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Anandakrishnan N, Yi Z, Sun Z, Liu T, Haydak J, Eddy S, Jayaraman P, DeFronzo S, Saha A, Sun Q, Yang D, Mendoza A, Mosoyan G, Wen HH, Schaub JA, Fu J, Kehrer T, Menon R, Otto EA, Godfrey B, Suarez-Farinas M, Leffters S, Twumasi A, Meliambro K, Charney AW, García-Sastre A, Campbell KN, Gusella GL, He JC, Miorin L, Nadkarni GN, Wisnivesky J, Li H, Kretzler M, Coca SG, Chan L, Zhang W, Azeloglu EU. Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.18.24304401. [PMID: 38562892 PMCID: PMC10984064 DOI: 10.1101/2024.03.18.24304401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
COVID-19 has been a significant public health concern for the last four years; however, little is known about the mechanisms that lead to severe COVID-associated kidney injury. In this multicenter study, we combined quantitative deep urinary proteomics and machine learning to predict severe acute outcomes in hospitalized COVID-19 patients. Using a 10-fold cross-validated random forest algorithm, we identified a set of urinary proteins that demonstrated predictive power for both discovery and validation set with 87% and 79% accuracy, respectively. These predictive urinary biomarkers were recapitulated in non-COVID acute kidney injury revealing overlapping injury mechanisms. We further combined orthogonal multiomics datasets to understand the mechanisms that drive severe COVID-associated kidney injury. Functional overlap and network analysis of urinary proteomics, plasma proteomics and urine sediment single-cell RNA sequencing showed that extracellular matrix and autophagy-associated pathways were uniquely impacted in severe COVID-19. Differentially abundant proteins associated with these pathways exhibited high expression in cells in the juxtamedullary nephron, endothelial cells, and podocytes, indicating that these kidney cell types could be potential targets. Further, single-cell transcriptomic analysis of kidney organoids infected with SARS-CoV-2 revealed dysregulation of extracellular matrix organization in multiple nephron segments, recapitulating the clinically observed fibrotic response across multiomics datasets. Ligand-receptor interaction analysis of the podocyte and tubule organoid clusters showed significant reduction and loss of interaction between integrins and basement membrane receptors in the infected kidney organoids. Collectively, these data suggest that extracellular matrix degradation and adhesion-associated mechanisms could be a main driver of COVID-associated kidney injury and severe outcomes.
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Mao Y, Chen Y, Li Y, Ma L, Wang X, Wang Q, He A, Liu X, Dong T, Gao W, Xu Y, Liu L, Ren L, Liu Q, Zhou P, Hu B, Zhou Y, Tian R, Shi ZL. Deep spatial proteomics reveals region-specific features of severe COVID-19-related pulmonary injury. Cell Rep 2024; 43:113689. [PMID: 38241149 DOI: 10.1016/j.celrep.2024.113689] [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: 08/31/2023] [Revised: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/21/2024] Open
Abstract
As a primary target of severe acute respiratory syndrome coronavirus 2, lung exhibits heterogeneous histopathological changes following infection. However, comprehensive insight into their protein basis with spatial resolution remains deficient, which hinders further understanding of coronavirus disease 2019 (COVID-19)-related pulmonary injury. Here, we generate a region-resolved proteomic atlas of hallmark pathological pulmonary structures by integrating histological examination, laser microdissection, and ultrasensitive proteomics. Over 10,000 proteins are quantified across 71 post-mortem specimens. We identify a spectrum of pathway dysregulations in alveolar epithelium, bronchial epithelium, and blood vessels compared with non-COVID-19 controls, providing evidence for transitional-state pneumocyte hyperplasia. Additionally, our data reveal the region-specific enrichment of functional markers in bronchiole mucus plugs, pulmonary fibrosis, airspace inflammation, and alveolar type 2 cells, uncovering their distinctive features. Furthermore, we detect increased protein expression associated with viral entry and inflammatory response across multiple regions, suggesting potential therapeutic targets. Collectively, this study provides a distinct perspective for deciphering COVID-19-caused pulmonary dysfunction by spatial proteomics.
