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Filippenkov IB, Remizova JA, Stavchansky VV, Denisova AE, Gubsky LV, Myasoedov NF, Limborska SA, Dergunova LV. Synthetic Adrenocorticotropic Peptides Modulate the Expression Pattern of Immune Genes in Rat Brain following the Early Post-Stroke Period. Genes (Basel) 2023; 14:1382. [PMID: 37510287 PMCID: PMC10379992 DOI: 10.3390/genes14071382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Ischemic stroke is an acute local decrease in cerebral blood flow due to a thrombus or embolus. Of particular importance is the study of the genetic systems that determine the mechanisms underlying the formation and maintenance of a therapeutic window (a time interval of up to 6 h after a stroke) when effective treatment can be provided. Here, we used a transient middle cerebral artery occlusion (tMCAO) model in rats to study two synthetic derivatives of adrenocorticotropic hormone (ACTH). The first was ACTH(4-7)PGP, which is known as Semax. It is actively used as a neuroprotective drug. The second was the ACTH(6-9)PGP peptide, which is elucidated as a prospective agent only. Using RNA-Seq analysis, we revealed hundreds of ischemia-related differentially expressed genes (DEGs), as well as 131 and 322 DEGs related to the first and second peptide at 4.5 h after tMCAO, respectively, in dorsolateral areas of the frontal cortex of rats. Furthermore, we showed that both Semax and ACTH(6-9)PGP can partially prevent changes in the immune- and neurosignaling-related gene expression profiles disturbed by the action of ischemia at 4.5 h after tMCAO. However, their different actions with regard to predominantly immune-related genes were also revealed. This study gives insight into how the transcriptome depends on the variation in the structure of the related peptides, and it is valuable from the standpoint of the development of measures for early post-stroke therapy.
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Affiliation(s)
- Ivan B Filippenkov
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Kurchatov Sq. 2, Moscow 123182, Russia
| | - Julia A Remizova
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Kurchatov Sq. 2, Moscow 123182, Russia
| | - Vasily V Stavchansky
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Kurchatov Sq. 2, Moscow 123182, Russia
| | - Alina E Denisova
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, Moscow 117997, Russia
| | - Leonid V Gubsky
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, Moscow 117997, Russia
- Federal Center for the Brain and Neurotechnologies, Federal Biomedical Agency, Ostrovitianov Str. 1, Building 10, Moscow 117997, Russia
| | - Nikolay F Myasoedov
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Kurchatov Sq. 2, Moscow 123182, Russia
| | - Svetlana A Limborska
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Kurchatov Sq. 2, Moscow 123182, Russia
| | - Lyudmila V Dergunova
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Kurchatov Sq. 2, Moscow 123182, Russia
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Filippenkov IB, Remizova JA, Denisova AE, Stavchansky VV, Golovina KD, Gubsky LV, Limborska SA, Dergunova LV. Differential gene expression in the contralateral hemisphere of the rat brain after focal ischemia. Sci Rep 2023; 13:573. [PMID: 36631528 PMCID: PMC9834327 DOI: 10.1038/s41598-023-27663-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Ischemic stroke is one of the most severe polygenic brain diseases. Here, we performed further functional genetic analysis of the processes occurring in the contralateral hemisphere (CH) after ischemia-reperfusion injury in rat brain. Comparison of RNA sequencing data for subcortical samples from the ipsilateral hemisphere (IH) and CH after 90 min of transient middle cerebral artery occlusion (tMCAO) and corresponding sham-operated (SO) controls showed four groups of genes that were associated with ischemic processes in rat brain at 24 h after tMCAO. Among them, 2672 genes were differentially expressed genes (DEGs) for IH but non-DEGs for CH, 34 genes were DEGs for CH but non-DEGs for IH, and 114 genes had codirected changes in expression in both hemispheres. The remaining 16 genes exhibited opposite changes at the mRNA level in the two brain hemispheres after tMCAO. These findings suggest that the ischemic process caused by a focal ischemia induces complex bilateral reactions at the transcriptome level in the rat brain. We believe that specific genome responses in the CH and IH may provide a useful model for the study of the potential for brain repair after stroke.
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Affiliation(s)
- Ivan B. Filippenkov
- grid.18919.380000000406204151Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Julia A. Remizova
- grid.18919.380000000406204151Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Alina E. Denisova
- grid.78028.350000 0000 9559 0613Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, 117997 Moscow, Russia
| | - Vasily V. Stavchansky
- grid.18919.380000000406204151Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Ksenia D. Golovina
- grid.18919.380000000406204151Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Leonid V. Gubsky
- grid.78028.350000 0000 9559 0613Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, 117997 Moscow, Russia ,Federal Center for the Brain and Neurotechnologies, Federal Biomedical Agency, Ostrovitianov Str. 1, Building 10, 117997 Moscow, Russia
| | - Svetlana A. Limborska
- grid.18919.380000000406204151Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Lyudmila V. Dergunova
- grid.18919.380000000406204151Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia
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Filippenkov IB, Remizova JA, Denisova AE, Stavchansky VV, Golovina KD, Gubsky LV, Limborska SA, Dergunova LV. 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 2022; 23:ijms23137308. [PMID: 35806305 PMCID: PMC9266805 DOI: 10.3390/ijms23137308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Ischemic stroke is a multifactorial disease with a complex etiology and global consequences. Model animals are widely used in stroke studies. Various controls, either brain samples from sham-operated (SO) animals or symmetrically located brain samples from the opposite (contralateral) hemisphere (CH), are often used to analyze the processes in the damaged (ipsilateral) hemisphere (IH) after focal stroke. However, previously, it was shown that focal ischemia can lead to metabolic and transcriptomic changes not only in the IH but also in the CH. Here, using a transient middle cerebral artery occlusion (tMCAO) model and genome-wide RNA sequencing, we identified 1941 overlapping differentially expressed genes (DEGs) with a cutoff value >1.5 and Padj < 0.05 that reflected the general transcriptome response of IH subcortical cells at 24 h after tMCAO using both SO and CH controls. Concomitantly, 861 genes were differentially expressed in IH vs. SO, whereas they were not vs. the CH control. Furthermore, they were associated with apoptosis, the cell cycle, and neurotransmitter responses. In turn, we identified 221 DEGs in IH vs. CH, which were non-DEGs vs. the SO control. Moreover, they were predominantly associated with immune-related response. We believe that both sets of non-overlapping genes recorded transcriptome changes in IH cells associated with transhemispheric differences after focal cerebral ischemia. Thus, the specific response of the CH transcriptome should be considered when using it as a control in studies of target brain regions in diseases that induce a global bilateral genetic response, such as stroke.
