Inflammation plays a key role in the pathogenesis of many diseases, including cardiovascular disease and ischemic stroke. However, despite the existence of known inflammatory genes, the question of estimating their total number and the possibility of discovering new ones remains open. This study sought and analyzed genes involved in inflammation among genes related to cardiovascular disease and ischemic stroke. Human genes associated with ischemic stroke (N = 1177) and cardiovascular disease (N = 1756) were retrieved from the DisGeNET platform. Inflammatory and immune response genes were obtained from the Gene Ontology, NCBI, and Reactome databases. An additional list of 140 inflammatory genes was compiled based on our previously obtained data on the differential gene expression in a rat brain under transient middle cerebral artery occlusion. Genes that occurred simultaneously in both the inflammatory gene lists and gene lists of diseases were selected and considered. The resulting combined gene list included 1285 inflammatory genes. The NFKB1 and RELA genes demonstrated the highest frequencies across the various inflammatory gene selection resources we examined. Using a combination of experimental and bioinformatics approaches, a representative list of inflammatory genes important for the pathogenesis of ischemic stroke was compiled. The identified genes may be crucial for the development of anti-inflammatory therapeutic strategies for this disease.

The aim. Determination of changes in the levels of circular RNAs (circRNAs) of the Mvp, Rgs9 and Dlgap4 genes in the frontal cortex of ischemic rats 24 h after transient occlusion of the right middle cerebral artery (tMCAO). CircRNAs are covalently closed biogenic RNA molecules that have increased metabolic stability, the ability to participate in the regulation of gene expression and act as potential biomarkers of diseases and therapeutic targets for treatment. Previously, we demonstrated the involvement of genes of the neurosignaling and inflammatory systems in the response to ischemic injury, and also revealed significant changes in the expression of circRNA of Rgs9 and Mvp genes in subcortical brain structures 24 h after tMCAO in rats. These genes encode proteins involved in the inflammatory response (Mvp) and nerve signal transmission (Rgs9). Here, the circRNA of the Mvp and Rgs9 genes were analyzed. Additionally, the circRNA of the Dlgap4 gene, which has been shown to play a role in ischemic stroke, was analyzed too. Materials and methods. Wistar rats, rat tMCAO model, real-time PCR, bioinformatics. Results. Changes in the levels of circRNAs of the Mvp, Rgs9, and Dlgap4 genes were studied in the frontal cortex, which contains predominantly regenerative penumbra cells, 24 h after tMCAO. We found that the circRNA of the Mvp gene demonstrated reliable increases in expression levels (fold change > 1.5; P < 0.05) in groups of ischemic rats relative to sham-operated animals, while the change in the level of circRNA of the Rgs9 and Dlgap4 genes was insignificant. Using bioinformatics, probable binding sites for microRNAs capable of controlling the work of genes of focal adhesion systems, neurotransmission and neurogenesis were identified in the circRNA sequences of the Dlgap4, Mvp and Rgs9 genes. Conclusions. The results allow us to assess the significance of circRNAs of Mvp, Rgs9 and Dlgap4 genes for the possibility of further creating promising diagnostic systems and choosing stroke treatment tactics on their basis.

Circular RNAs (circRNAs) are a unique class of covalently closed molecules formed through non-canonical splicing and characterized by a markedly greater stability compared to linear RNAs. Although the first circRNA was discovered half a century ago in 1976 in a viroid, they had remained largely overlooked for several decades. Over the past ten years, the however, interest in circRNAs has grown substantially, even as their biological functions and overall significance continue to be debated. It is now well established that circRNAs constitute a large and diverse group of molecules with varied origins and properties. They have been identified across a wide range of organisms, from prokaryotes to plants and mammals, where they participate in the regulation of numerous cellular processes. The unique properties of circRNAs are beginning to be exploited for practical applications, including their use as disease biomarkers and platforms for the development of novel therapeutic strategies. This review summarizes the knowledge accumulated on circRNAs since their discovery and highlights recent advances in understanding their biology and potential applications.

Circular RNAs (circRNAs) are long, covalently closed RNA molecules with unique properties. Most of them are thought to function as competitive endogenous RNAs, interacting with microRNA, DNA, and proteins to regulate gene expression both in health and in various pathologies. Recently, Maxim P. Nikitin described the phenomenon of strand commutation, the interaction of weakly complementary nucleic acid (NA) molecules, demonstrating in vitro that their role can be compared with classical complementary interactions. This discovery may be particularly important for understanding the functions of circRNAs as competitive endogenous RNAs. Given the resistance of circRNAs to nucleases compared with linear RNAs, their contribution to regulating interactions with NAs and proteins, including those with low affinity, may be quite significant. An analysis of possible circRNA interactions with NAs and proteins is presented. The review includes data from 35 published research results and systematic reviews available in the PubMed database. Conclusion. We believe that studying the role of circRNAs as regulators of gene expression, including due to low-affinity interactions, will allow us to understand how they form regulatory networks and thus open new possibilities for the future development of diagnostic and therapeutic methods for various diseases.

