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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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2
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Liang Y, Feng Q, Wang Z. Mass Spectrometry Imaging as a New Method: To Reveal the Pathogenesis and the Mechanism of Traditional Medicine in Cerebral Ischemia. Front Pharmacol 2022; 13:887050. [PMID: 35721195 PMCID: PMC9204101 DOI: 10.3389/fphar.2022.887050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Mass spectrometry imaging (MSI) can describe the spatial distribution of molecules in various complex biological samples, such as metabolites, lipids, peptides and proteins in a comprehensive way, and can provide highly relevant supplementary information when combined with other molecular imaging techniques and chromatography techniques, so it has been used more and more widely in biomedical research. The application of mass spectrometry imaging in neuroscience is developing. It is very advantageous and necessary to use MSI to study various pathophysiological processes involved in brain injury and functional recovery during cerebral ischemia. Therefore, this paper introduces the techniques of mass spectrometry, including the principle of mass spectrometry, the acquisition and preparation of imaging samples, the commonly used ionization techniques, and the optimization of the current applied methodology. Furthermore, the research on the mechanism of cerebral ischemia by mass spectrometry was reviewed, such as phosphatidylcholine involved, dopamine, spatial distribution and level changes of physiological substances such as ATP in the Krebs cycle; The characteristics of mass spectrometry imaging as one of the methods of metabolomics in screening biomarkers related to cerebral ischemia were analyzed the advantages of MSI in revealing drug distribution and the mechanism of traditional drugs were summarized, and the existing problems of MSI were also analyzed and relevant suggestions were put forward.
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Affiliation(s)
- Yan Liang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiaoqiao Feng
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhang Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Ethnomedicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Zhang Wang,
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3
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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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4
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Kim JA, Vetrivel P, Kim SM, Ha SE, Kim HH, Bhosale PB, Heo JD, Lee WS, Senthil K, Kim GS. Quantitative Proteomics Analysis for the Identification of Differential Protein Expression in Calf Muscles between Young and Old SD Rats Using Mass Spectrometry. ACS OMEGA 2021; 6:7422-7433. [PMID: 33778255 PMCID: PMC7992086 DOI: 10.1021/acsomega.0c05821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 05/04/2023]
Abstract
Aging is associated with loss of muscle mass and strength that leads to a condition termed sarcopenia. Impaired conditions, morbidity, and malnutrition are the factors of devaluation of muscle fibers in aged animals. Satellite cells play an important role in maintaining muscle homeostasis during tissue regeneration and repair. Proteomic profiling on the skeletal muscle tissues of different age group rats helps to determine the differentially expressed (DE) proteins, which may eventually lead to the development of biomarkers in treating the conditions of sarcopenia. In this study, nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) analysis was implemented in the calf tissues of young and old groups of rats. The mass spectrometry (MS) analysis revealed the presence of 335 differentially expressed proteins between the two different age conditions, among which those based on log-fold change 25 proteins were upregulated and 77 were downregulated. The protein-protein interaction network analysis revealed 18 upregulated proteins with three distinct interconnected networks and 57 downregulated proteins with two networks. Further, gene ontology (GO) enrichment analysis showed the biological process, cellular component, and molecular function of the differential proteins. Pathway enrichment analysis of the DE proteins identified nine significantly enriched pathways with a list of eight significant genes (Cryab, Hspb2, Acat1, Ak1, Adssl1, Anxa5, Gys1, Ogdh, Gc, and Adssl1). Quantification of significant genes by quantitative real-time polymerase chain reaction (qRT-PCR) confirmed the downregulation at the mRNA level. Western blot analysis of their protein expression showed concordant results on two candidate proteins (Ogdh and annexin 5) confirming their differential regulation between the two age groups of rats. Thus, these proteomic approaches on young and aged rats provide insights into the development of protein targets in the treatment of sarcopenia (muscle loss).
