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Circular RNA CircPDS5B impairs angiogenesis following ischemic stroke through its interaction with hnRNPL to inactivate VEGF-A. Neurobiol Dis 2023; 181:106080. [PMID: 36925052 DOI: 10.1016/j.nbd.2023.106080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/26/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Ischemic stroke (IS) is the primary cause of mortality and disability worldwide. Circular RNAs (circRNAs) have been proposed as crucial regulators in IS. This study focused on the role of circPDS5B in IS and its underlying mechanism. METHOD Transient middle cerebral artery occlusion (tMCAO) mice and glucose deprivation/reoxygenation (OGD/R)-exposed human brain microvascular endothelial cells (BMECs) were used as IS models. Expression levels of circPDS5B, heterogenous nuclear ribonucleoprotein L (hnRNPL), runt-related transcription factor-1 (Runx1), and Zinc finger protein 24 (ZNF24) were quantified by qRT-PCR. MTT, wound healing, transwell and tube formation assays were employed to evaluate the cell proliferation, migration, and angiogenesis, respectively. Moreover, RNA pull-down, and RIP assay were performed to investigate the interaction among circPDS5B, hnRNPL and vascular endothelial growth factor-A (VEGFA). RESULTS circPDS5B was significantly up-regulated in IS patients and tMCAO mice. Deficiency of circPDS5B relieved brain infarction and neuronal injury of tMCAO mice. OGD/R-induced apoptosis, inhibition in viability, migration, and angiogenesis in BMECs were dramatically abrogated by circPDS5B knockdown. Mechanistically, circPDS5B stabilized Runx1 and ZNF24 via recruiting hnRNPL, thereby suppressing the transcription and expression of VEGFA. hnRNPL silencing strengthened circPDS5B knockdown-mediated beneficial effect on IS. CONCLUSION Altogether, our study showed that high expression of circPDS5B exacerbated IS through recruitment of hnRNP to stabilize Runx1/ZNF24 and subsequently inactivate VEGF-A. Our findings suggest circPDS5B may be a novel therapeutic target for IS.
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Abstract
Stroke remains a leading cause of death and disability, with limited therapeutic options and suboptimal tools for diagnosis and prognosis. High throughput technologies such as proteomics generate large volumes of experimental data at once, thus providing an advanced opportunity to improve the status quo by facilitating identification of novel therapeutic targets and molecular biomarkers. Proteomics studies in animals are largely designed to decipher molecular pathways and targets altered in brain tissue after stroke, whereas studies in human patients primarily focus on biomarker discovery in biofluids and, more recently, in thrombi and extracellular vesicles. Here, we offer a comprehensive review of stroke proteomics studies conducted in both animal and human specimen and present our view on limitations, challenges, and future perspectives in the field. In addition, as a unique resource for the scientific community, we provide extensive lists of all proteins identified in proteomic studies as altered by stroke and perform postanalysis of animal data to reveal stroke-related cellular processes and pathways.
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Affiliation(s)
- Karin Hochrainer
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY (K.H.)
| | - Wei Yang
- Center for Perioperative Organ Protection, Department of Anesthesiology, Duke University School of Medicine, Durham, NC (W.Y.)
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SWATH-MS for prospective identification of protein blood biomarkers of rtPA-associated intracranial hemorrhage in acute ischemic stroke: a pilot study. Sci Rep 2021; 11:18765. [PMID: 34548538 PMCID: PMC8455557 DOI: 10.1038/s41598-021-97710-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 08/27/2021] [Indexed: 11/08/2022] Open
Abstract
Intravenous recombinant tissue plasminogen activator (rtPA) is, besides mechanical thrombectomy, the highest class evidence based reperfusion treatment of acute ischemic stroke (AIS). The biggest concern of the therapy is symptomatic intracranial hemorrhage (sICH), which occurs in 3-7% of all treated patients, and is associated with worse functional outcome. Finding a method of the powerful identification of patients at highest risk of sICH, in order to increase the percentage of stroke patients safely treated with rtPA, is one of the most important challenges in stroke research. To address this problem, we designed a complex project to identify blood, neuroimaging, and clinical biomarkers combined for prospective assessment of the risk of rtPA-associated ICH. In this paper we present results of blood proteomic and peptide analysis of pilot 41 AIS patients before rtPA administration (the test ICH group, n = 9 or the controls, without ICH, n = 32). We demonstrated that pre-treatment blood profiles of 15 proteins differ depending on whether the patients develop rtPA-associated ICH or not. SWATH-MS quantification of serum or plasma proteins might allow for robust selection of blood biomarkers to increase the prospective assessment of rtPA-associated ICH over that based solely on clinical and neuroimaging characteristics.