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Affiliation(s)
- Ivan B. Filippenkov
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (J.A.R.); (V.V.S.); (K.D.G.); (S.A.L.); (L.V.D.)
- Correspondence: ; Tel.: +7-499-196-1858
| | - Julia A. Remizova
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (J.A.R.); (V.V.S.); (K.D.G.); (S.A.L.); (L.V.D.)
| | - Alina E. Denisova
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, 117997 Moscow, Russia; (A.E.D.); (L.V.G.)
| | - Vasily V. Stavchansky
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (J.A.R.); (V.V.S.); (K.D.G.); (S.A.L.); (L.V.D.)
| | - Ksenia D. Golovina
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (J.A.R.); (V.V.S.); (K.D.G.); (S.A.L.); (L.V.D.)
| | - Leonid V. Gubsky
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, 117997 Moscow, Russia; (A.E.D.); (L.V.G.)
- Federal Center for the Brain and Neurotechnologies, Federal Biomedical Agency, Ostrovitianov Str. 1, Building 10, 117997 Moscow, Russia
| | - Svetlana A. Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (J.A.R.); (V.V.S.); (K.D.G.); (S.A.L.); (L.V.D.)
| | - Lyudmila V. Dergunova
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (J.A.R.); (V.V.S.); (K.D.G.); (S.A.L.); (L.V.D.)
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Filippenkov IB, Stavchansky VV, Denisova AE, Valieva LV, Remizova JA, Mozgovoy IV, Zaytceva EI, Gubsky LV, Limborska SA, Dergunova LV. Genome-Wide RNA-Sequencing Reveals Massive Circular RNA Expression Changes of the Neurotransmission Genes in the Rat Brain after Ischemia-Reperfusion. Genes (Basel) 2021; 12:genes12121870. [PMID: 34946819 PMCID: PMC8701796 DOI: 10.3390/genes12121870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Ischemic brain stroke is one of the most serious and socially significant diseases. In addition to messenger RNAs (mRNAs), encoding protein, the study of regulatory RNAs in ischemic has exceptional importance for the development of new strategies for neuroprotection. Circular RNAs (circRNAs) have a closed structure, predominantly brain-specific expression, and remain highly promising targets of research. They can interact with microRNAs (miRNAs), diminish their activity and thereby inhibit miRNA-mediated repression of mRNA. Genome-wide RNA-Seq analysis of the subcortical structures of the rat brain containing an ischemic damage focus and penumbra area revealed 395 circRNAs changed their expression significantly at 24 h after transient middle cerebral artery occlusion model (tMCAO) conditions. Furthermore, functional annotation revealed their association with neuroactive signaling pathways. It was found that about a third of the differentially expressed circRNAs (DECs) originate from genes whose mRNA levels also changed at 24 h after tMCAO. The other DECs originate from genes encoding non-regulated mRNAs under tMCAO conditions. In addition, bioinformatic analysis predicted a circRNA–miRNA–mRNA network which was associated with the neurotransmission signaling regulation. Our results show that such circRNAs can persist as potential miRNA sponges for the protection of mRNAs of neurotransmitter genes. The results expanded our views about the neurotransmission regulation in the rat brain after ischemia–reperfusion with circRNA action.
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Affiliation(s)
- Ivan B. Filippenkov
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (V.V.S.); (L.V.V.); (J.A.R.); (I.V.M.); (S.A.L.); (L.V.D.)
- Correspondence: ; Tel.: +7-499-196-1858
| | - Vasily V. Stavchansky
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (V.V.S.); (L.V.V.); (J.A.R.); (I.V.M.); (S.A.L.); (L.V.D.)
| | - Alina E. Denisova
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; (A.E.D.); (L.V.G.)
| | - Liya V. Valieva
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (V.V.S.); (L.V.V.); (J.A.R.); (I.V.M.); (S.A.L.); (L.V.D.)
| | - Julia A. Remizova
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (V.V.S.); (L.V.V.); (J.A.R.); (I.V.M.); (S.A.L.); (L.V.D.)
| | - Ivan V. Mozgovoy
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (V.V.S.); (L.V.V.); (J.A.R.); (I.V.M.); (S.A.L.); (L.V.D.)
| | - Elizaveta I. Zaytceva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia;
| | - Leonid V. Gubsky
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; (A.E.D.); (L.V.G.)
- Federal Center for the Brain and Neurotechnologies, Federal Biomedical Agency, Ostrovitianov str. 1, Building 10, 117997 Moscow, Russia
| | - Svetlana A. Limborska
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (V.V.S.); (L.V.V.); (J.A.R.); (I.V.M.); (S.A.L.); (L.V.D.)
| | - Lyudmila V. Dergunova
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, 123182 Moscow, Russia; (V.V.S.); (L.V.V.); (J.A.R.); (I.V.M.); (S.A.L.); (L.V.D.)
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