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Affiliation(s)
- Yiheng Mao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430030, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Li
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Longda Ma
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xi Wang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430030, China; University of Chinese Academy of Sciences, Beijing, China
| | - An He
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430030, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tianyi Dong
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430030, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weina Gao
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yanfen Xu
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liang Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Ren
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qian Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Peng Zhou
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Ben Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430030, China
| | - Yiwu Zhou
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Ruijun Tian
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Zheng-Li Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430030, China.
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Ebrahimi M, Farhadian N, Soflaei SS, Amiri A, Tanbakuchi D, Oskooee RK, Karimi M. Utilizing the sublingual form of squalene in COVID-19 patients: a randomized clinical trial. Sci Rep 2024; 14:4532. [PMID: 38402329 PMCID: PMC10894301 DOI: 10.1038/s41598-024-54843-x] [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: 01/01/2023] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
In this study, the efficacy of sublingual squalene in decreasing the mortality rate among patients with COVID-19 was investigated. Squalene was extracted from pumpkin seed oil with a novel method. Then, the microemulsion form of squalene was prepared for sublingual usage. In the clinical study, among 850 admitted patients, 602 eligible COVID-19 patients were divided in two groups of control (N = 301) and cases (N = 301) between Nov 2021 and Jan 2022. Groups were statistically the same in terms of age, sex, BMI, lymphocyte count on 1st admission day, hypertension, chronic kidney disease, chronic respiratory disease, immunosuppressive disease, and required standard treatments. The treatment group received five drops of sublingual squalene every 4 h for 5 days plus standard treatment, while the control group received only standard treatment. Patients were followed up for 30 days after discharge from the hospital. The sublingual form of squalene in the microemulsion form was associated with a significant decrease in the mortality rate (p < 0.001), in which 285 (94.7%) cases were alive after one month while 245 (81.4%) controls were alive after 1 month of discharge from the hospital. In addition, squalene appears to be effective in preventing re-hospitalization due to COVID-19 (p < 0.001), with 141 of controls (46.8%) versus 58 cases (19.3%). This study suggests sublingual squalene in the microemulsion as an effective drug for reducing mortality and re-hospitalization rates in COVID-19 patients.Trial Registration Number: IRCT20200927048848N3.
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Affiliation(s)
- Mahmoud Ebrahimi
- Cardiovascular Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nafiseh Farhadian
- Chemical Engineering Department, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Sara Saffar Soflaei
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Amiri
- Emergency Medicine Department, Golestan University of Medical Sciences, Gorgan, Iran
| | - Davoud Tanbakuchi
- Department of Biostatistics, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohammad Karimi
- Emergency Medicine Department, Birjand University of Medical Sciences, Birjand, Iran
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Tofaute M, Weller B, Graß C, Halder H, Dohai B, Falter-Braun P, Krappmann D. SARS-CoV-2 NSP14 MTase activity is critical for inducing canonical NF-κB activation. Biosci Rep 2024; 44:BSR20231418. [PMID: 38131452 PMCID: PMC10776897 DOI: 10.1042/bsr20231418] [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: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
Upon SARS-CoV-2 infection, patients with severe forms of COVID-19 often suffer from a dysregulated immune response and hyperinflammation. Aberrant expression of cytokines and chemokines is associated with strong activation of the immunoregulatory transcription factor NF-κB, which can be directly induced by the SARS-CoV-2 protein NSP14. Here, we use NSP14 mutants and generated cells with host factor knockouts (KOs) in the NF-κB signaling pathways to characterize the molecular mechanism of NSP14-induced NF-κB activation. We demonstrate that full-length NSP14 requires methyltransferase (MTase) activity to drive NF-κB induction. NSP14 WT, but not an MTase-defective mutant, is poorly expressed and inherent post-translational instability is mediated by proteasomal degradation. Binding of SARS-CoV-2 NSP10 or addition of the co-factor S-adenosylmethionine (SAM) stabilizes NSP14 and augments its potential to activate NF-κB. Using CRISPR/Cas9-engineered KO cells, we demonstrate that NSP14 stimulation of canonical NF-κB activation relies on NF-κB factor p65/RELA downstream of the NEMO/IKK complex, while c-Rel or non-canonical RelB are not required to induce NF-κB transcriptional activity. However, NSP14 overexpression is unable to induce canonical IκB kinase β (IKKβ)/NF-κB signaling and in co-immunoprecipitation assays we do not detect stable associations between NSP14 and NEMO or p65, suggesting that NSP14 activates NF-κB indirectly through its methyltransferase activity. Taken together, our data provide a framework how NSP14 can augment basal NF-κB activation, which may enhance cytokine expression in SARS-CoV-2 infected cells.
