{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T01:00:43Z","timestamp":1774832443207,"version":"3.50.1"},"reference-count":78,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,3,6]],"date-time":"2025-03-06T00:00:00Z","timestamp":1741219200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"NRC \u201cKurchatov Institute\u201d (bioinformatics data processing) and with financial support of the Russian Science Foundation (RSF)","doi-asserted-by":"publisher","award":["24-14-00027"],"award-info":[{"award-number":["24-14-00027"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Ischemic stroke is a multifactorial disease that leads to brain tissue damage and severe neurological deficit. Transient middle cerebral artery occlusion (tMCAO) models are actively used for the molecular, genetic study of stroke. Previously, using high-throughput RNA sequencing (RNA-Seq), we revealed 3774 differentially expressed genes (DEGs) in the penumbra-associated region of the frontal cortex (FC) of rats 24 h after applying the tMCAO model. Here, we studied the gene expression pattern in the striatum that contained an ischemic focus. Striatum samples were obtained from the same rats from which we previously obtained FC samples. Therefore, we compared DEG profiles between two rat brain tissues 24 h after tMCAO. Tissues were selected based on magnetic resonance imaging (MRI) and histological examination (HE) data. As a result, 4409 DEGs were identified 24 h after tMCAO in striatum. Among them, 2609 DEGs were overlapped in the striatum and FC, whereas more than one thousand DEGs were specific for each studied tissue. Furthermore, 54 DEGs exhibited opposite changes at the mRNA level in the two brain tissues after tMCAO. Thus, the spatial regulation of the ischemic process in the ipsilateral hemisphere of rat brain at the transcriptome level was revealed. We believe that the targeted adjustment of the genome responses identified can be the key for the induction of regeneration processes in brain cells after stroke.<\/jats:p>","DOI":"10.3390\/ijms26052347","type":"journal-article","created":{"date-parts":[[2025,3,6]],"date-time":"2025-03-06T04:55:08Z","timestamp":1741236908000},"page":"2347","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Differentially Expressed Genes in Rat Brain Regions with Different Degrees of Ischemic Damage"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6964-3405","authenticated-orcid":false,"given":"Ivan B.","family":"Filippenkov","sequence":"first","affiliation":[{"name":"Laboratory of Human Molecular Genetics, National Research Centre \u201cKurchatov Institute\u201d, Kurchatov Sq. 2, Moscow 123182, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4586-0384","authenticated-orcid":false,"given":"Yana Yu.","family":"Shpetko","sequence":"additional","affiliation":[{"name":"Laboratory of Human Molecular Genetics, National Research Centre \u201cKurchatov Institute\u201d, Kurchatov Sq. 2, Moscow 123182, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vasily V.","family":"Stavchansky","sequence":"additional","affiliation":[{"name":"Laboratory of Human Molecular Genetics, National Research Centre \u201cKurchatov Institute\u201d, Kurchatov Sq. 2, Moscow 123182, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alina E.","family":"Denisova","sequence":"additional","affiliation":[{"name":"Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, Moscow 117997, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vadim V.","family":"Yuzhakov","sequence":"additional","affiliation":[{"name":"A. Tsyb Medical Radiological Research Center\u2014Branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Koroleva Str. 4B, Obninsk 249036, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1499-1349","authenticated-orcid":false,"given":"Natalia K.","family":"Fomina","sequence":"additional","affiliation":[{"name":"A. Tsyb Medical Radiological Research Center\u2014Branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Koroleva Str. 4B, Obninsk 249036, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leonid V.","family":"Gubsky","sequence":"additional","affiliation":[{"name":"Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, Moscow 117997, Russia"},{"name":"Federal Center for the Brain and Neurotechnologies, Federal Biomedical Agency, Ostrovitianov Str. 1, Building 10, Moscow 117997, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Svetlana A.","family":"Limborska","sequence":"additional","affiliation":[{"name":"Laboratory of Human Molecular Genetics, National Research Centre \u201cKurchatov Institute\u201d, Kurchatov Sq. 2, Moscow 123182, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lyudmila V.","family":"Dergunova","sequence":"additional","affiliation":[{"name":"Laboratory of Human Molecular Genetics, National Research Centre \u201cKurchatov Institute\u201d, Kurchatov Sq. 2, Moscow 123182, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"100527","DOI":"10.1016\/j.ejro.2023.100527","article-title":"Epidemiology, organization, diagnosis and treatment of acute ischemic stroke","volume":"11","author":"Capirossi","year":"2023","journal-title":"Eur. J. Radiol. Open"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2133","DOI":"10.1016\/S0140-6736(24)00757-8","article-title":"Global incidence, prevalence, years lived with disability (YLDs), disability-adjusted life-years (DALYs), and healthy life expectancy (HALE) for 371 diseases and injuries in 204 countries and territories and 811 subnational locations, 1990\u20132021: A systematic analysis for the Global Burden of Disease Study 2021","volume":"403","author":"Ferrari","year":"2024","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1177\/17474930241308142","article-title":"World Stroke Organization: Global Stroke Fact Sheet 2025","volume":"20","author":"Feigin","year":"2025","journal-title":"Int. J. Stroke"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1161\/STROKEAHA.124.048033","article-title":"Global, Regional, and National Burden of Stroke, 1990\u20132021: A Systematic Analysis for Global Burden of Disease 2021","volume":"55","author":"He","year":"2024","journal-title":"Stroke"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Filippenkov, I.B., Khrunin, A.V., Mozgovoy, I.V., Dergunova, L.V., and Limborska, S.A. (2023). Are Ischemic Stroke and Alzheimer\u2019s Disease Genetically Consecutive Pathologies?. Biomedicines, 11.","DOI":"10.3390\/biomedicines11102727"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Elman-Shina, K., and Efrati, S. (2022). Ischemia as a common trigger for Alzheimer\u2019s disease. Front. Aging Neurosci., 14.","DOI":"10.3389\/fnagi.2022.1012779"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/0006-8993(92)91274-I","article-title":"Amyloid precursor protein accumulates in regions of neurodegeneration following focal cerebral ischemia in the rat","volume":"593","author":"Stephenson","year":"1992","journal-title":"Brain Res."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"335","DOI":"10.3233\/JAD-2007-12406","article-title":"Cerebral ischemia and Alzheimer\u2019s disease: The expression of amyloid-\u03b2 and apolipoprotein E in human hippocampus","volume":"12","author":"Qi","year":"2007","journal-title":"J. Alzheimer\u2019s Dis."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Ziaunys, M., Sakalauskas, A., Mikalauskaite, K., and Smirnovas, V. (2021). Polymorphism of alpha-synuclein amyloid fibrils depends on ionic strength and protein concentration. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222212382"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Carapeto, A.P., Marcuello, C., Fa\u00edsca, P.F.N., and Rodrigues, M.S. (2024). Morphological and Biophysical Study of S100A9 Protein Fibrils by Atomic Force Microscopy Imaging and Nanomechanical Analysis. Biomolecules, 14.","DOI":"10.3390\/biom14091091"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"74607","DOI":"10.18632\/oncotarget.20253","article-title":"Global gene expression profile of cerebral ischemia-reperfusion injury in rat MCAO model","volume":"8","author":"Wang","year":"2017","journal-title":"Oncotarget"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/0304-3940(92)90717-L","article-title":"Are Ca2+-permeable kainate\/AMPA receptors more abundant in immature brain?","volume":"144","author":"Bennett","year":"1992","journal-title":"Neurosci. Lett."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.ceca.2010.01.003","article-title":"Calcium, ischemia and excitotoxicity","volume":"47","author":"Szydlowska","year":"2010","journal-title":"Cell Calcium"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1152\/physrev.1999.79.4.1431","article-title":"Ischemic cell death in brain neurons","volume":"79","author":"Lipton","year":"1999","journal-title":"Physiol. Rev."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Jurcau, A., and Ardelean, A.I. (2022). Oxidative Stress in Ischemia\/Reperfusion Injuries following Acute Ischemic Stroke. Biomedicines, 10.","DOI":"10.3390\/biomedicines10030574"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1160\/TH14-01-0007","article-title":"Analysis of the expression of nine secreted matrix metalloproteinases and their endogenous inhibitors in the brain of mice subjected to ischaemic stroke","volume":"112","author":"Lenglet","year":"2014","journal-title":"Thromb. Haemost."