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Affiliation(s)
- Jin A. Kim
- Department
of Physical Therapy, International University
of Korea, Jinju 52833, Republic of Korea
| | - Preethi Vetrivel
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Seong Min Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Sang Eun Ha
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Hun Hwan Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
| | - Jeong Doo Heo
- Gyeongnam
Department of Environment Toxicology and Chemistry, Toxicity Screening
Research Center, Korea Institute of Toxicology, Munsan-eup, Jinju, Gyeongnam 52834, Republic of Korea
| | - Won Sup Lee
- Department
of Internal Medicine, Institute of Health Sciences, Gyeongsang National
University Hospital, Gyeongsang National
University School of Medicine, Jinju 660-702, Republic
of Korea
| | - Kalaiselvi Senthil
- Department
of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for
Women, Coimbatore 641043, India
| | - Gon Sup Kim
- Research
Institute of Life Science and College of Veterinary Medicine, Gyeongsang National University, Gazwa, Jinju 52828, Republic of Korea
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5
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Gao Y, Han X, Wei L, Yuan Y, Zhao C, Zhang M, Wang Z, Li X, Xu W. Study on the differential proteomics of rat hippocampal mitochondria during deep hypothermic circulatory arrest. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:346. [PMID: 33708973 PMCID: PMC7944285 DOI: 10.21037/atm-21-95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/10/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND This study aimed to investigate the effect of deep hypothermic circulatory arrest (DHCA) on rat hippocampal mitochondrial protein expression and its differential proteomics, and explore the potential mechanisms behind the effect. METHODS We used internal jugular vein reflux and tail artery perfusion methods to establish the rat cardiopulmonary bypass (CPB) model. Rats were dissected to obtain the hippocampus, and the hippocampal mitochondria were purified. The mitochondrial morphology and the mitochondrial marker cytochrome C oxidase (COX) qualitatively examined via transmission electron microscopy and western-blot analysis, respectively. The qualified samples were subjected to isobaric tags for relative and absolute quantification (iTRAQ); we then established the CPB model again to obtain the rat hippocampus for cryoultramicrotomy, and used immunofluorescent double staining technique to qualitatively and semi-quantitatively verify two representative differentially expressed proteins. RESULTS By searching the Mascot 2.2 database, 29 differentially expressed proteins were obtained with statistical significance, including 21 known proteins and 8 unknowns. The expression level of COX and monoacylglycerol lipase did not change significantly (P>0.05) during the hyperacute phase; however, their intracellular localizations were altered. CONCLUSIONS DHCA induced the differential expression of 29 rat hippocampal mitochondrial proteins, some of which had altered intracellular localization. We speculated that the localized alteration of these proteins is one of the neuroprotection mechanisms that occurs during DHCA.
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Affiliation(s)
- Yongjun Gao
- Department of Neurosurgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiuli Han
- Department of Stomatology, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Liang Wei
- Department of Neurosurgery, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yong Yuan
- Department of Neurosurgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chengbin Zhao
- Department of Neurosurgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ming Zhang
- Department of Neurosurgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zheng Wang
- Department of Neurosurgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuhui Li
- Department of Neurosurgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wei Xu
- Department of Neurosurgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
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6
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Saponaro F, Kim JH, Chiellini G. Transthyretin Stabilization: An Emerging Strategy for the Treatment of Alzheimer's Disease? Int J Mol Sci 2020; 21:ijms21228672. [PMID: 33212973 PMCID: PMC7698513 DOI: 10.3390/ijms21228672] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/14/2020] [Accepted: 11/15/2020] [Indexed: 12/27/2022] Open
Abstract
Transthyretin (TTR), previously named prealbumin is a plasma protein secreted mainly by the liver and choroid plexus (CP) that is a carrier for thyroid hormones (THs) and retinol (vitamin A). The structure of TTR, with four monomers rich in β-chains in a globular tetrameric protein, accounts for the predisposition of the protein to aggregate in fibrils, leading to a rare and severe disease, namely transthyretin amyloidosis (ATTR). Much effort has been made and still is required to find new therapeutic compounds that can stabilize TTR ("kinetic stabilization") and prevent the amyloid genetic process. Moreover, TTR is an interesting therapeutic target for neurodegenerative diseases due to its recognized neuroprotective properties in the cognitive impairment context and interestingly in Alzheimer's disease (AD). Much evidence has been collected regarding the neuroprotective effects in AD, including through in vitro and in vivo studies as well as a wide range of clinical series. Despite this supported hypothesis of neuroprotection for TTR, the mechanisms are still not completely clear. The aim of this review is to highlight the most relevant findings on the neuroprotective role of TTR, and to summarize the recent progress on the development of TTR tetramer stabilizers.
