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Tian X, Yang W, Jiang W, Zhang Z, Liu J, Tu H. Multi-Omics Profiling Identifies Microglial Annexin A2 as a Key Mediator of NF-κB Pro-inflammatory Signaling in Ischemic Reperfusion Injury. Mol Cell Proteomics 2024; 23:100723. [PMID: 38253182 PMCID: PMC10879806 DOI: 10.1016/j.mcpro.2024.100723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Cerebral stroke is one of the leading causes of mortality and disability worldwide. Restoring the cerebral circulation following a period of occlusion and subsequent tissue oxygenation leads to reperfusion injury. Cerebral ischemic reperfusion (I/R) injury triggers immune and inflammatory responses, apoptosis, neuronal damage, and even death. However, the cellular function and molecular mechanisms underlying cerebral I/R-induced neuronal injury are incompletely understood. By integrating proteomic, phosphoproteomic, and transcriptomic profiling in mouse hippocampi after cerebral I/R, we revealed that the differentially expressed genes and proteins mainly fall into several immune inflammatory response-related pathways. We identified that Annexin 2 (Anxa2) was exclusively upregulated in microglial cells in response to cerebral I/R in vivo and oxygen-glucose deprivation and reoxygenation (OGD/R) in vitro. RNA-seq analysis revealed a critical role of Anxa2 in the expression of inflammation-related genes in microglia via the NF-κB signaling. Mechanistically, microglial Anxa2 is required for nuclear translocation of the p65 subunit of NF-κB and its transcriptional activity upon OGD/R in BV2 microglial cells. Anxa2 knockdown inhibited the OGD/R-induced microglia activation and markedly reduced the expression of pro-inflammatory factors, including TNF-α, IL-1β, and IL-6. Interestingly, conditional medium derived from Anxa2-depleted BV2 cell cultures with OGD/R treatment alleviated neuronal death in vitro. Altogether, our findings revealed that microglia Anxa2 plays a critical role in I/R injury by regulating NF-κB inflammatory responses in a non-cell-autonomous manner, which might be a potential target for the neuroprotection against cerebral I/R injury.
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Affiliation(s)
- Xibin Tian
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Wuyan Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Wei Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Zhen Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Junqiang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China
| | - Haijun Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan, China; Shenzhen Research Institute, Hunan University, Shenzhen, Guangdong, China.
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2
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Furman M, Sihotsky V, Virag M, Kopolovets I, Nemethova M, Mucha R. Quantitative analysis of selected genetic markers of induced brain stroke ischemic tolerance detected in human blood. Brain Res 2023; 1821:148590. [PMID: 37739332 DOI: 10.1016/j.brainres.2023.148590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
A brain stroke is a serious disease and the second leading cause of death in the European Union. Carotid stenosis accounts for 15% of all ischemic cerebral strokes. However, there is currently no effective screening for carotid disease. Analysis of the DNA from peripheral blood is increasingly being used for several disease diagnoses. The potentially beneficial therapeutic method of inducing tissue tolerance to ischemia has so far been studied mainly in animal models. The aim of this study is to investigate changes in the gene expression of selected markers of brain ischemia during carotid endarterectomy, considered in this study as an activator of ischemic tolerance. During the carotid endarterectomy, there is a short-term occlusion of the internal carotid artery. Using the RT-qPCR method, we detected changes in the early identified gene markers of brain ischemia (ADM, CDKN1A, GADD45G, IL6, TM4SF1) in peripheral blood during sub lethal cerebral ischemia caused by carotid endarterectomy. Patients underwenting surgical procedure were divided into three groups: asymptomatic, symptomatic, and those who underwent carotid endarterectomy after an acute stroke. The results were compared to a negative/control group. Carotid endarterectomy had an impact on the expression of all monitored biomarkers. We observed statistically significant changes (p value 0.05-0.001) when comparing the groups among themselves, as well as the presence of ischemic tolerance of brain tissue to ischemic attacks. In conclusion, ADM, GADD45G, and TM4SF1 were affected in symptomatic patients, GADD45G and IL6 in acute patients, and CDKN1A and ADM in asymptomatic group after application of carotid endarterectomy.
