimentally Supported Human Microrna-Disease Associations. Nucleic Acids Res. 2019;47(D1):D1013–d7. doi:10.1093/nar/gky1010
   PubMed Web of Science ®Google Scholar
• Li XJ, Wen R, Wen DY, et al. Downregulation of Mir‑193a‑3p Via Targeting Cyclin d1 in Thyroid Cancer. Mol Med Rep. 2020;22(3):2199–2218. doi:10.3892/mmr.2020.11310
   PubMed Web of Science ®Google Scholar
• Bu D, Luo H, Huo P, et al. Kobas-I: intelligent Prioritization and Exploratory Visualization of Biological Functions for Gene Enrichment Analysis. Nucleic Acids Res. 2021;49(W1):W317–w25. doi:10.1093/nar/gkab447
   PubMed Web of Science ®Google Scholar
• Vlachos IS, Zagganas K, Paraskevopoulou MD, et al. Diana-Mirpath V3.0: deciphering Microrna Function with Experimental Support. Nucleic Acids Res. 2015;43(W1):W460–6. doi:10.1093/nar/gkv403
   PubMed Web of Science ®Google Scholar
• Koutsaliaris IK, Moschonas IC, Pechlivani LM, Tsouka AN, Tselepis AD. Inflammation, Oxidative Stress, Vascular Aging and Atherosclerotic Ischemic Stroke. Curr. Med. Chem. 2022;29(34):5496–5509. doi:10.2174/0929867328666210921161711
   PubMed Web of Science ®Google Scholar
• Zhan M, Sun LJ, Zhang YH, Gao JM, Liu JX. Correlation and Predictive Value of Platelet Biological Indicators and Recurrence of Large-Artery Atherosclerosis Type of Ischemic Stroke. Biotechnol Genet Eng Rev. 2023;1–19. doi:10.1080/02648725.2023.2196879
   Web of Science ®Google Scholar
• Zhang Y, Chen Z, Tang Y, et al. Association between Procalcitonin Levels and Carotid Atherosclerosis in Acute Ischemic Stroke Patients. Int j Neurosci. 2018;128(3):237–242. doi:10.1080/00207454.2017.1387114
   PubMed Web of Science ®Google Scholar
• Zhao FF, Gao HY, Gao Y, et al. A Correlational Study on Cerebral Microbleeds and Carotid Atherosclerosis in Patients with Ischemic Stroke. J Stroke Cerebrovascular Dis. 2018;27(8):2228–2234. doi:10.1016/j.jstrokecerebrovasdis.2018.04.009
   PubMed Web of Science ®Google Scholar
• Yan J, Zuo G, Sherchan P, et al. Ccr1 Activation Promotes Neuroinflammation through Ccr1/Tpr1/Erk1/2 Signaling Pathway after Intracerebral Hemorrhage in Mice. Neurotherapeutics. 2020;17(3):1170–1183. doi:10.1007/s13311-019-00821-5
   PubMed Web of Science ®Google Scholar
• Halks-Miller M, Schroeder ML, Haroutunian V, et al. Ccr1 Is an Early and Specific Marker of Alzheimer’s Disease. Ann. Neurol. 2003;54(5):638–646. doi:10.1002/ana.10733
   PubMed Web of Science ®Google Scholar
• Potteaux S, Combadière C, Esposito B, et al. Chemokine Receptor Ccr1 Disruption in Bone Marrow Cells Enhances Atherosclerotic Lesion Development and Inflammation in Mice. Molecular med. 2005;11(1–12):16–20. doi:10.2119/2005-00028.Potteaux
   PubMed Web of Science ®Google Scholar
• Veillard NR, Kwak B, Pelli G, et al. Antagonism of Rantes Receptors Reduces Atherosclerotic Plaque Formation in Mice. Circulation Res. 2004;94(2):253–261. doi:10.1161/01.Res.0000109793.17591.4e
   PubMed Web of Science ®Google Scholar
• Shi C, Jin J, Xu H, et al. Ccr1 Enhances Sumoylation of Dgcr8 by up-Regulating Erk Phosphorylation to Promote Spinal Nerve Ligation-Induced Neuropathic Pain. Genet Ther. 2022;29(6):379–389. doi:10.1038/s41434-021-00285-3
   PubMed Web of Science ®Google Scholar
• Zhao P, Huo H, Li J, et al. Jnk Pathway-Associated Phosphatase in Acute Ischemic Stroke Patients: its Correlation with T Helper Cells, Clinical Properties, and Recurrence Risk. J Clin Lab Analysis. 2022;36(8):e24535. doi:10.1002/jcla.24535
   PubMed Web of Science ®Google Scholar
• Lucaciu A, Kuhn H, Trautmann S, et al. A Sphingosine 1-Phosphate Gradient Is Linked to the Cerebral Recruitment of T Helper and Regulatory T Helper Cells During Acute Ischemic Stroke. Int J Mol Sci. 2020;21(17). doi:10.3390/ijms21176242
   Web of Science ®Google Scholar
• Iadecola C, Anrather J. The Immunology of Stroke: from Mechanisms to Translation. Nature Med. 2011;17(7):796–808. doi:10.1038/nm.2399
   PubMed Web of Science ®Google Scholar
• Zheng Z, Hou F, He G, Jiang F, Bao X, Tong M. Carvedilol Reduces the Neuronal Apoptosis after Ischemic Stroke by Modulating Activator of Transcription 3 Expression in Vitro. Dev. Neurosci. 2023;45(2):94–104. doi:10.1159/000527484
   PubMed Web of Science ®Google Scholar