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Affiliation(s)
| | - Jin Hae Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea;
| | - Grazia Chiellini
- Department of Pathology, University of Pisa, 56100 Pisa, Italy;
- Correspondence:
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7
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Li H, You W, Li X, Shen H, Chen G. Proteomic-Based Approaches for the Study of Ischemic Stroke. Transl Stroke Res 2019; 10:601-606. [PMID: 31278685 DOI: 10.1007/s12975-019-00716-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Wanchun You
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Haitao Shen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China.
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8
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Goulding DR, Nikolova VD, Mishra L, Zhuo L, Kimata K, McBride SJ, Moy SS, Harry GJ, Garantziotis S. Inter-α-inhibitor deficiency in the mouse is associated with alterations in anxiety-like behavior, exploration and social approach. GENES, BRAIN, AND BEHAVIOR 2019; 18:e12505. [PMID: 29987918 PMCID: PMC6328341 DOI: 10.1111/gbb.12505] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 12/30/2022]
Abstract
In recent years, several genome-wide association studies have identified candidate regions for genetic susceptibility in major mood disorders. Most notable are regions in a locus in chromosome 3p21, encompassing the genes NEK4-ITIH1-ITIH3-ITIH4. Three of these genes represent heavy chains of the composite protein inter-α-inhibitor (IαI). In order to further establish associations of these genes with mood disorders, we evaluated behavioral phenotypes in mice deficient in either Ambp/bikunin, which is necessary for functional ITIH1 and ITIH3 complexes, or in Itih4, the gene encoding the heavy chain Itih4. We found that loss of Itih4 had no effect on the behaviors tested, but loss of Ambp/bikunin led to increased anxiety-like behavior in the light/dark and open field tests and reduced exploratory activity in the elevated plus maze, light/dark preference and open field tests. Ambp/bikunin knockout mice also exhibited a sex-dependent exaggeration of acoustic startle responses, alterations in social approach during a three-chamber choice test, and an elevated fear conditioning response. These results provide experimental support for the role of ITIH1/ITIH3 in the development of mood disorders.
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Affiliation(s)
- David R Goulding
- Comparative Medicine Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Viktoriya D Nikolova
- Carolina Institute for Developmental Disabilities and Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery, Georgetown University, Washington, District of Columbia
| | - Lisheng Zhuo
- Multidisciplinary Pain Center and the Research Creation Support Center, Aichi Medical University, Nagakute, Japan
| | - Koji Kimata
- Multidisciplinary Pain Center and the Research Creation Support Center, Aichi Medical University, Nagakute, Japan
| | | | - Sheryl S Moy
- Carolina Institute for Developmental Disabilities and Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - G J Harry
- Neurotoxicology Group, National Toxicology Program Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Stavros Garantziotis
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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9
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Zhang Z, Yan Q, Guo J, Wang X, Yuan W, Wang L, Chen L, Su G, Wang M. A plasma proteomics method reveals links between ischemic stroke and MTHFR C677T genotype. Sci Rep 2017; 7:13390. [PMID: 29042595 PMCID: PMC5645471 DOI: 10.1038/s41598-017-13542-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/26/2017] [Indexed: 02/02/2023] Open
Abstract
Methylene Tetrahydrofolate Reductase (MTHFR) catalyzes the conversion of methylene tetrahydrofolate to methylte trahydrofolate. The 677th nucleotide of the MTHFR gene is often regarded as a risk factor of cardiovascular disease. Previous studies demonstrated an elevated risk of ischemic stroke with the MTHFR677TT genotype. In this study, we employed a plasma proteomics method to investigate the connection between the polymorphism of the target nucleotide and stroke. In total, 28 protein spots were differentially expressed between the two groups, and of which, 25 protein spots were up-regulated and 3 were down-regulated. Five randomly selected spots were successfully identified as Haptoglobin (HPT) and Transferrin (TRFE). A functional analysis indicated that most of the differential expressed proteins (DEPs) were related to the inflammatory immune response. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEPs were involved in the complement cascade reaction. Meanwhile, protein-protein interactions (PPIs) analysis highlighted the novel association between the C677T MTHFR genotype and Vitamin D binding protein (DBP), which was confirmed by a molecular genetic analysis. The results suggested that the phenotype of the MTHFR might be associated with multiple proteins that have a synergistic effect, which might be related to the mechanism of ischemic stroke.