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Affiliation(s)
- Marek Furman
- Institute of Neurobiology of Biomedical Research Center, Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia
| | - Vladimir Sihotsky
- Eastern Slovak Institute of Cardiovascular Diseases and Faculty of Medicine, Pavol Jozef Safarik University, Kosice, Ondavska 8, 040 01 Kosice, Slovakia
| | - Michal Virag
- Eastern Slovak Institute of Cardiovascular Diseases and Faculty of Medicine, Pavol Jozef Safarik University, Kosice, Ondavska 8, 040 01 Kosice, Slovakia
| | - Ivan Kopolovets
- Eastern Slovak Institute of Cardiovascular Diseases and Faculty of Medicine, Pavol Jozef Safarik University, Kosice, Ondavska 8, 040 01 Kosice, Slovakia
| | - Miroslava Nemethova
- Institute of Neurobiology of Biomedical Research Center, Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia
| | - Rastislav Mucha
- Institute of Neurobiology of Biomedical Research Center, Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia.
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Zhao T, Zeng J, Zhang R, Pu L, Wang H, Pan L, Jiang Y, Dai X, Sha Y, Han L. Proteomic advance of ischemic stroke: preclinical, clinical, and intervention. Metab Brain Dis 2023; 38:2521-2546. [PMID: 37440002 DOI: 10.1007/s11011-023-01262-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023]
Abstract
Ischemic stroke (IS) is the most common type of stroke and is characterized by high rates of mortality and long-term injury. The prediction and early diagnosis of IS are therefore crucial for optimal clinical intervention. Proteomics has provided important techniques for exploring protein markers associated with IS, but there has been no systematic evaluation and review of research that has used these techniques. Here, we review the differential proteins that have been found in cell- and animal- based studies and clinical trials of IS in the past 10 years; determine the key pathological proteins that have been identified in clinical trials; summarize the target proteins affected by interventions aimed at treating IS, with a focus on traditional Chinese medicine treatments. Overall, we clarify findings and problems that have been identified in recent proteomics research on IS and provide suggestions for improvements in this area. We also suggest areas that could be explored for determining the pathogenesis and developing interventions for IS.
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Affiliation(s)
- Tian Zhao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Jingjing Zeng
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Ruijie Zhang
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Liyuan Pu
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Han Wang
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Lifang Pan
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Yannan Jiang
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China
| | - Xiaoyu Dai
- Department of Anus & Intestine Surgery, Ningbo No.2 Hospital, Ningbo, 315000, China
| | - Yuyi Sha
- Department of Intensive Care Medicine, Ningbo No.2 Hospital, Ningbo, 315000, China.
| | - Liyuan Han
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo No.2 Hospital, 41 Northwest Street, Ningbo, 315000, Zhejiang, China.
- Center for Cardiovascular and Cerebrovascular Epidemiology and Translational Medicine, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China.
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Li Q, Zhao L, Chan CL, Zhang Y, Tong SW, Zhang X, Ho JWK, Jiao Y, Rainer TH. Multi-Level Biomarkers for Early Diagnosis of Ischaemic Stroke: A Systematic Review and Meta-Analysis. Int J Mol Sci 2023; 24:13821. [PMID: 37762122 PMCID: PMC10530879 DOI: 10.3390/ijms241813821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Blood biomarkers hold potential for the early diagnosis of ischaemic stroke (IS). We aimed to evaluate the current weight of evidence and identify potential biomarkers and biological pathways for further investigation. We searched PubMed, EMBASE, the Cochrane Library and Web of Science, used R package meta4diag for diagnostic meta-analysis and applied Gene Ontology (GO) analysis to identify vital biological processes (BPs). Among 8544 studies, we included 182 articles with a total of 30,446 participants: 15675 IS, 2317 haemorrhagic stroke (HS), 1798 stroke mimics, 846 transient ischaemic attack and 9810 control subjects. There were 518 pooled biomarkers including 203 proteins, 114 genes, 108 metabolites and 88 transcripts. Our study generated two shortlists of biomarkers for future research: one with optimal diagnostic performance and another with low selection bias. Glial fibrillary acidic protein was eligible for diagnostic meta-analysis, with summary sensitivities and specificities for differentiating HS from IS between 3 h and 24 h after stroke onset ranging from 73% to 80% and 77% to 97%, respectively. GO analysis revealed the top five BPs associated with IS. This study provides a holistic view of early diagnostic biomarkers in IS. Two shortlists of biomarkers and five BPs warrant future investigation.
