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Mansueto G, Fusco G, Colonna G. A Tiny Viral Protein, SARS-CoV-2-ORF7b: Functional Molecular Mechanisms. Biomolecules 2024; 14:541. [PMID: 38785948 PMCID: PMC11118181 DOI: 10.3390/biom14050541] [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: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study presents the interaction with the human host metabolism of SARS-CoV-2 ORF7b protein (43 aa), using a protein-protein interaction network analysis. After pruning, we selected from BioGRID the 51 most significant proteins among 2753 proven interactions and 1708 interactors specific to ORF7b. We used these proteins as functional seeds, and we obtained a significant network of 551 nodes via STRING. We performed topological analysis and calculated topological distributions by Cytoscape. By following a hub-and-spoke network architectural model, we were able to identify seven proteins that ranked high as hubs and an additional seven as bottlenecks. Through this interaction model, we identified significant GO-processes (5057 terms in 15 categories) induced in human metabolism by ORF7b. We discovered high statistical significance processes of dysregulated molecular cell mechanisms caused by acting ORF7b. We detected disease-related human proteins and their involvement in metabolic roles, how they relate in a distorted way to signaling and/or functional systems, in particular intra- and inter-cellular signaling systems, and the molecular mechanisms that supervise programmed cell death, with mechanisms similar to that of cancer metastasis diffusion. A cluster analysis showed 10 compact and significant functional clusters, where two of them overlap in a Giant Connected Component core of 206 total nodes. These two clusters contain most of the high-rank nodes. ORF7b acts through these two clusters, inducing most of the metabolic dysregulation. We conducted a co-regulation and transcriptional analysis by hub and bottleneck proteins. This analysis allowed us to define the transcription factors and miRNAs that control the high-ranking proteins and the dysregulated processes within the limits of the poor knowledge that these sectors still impose.
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Affiliation(s)
- Gelsomina Mansueto
- Dipartimento di Scienze Mediche e Chirurgiche Avanzate, Università della Campania, L. Vanvitelli, 80138 Naples, Italy;
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Giovanni Colonna
- Medical Informatics AOU, Università della Campania, L. Vanvitelli, 80138 Naples, Italy
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2
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Tukacs V, Mittli D, Hunyadi-Gulyás É, Darula Z, Juhász G, Kardos J, Kékesi KA. Comparative analysis of hippocampal extracellular space uncovers widely altered peptidome upon epileptic seizure in urethane-anaesthetized rats. Fluids Barriers CNS 2024; 21:6. [PMID: 38212833 PMCID: PMC10782730 DOI: 10.1186/s12987-024-00508-w] [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: 08/24/2023] [Accepted: 10/31/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND The brain extracellular fluid (ECF), composed of secreted neurotransmitters, metabolites, peptides, and proteins, may reflect brain processes. Analysis of brain ECF may provide new potential markers for synaptic activity or brain damage and reveal additional information on pathological alterations. Epileptic seizure induction is an acute and harsh intervention in brain functions, and it can activate extra- and intracellular proteases, which implies an altered brain secretome. Thus, we applied a 4-aminopyridine (4-AP) epilepsy model to study the hippocampal ECF peptidome alterations upon treatment in rats. METHODS We performed in vivo microdialysis in the hippocampus for 3-3 h of control and 4-AP treatment phase in parallel with electrophysiology measurement. Then, we analyzed the microdialysate peptidome of control and treated samples from the same subject by liquid chromatography-coupled tandem mass spectrometry. We analyzed electrophysiological and peptidomic alterations upon epileptic seizure induction by two-tailed, paired t-test. RESULTS We detected 2540 peptides in microdialysate samples by mass spectrometry analysis; and 866 peptides-derived from 229 proteins-were found in more than half of the samples. In addition, the abundance of 322 peptides significantly altered upon epileptic seizure induction. Several proteins of significantly altered peptides are neuropeptides (Chgb) or have synapse- or brain-related functions such as the regulation of synaptic vesicle cycle (Atp6v1a, Napa), astrocyte morphology (Vim), and glutamate homeostasis (Slc3a2). CONCLUSIONS We have detected several consequences of epileptic seizures at the peptidomic level, as altered peptide abundances of proteins that regulate epilepsy-related cellular processes. Thus, our results indicate that analyzing brain ECF by in vivo microdialysis and omics techniques is useful for monitoring brain processes, and it can be an alternative method in the discovery and analysis of CNS disease markers besides peripheral fluid analysis.
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Affiliation(s)
- Vanda Tukacs
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Dániel Mittli
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Hungarian Research Network (HUN-REN), Temesvári Körút 62, Szeged, 6726, Hungary
| | - Zsuzsanna Darula
- Laboratory of Proteomics Research, Biological Research Centre, Hungarian Research Network (HUN-REN), Temesvári Körút 62, Szeged, 6726, Hungary
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, Temesvári Körút 62, Szeged, 6726, Hungary
| | - Gábor Juhász
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- InnoScience Hungary Ltd., Bátori Út 9, Mátranovák, 3142, Hungary
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Katalin Adrienna Kékesi
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
- InnoScience Hungary Ltd., Bátori Út 9, Mátranovák, 3142, Hungary.