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Lee J, Mun S, Park A, Kim D, Lee YJ, Kim HJ, Choi H, Shin M, Lee SJ, Kim JG, Chun YT, Kang HG. Proteomics Reveals Plasma Biomarkers for Ischemic Stroke Related to the Coagulation Cascade. J Mol Neurosci 2020; 70:1321-1331. [DOI: 10.1007/s12031-020-01545-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/13/2020] [Indexed: 12/20/2022]
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Ostolaza A, Blanco-Luquin I, Urdánoz-Casado A, Rubio I, Labarga A, Zandio B, Roldán M, Martínez-Cascales J, Mayor S, Herrera M, Aymerich N, Gallego J, Muñoz R, Mendioroz M. Circular RNA expression profile in blood according to ischemic stroke etiology. Cell Biosci 2020; 10:34. [PMID: 32175077 PMCID: PMC7063791 DOI: 10.1186/s13578-020-00394-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 02/24/2020] [Indexed: 02/03/2023] Open
Abstract
Background The discovery of novel biomarkers of stroke etiology would be most helpful in management of acute ischemic stroke patients. Recently, circular RNAs (circRNAs) have been proposed as candidate biomarkers of neurological conditions due to its high stability. circRNAs function as sponges, sequestering miRNAs and are involved in most relevant biological functions. Our aim was to identify differentially expressed circRNAs in acute ischemic stroke patients according to stroke etiology. Methods A comprehensive expression profile of blood circRNAs was conducted by Arraystar Human circRNA arrays (13,617 probes) on a discovery cohort of 30 stroke patients with different stroke etiologies by TOAST classification. Real-time quantitative PCR (RT-qPCR) was used to validate array results in a cohort of 50 stroke patients. Functional in silico analysis was performed to identify potential interactions with microRNAs (miRNAs) and pathways underlying deregulated circRNAs. Results A set of 60 circRNAs were found to be upregulated in atherotrombotic versus cardioembolic strokes (fold-change > = 1.5 and p-value ≤ 0.05). Differential expression of hsa_circRNA_102488, originated from UBA52 gene, was replicated in the validation cohort. RNA-binding proteins (RBPs) sites of hsa_circRNA_102488 clustered around AGO2 and FUS proteins. Further functional analysis revealed interactions between deregulated circRNAs and a set of miRNAs involved in stroke-related pathways, such as fatty acid biogenesis or lysine degradation. Conclusion Different stroke subtypes show specific profiles of circRNAs expression. circRNAs may serve as a new source of biomarkers of stroke etiology in acute ischemic stroke patients.
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Affiliation(s)
- Aiora Ostolaza
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - Idoia Blanco-Luquin
- Neuroepigenetics Laboratory-Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/Irunlarrea, 3, 31008 Pamplona, Navarra Spain
| | - Amaya Urdánoz-Casado
- Neuroepigenetics Laboratory-Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/Irunlarrea, 3, 31008 Pamplona, Navarra Spain
| | - Idoya Rubio
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - Alberto Labarga
- 4Bioinformatics Unit, Navarrabiomed, Public University of Navarre (UPNA), IdiSNA (Navarra Institute for Health Research), C/Irunlarrea, 3, 31008 Pamplona, Navarra Spain
| | - Beatriz Zandio
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain.,3Stroke Unit, Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - Miren Roldán
- Neuroepigenetics Laboratory-Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/Irunlarrea, 3, 31008 Pamplona, Navarra Spain
| | - Judith Martínez-Cascales
- Neuroepigenetics Laboratory-Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/Irunlarrea, 3, 31008 Pamplona, Navarra Spain
| | - Sergio Mayor
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain.,3Stroke Unit, Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - María Herrera
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain.,3Stroke Unit, Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - Nuria Aymerich
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain.,3Stroke Unit, Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - Jaime Gallego
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain.,3Stroke Unit, Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - Roberto Muñoz
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain.,3Stroke Unit, Department of Neurology, Complejo Hospitalario de Navarra- IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain
| | - Maite Mendioroz
- 1Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), 31008 Pamplona, Navarra Spain.,Neuroepigenetics Laboratory-Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), C/Irunlarrea, 3, 31008 Pamplona, Navarra Spain
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Valdés A, Bergström Lind S. Mass Spectrometry-Based Analysis of Time-Resolved Proteome Quantification. Proteomics 2019; 20:e1800425. [PMID: 31652013 DOI: 10.1002/pmic.201800425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/20/2019] [Indexed: 11/09/2022]
Abstract
The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time-dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners-both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS-based analysis of time-resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.