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Affiliation(s)
- Qianyun Li
- Department of Emergency Medicine, University of Hong Kong, Hong Kong, China; (Q.L.)
| | - Lingyun Zhao
- Department of Emergency Medicine, University of Hong Kong, Hong Kong, China; (Q.L.)
| | - Ching Long Chan
- Department of Emergency Medicine, University of Hong Kong, Hong Kong, China; (Q.L.)
| | - Yilin Zhang
- Department of Emergency Medicine, University of Hong Kong, Hong Kong, China; (Q.L.)
| | - See Wai Tong
- Department of Emergency Medicine, University of Hong Kong, Hong Kong, China; (Q.L.)
| | - Xiaodan Zhang
- Department of Emergency Medicine, University of Hong Kong, Hong Kong, China; (Q.L.)
| | - Joshua Wing Kei Ho
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Yaqing Jiao
- Department of Emergency Medicine, University of Hong Kong, Hong Kong, China; (Q.L.)
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5
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Hernandez VG, Lechtenberg KJ, Peterson TC, Zhu L, Lucas TA, Bradshaw KP, Owah JO, Dorsey AI, Gentles AJ, Buckwalter MS. Translatome analysis reveals microglia and astrocytes to be distinct regulators of inflammation in the hyperacute and acute phases after stroke. Glia 2023; 71:1960-1984. [PMID: 37067534 PMCID: PMC10330240 DOI: 10.1002/glia.24377] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/08/2023] [Accepted: 04/04/2023] [Indexed: 04/18/2023]
Abstract
Neuroinflammation is a hallmark of ischemic stroke, which is a leading cause of death and long-term disability. Understanding the exact cellular signaling pathways that initiate and propagate neuroinflammation after stroke will be critical for developing immunomodulatory stroke therapies. In particular, the precise mechanisms of inflammatory signaling in the clinically relevant hyperacute period, hours after stroke, have not been elucidated. We used the RiboTag technique to obtain microglia and astrocyte-derived mRNA transcripts in a hyperacute (4 h) and acute (3 days) period after stroke, as these two cell types are key modulators of acute neuroinflammation. Microglia initiated a rapid response to stroke at 4 h by adopting an inflammatory profile associated with the recruitment of immune cells. The hyperacute astrocyte profile was marked by stress response genes and transcription factors, such as Fos and Jun, involved in pro-inflammatory pathways such as TNF-α. By 3 days, microglia shift to a proliferative state and astrocytes strengthen their inflammatory response. The astrocyte pro-inflammatory response at 3 days is partially driven by the upregulation of the transcription factors C/EBPβ, Spi1, and Rel, which comprise 25% of upregulated transcription factor-target interactions. Surprisingly, few sex differences across all groups were observed. Expression and log2 fold data for all sequenced genes are available on a user-friendly website for researchers to examine gene changes and generate hypotheses for stroke targets. Taken together, our data comprehensively describe the microglia and astrocyte-specific translatome response in the hyperacute and acute period after stroke and identify pathways critical for initiating neuroinflammation.