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Affiliation(s)
- Marie J. Tofaute
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Benjamin Weller
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Carina Graß
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Hridi Halder
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Bushra Dohai
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität (LMU) München, Planegg-Martinsried, Germany
| | - Daniel Krappmann
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
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Zaidi AK, Singh RB, A A Rizvi S, Dehgani-Mobaraki P, Palladino N. COVID-19 pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:67-112. [PMID: 38237991 DOI: 10.1016/bs.pmbts.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
The pathogenesis of COVID-19 involves a complex interplay between host factors and the SARS-CoV-2 virus, leading to a multitude of clinical manifestations beyond the respiratory system. This chapter provides an overview of the risk factors, genetic predisposition, and multisystem manifestations of COVID-19, shedding light on the underlying mechanisms that contribute to extrapulmonary manifestations. The chapter discusses the direct invasion of SARS-CoV-2 into various organs as well as the indirect mechanisms such as dysregulation of the renin-angiotensin-aldosterone system (RAAS), immune response dysfunctions within the innate and adaptive immune systems, endothelial damage, and immunothrombosis. Furthermore, the multisystem manifestations of COVID-19 across different organ systems, including the cardiovascular, renal, gastrointestinal, hepatobiliary, nervous, endocrine and metabolic, ophthalmic, ear-nose-throat, reproductive, hematopoietic, and immune systems are discussed in detail. Each system exhibits unique manifestations that contribute to the complexity of the disease.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia
| | - Syed A A Rizvi
- College of Biomedical Sciences, Larkin University, Miami, Florida, United States.
| | - Puya Dehgani-Mobaraki
- Founder and President, Associazione Naso Sano, Ringgold Institution ID 567754, San Mariano, Italy.
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Rajoria S, Kavuru SR, Pyda HS, Bihani S, Borishetty D, Biswas D, Prajapati J, Paladi H, Srivastava S. CoVProt: Toward a Mass Spectrometry Data Portal for COVID-19 Proteomics Research and Development. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:24-31. [PMID: 38193774 DOI: 10.1089/omi.2023.0274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has wreaked havoc globally. Beyond the pandemic, the long-term effects of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in multiple organ systems are yet to be deciphered. This calls for continued systems science research. Moreover, the host response to SARS-CoV-2 varies person-to-person and gives rise to different degrees of morbidity and mortality. Mass spectrometry (MS) has been a proven asset in studies of the SARS-CoV-2 from an omics systems science lens. To strengthen the proteomics research dedicated to COVID-19, we introduce here a web-based portal, CoVProt. The portal is work in progress and aims for a comprehensive curation of MS-based proteomics data of COVID-19 clinical samples for deep proteomic investigations, data visualization, and easy data accessibility for life sciences innovations and planetary health research community. Currently, CoVProt contains information on 2725 different proteins and 37,125 different peptides from six data sets covering a total of 202 clinical samples. Moreover, all pertinent data sets extracted from the literature have been reanalyzed using a common analysis pipeline developed by combining multiple tools. Going forward, we anticipate that the CoVProt portal will also provide access to the clinical parameters of the patients. The CoVProt (v1.0) portal addresses an existing significant gap to study COVID-19 host proteomics, which, to the best of our knowledge, is the first effort in this direction. We believe that CoVProt is poised to make contributions as a community resource for proteomic applications and aims to broadly support clinical studies to facilitate the discovery of COVID-19 biomarkers and therapeutics with translational potential.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sai Rohith Kavuru
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Hari Sundar Pyda