Circular RNAs (circRNAs) are covalently closed non-coding RNAs with an increased metabolic stability, capable of regulating gene expression. CircRNAs can be potentially used as biomarkers and therapeutic targets in various diseases, including ischemic stroke. Transient middle cerebral artery occlusion (tMCAO) is commonly used as a model in stroke transcriptomics. Here, we used genome-wide RNA sequencing to investigate expression profiles of circRNAs in the frontal cortex of rats 24 h after tMCAO. Sixty-four differentially expressed circRNAs (fold change > 1.5; Padj < 0.05) were identified; most of them were upregulated compared to sham-operated animals. According to on the MRI data, the analyzed region of the frontal cortex included the penumbra, an area containing damaged but viable cells, whose survival is crucial for the poststroke recovery. Based on bioinformatics analysis of identified circRNAs and previously obtained data on differential mRNA expression in this brain region, we predicted regulatory circRNA–microRNA–mRNA networks involved in ischemic stroke. Functional analysis of these networks revealed that genes whose expression in ischemia was presumably regulated by circRNAs, are involved in synaptic signaling and inflammatory response. Our data indicate a significant role of circRNA-mediated transcriptome regulation in the penumbra region in ischemia and suggest circRNA as potential targets in the development of new strategies in the therapy of stroke and poststroke complications.

Circular RNAs (circRNAs) are non-coding RNAs that can significantly influence the regulation of gene expression in health and disease, including ischemic stroke. We identified 597 differentially expressed circRNAs (DECs) (fold change > 1.5; Padj < 0.05) in the striatum region encompassing the ischemic lesion and penumbra 24 h after ischemia-reperfusion injury (tMCAO) in rats, according to high-throughput RNA sequencing data (RNA-Seq). The DECs predominantly increased expression levels relative to those in sham-operated animals. In this study, we also compared these data with DECs we previously identified in the frontal cortex region containing the penumbra and healthy tissue. Furthermore, we bioinformatically constructed a network of competitive circRNA-microRNA-mRNA interactions characterizing the possible functions of DECs in brain areas with varying degrees of ischemic injury. We found that in both tissues, the identified DECs were involved in regulating the expression of genes associated with inflammation and neurotransmission. Moreover, in the striatum, most DECs decreased their expression, while in the frontal cortex, most DECs increased their expression. Thus, we demonstrated different circRNA activities in brain areas with varying degrees of injury. This result may indicate a role for these molecules in regulating brain cell responses, including those important for functional recovery after cerebral ischemia.

In the treatment of ischemic stroke, an innovative approach is the use of neuroprotective compounds. Natural peptides, including adrenocorticotropic hormone (ACTH), can serve as the basis for such drugs. Previously, a significant effect of non-hormonal ACTH(4-7)PGP (Semax) and ACTH(6-9)PGP peptides on the functions of the nervous system was shown. Also, while using RNA-Seq, we firstly revealed differentially expressed genes (DEGs) that associated with peptides in the penumbra-associated region of the frontal cortex (FC) of rats at 24 h after transient middle cerebral artery occlusion (tMCAO) model. Peptides significantly reduced profile disturbances caused by ischemia for almost two-thousand DEGs in FC related to the neurotransmitter and inflammatory response. Here, we studied how peptides affected the expression of genes in the striatum with an ischemic focus, predominantly. The same animals from which we previously acquired FC were used to collect striatum samples. Peptides generated fewer DEGs in the striatum than in the FC. Both peptides tended to normalize the profile of disturbances caused by ischemia for hundreds of DEGs, whereas 152 genes showed an even more affected profile in the striatum under ACTH(6-9)PGP action. These DEGs were associated with inflammation, predominantly. About hundred genes were overlapped between both peptides in both tissues and were associated with neuroactive ligand-receptor interaction, predominantly. Thus, genes that are associated with the ACTH-like peptide action in rat brain regions with varying levels of ischemia injury were identified. Moreover, differential spatial regulation of the ischemia process in the rat brain at the transcriptome levels was discovered under peptides with different ACTH structures. We suppose that our results may be useful for selecting more effective neuroprotective drug structures in accordance with their specific tissue/damage therapeutic impact.

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.

Stroke remains the second leading cause of death worldwide. The development of new therapeutic agents focused on restoring vascular function and neuroprotection of viable tissues is required. In this study the neuroprotective activity of melanocortin-like ACTH(4-7)PGP and ACTH(6-9)PGP peptides was investigated in rat brain at 24 h after transient middle cerebral artery occlusion (tMCAO). The severity of ischemic damage, changes in the proliferative activity of neuroglial cells and vascularization of rat brain tissue were analyzed. The administration of peptides resulted in a significant increase in the volume density of neurons in the perifocal zone of infarction compared to rats subjected to ischemia and receiving saline. Immunohistochemical analysis of the proliferative activity of neuroglia cells using PCNA antibodies showed a significant increase in the number of proliferating cells in the penumbra and in the intact cerebral cortex of rats receiving peptide treatment. The effect of peptides on vascularization was examined using CD31 antibodies under tMCAO conditions, revealing a significant increase in the volume density of vessels and their sizes in the penumbra after administration of ACTH(4-7)PGP and ACTH(6-9)PGP. These findings confirm the neuroprotective effect of peptides due to the activation of neuroglia proliferation and the enhancement of collateral blood flow.