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Affiliation(s)
- Victoria G Hernandez
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Kendra J Lechtenberg
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Todd C Peterson
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Li Zhu
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Tawaun A Lucas
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Karen P Bradshaw
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Justice O Owah
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Alanna I Dorsey
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
| | - Andrew J Gentles
- Department of Pathology, Stanford University, Stanford, California, USA
- Department of Medicine - Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Marion S Buckwalter
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Palo Alto, California, USA
- Department of Neurosurgery, Stanford School of Medicine, Palo Alto, California, USA
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6
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Granata A. Functional genomics in stroke: current and future applications of iPSCs and gene editing to dissect the function of risk variants. BMC Cardiovasc Disord 2023; 23:223. [PMID: 37120540 PMCID: PMC10148993 DOI: 10.1186/s12872-023-03227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/04/2023] [Indexed: 05/01/2023] Open
Abstract
Stroke is an important disease with unmet clinical need. To uncover novel paths for treatment, it is of critical importance to develop relevant laboratory models that may help to shed light on the pathophysiological mechanisms of stroke. Induced pluripotent stem cells (iPSCs) technology has enormous potential to advance our knowledge into stroke by creating novel human models for research and therapeutic testing. iPSCs models generated from patients with specific stroke types and specific genetic predisposition in combination with other state of art technologies including genome editing, multi-omics, 3D system, libraries screening, offer the opportunity to investigate disease-related pathways and identify potential novel therapeutic targets that can then be tested in these models. Thus, iPSCs offer an unprecedented opportunity to make rapid progress in the field of stroke and vascular dementia research leading to clinical translation. This review paper summarizes some of the key areas in which patient-derived iPSCs technology has been applied to disease modelling and discusses the ongoing challenges and the future directions for the application of this technology in the field of stroke research.
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Affiliation(s)
- Alessandra Granata
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart & Lung Research Institute, Papworth Road, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0BB, UK.
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7
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Hernandez VG, Lechtenberg KJ, Peterson TC, Zhu L, Lucas TA, Owah JO, Dorsey AI, Gentles AJ, Buckwalter MS. Translatome analysis reveals microglia and astrocytes to be distinct regulators of inflammation in the hyperacute and acute phases after stroke. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.520351. [PMID: 36824949 PMCID: PMC9949064 DOI: 10.1101/2023.02.14.520351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Neuroinflammation is a hallmark of ischemic stroke, which is a leading cause of death and long-term disability. Understanding the exact cellular signaling pathways that initiate and propagate neuroinflammation after stroke will be critical for developing immunomodulatory stroke therapies. In particular, the precise mechanisms of inflammatory signaling in the clinically relevant hyperacute period, hours after stroke, have not been elucidated. We used the RiboTag technique to obtain astrocyte and microglia-derived mRNA transcripts in a hyperacute (4 hours) and acute (3 days) period after stroke, as these two cell types are key modulators of acute neuroinflammation. Microglia initiated a rapid response to stroke at 4 hours by adopting an inflammatory profile associated with the recruitment of immune cells. The hyperacute astrocyte profile was marked by stress response genes and transcription factors, such as Fos and Jun , involved in pro-inflammatory pathways such as TNF-α. By 3 days, microglia shift to a proliferative state and astrocytes strengthen their inflammatory response. The astrocyte pro-inflammatory response at 3 days is partially driven by the upregulation of the transcription factors C/EBPβ, Spi1 , and Rel , which comprise 25% of upregulated transcription factor-target interactions. Surprisingly, few sex differences across all groups were observed. Expression and log 2 fold data for all sequenced genes are available on a user-friendly website for researchers to examine gene changes and generate hypotheses for stroke targets. Taken together our data comprehensively describe the astrocyte and microglia-specific translatome response in the hyperacute and acute period after stroke and identify pathways critical for initiating neuroinflammation.