- Department of Physiology and Neurobiology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
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Rabaglino MB, Wakabayashi M, Pearson JT, Jensen LJ. Effect of age on the vascular proteome in middle cerebral arteries and mesenteric resistance arteries in mice. Mech Ageing Dev 2021; 200:111594. [PMID: 34756926 DOI: 10.1016/j.mad.2021.111594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 10/20/2022]
Abstract
Aging is associated with hypertension and brain blood flow dysregulation, which are major risk factors for cardiovascular and neurodegenerative diseases. Structural remodeling, endothelial dysfunction, or hypercontractility of resistance vessels may cause increased total peripheral resistance and hypertension. Recent studies showed that G protein- and RhoA/Rho-kinase pathways are involved in increased mean arterial pressure (MAP) and arterial tone in middle-aged mice. We aimed to characterize the age-dependent changes in the vascular proteome in normal laboratory mice using mass spectrometry and bioinformatics analyses on middle cerebral arteries and mesenteric resistance arteries from young (3 months) vs. middle-aged (14 months) mice. In total, 31 proteins were significantly affected by age whereas 172 proteins were differentially expressed by vessel type. Hierarchical clustering revealed that 207 proteins were significantly changed or clustered by age. Vitamin B6 pathway, Biosynthesis of antibiotics, Regulation of actin cytoskeleton and Endocytosis were the top enriched KEGG pathways by age. Several proteins in the RhoA/Rho-kinase pathway changed in a manner consistent with hypertension and dysregulation of cerebral perfusion. Although aging had a less profound effect than vessel type on the resistance artery proteome, regulation of actin cytoskeleton, including the RhoA/Rho-kinase pathway, is an important target for age-dependent hypertension.
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Affiliation(s)
- Maria Belen Rabaglino
- Dept. of Applied Mathematics and Computer Science, Danish Technical University, Denmark
| | - Masaki Wakabayashi
- Omics Research Center, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - James Todd Pearson
- Dept. of Cardiac Physiology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan; Monash Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Australia
| | - Lars Jørn Jensen
- Dept. of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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Gorski K, Spoljaric A, Nyman TA, Kaila K, Battersby BJ, Lehesjoki AE. Quantitative Changes in the Mitochondrial Proteome of Cerebellar Synaptosomes From Preclinical Cystatin B-Deficient Mice. Front Mol Neurosci 2020; 13:570640. [PMID: 33281550 PMCID: PMC7691638 DOI: 10.3389/fnmol.2020.570640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/21/2020] [Indexed: 12/04/2022] Open
Abstract
Progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1) is a neurodegenerative disorder caused by loss-of-function mutations in the cystatin B (CSTB) gene. Progression of the clinical symptoms in EPM1 patients, including stimulus-sensitive myoclonus, tonic-clonic seizures, and ataxia, are well described. However, the cellular dysfunction during the presymptomatic phase that precedes the disease onset is not understood. CSTB deficiency leads to alterations in GABAergic signaling, and causes early neuroinflammation followed by progressive neurodegeneration in brains of a mouse model, manifesting as progressive myoclonus and ataxia. Here, we report the first proteome atlas from cerebellar synaptosomes of presymptomatic Cstb-deficient mice, and propose that early mitochondrial dysfunction is important to the pathogenesis of altered synaptic function in EPM1. A decreased sodium- and chloride dependent GABA transporter 1 (GAT-1) abundance was noted in synaptosomes with CSTB deficiency, but no functional difference was seen between the two genotypes in electrophysiological experiments with pharmacological block of GAT-1. Collectively, our findings provide novel insights into the early onset and pathogenesis of CSTB deficiency, and reveal greater complexity to the molecular pathogenesis of EPM1.
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Affiliation(s)
- Katarin Gorski
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Albert Spoljaric
- Molecular and Integrative Biosciences, and Neuroscience Center (HiLIFE), Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tuula A Nyman
- Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kai Kaila
- Molecular and Integrative Biosciences, and Neuroscience Center (HiLIFE), Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Anna-Elina Lehesjoki
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
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Zhao X, Wang Y, Cai A, Mei S, Liu N, Kong X. A novel NAPB splicing mutation identified by Trio-based exome sequencing is associated with early-onset epileptic encephalopathy. Eur J Med Genet 2020; 64:104101. [PMID: 33189936 DOI: 10.1016/j.ejmg.2020.104101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 11/25/2022]
Abstract
N-ethylmaleimide-sensitive factor attachment proteins (NAP: NAPA and NAPB) play a role in Soluble N-ethylmaleimide-sensitive accessory protein receptor (SNARE) complex dissociation and recycling, associated with neuronal regulation and brain development and various severe early-onset epilepsies. Here, we report two patients from a Chinese family presenting with unexplained early-onset epileptic encephalopathies (EOEE) syndrome characterized by multifocal seizures, profound intellectual disability and global developmental delay. We identified the homozygous c.433-1G > A variant of the NAPB as the causative by trio-based exome sequencing. The novel splicing mutation in NAPB was third variant reported associated with EOEE syndrome. Our results gave further hints on the associations of variants in NAPB with EOEE and indicated that for patients with unexplained EOEE, the NAPB gene should be included into the data analysis from whole exome sequencing, which contributes to uncover more patients affected and rich the phenotypic spectrum.
