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Alexovič M, Bondarchuk T, Uličná C, Sabo J. Blood proteomics of COVID-19 infection: An update. Clin Chim Acta 2024; 562:119881. [PMID: 39033952 DOI: 10.1016/j.cca.2024.119881] [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: 05/10/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Despite significant progress in understanding SARS-CoV-2 and its impact, a deeper comprehension of the molecular changes in the host following infection is still lacking. Proteomic analysis of COVID-19 infected patients can provide valuable data about the events and mechanisms related to the initial, progression, and terminal stages of the disease. Such information can lead to better prevention, treatment, and convalescence strategies. In this review, we discuss blood proteomic studies based on mass spectrometry in COVID-19 patients. The analysis focuses on various blood components including plasma, platelets, serum, red blood cells, and peripheral blood mononuclear cells. Scientific papers published since 2022 are covered, with approaches categorised based on whether they use in-gel, in-solution, or on-beads/on-filter digestion modes. Additionally, candidate protein biomarkers related to COVID-19 are surveyed and discussed.
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011, Košice, Slovakia.
| | - Tetiana Bondarchuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, 03143, Kyiv, Ukraine
| | - Csilla Uličná
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011, Košice, Slovakia; University Library, University of Prešov, 08001, Prešov, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011, Košice, Slovakia
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Tsuji C, Bradshaw M, Allen MF, Jackson ML, Mantell J, Borucu U, Poole AW, Verkade P, Hers I, Paul DM, Dodding MP. CryoET reveals actin filaments within platelet microtubules. Nat Commun 2024; 15:5967. [PMID: 39013865 PMCID: PMC11252303 DOI: 10.1038/s41467-024-50424-8] [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: 01/02/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
Crosstalk between the actin and microtubule cytoskeletons is important for many cellular processes. Recent studies have shown that microtubules and F-actin can assemble to form a composite structure where F-actin occupies the microtubule lumen. Whether these cytoskeletal hybrids exist in physiological settings and how they are formed is unclear. Here, we show that the short-crossover Class I actin filament previously identified inside microtubules in human HAP1 cells is cofilin-bound F-actin. Lumenal F-actin can be reconstituted in vitro, but cofilin is not essential. Moreover, actin filaments with both cofilin-bound and canonical morphologies reside within human platelet microtubules under physiological conditions. We propose that stress placed upon the microtubule network during motor-driven microtubule looping and sliding may facilitate the incorporation of actin into microtubules.
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Affiliation(s)
- Chisato Tsuji
- School of Biochemistry, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Marston Bradshaw
- School of Physiology, Pharmacology and Neuroscience, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Megan F Allen
- School of Physiology, Pharmacology and Neuroscience, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Molly L Jackson
- School of Physiology, Pharmacology and Neuroscience, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Judith Mantell
- School of Biochemistry, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Ufuk Borucu
- GW4 Facility for High-Resolution Electron Cryo-Microscopy, University of Bristol, Bristol, UK
| | - Alastair W Poole
- School of Physiology, Pharmacology and Neuroscience, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Paul Verkade
- School of Biochemistry, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Ingeborg Hers
- School of Physiology, Pharmacology and Neuroscience, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK.
| | - Danielle M Paul
- School of Physiology, Pharmacology and Neuroscience, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK.
| | - Mark P Dodding
- School of Biochemistry, Faculty of Health and Life Sciences, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK.
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Lopuhaä BV, Guzel C, van der Lee A, van den Bosch TPP, van Kemenade FJ, Huisman MV, Kruip MJHA, Luider TM, von der Thüsen JH. Increase in venous thromboembolism in SARS-CoV-2 infected lung tissue: proteome analysis of lung parenchyma, isolated endothelium, and thrombi. Histopathology 2024; 84:967-982. [PMID: 38253958 DOI: 10.1111/his.15143] [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: 07/13/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
AIMS COVID-19 pneumonia is characterized by an increased rate of deep venous thrombosis and pulmonary embolism. To better understand the pathophysiology behind thrombosis in COVID-19, we performed proteomics analysis on SARS-CoV-2 infected lung tissue. METHODS Liquid chromatography mass spectrometry was performed on SARS-CoV-2 infected postmortem lung tissue samples. Five protein profiling analyses were performed: whole slide lung parenchyma analysis, followed by analysis of isolated thrombi and endothelium, both stratified by disease (COVID-19 versus influenza) and thrombus morphology (embolism versus in situ). Influenza autopsy cases with pulmonary thrombi were used as controls. RESULTS Compared to influenza controls, both analyses of COVID-19 whole-tissue and isolated endothelium showed upregulation of proteins and pathways related to liver metabolism including urea cycle activation, with arginase being among the top upregulated proteins in COVID-19 lung tissue. Analysis of isolated COVID-19 thrombi showed significant downregulation of pathways related to platelet activation compared to influenza thrombi. Analysis of isolated thrombi based on histomorphology shows that in situ thrombi have significant upregulation of coronavirus pathogenesis proteins. CONCLUSIONS The decrease in platelet activation pathways in severe COVID-19 thrombi suggests a relative increase in venous thromboembolism, as thrombi from venous origin tend to contain fewer platelets than arterial thrombi. Based on histomorphology, in situ thrombi show upregulation of various proteins related to SARS-CoV-2 pathogenesis compared to thromboemboli, which may indicate increased in situ pulmonary thrombosis in COVID-19. Therefore, this study supports the increase of venous thromboembolism without undercutting the involvement of in situ thrombosis in severe COVID-19.