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8
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Influence of sex, age and diabetes on brain transcriptome and proteome modifications following cerebral ischemia. BMC Neurosci 2023; 24:7. [PMID: 36707762 PMCID: PMC9881265 DOI: 10.1186/s12868-023-00775-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/10/2023] [Indexed: 01/28/2023] Open
Abstract
Ischemic stroke is a major cause of death and disability worldwide. Translation into the clinical setting of neuroprotective agents showing promising results in pre-clinical studies has systematically failed. One possible explanation is that the animal models used to test neuroprotectants do not properly represent the population affected by stroke, as most of the pre-clinical studies are performed in healthy young male mice. Therefore, we aimed to determine if the response to cerebral ischemia differed depending on age, sex and the presence of comorbidities. Thus, we explored proteomic and transcriptomic changes triggered during the hyperacute phase of cerebral ischemia (by transient intraluminal middle cerebral artery occlusion) in the brain of: (1) young male mice, (2) young female mice, (3) aged male mice and (4) diabetic young male mice. Moreover, we compared each group's proteomic and transcriptomic changes using an integrative enrichment pathways analysis to disclose key common and exclusive altered proteins, genes and pathways in the first stages of the disease. We found 61 differentially expressed genes (DEG) in male mice, 77 in females, 699 in diabetics and 24 in aged mice. Of these, only 14 were commonly dysregulated in all groups. The enrichment pathways analysis revealed that the inflammatory response was the biological process with more DEG in all groups, followed by hemopoiesis. Our findings indicate that the response to cerebral ischemia regarding proteomic and transcriptomic changes differs depending on sex, age and comorbidities, highlighting the importance of incorporating animals with different phenotypes in future stroke research studies.
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Proteomic investigations of acute ischemic stroke in animal models: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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Skvortsov V, Ivanova Y, Voronina A. Acetylation, methylation, and ubiquitination of proteins in experimental ischemic stroke in mice: a bioinformatics analysis. BIOMEDITSINSKAYA KHIMIYA 2022; 68:390-397. [DOI: 10.18097/pbmc20226805390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The experimental results available in the ProteomeXchange database (accession code PXD016538) (Simats et al. (2020) Molecular and Cellular Proteomics, 19(12), 1921-1936) obtained using a comprehensive multi-omics approach were analyzed in mouse blood to identify potential biomarkers of ischemic stroke. Acetylation, methylation, and ubiquitination were considered as post-translational modifications. The analysis of the significance of changes in the level of protein modification was evaluated for ischemic tissue in comparison with tissue undamaged by stroke and control taken from mice after sham operation. At the level of statistically significant differences according to the Mann-Whitney test (p < 0.05), 2 proteins were found (Q02248 and Q8BL66); for additional 7 proteins, the differences were at the level of a statistical trend (p < 0.1). For 7 of 9 selected proteins there are reports in the literature, for their association with cerebral ischemia.
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Affiliation(s)
| | - Y.O. Ivanova
- Institute of Biomedical Chemistry, Moscow, Russia
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11
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Dias A, Silva L, Moura J, Gabriel D, Maia LF. Fluid biomarkers in stroke: From animal models to clinical care. Acta Neurol Scand 2022; 146:332-347. [PMID: 35838031 DOI: 10.1111/ane.13668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/17/2022] [Accepted: 06/24/2022] [Indexed: 12/12/2022]
Abstract
Stroke is a leading cause of death and disability worldwide. Stroke prevention, early diagnosis, and efficient acute treatment are priorities to successfully impact stroke death and disability. Fluid biomarkers may improve stroke differential diagnostic, patient stratification for acute treatment, and post-stroke individualized rehabilitation. In the present work, we characterized the use of stroke animal models in fluid biomarker research through a systematic review of PubMed and Scopus databases, followed by a literature review on the translation to the human stroke care setting and future perspectives in the field. We found increasing numbers of publications but with limited translation to the clinic. Animal studies are very heterogeneous, do not account for several human features present in stroke, and, importantly, only a minority of such studies used human cohorts to validate biomarker findings. Clinical studies have found appealing candidates, both protein and circulating nucleic acids, to contribute to a more personalized stroke care pathway. Still, brain tissue complexity and the fact that different brain pathologies share lesion biomarkers make this task challenging due to biomarker low specificity. Moreover, the study design and lack of validation cohorts may have precluded a formal integration of biomarkers in different steps of stroke diagnosis and treatment. To overcome such issues, recent pivotal studies on biomarker dynamics in individual patients are providing added value to diagnosis and anticipating patients' early prognosis. Presently, the most consistent protein biomarkers for stroke diagnosis and short- and long-term prognosis are associated with tissue damage at neuronal (TAU), axonal (NFL), or astroglial (GFAP and S100β) levels. Most promising nucleic acids are microRNAs (miR), due to their stability in plasma and ease of access. Still, clinical validation and standardized quantitation place them a step behind compared protein as stroke biomarkers. Ultimately, the definition of clinically relevant biomarker panels and optimization of fast and sensitive biomarker measurements in the blood, together with their combination with clinical and neuroimaging data, will pave the way toward personalized stroke care.