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Affiliation(s)
- Zhenchang Zhang
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Qi Yan
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Jia Guo
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Xueping Wang
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Wei Yuan
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Lei Wang
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Lixia Chen
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Gang Su
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.
| | - Manxia Wang
- Department of Neurology, the Second Hospital of Lanzhou University, Lanzhou, 730030, China.
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10
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Glushakov AV, Arias RA, Tolosano E, Doré S. Age-Dependent Effects of Haptoglobin Deletion in Neurobehavioral and Anatomical Outcomes Following Traumatic Brain Injury. Front Mol Biosci 2016; 3:34. [PMID: 27486583 PMCID: PMC4949397 DOI: 10.3389/fmolb.2016.00034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/05/2016] [Indexed: 12/11/2022] Open
Abstract
Cerebral hemorrhages are common features of traumatic brain injury (TBI) and their presence is associated with chronic disabilities. Recent clinical and experimental evidence suggests that haptoglobin (Hp), an endogenous hemoglobin-binding protein most abundant in blood plasma, is involved in the intrinsic molecular defensive mechanism, though its role in TBI is poorly understood. The aim of this study was to investigate the effects of Hp deletion on the anatomical and behavioral outcomes in the controlled cortical impact model using wildtype (WT) C57BL/6 mice and genetically modified mice lacking the Hp gene (Hp(-∕-)) in two age cohorts [2-4 mo-old (young adult) and 7-8 mo-old (older adult)]. The data obtained suggest age-dependent significant effects on behavioral and anatomical TBI outcomes and recovery from injury. Moreover, in the adult cohort, neurological deficits in Hp(-∕-) mice at 24 h were significantly improved compared to WT, whereas there were no significant differences in brain pathology between these genotypes. In contrast, in the older adult cohort, Hp(-∕-) mice had significantly larger lesion volumes compared to WT, but neurological deficits were not significantly different. Immunohistochemistry for ionized calcium-binding adapter molecule 1 (Iba1) and glial fibrillary acidic protein (GFAP) revealed significant differences in microglial and astrocytic reactivity between Hp(-∕-) and WT in selected brain regions of the adult but not the older adult-aged cohort. In conclusion, the data obtained in the study provide clarification on the age-dependent aspects of the intrinsic defensive mechanisms involving Hp that might be involved in complex pathways differentially affecting acute brain trauma outcomes.
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Affiliation(s)
- Alexander V Glushakov
- Department of Anesthesiology, Center for Translational Research in Neurodegenerative Disease, University of Florida College of Medicine Gainesville, FL, USA
| | - Rodrigo A Arias
- Department of Anesthesiology, Center for Translational Research in Neurodegenerative Disease, University of Florida College of Medicine Gainesville, FL, USA
| | - Emanuela Tolosano
- Departments of Molecular Biotechnology and Health Sciences, University of Torino Torino, Italy
| | - Sylvain Doré
- Department of Anesthesiology, Center for Translational Research in Neurodegenerative Disease, University of Florida College of MedicineGainesville, FL, USA; Departments of Anesthesiology, Neurology, Psychiatry, Psychology, Pharmaceutics and Neuroscience, University of Florida College of MedicineGainesville, FL, USA
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11
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Ménoret A, Crocker SJ, Rodriguez A, Rathinam VA, Clark RB, Vella AT. Transition from identity to bioactivity-guided proteomics for biomarker discovery with focus on the PF2D platform. Proteomics Clin Appl 2015. [PMID: 26201056 DOI: 10.1002/prca.201500029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic strategies provide a valuable tool kit to identify proteins involved in diseases. With recent progress in MS technology, high throughput proteomics has accelerated protein identification for potential biomarkers. Numerous biomarker candidates have been identified in several diseases, and many are common among pathologies. An overall strategy that could complement and strengthen the search for biomarkers is combining protein identity with biological outcomes. This review describes an emerging framework of bridging bioactivity to protein identity, exploring the possibility that some biomarkers will have a mechanistic role in the disease process. A review of pulmonary, cardiovascular, and CNS biomarkers will be discussed to demonstrate the utility of combining bioactivity with identification as a means to not only find meaningful biomarkers, but also to uncover functional mediators of disease.