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Affiliation(s)
- Alberto Valdés
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, 75124, Uppsala, Sweden
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Wen M, Jin Y, Zhang H, Sun X, Kuai Y, Tan W. Proteomic Analysis of Rat Cerebral Cortex in the Subacute to Long-Term Phases of Focal Cerebral Ischemia-Reperfusion Injury. J Proteome Res 2019; 18:3099-3118. [PMID: 31265301 DOI: 10.1021/acs.jproteome.9b00220] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Stroke is a leading cause of mortality and disability, and ischemic stroke accounts for more than 80% of the disease occurrence. Timely reperfusion is essential in the treatment of ischemic stroke, but it is known to cause ischemia-reperfusion (I/R) injury and the relevant studies have mostly focused on the acute phase. Here we reported on a global proteomic analysis to investigate the development of cerebral I/R injury in the subacute and long-term phases. A rat model was used, with 2 h-middle cerebral artery occlusion (MCAO) followed with 1, 7, and 14 days of reperfusion. The proteins of cerebral cortex were analyzed by SDS-PAGE, whole-gel slicing, and quantitative LC-MS/MS. Totally 5621 proteins were identified, among which 568, 755, and 492 proteins were detected to have significant dys-regulation in the model groups with 1, 7, and 14 days of reperfusion, respectively, when compared with the corresponding sham groups (n = 4, fold change ≥1.5 or ≤0.67 and p ≤ 0.05). Bioinformatic analysis on the functions and reperfusion time-dependent dys-regulation profiles of the proteins exhibited changes of structures and biological processes in cytoskeleton, synaptic plasticity, energy metabolism, inflammation, and lysosome from subacute to long-term phases of cerebral I/R injury. Disruption of cytoskeleton and synaptic structures, impairment of energy metabolism processes, and acute inflammation responses were the most significant features in the subacute phase. With the elongation of reperfusion time to the long-term phase, a tendency of recovery was detected on cytoskeleton, while inflammation pathways different from the subacute phase were activated. Also, lysosomal structures and functions might be restored. This is the first work reporting the proteome changes that occurred at different time points from the subacute to long-term phases of cerebral I/R injury and we expect it would provide useful information to improve the understanding of the mechanisms involved in the development of cerebral I/R injury and suggest candidates for treatment.
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Affiliation(s)
- Meiling Wen
- School of Biology and Biological Engineering , South China University of Technology , Guangzhou 510006 , P. R. China
| | - Ya Jin
- Institute of Biomedical and Pharmaceutical Sciences , Guangdong University of Technology , Guangzhou 510006 , P. R. China
| | - Hao Zhang
- Institute of Biomedical and Pharmaceutical Sciences , Guangdong University of Technology , Guangzhou 510006 , P. R. China
| | - Xiaoou Sun
- Institute of Biomedical and Pharmaceutical Sciences , Guangdong University of Technology , Guangzhou 510006 , P. R. China
| | - Yihe Kuai
- Institute of Biomedical and Pharmaceutical Sciences , Guangdong University of Technology , Guangzhou 510006 , P. R. China
| | - Wen Tan
- Institute of Biomedical and Pharmaceutical Sciences , Guangdong University of Technology , Guangzhou 510006 , P. R. China
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Dagonnier M, Wilson WJ, Favaloro JM, Rewell SSJ, Lockett LJ, Sastra SA, Jeffreys AL, Dewey HM, Donnan GA, Howells DW. Hyperacute changes in blood mRNA expression profiles of rats after middle cerebral artery occlusion: Towards a stroke time signature. PLoS One 2018; 13:e0206321. [PMID: 30439964 PMCID: PMC6237327 DOI: 10.1371/journal.pone.0206321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023] Open
Abstract
Stroke evolution is a highly dynamic but variable disease which makes clinical decision making difficult. Biomarker discovery programs intended to aid clinical decision making have however largely ignored the rapidity of stroke evolution. We have used gene array technology to determine blood mRNA expression changes over the first day after stroke in rats. Blood samples were collected from 8 male spontaneously hypertensive rats at 0, 1, 2, 3, 6 and 24h post stroke induction by middle cerebral artery occlusion. RNA was extracted from whole blood stabilized in PAXgene tubes and mRNA expression was detected by oligonucleotide Affymetrix microarray. Using a pairwise comparison model, 1932 genes were identified to vary significantly over time (p≤0.5x10-7) within 24h after stroke. Some of the top20 most changed genes are already known to be relevant to the ischemic stroke physiopathology (e.g. Il-1R, Nos2, Prok2). Cluster analysis showed multiple stereotyped and time dependent profiles of gene expression. Direction and rate of change of expression for some profiles varied dramatically during these 24h. Profiles with potential clinical utility including hyper acute or acute transient upregulation (with expression peaking from 2 to 6h after stroke and normalisation by 24h) were identified. We found that blood gene expression varies rapidly and stereotypically after stroke in rats. Previous researchers have often missed the optimum time for biomarker measurement. Temporally overlapping profiles have the potential to provide a biological “stroke clock” able to tell the clinician how far an individual stroke has evolved.
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Affiliation(s)
- Marie Dagonnier
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
- * E-mail:
| | - William John Wilson
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia
| | - Jenny Margaret Favaloro
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
| | - Sarah Susan Jane Rewell
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
| | - Linda Jane Lockett
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia
| | - Stephen Andrew Sastra
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
| | - Amy Lucienne Jeffreys
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
| | - Helen Margaret Dewey
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
| | - Geoffrey Alan Donnan
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
| | - David William Howells
- The Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, Austin Campus, Heidelberg, Australia
- School of Medicine, Faculty of Health, University of Tasmania, Hobart, Australia
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