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Affiliation(s)
- Alexandre Dias
- Department of Neurology, Centro Hospitalar Universitário do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Lénia Silva
- Department of Neurology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - João Moura
- Department of Neurology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Denis Gabriel
- Department of Neurology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Luis F Maia
- Department of Neurology, Centro Hospitalar Universitário do Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
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12
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Qiao H, Mei J, Yuan K, Zhang K, Zhou F, Tang T, Zhao J. Immune-regulating strategy against rheumatoid arthritis by inducing tolerogenic dendritic cells with modified zinc peroxide nanoparticles. J Nanobiotechnology 2022; 20:323. [PMID: 35836178 PMCID: PMC9281050 DOI: 10.1186/s12951-022-01536-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
In hypoxic dendritic cells (DCs), a low level of Zn2+ can induce the activation of immunogenic DCs (igDCs), thereby triggering an active T-cell response to propel the immune progression of rheumatoid arthritis (RA). This finding indicates the crucial roles of zinc and oxygen homeostasis in DCs during the pathogenesis of RA. However, very few studies have focused on the modulation of zinc and oxygen homeostasis in DCs during RA treatment. Proposed herein is a DC-targeting immune-regulating strategy to induce igDCs into tolerogenic DCs (tDCs) and inhibit subsequent T-cell activation, referred to as ZnO2/Catalase@liposome-Mannose nanoparticles (ZnCM NPs). ZnCM NPs displayed targeted intracellular delivery of Zn2+ and O2 towards igDCs in a pH-responsive manner. After inactivating OTUB1 deubiquitination, the ZnCM NPs promoted CCL5 degradation via NF-κB signalling, thereby inducing the igDC-tDC transition to further inhibit CD4+ T-cell homeostasis. In collagen-induced arthritis (CIA) mice, this nanoimmunoplatform showed significant accumulation in the spleen, where immature DCs (imDCs) differentiated into igDCs. Splenic tDCs were induced to alleviate ankle swelling, improve walking posture and safely inhibit ankle/spleen inflammation. Our work pioneers the combination of DC-targeting nanoplatforms with RA treatments and highlights the significance of zinc and oxygen homeostasis for the immunoregulation of RA by inducing tDCs with modified ZnO2 NPs, which provides novel insight into ion homeostasis regulation for the treatment of immune diseases with a larger variety of distinct metal or nonmetal ions. The DC-targeting immune-regulating nanostrategy was firstly employed to treat RA. The complex immune regulating effects was realized through a portable, convenient and green nanomaterial. Highlighting the significance of zinc and oxygen homeostasis for the immunoregulation of RA by inducing tDCs with modified ZnO2 NPs. Expanding the notion of ion homeostasis regulation with a larger variety of distinct metal or nonmetal ions.