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Affiliation(s)
- Antoine Ménoret
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Stephen J Crocker
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT, USA
| | - Annabelle Rodriguez
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Vijay A Rathinam
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Robert B Clark
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Anthony T Vella
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
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12
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Connaughton SM, Wheeler JX, Vitková E, Minor P, Schepelmann S. In vitro and in vivo growth alter the population dynamic and properties of a Jeryl Lynn mumps vaccine. Vaccine 2015; 33:4586-93. [PMID: 26187256 PMCID: PMC4550476 DOI: 10.1016/j.vaccine.2015.06.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/26/2015] [Accepted: 06/27/2015] [Indexed: 11/26/2022]
Abstract
Mumps vaccines are live attenuated viruses. They are known to vary in effectiveness, degree of attenuation and adverse event profile. However, the underlying reasons are poorly understood. We studied two closely related mumps vaccines which originate from the same attenuated Jeryl Lynn-5 strain but have different efficacies. Jeryl Lynn-Canine Kidney (JL-CK), produced on primary canine kidney cells, is less effective than RIT4385, which is produced on chicken embryo fibroblasts. JL-CK and RIT4385 could be distinguished by a number of in vitro and in vivo properties. JL-CK produced heterogeneous, generally smaller plaques than RIT4385, but gave 100-fold higher titres when grown in cells and showed a higher degree of hydrocephalus formation in neonatal rat brains. Sanger sequencing of JL-CK identified 14 regions of heterogeneity throughout the genome. Plaque purification of JL-CK demonstrated the presence of five different Jeryl Lynn-5 variants encompassing the 14 mutations. One JL-CK mutation was associated with a small plaque phenotype, the effects of the others in vitro or in vivo were less clear. Only 4% of the JL-CK population corresponded to the parental Jeryl Lynn-5 strain. Next generation sequencing of JL-CK and virus before and after growth in cell lines or neonatal rat brains showed that propagation in vitro or in vivo altered the population dramatically. Our findings indicate that growth of JL-CK in primary canine kidney cells resulted in the selection of a mixture of mumps virus variants that have different biological properties compared to the parent Jeryl Lynn-5 virus. We also report three previously unknown heterogenic regions within the N gene of the RIT4385 vaccine.
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Affiliation(s)
- Sarah M Connaughton
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom.
| | - Jun X Wheeler
- Laboratory for Molecular Structure, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom.
| | - Eva Vitková
- State Institute for Drug Control, Srobarova 48, 10041 Prague 10, Czech Republic
| | - Philip Minor
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom.
| | - Silke Schepelmann
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom.
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13
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Sharma R, Gowda H, Chavan S, Advani J, Kelkar D, Kumar GSS, Bhattacharjee M, Chaerkady R, Prasad TSK, Pandey A, Nagaraja D, Christopher R. Proteomic Signature of Endothelial Dysfunction Identified in the Serum of Acute Ischemic Stroke Patients by the iTRAQ-Based LC–MS Approach. J Proteome Res 2015; 14:2466-79. [DOI: 10.1021/pr501324n] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rakesh Sharma
- Department
of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
- Department of Biochemistry, Faculty of Medicine, The University of Hong Kong, Hong Kong
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong
| | - Harsha Gowda
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Sandip Chavan
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - Jayshree Advani
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - Dhanashree Kelkar
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - G. S. Sameer Kumar
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Mitali Bhattacharjee
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Raghothama Chaerkady
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - T. S. Keshava Prasad
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
- Manipal University, Manipal 576 104, India
| | - Akhilesh Pandey
- Institute
of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Dindagur Nagaraja
- Department
of Neurology, Dharwad Institute of Mental Health and Neuro Sciences, Dharwad 580001, India
| | - Rita Christopher
- Department
of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
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14
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Chen YH, Chiang YH, Ma HI. Analysis of spatial and temporal protein expression in the cerebral cortex after ischemia-reperfusion injury. J Clin Neurol 2014; 10:84-93. [PMID: 24829593 PMCID: PMC4017024 DOI: 10.3988/jcn.2014.10.2.84] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 01/26/2023] Open