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Affiliation(s)
- Xuechao Zhao
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, People's Republic of China.
| | - Yanhong Wang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, No-33, Longhu Waihuan East Road, 450018, Zhengzhou, Henan Province, China.
| | - Aojie Cai
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China.
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, No-33, Longhu Waihuan East Road, 450018, Zhengzhou, Henan Province, China.
| | - Ning Liu
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, People's Republic of China.
| | - Xiangdong Kong
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, People's Republic of China.
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Ciampa E, Li Y, Dillon S, Lecarpentier E, Sorabella L, Libermann TA, Karumanchi SA, Hess PE. Cerebrospinal Fluid Protein Changes in Preeclampsia. Hypertension 2018; 72:219-226. [PMID: 29844151 DOI: 10.1161/hypertensionaha.118.11153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/15/2018] [Accepted: 05/06/2018] [Indexed: 01/21/2023]
Abstract
The molecular mechanisms underlying seizure susceptibility in preeclampsia are unknown. We hypothesized that altered expression of distinct proteins in the cerebrospinal fluid (CSF) may reflect pathophysiological changes in the central nervous system that contribute to the neurological manifestations of severe preeclampsia. We obtained CSF samples from 13 patients with preeclampsia and 14 control patients during spinal anesthesia before delivery and analyzed them by SOMAscan, an aptamer-based proteomics platform for alterations in 1310 protein levels. Ingenuity Pathway Analysis was conducted to highlight relationships between preeclampsia-specific proteins found to be significantly altered. For 2 of the target proteins, we validated the difference in CSF concentrations by ELISA. SOMAscan revealed 82 proteins, whose expression levels were significantly different (P<0.05) in CSF from patients with preeclampsia versus controls. Principal component analysis achieved perfect separation of the preeclampsia and control groups in 2 dimensions. The differentially expressed proteins converge around 4 signaling molecules: TGF-β (transforming growth factor-β), VEGFA (vascular endothelial growth factor A), angiotensinogen, and IL-6 (interleukin-6). Within the TGF-β pathway, upregulation of activin A (301.6±47.4 versus 151.6±20.5 pg/mL; P=0.0074) and follistatin-related gene (5129±347 versus 3016±188 pg/mL; P<0.0001) in preeclampsia was confirmed by ELISA. In summary, signaling pathways important for vascular remodeling, inflammation, and neuronal growth, signaling, and electrophysiology were well represented among the proteins found to be altered in CSF in patients with preeclampsia.
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Affiliation(s)
- Erin Ciampa
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.)
| | - Yunping Li
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.)
| | - Simon Dillon
- Medicine (S.D., E.L., T.A.L., S.A.K.).,Genomics, Proteomics, Bioinformatics, and Systems Biology Center (S.D., T.A.L.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Edouard Lecarpentier
- Medicine (S.D., E.L., T.A.L., S.A.K.).,Faculté de médecine de Créteil Université Paris Est Créteil - Paris XII, and Service de Gynécologie-Obstétrique et Médecine de la Reproduction, Centre Hospitalier Intercommunal de Créteil, France (E.L.)
| | - Laura Sorabella
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.).,Department of Anesthesia, Vanderbilt University Medical Center, Nashville, TN (L.S.)
| | - Towia A Libermann
- Medicine (S.D., E.L., T.A.L., S.A.K.).,Genomics, Proteomics, Bioinformatics, and Systems Biology Center (S.D., T.A.L.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - S Ananth Karumanchi
- Medicine (S.D., E.L., T.A.L., S.A.K.) .,Obstetrics and Gynecology (S.A.K.).,Departments of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA (S.A.K.)
| | - Philip E Hess
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.)
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Herold C, Bidmon HJ, Pannek HW, Hans V, Gorji A, Speckmann EJ, Zilles K. ATPase N-ethylmaleimide-sensitive Fusion Protein: A Novel Key Player for Causing Spontaneous Network Excitation in Human Temporal Lobe Epilepsy. Neuroscience 2018; 371:371-383. [DOI: 10.1016/j.neuroscience.2017.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/27/2017] [Accepted: 12/11/2017] [Indexed: 11/26/2022]
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