Synthetic peptides have a wide range of clinical effects. Of particular interest are peptides based on adrenocorticotropic hormone (ACTH) both as already used and as potential drugs for preventing consequences of cerebral ischemia. However, it is necessary to study influence of the peptide on the brain cells under normal physiological conditions, including understanding the risks of their use. Here, we used high-throughput RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in the brain frontal cortex of rat receiving intraperitoneal administration of ACTH-like peptides ACTH(4-7)PGP (Semax) and ACTH(6-9)PGP, or saline. We identified 258 and 228 DEGs, respectively, with the fold change > 1.5 and Padj < 0.05 at 22.5 h after the first administration of Semax and ACTH(6-9)PGP. Metabolic pathways, characterizing both common and specific effects of the peptides on the transcriptome were identified. Both peptides predominantly caused decrease in expression of the genes associated with the immune system. At the same time, when comparing the effects of ACTH(6-9)PGP relative to Semax, DEGs were identified that characterized the main differences in the effects of the peptides. These genes were mostly downregulated and associated with neurosignaling systems and regulation of ion channels, thus characterizing differences in the effects of the peptides. Our data show how differences in the structure of ACTH derivatives are associated with the changes in the brain cell transcriptome following exposure to these related peptides. Furthermore, our results demonstrate that when studying influence of regulatory peptides on transcriptome under pathological conditions, it is necessary to take into account their actions under normal physiological conditions.

Stress is a risk factor for the development of anxiety-depressive disorders, cardiovascular diseases, and cognitive impairment. The peptide drug ThrLysProArgProGlyPro (Selank), an analogue of endogenous tuftsin, has entered clinical practice as an anxiolytic agent acting as a positive allosteric modulator. In a model of acute restraint stress, high-throughput RNA sequencing (RNA-Seq) is used to demonstrate that Selank is able to significantly alter gene expression in the rat hippocampus 2 h after stress exposure. Thus, the introduction of Selank (300 μg/kg) to rats 30 min before the start of immobilization lasting 1 h leads to a change in the expression of 549 genes (fold change >1.5 and Padj < 0.05), which are related to the systems of processing and presentation of antigens and transmission of nerve impulses. At the same time, when Selank is administered to rats in the absence of stress, no significant change in gene expression in the hippocampus is observed. Thus, Selank can regulate the processes caused by acute stress at the molecular-genetic level already in the early hours after acute stress, without affecting genomic activity in the absence of such an impact.

Background: Ischemic stroke results from a disruption of cerebral blood flow. Adrenocorticotropic hormone (ACTH) serves as the basis for the creation of synthetic peptides as neuroprotective agents for stroke therapy. Previously, using RNA-Seq we first revealed differential expressed genes (DEGs) associated with ACTH(4-7)PGP (Semax) and ACTH(6-9)PGP peptides under cerebral ischemia conditions. Analysis was carried out at 4.5 h after transient middle cerebral artery occlusion (tMCAO) model in the ipsilateral frontal cortex of a rat brain. Methods: Here, we analyzed the penumbra-associated frontal cortex of rats and actions under the same peptides at 24 h after tMCAO using RNA-Seq. Results: 3774 DEGs (fold change > 1.5 and Padj < 0.05) were identified under ischemia conditions, whereas 1539 and 2066 DEGs were revealed under Semax and ACTH(6-9)PGP peptides at 24 h after tMCAO. Furthermore, both peptides significantly reduced expression distortions caused by ischemia for 1171 genes associated with immune and neurosignaling pathways. Concomitantly, there were 32 DEGs under ACTH(6-9)PGP versus Semax administration at 24 h after tMCAO. Besides, neurogenesis-, angiogenesis-, protein kinase- and growth factor-related DEGs were revealed under peptides action. Previously, we observed the neuroprotective effect of peptides at the histological level in rat brains at 24 h after tMCAO. Thus, here we demonstrate the transcriptome manifestation of this histological effect. Furthermore, comparison with previous data at the 4.5 h post-tMCAO time point showed that the pattern of peptide action on the transcriptome depends on the time elapsed after tMCAO. Conclusions: We revealed that the effect of ACTH(6-9)PGP was more similar to Semax than different from it a day after tMCAO. At this time point, ACTH-like peptides compensated rat brain gene expression profiles disrupted by ischemia. Thus, our results may be useful for selecting more effective structures for future anti-stroke drugs and appropriate post-stroke time points for their testing.