Abstract
Background and Purpose Hypoxia, or ischemia, is a common cause of neurological deficits in the elderly. This study elucidated the mechanisms underlying ischemia-induced brain injury that results in neurological sequelae. Methods Cerebral ischemia was induced in male Sprague-Dawley rats by transient ligation of the left carotid artery followed by 60 min of hypoxia. A two-dimensional differential proteome analysis was performed using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry to compare changes in protein expression on the lesioned side of the cortex relative to that on the contralateral side at 0, 6, and 24 h after ischemia. Results The expressions of the following five proteins were up-regulated in the ipsilateral cortex at 24 h after ischemia-reperfusion injury compared to the contralateral (i.e., control) side: aconitase 2, neurotensin-related peptide, hypothetical protein XP-212759, 60-kDa heat-shock protein, and aldolase A. The expression of one protein, dynamin-1, was up-regulated only at the 6-h time point. The level of 78-kDa glucose-regulated protein precursor on the lesioned side of the cerebral cortex was found to be high initially, but then down-regulated by 24 h after the induction of ischemia-reperfusion injury. The expressions of several metabolic enzymes and translational factors were also perturbed soon after brain ischemia. Conclusions These findings provide insights into the mechanisms underlying the neurodegenerative events that occur following cerebral ischemia.
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Affiliation(s)
- Yuan-Hao Chen
- Department of Neurological Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Yung-Hsiao Chiang
- Section of Neurosurgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan, ROC
| | - Hsin-I Ma
- Department of Neurological Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
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15
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Chen CP, Hsu CC, Pei YC, Chen RL, Zhou S, Shen HC, Lin SC, Tsai WC. Changes of synovial fluid protein concentrations in supra-patellar bursitis patients after the injection of different molecular weights of hyaluronic acid. Exp Gerontol 2014; 52:30-5. [DOI: 10.1016/j.exger.2014.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 01/16/2023]
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16
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Vieira M, Saraiva MJ. Transthyretin: a multifaceted protein. Biomol Concepts 2014; 5:45-54. [DOI: 10.1515/bmc-2013-0038] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/15/2014] [Indexed: 11/15/2022] Open
Abstract
AbstractTransthyretin is a highly conserved homotetrameric protein, mainly synthetized by the liver and the choroid plexus of brain. The carrier role of TTR is well-known; however, many other functions have emerged, namely in the nervous system. Behavior, cognition, neuropeptide amidation, neurogenesis, nerve regeneration, axonal growth and 14-3-3ζ metabolism are some of the processes where TTR has an important role. TTR aggregates are responsible for many amyloidosis such as familial amyloidotic polyneuropathy and cardiomyopathy. Normal TTR can also aggregate and deposit in the heart of old people and in preeclampsia placental tissue. Differences in TTR levels have been found in several neuropathologies, but its neuroprotective role, until now, was described in ischemia and Alzheimer’s disease. The aim of this review is to stress the relevance of TTR, besides its well-known role on transport of thyroxine and retinol-binding protein.
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17
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Laborde CM, Mourino-Alvarez L, Akerstrom F, Padial LR, Vivanco F, Gil-Dones F, Barderas MG. Potential blood biomarkers for stroke. Expert Rev Proteomics 2013; 9:437-49. [PMID: 22967080 DOI: 10.1586/epr.12.33] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Stroke is one of the most common causes of death worldwide and a major cause of acquired disability in adults. Despite advances in research during the last decade, prevention and treatment strategies still suffer from significant limitations, and therefore new theoretical and technical approaches are required. Technological advances in the proteomic and metabolomic areas, during recent years, have permitted a more effective search for novel biomarkers and therapeutic targets that may allow for effective risk stratification and early diagnosis with subsequent rapid treatment. This review provides a comprehensive overview of the latest candidate proteins and metabolites proposed as new potential biomarkers in stroke.
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Affiliation(s)
- Carlos M Laborde
- Laboratory of Vascular Pathophysiology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
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