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Affiliation(s)
- Han Qiao
- Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China.,Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jingtian Mei
- Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China.,Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Kai Yuan
- Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China.,Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Kai Zhang
- Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China.,Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Feng Zhou
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, People's Republic of China
| | - Tingting Tang
- Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China. .,Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
| | - Jie Zhao
- Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China. .,Shanghai Key Laboratory of Orthopaedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
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13
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Lai M, Zhang X, Zhou D, Zhang X, Zhu M, Liu Q, Zhang Y, Wang D. Integrating serum proteomics and metabolomics to compare the common and distinct features between acute aggressive ischemic stroke (APIS) and acute non-aggressive ischemic stroke (ANPIS). J Proteomics 2022; 261:104581. [PMID: 35421619 DOI: 10.1016/j.jprot.2022.104581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/02/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023]
Abstract
Understanding common and distinct pathophysiological features between acute progressive ischemic stroke (APIS) and acute non-progressive ischemic stroke (ANPIS) is a prerequisite to making clear the mechanism to determine the prognosis of acute ischemic stroke (AIS). Here, we recruited three independent sets of subjects, all of which included the APIS, ANPIS, and control groups. They were used for serum proteomic and metabolomic analyses, and validation of the critical pathophysiological processes and potential biomarkers of APIS, respectively. Results showed that there were both common and distinct metabolome and proteome between APIS and ANPIS. APIS and ANPIS shared basic processes of AIS in inflammation and oxidative stress response. Coagulation and lipid metabolism disorder, activation of the complement system, and inflammation may enhance with each other in the symptom worsening of APIS. The contents of serum amyloid A1 (SAA1) and S100 calcium-binding protein A9 (S100-A9) in the validation set confirmed the key pathophysiological processes indicated by omics data; they also jointly conferred a moderate value to distinguish APIS from ANPIS. Collectively, disturbance in coagulation and lipid metabolism, complement activation, and inflammation may be synergistically involved in symptom deterioration in APIS. SAA1 and S100-A9 serve as a potential biomarker panel to distinguish APIS from ANPIS. THE SIGNIFICANCE: In this study, we integrated serum proteomics and metabolomics to explore the similarities and differences in pathophysiological processes between APIS and ANPIS. The global metabolic networks have been constructed, and the crucial common pathophysiological processes and the key distinct pathophysiological features between APIS and ANPIS were investigated based on the differentially expressed proteins and metabolites (DEPs/DEMs). Furthermore, pivotal serum proteins (SAA1 and S100A9) were detected in a dependent set to validate the key pathophysiological characteristics, as well as to assess the possibility of them being used as a biomarker panel. Taken together, the multi-omics integration strategy used in this clinical study shows potential to comprehensively interpret and compare the pathophysiological processes of AIS in various conditions, as well as to screen a reliable new biomarker panel.
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Affiliation(s)
- Minchao Lai
- Department of Neurology, First Affiliated Hospital of Shantou University Medical College, China
| | - Xiaojun Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Danya Zhou
- Department of Forensic Medicine, Shantou, China; School of Basic Medicine, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | | | | | - Qingxian Liu
- Department of Nursing, Shantou University Medical College (SUMC), China
| | - Ye Zhang
- Department of Forensic Medicine, Shantou, China
| | - Dian Wang
- Department of Forensic Medicine, Shantou, China.
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14
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Sonawane AR, Aikawa E, Aikawa M. Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:873582. [PMID: 35665246 PMCID: PMC9160390 DOI: 10.3389/fcvm.2022.873582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/19/2022] [Indexed: 01/18/2023] Open
Abstract
Cardiovascular diseases (CVD) are diverse disorders affecting the heart and vasculature in millions of people worldwide. Like other fields, CVD research has benefitted from the deluge of multiomics biomedical data. Current CVD research focuses on disease etiologies and mechanisms, identifying disease biomarkers, developing appropriate therapies and drugs, and stratifying patients into correct disease endotypes. Systems biology offers an alternative to traditional reductionist approaches and provides impetus for a comprehensive outlook toward diseases. As a focus area, network medicine specifically aids the translational aspect of in silico research. This review discusses the approach of network medicine and its application to CVD research.
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Affiliation(s)
- Abhijeet Rajendra Sonawane
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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15
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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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16
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Skvortsov VS, Ivanova YO, Voronina AI. [The bioinformatic identification of proteins with varying levels of post-translational modifications in experimental ischemic stroke in mice]. BIOMEDITSINSKAIA KHIMIIA 2021; 67:475-484. [PMID: 34964441 DOI: 10.18097/pbmc20216706475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The experimental data obtained by Simats A. et al. (Molecular and Cellular Proteomics, 2020, 19(12), 1921-1936) was analysed using a bioinformatic approach. Original experimental results available in the ProteomeXchange database were obtained using a comprehensive multidomain approach to identify potential blood biomarkers in ischemic stroke in mice. The identification of peptides with post-translational modification (PTM) was performed by us using the raw data (accession code PXD016538). Only phosphorylation and deamination were considered as PTMs. Different combinations of data sets (ischemic tissue with intact tissue, ischemic tissue with control taken from mice after sham surgery, etc.) were compared both in terms of the ratio of abundance for the modified peptide to the unmodified variant and in terms of absolute values of abundance. The most likely change in precisely PTM levels was shown for 27 proteins, which include dynamin, glycogen phosphorylase and 70 kDa heat shock protein.