• Thompson MR, Xu D, Williams BR. Atf3 Transcription Factor and Its Emerging Roles in Immunity and Cancer. J Mol Med. 2009;87(11):1053–1060. doi:10.1007/s00109-009-0520-x
   PubMed Web of Science ®Google Scholar
• Ye J, Zhang F, Li B, Liu Q, Zeng G. Knockdown of Atf3 Suppresses the Progression of Ischemic Stroke through Inhibiting Ferroptosis. Front Mol Neurosci. 2022;15:1079338. doi:10.3389/fnmol.2022.1079338
   PubMed Web of Science ®Google Scholar
• Komissarov A, Potashnikova D, Freeman ML, et al. Driving T Cells to Human Atherosclerotic Plaques: ccl3/Ccr5 and Cx3cl1/Cx3cr1 Migration Axes. Eur j Immunol. 2021;51(7):1857–1859. doi:10.1002/eji.202049004
   PubMedGoogle Scholar
• Chang TT, Yang HY, Chen C, Chen JW. Ccl4 Inhibition in Atherosclerosis: effects on Plaque Stability, Endothelial Cell Adhesiveness, and Macrophages Activation. Int J Mol Sci. 2020;21(18). doi:10.3390/ijms21186567
   Web of Science ®Google Scholar
• Zhang D, Li X, Jing B, et al. Identification of Pathways and Key Genes in Male Late-Stage Carotid Atherosclerosis Using Bioinformatics Analysis. Exp Ther Med. 2022;24(1):460. doi:10.3892/etm.2022.11387
   PubMed Web of Science ®Google Scholar
• Guo A, Gao B, Zhang M, Shi X, Jin W, Tian D. Bioinformatic Identification of Hub Genes Myd88 and Ccl3 and Tws-119 as a Potential Agent for the Treatment of Massive Cerebral Infarction. Front Neurosci. 2023;17:1171112. doi:10.3389/fnins.2023.1171112
   PubMed Web of Science ®Google Scholar
• Martha SR, Cheng Q, Fraser JF, et al. Expression of Cytokines and Chemokines as Predictors of Stroke Outcomes in Acute Ischemic Stroke. Front Neurol. 2019;10:1391. doi:10.3389/fneur.2019.01391
   PubMed Web of Science ®Google Scholar
• Li P, Zhu N, Yi B, et al. Microrna-663 Regulates Human Vascular Smooth Muscle Cell Phenotypic Switch and Vascular Neointimal Formation. Circulation Res. 2013;113(10):1117–1127. doi:10.1161/circresaha.113.301306
   PubMed Web of Science ®Google Scholar
• Zhao X, Miao G, Zhang L, et al. Chlamydia Pneumoniae Infection Induces Vascular Smooth Muscle Cell Migration and Atherosclerosis through Mitochondrial Reactive Oxygen Species-Mediated Junb-Fra-1 Activation. Front Cell Develop Biol. 2022;10:879023. doi:10.3389/fcell.2022.879023
   PubMed Web of Science ®Google Scholar
• Rehnström M, Frederiksen SD, Ansar S, Edvinsson L. Transcriptome Profiling Revealed Early Vascular Smooth Muscle Cell Gene Activation Following Focal Ischemic Stroke in Female Rats - Comparisons with Males. BMC Genomics. 2020;21(1):883. doi:10.1186/s12864-020-07295-2
   PubMed Web of Science ®Google Scholar
• Zhai K, Kong X, Liu B, Lou J. Bioinformatics Analysis of Gene Expression Profiling for Identification of Potential Key Genes among Ischemic Stroke. Medicine. 2017;96(34):e7564. doi:10.1097/md.0000000000007564
   PubMed Web of Science ®Google Scholar
• Li Y, Huang S, Huang X, et al. Pharmacological Inhibition of Malt1 Protease Activity Suppresses Endothelial Activation Via Enhancing Mcpip1 Expression. Cell. Signalling. 2018;50:1–8. doi:10.1016/j.cellsig.2018.05.009
   PubMed Web of Science ®Google Scholar
• Yu F, Du F, Wang Y, et al. Bone Marrow Deficiency of Mcpip1 Results in Severe Multi-Organ Inflammation but Diminishes Atherogenesis in Hyperlipidemic Mice. PLoS One. 2013;8(11):e80089. doi:10.1371/journal.pone.0080089
   PubMed Web of Science ®Google Scholar
• Shen W, Wang X, Tang M, et al. Huoluo Xiaoling Pellet Promotes Microglia M2 Polarization through Increasing Mcpip1 Expression for Ischemia Stroke Alleviation. Biomed. Pharmacother. 2023;164:114914. doi:10.1016/j.biopha.2023.114914
   PubMed Web of Science ®Google Scholar
• Yang X, Yan S, Wang P, Wang G. Identification of Hub Genes in the Pathogenesis of Ischemic Stroke Based on Bioinformatics Analysis. J Korean Neurosurgical Soc. 2022;65(5):697–709. doi:10.3340/jkns.2021.0200
   PubMed Web of Science ®Google Scholar
• Chen CP, Wu YL, Chan KC, Ho HH, Wang CJ, Hsu LS. Mulberry Polyphenols Ameliorate Atherogenic Migration and Proliferation by Degradation of K-Ras and Downregulation of Its Signals in Vascular Smooth Muscle Cell. Int J Med Sci. 2022;19(10):1557–1566. doi:10.7150/ijms.76006
   PubMed Web of Science ®Google Scholar