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Affiliation(s)
- Boaz V Lopuhaä
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Coşkun Guzel
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | | | | | - Menno V Huisman
- Department of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke J H A Kruip
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Theo M Luider
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, the Netherlands
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Mahin A, Soman SP, Modi PK, Raju R, Keshava Prasad TS, Abhinand CS. Meta-analysis of the serum/plasma proteome identifies significant associations between COVID-19 with Alzheimer's/Parkinson's diseases. J Neurovirol 2024; 30:57-70. [PMID: 38167982 DOI: 10.1007/s13365-023-01191-7] [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: 10/14/2023] [Revised: 11/22/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
In recent years, we have seen the widespread devastations and serious health complications manifested by COVID-19 globally. Although we have effectively controlled the pandemic, uncertainties persist regarding its potential long-term effects, including prolonged neurological issues. To gain comprehensive insights, we conducted a meta-analysis of mass spectrometry-based proteomics data retrieved from different studies with a total of 538 COVID-19 patients and 523 healthy controls. The meta-analysis revealed that top-enriched pathways were associated with neurological disorders, including Alzheimer's (AD) and Parkinson's disease (PD). Further analysis confirmed a direct correlation in the expression patterns of 24 proteins involved in Alzheimer's and 23 proteins in Parkinson's disease with COVID-19. Protein-protein interaction network and cluster analysis identified SNCA as a hub protein, a known biomarker for Parkinson's disease, in both AD and PD. To the best of our knowledge, this is the first meta-analysis study providing proteomic profiling evidence linking COVID-19 to neurological complications.
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Affiliation(s)
- Althaf Mahin
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Sreelakshmi Pathappillil Soman
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India.
| | | | - Chandran S Abhinand
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, India.
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Wolny M, Rozanova S, Knabbe C, Pfeiffer K, Barkovits K, Marcus K, Birschmann I. Changes in the Proteome of Platelets from Patients with Critical Progression of COVID-19. Cells 2023; 12:2191. [PMID: 37681923 PMCID: PMC10486756 DOI: 10.3390/cells12172191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
Platelets, the smallest cells in human blood, known for their role in primary hemostasis, are also able to interact with pathogens and play a crucial role in the immune response. In severe coronavirus disease 2019 (COVID-19) cases, platelets become overactivated, resulting in the release of granules, exacerbating inflammation and contributing to the cytokine storm. This study aims to further elucidate the role of platelets in COVID-19 progression and to identify predictive biomarkers for disease outcomes. A comparative proteome analysis of highly purified platelets from critically diseased COVID-19 patients with different outcomes (survivors and non-survivors) and age- and sex-matched controls was performed. Platelets from critically diseased COVID-19 patients exhibited significant changes in the levels of proteins associated with protein folding. In addition, a number of proteins with isomerase activity were found to be more highly abundant in patient samples, apparently exerting an influence on platelet activity via the non-genomic properties of the glucocorticoid receptor (GR) and the nuclear factor κ-light-chain-enhancer of activated B cells (NFκB). Moreover, carbonic anhydrase 1 (CA-1) was found to be a candidate biomarker in platelets, showing a significant increase in COVID-19 patients.
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Affiliation(s)
- Monika Wolny
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum NRW, Universitätsklinik der Ruhr-Universität Bochum, 32545 Bad Oeynhausen, Germany
| | - Svitlana Rozanova
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Cornelius Knabbe
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum NRW, Universitätsklinik der Ruhr-Universität Bochum, 32545 Bad Oeynhausen, Germany
| | - Kathy Pfeiffer
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, 44801 Bochum, Germany
| | - Ingvild Birschmann
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum NRW, Universitätsklinik der Ruhr-Universität Bochum, 32545 Bad Oeynhausen, Germany
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