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Kestner, R.I., Mayser, F., Vutukuri, R., Hansen, L., G\u00fcnther, S., Brunkhorst, R., Devraj, K., and Pfeilschifter, W. (2020). Gene Expression Dynamics at the Neurovascular Unit During Early Regeneration After Cerebral Ischemia\/Reperfusion Injury in Mice. Front. Neurosci., 14.","DOI":"10.3389\/fnins.2020.00280"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/jcbfm.2014.199","article-title":"Blood-brain barrier breakdown involves four distinct stages of vascular damage in various models of experimental focal cerebral ischemia","volume":"35","author":"Krueger","year":"2015","journal-title":"J. Cereb. Blood Flow Metab."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1007\/s12192-017-0794-9","article-title":"Upregulation and phosphorylation of HspB1\/Hsp25 and HspB5\/\u03b1B-crystallin after transient middle cerebral artery occlusion in rats","volume":"22","author":"Slowik","year":"2017","journal-title":"Cell Stress Chaperones"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5734","DOI":"10.1007\/s12035-022-02942-z","article-title":"Astrocyte-Derived TNF-\u03b1-Activated Platelets Promote Cerebral Ischemia\/Reperfusion Injury by Regulating the RIP1\/RIP3\/AKT Signaling Pathway","volume":"59","author":"Li","year":"2022","journal-title":"Mol. Neurobiol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Dergunova, L.V., Filippenkov, I.B., Stavchansky, V.V., Denisova, A.E., Yuzhakov, V.V., Mozerov, S.A., Gubsky, L.V., and Limborska, S.A. (2018). Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model. BMC Genom., 19.","DOI":"10.1186\/s12864-018-5039-5"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Filippenkov, I.B., Remizova, J.A., Denisova, A.E., Stavchansky, V.V., Golovina, K.D., Gubsky, L.V., Limborska, S.A., and Dergunova, L.V. (2023). Differential gene expression in the contralateral hemisphere of the rat brain after focal ischemia. Sci. Rep., 13.","DOI":"10.1038\/s41598-023-27663-8"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.brainres.2005.11.090","article-title":"Expression Analysis Systematic Explorer (EASE) analysis reveals differential gene expression in permanent and transient focal stroke rat models","volume":"1071","author":"Ford","year":"2006","journal-title":"Brain Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1007\/978-1-61779-328-8_13","article-title":"Modeling focal cerebral ischemia in vivo","volume":"Volume 793","author":"Jackman","year":"2011","journal-title":"Neurodegeneration"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Ma, R., Xie, Q., Li, Y., Chen, Z., Ren, M., Chen, H., Li, H., Li, J., and Wang, J. (2020). Animal models of cerebral ischemia: A review. Biomed. Pharmacother., 131.","DOI":"10.1016\/j.biopha.2020.110686"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"111050","DOI":"10.1016\/j.brainresbull.2024.111050","article-title":"Neuroprotective effects of GPR68 against cerebral ischemia-reperfusion injury via the NF-\u03baB\/Hif-1\u03b1 pathway","volume":"216","author":"Li","year":"2024","journal-title":"Brain Res. Bull."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1177\/0271678X17747193","article-title":"A peptide mimetic of tyrosine phosphatase STEP as a potential therapeutic agent for treatment of cerebral ischemic stroke","volume":"39","author":"Poddar","year":"2019","journal-title":"J. Cereb. Blood Flow Metab."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1007\/s11064-018-2523-x","article-title":"Xueshuantong Injection (Lyophilized) Attenuates Cerebral Ischemia\/Reperfusion Injury by the Activation of Nrf2-VEGF Pathway","volume":"43","author":"Guo","year":"2018","journal-title":"Neurochem. Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2364","DOI":"10.1080\/21655979.2021.1935403","article-title":"The functions of fluoxetine and identification of fluoxetine-mediated circular RNAs and messenger RNAs in cerebral ischemic stroke","volume":"12","author":"He","year":"2021","journal-title":"Bioengineered"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Filippenkov, I.B., Stavchansky, V.V., Denisova, A.E., Yuzhakov, V.V., Sevan\u2019kaeva, L.E., Sudarkina, O.Y., Dmitrieva, V.G., Gubsky, L.V., Myasoedov, N.F., and Limborska, S.A. (2020). Novel Insights into the Protective Properties of ACTH(4-7)PGP (Semax) Peptide at the Transcriptome Level Following Cerebral Ischaemia\u2013Reperfusion in Rats. Genes, 11.","DOI":"10.3390\/genes11060681"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Filippenkov, I.B., Shpetko, Y.Y., Stavchansky, V.V., Denisova, A.E., Gubsky, L.V., Andreeva, L.A., Myasoedov, N.F., Limborska, S.A., and Dergunova, L.V. (2024). ACTH-like Peptides Compensate Rat Brain Gene Expression Profile Disrupted by Ischemia a Day After Experimental Stroke. Biomedicines, 12.","DOI":"10.3390\/biomedicines12122830"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e2404203121","DOI":"10.1073\/pnas.2404203121","article-title":"Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia","volume":"121","author":"Zucha","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Li, K., Gong, Y., Chang, W., Yan, J., Hu, Y., Pan, Z., and Huang, P. (2024). Unraveling Spatiotemporal Metabolic Perturbation of Amino Acids Associated with Ischemia\u2013Reperfusion Injury by MALDI MS Imaging. Mol. Neurobiol.","DOI":"10.1007\/s12035-024-04649-9"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1161\/STROKEAHA.118.021508","article-title":"RNA-Sequencing Analysis Revealed a Distinct Motor Cortex Transcriptome in Spontaneously Recovered Mice After Stroke","volume":"49","author":"Ito","year":"2018","journal-title":"Stroke"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1002\/cphy.c160006","article-title":"Ischemia\/Reperfusion","volume":"Volume 7","author":"Kalogeris","year":"2016","journal-title":"Comprehensive Physiology"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/s41593-017-0033-9","article-title":"The diversity and disparity of the glial scar","volume":"21","author":"Adams","year":"2018","journal-title":"Nat. Neurosci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1038\/s41593-022-01183-6","article-title":"CD8+ T cells induce interferon-responsive oligodendrocytes and microglia in white matter aging","volume":"25","author":"Kaya","year":"2022","journal-title":"Nat. Neurosci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: A revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Corley, S.M., MacKenzie, K.L., Beverdam, A., Roddam, L.F., and Wilkins, M.R. (2017). Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3797-0"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1016\/j.csbj.2024.02.018","article-title":"Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review","volume":"23","author":"Rosati","year":"2024","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Ryang, Y.-M., Dang, J., Kipp, M., Petersen, K.-U., Fahlenkamp, A.V., Gempt, J., Wesp, D., Rossaint, R., Beyer, C., and Coburn, M. (2011). Solulin reduces infarct volume and regulates gene-expression in transient middle cerebral artery occlusion in rats. BMC Neurosci., 12.","DOI":"10.1186\/1471-2202-12-113"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1007\/BF00304474","article-title":"Induction of FOS and JUN proteins after focal ischemia in the rat: Differential effect of the N-methyl-d-aspartate receptor antagonist MK-801","volume":"84","author":"Gass","year":"1992","journal-title":"Acta Neuropathol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1002\/iub.2453","article-title":"Mitochondrial\u2013nuclear p53 trafficking controls neuronal susceptibility in stroke","volume":"73","author":"Almeida","year":"2021","journal-title":"IUBMB Life"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Maes, M., Nikiforov, N.G., Plaimas, K., Suratanee, A., Alfieri, D.F., and Reiche, E.M.V. (2021). New drug targets to prevent death due to stroke: A review based on results of protein-protein interaction network, enrichment, and annotation analyses. Int. J. Mol. Sci., 22.","DOI":"10.20944\/preprints202109.0070.v1"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/s12974-024-03205-5","article-title":"Systemic inflammation following traumatic injury and its impact on neuroinflammatory gene expression in the rodent brain","volume":"21","author":"Rowe","year":"2024","journal-title":"J. Neuroinflamm."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/bs.vh.2017.05.005","article-title":"Thyroid Hormone in the CNS: Contribution of Neuron\u2013Glia Interaction","volume":"Volume 106","author":"Noda","year":"2018","journal-title":"Vitamins and Hormones"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"110983","DOI":"10.1016\/j.brainresbull.2024.110983","article-title":"Thyroid hormones and stroke, the gap between clinical and experimental studies","volume":"213","author":"Shafia","year":"2024","journal-title":"Brain Res. Bull."