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Affiliation(s)
| | - Ya O Ivanova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Voronina
- Institute of Biomedical Chemistry, Moscow, Russia
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17
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Multi-Omics Approach to Elucidate Cerebrospinal Fluid Changes in Dogs with Intervertebral Disc Herniation. Int J Mol Sci 2021; 22:ijms222111678. [PMID: 34769107 PMCID: PMC8583948 DOI: 10.3390/ijms222111678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
Herniation of the intervertebral disc (IVDH) is the most common cause of neurological and intervertebral disc degeneration-related diseases. Since the disc starts to degenerate before it can be observed by currently available diagnostic methods, there is an urgent need for novel diagnostic approaches. To identify molecular networks and pathways which may play important roles in intervertebral disc herniation, as well as to reveal the potential features which could be useful for monitoring disease progression and prognosis, multi-omics profiling, including high-resolution liquid chromatography-mass spectrometry (LC-MS)-based metabolomics and tandem mass tag (TMT)-based proteomics was performed. Cerebrospinal fluid of nine dogs with IVDH and six healthy controls were used for the analyses, and an additional five IVDH samples were used for proteomic data validation. Furthermore, multi-omics data were integrated to decipher a complex interaction between individual omics layers, leading to an improved prediction model. Together with metabolic pathways related to amino acids and lipid metabolism and coagulation cascades, our integromics prediction model identified the key features in IVDH, namely the proteins follistatin Like 1 (FSTL1), secretogranin V (SCG5), nucleobindin 1 (NUCB1), calcitonin re-ceptor-stimulating peptide 2 precursor (CRSP2) and the metabolites N-acetyl-D-glucosamine and adenine, involved in neuropathic pain, myelination, and neurotransmission and inflammatory response, respectively. Their clinical application is to be further investigated. The utilization of a novel integrative interdisciplinary approach may provide new opportunities to apply innovative diagnostic and monitoring methods as well as improve treatment strategies and personalized care for patients with degenerative spinal disorders.
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18
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Integrative Multi-omics Analysis to Characterize Human Brain Ischemia. Mol Neurobiol 2021; 58:4107-4121. [PMID: 33939164 DOI: 10.1007/s12035-021-02401-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/21/2021] [Indexed: 01/14/2023]
Abstract
Stroke is a major cause of death and disability. A better comprehension of stroke pathophysiology is fundamental to reduce its dramatic outcome. The use of high-throughput unbiased omics approaches and the integration of these data might deepen the knowledge of stroke at the molecular level, depicting the interaction between different molecular units. We aimed to identify protein and gene expression changes in the human brain after ischemia through an integrative approach to join the information of both omics analyses. The translational potential of our results was explored in a pilot study with blood samples from ischemic stroke patients. Proteomics and transcriptomics discovery studies were performed in human brain samples from six deceased stroke patients, comparing the infarct core with the corresponding contralateral brain region, unveiling 128 proteins and 2716 genes significantly dysregulated after stroke. Integrative bioinformatics analyses joining both datasets exposed canonical pathways altered in the ischemic area, highlighting the most influential molecules. Among the molecules with the highest fold-change, 28 genes and 9 proteins were selected to be validated in five independent human brain samples using orthogonal techniques. Our results were confirmed for NCDN, RAB3C, ST4A1, DNM1L, A1AG1, A1AT, JAM3, VTDB, ANXA1, ANXA2, and IL8. Finally, circulating levels of the validated proteins were explored in ischemic stroke patients. Fluctuations of A1AG1 and A1AT, both up-regulated in the ischemic brain, were detected in blood along the first week after onset. In summary, our results expand the knowledge of ischemic stroke pathology, revealing key molecules to be further explored as biomarkers and/or therapeutic targets.
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