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"926","DOI":"10.3390\/neurolint15030060","article-title":"Investigating the Predictive Value of Thyroid Hormone Levels for Stroke Prognosis","volume":"15","author":"Gkantzios","year":"2023","journal-title":"Neurol. Int."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"114728","DOI":"10.1016\/j.expneurol.2024.114728","article-title":"PI3K\u03b4 inhibition alleviates the brain injury during cerebral ischemia reperfusion via suppressing pericyte contraction in a TNF-\u03b1 dependent manner","volume":"375","author":"Qiu","year":"2024","journal-title":"Exp. Neurol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1136\/jim-2017-000485","article-title":"MicroRNA-15b deteriorates hypoxia\/reoxygenation-induced cardiomyocyte apoptosis by downregulating Bcl-2 and MAPK3","volume":"66","author":"Liu","year":"2018","journal-title":"J. Investig. Med."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.ejphar.2008.12.028","article-title":"Mitogen-activated protein kinase 3\/mitogen-activated protein kinase 1 activates apoptosis during testicular ischemia-reperfusion injury in a nuclear factor-\u03baB-independent manner","volume":"604","author":"Minutoli","year":"2009","journal-title":"Eur. J. Pharmacol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1097\/FJC.0000000000000971","article-title":"Cryptotanshinone Attenuates Ischemia\/Reperfusion-induced Apoptosis in Myocardium by Upregulating MAPK3","volume":"77","author":"Wang","year":"2021","journal-title":"J. Cardiovasc. Pharmacol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Zhao, L., Ding, L.D., Xia, Z.H., Sheng, P., Shen, M.M., Cai, Z.M., and Yan, B.C. (2022). A Network-Based Approach to Investigate the Neuroprotective Effects and Mechanisms of Action of Huangqi-Chuanxiong and Sanleng-Ezhu Herb Pairs in the Treatment of Cerebral Ischemic Stroke. Front. Pharmacol., 13.","DOI":"10.3389\/fphar.2022.844186"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Sun, Z., Wang, Y., Pang, X., Wang, X., and Zeng, H. (2023). Mechanisms of polydatin against spinal cord ischemia\u2013reperfusion injury based on network pharmacology, molecular docking and molecular dynamics simulation. Bioorganic Chem., 140.","DOI":"10.1016\/j.bioorg.2023.106840"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"113421","DOI":"10.1016\/j.intimp.2024.113421","article-title":"Molecular mechanisms and potential targets of lycopene for alleviating renal ischemia-reperfusion injury revealed by network pharmacology and animal experiments","volume":"143","author":"Pan","year":"2024","journal-title":"Int. Immunopharmacol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1038\/jcbfm.2011.186","article-title":"The two pathophysiologies of focal brain ischemia: Implications for translational stroke research","volume":"32","author":"Hossmann","year":"2012","journal-title":"J. Cereb. Blood Flow Metab."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Kossatz, E., Silva-Pe\u00f1a, D., Su\u00e1rez, J., de Fonseca, F.R., Maldonado, R., and Robledo, P. (2018). Octadecylpropyl sulfamide reduces neurodegeneration and restores the memory deficits induced by hypoxia-ischemia in mice. Front. Pharmacol., 9.","DOI":"10.3389\/fphar.2018.00376"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1016\/j.neuroscience.2008.01.022","article-title":"Modulation of the balance between cannabinoid CB1 and CB2 receptor activation during cerebral ischemic\/reperfusion injury","volume":"152","author":"Zhang","year":"2008","journal-title":"Neuroscience"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1089\/thy.2005.15.855","article-title":"Pretranslational regulation of type 2 deiodinase","volume":"15","author":"Gereben","year":"2005","journal-title":"Thyroid"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"105040","DOI":"10.1016\/j.jstrokecerebrovasdis.2020.105040","article-title":"Deiodinases, organic anion transporter polypeptide polymorphisms and symptoms of anxiety and depression after ischemic stroke","volume":"29","author":"Taroza","year":"2020","journal-title":"J. Stroke Cerebrovasc. Dis."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Zhang, Z., Zheng, Z., Luo, W., Li, J., Liao, J., Chen, F., Wang, D., and Lin, Y. (2024). Identifying immune cell infiltration and effective diagnostic biomarkers for ischemic stroke using bioinformatics analysis. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0310108"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"3098","DOI":"10.1007\/s12035-024-04433-9","article-title":"The Use of Identified Hypoxia-related Genes to Generate Models for Predicting the Prognosis of Cerebral Ischemia\u2013reperfusion Injury and Developing Treatment Strategies","volume":"62","author":"Sun","year":"2024","journal-title":"Mol. Neurobiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e17208","DOI":"10.7717\/peerj.17208","article-title":"Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients","volume":"12","author":"Cong","year":"2024","journal-title":"PeerJ"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"147982","DOI":"10.1016\/j.brainres.2022.147982","article-title":"Exploring biomarkers for ischemic stroke through integrated microarray data analysis","volume":"1790","author":"Lv","year":"2022","journal-title":"Brain Res."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Khrunin, A.V., Khvorykh, G.V., Arapova, A.S., Kulinskaya, A.E., Koltsova, E.A., Petrova, E.A., Kimelfeld, E.I., and Limborska, S.A. (2023). The Study of the Association of Polymorphisms in LSP1, GPNMB, PDPN, TAGLN, TSPO, and TUBB6 Genes with the Risk and Outcome of Ischemic Stroke in the Russian Population. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24076831"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Khrunin, A.V., Khvorykh, G.V., Rozhkova, A.V., Koltsova, E.A., Petrova, E.A., Kimelfeld, E.I., and Limborska, S.A. (2021). Examination of Genetic Variants Revealed from a Rat Model of Brain Ischemia in Patients with Ischemic Stroke: A Pilot Study. Genes, 12.","DOI":"10.3390\/genes12121938"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s12031-025-02309-8","article-title":"Identification of Novel Biomarkers for Ischemic Stroke Through Integrated Bioinformatics Analysis and Machine Learning","volume":"75","author":"Jia","year":"2025","journal-title":"J. Mol. Neurosci."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1049\/syb2.12095","article-title":"Revealing the potential role of hub metabolism-related genes and their correlation with immune cells in acute ischemic stroke","volume":"18","author":"Zhang","year":"2024","journal-title":"IET Syst. Biol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Filippenkov, I.B., Remizova, J.A., Denisova, A.E., Stavchansky, V.V., Golovina, K.D., Gubsky, L.V., Limborska, S.A., and Dergunova, L.V. (2022). Comparative Use of Contralateral and Sham-Operated Controls Reveals Traces of a Bilateral Genetic Response in the Rat Brain after Focal Stroke. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23137308"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3995\/jstroke.8.1","article-title":"Experimental studies of ischemic brain edema","volume":"8","author":"Koizumi","year":"1986","journal-title":"Jpn. J. Stroke"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.3390\/cimb46030133","article-title":"Melanocortin Derivatives Induced Vascularization and Neuroglial Proliferation in the Rat Brain under Conditions of Cerebral Ischemia","volume":"46","author":"Stavchansky","year":"2024","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1023\/B:BILE.0000019559.84305.47","article-title":"Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper\u2014Excel-based tool using pair-wise correlations","volume":"26","author":"Pfaffl","year":"2004","journal-title":"Biotechnol. Lett."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394CT Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"W147","DOI":"10.1093\/nar\/gkw419","article-title":"Heatmapper: Web-enabled heat mapping for all","volume":"44","author":"Babicki","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software Environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_77","unstructured":"National Center for Biotechnology Information (2024, June 25). Available online: https:\/\/dataview.ncbi.nlm.nih.gov\/object\/PRJNA1119923?reviewer=plp0lftpig94lmq8vmup84at3d."},{"key":"ref_78","unstructured":"National Center for Biotechnology Information (2024, June 25). Available online: https:\/\/dataview.ncbi.nlm.nih.gov\/object\/PRJNA1128447?reviewer=vkci32ofqame6mkpbivjt1pqn8."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/5\/2347\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:48:07Z","timestamp":1760028487000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/5\/2347"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,6]]},"references-count":78,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["ijms26052347"],"URL":"https:\/\/doi.org\/10.3390\/ijms26052347","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,6]]}}}