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai- Indian Oil Odisha Campus, Bhubaneswar, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Dhanush Borishetty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptrup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Jeel Prajapati
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Gandhinagar, India
| | - Harshith Paladi
- Department of Computer Science, School of Computing, SASTRA Deemed to be University, Thanjavur, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Zhang Y, Li Z, Wang H, Pei Z, Zhao S. Molecular biomarkers of diffuse axonal injury: recent advances and future perspectives. Expert Rev Mol Diagn 2024; 24:39-47. [PMID: 38183228 DOI: 10.1080/14737159.2024.2303319] [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: 06/30/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024]
Abstract
INTRODUCTION Diffuse axonal injury (DAI), with high mortality and morbidity both in children and adults, is one of the most severe pathological consequences of traumatic brain injury. Currently, clinical diagnosis, disease assessment, disability identification, and postmortem diagnosis of DAI is mainly limited by the absent of specific molecular biomarkers. AREAS COVERED In this review, we first introduce the pathophysiology of DAI, summarized the reported biomarkers in previous animal and human studies, and then the molecular biomarkers such as β-Amyloid precursor protein, neurofilaments, S-100β, myelin basic protein, tau protein, neuron-specific enolase, Peripherin and Hemopexin for DAI diagnosis is summarized. Finally, we put forward valuable views on the future research direction of diagnostic biomarkers of DAI. EXPERT OPINION In recent years, the advanced technology has ultimately changed the research of DAI, and the numbers of potential molecular biomarkers was introduced in related studies. We summarized the latest updated information in such studies to provide references for future research and explore the potential pathophysiological mechanism on diffuse axonal injury.
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Affiliation(s)
- Youyou Zhang
- Department of Geriatrics Neurology, the Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Linfen People's Hosiptal, the Seventh Clinical Medical College of Shanxi Medical University, Linfen, Shanxi, China
| | - Zhaoyang Li
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hui Wang
- Department of Geriatrics Neurology, the Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhiyong Pei
- Linfen People's Hosiptal, the Seventh Clinical Medical College of Shanxi Medical University, Linfen, Shanxi, China
| | - Shuquan Zhao
- Department of Forensic Pathology, Zhongshan School of Medicine Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, Guangdong, China
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Gómez-Carballa A, Albericio G, Montoto-Louzao J, Pérez P, Astorgano D, Rivero-Calle I, Martinón-Torres F, Esteban M, Salas A, García-Arriaza J. Lung transcriptomics of K18-hACE2 mice highlights mechanisms and genes involved in the MVA-S vaccine-mediated immune response and protection against SARS-CoV-2 infection. Antiviral Res 2023; 220:105760. [PMID: 37992765 DOI: 10.1016/j.antiviral.2023.105760] [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: 07/27/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023]
Abstract
Unravelling the molecular mechanism of COVID-19 vaccines through transcriptomic pathways involved in the host response to SARS-CoV-2 infection is key to understand how vaccines work, and for the development of optimized COVID-19 vaccines that can prevent the emergence of SARS-CoV-2 variants of concern (VoCs) and future outbreaks. In this study, we investigated the effects of vaccination with a modified vaccinia virus Ankara (MVA)-based vector expressing the full-length SARS-CoV-2 spike protein (MVA-S) on the lung transcriptome from susceptible K18-hACE2 mice after SARS-CoV-2 infection. One dose of MVA-S regulated genes related to viral infection control, inflammation processes, T-cell response, cytokine production and IFN-γ signalling. Down-regulation of Rhcg and Tnfsf18 genes post-vaccination with one and two doses of MVA-S may represent a mechanism for controlling infection immunity and vaccine-induced protection. One dose of MVA-S provided partial protection with a distinct lung transcriptomic profile to healthy animals, while two doses of MVA-S fully protected against infection with a transcriptomic profile comparable to that of non-vaccinated healthy animals. This suggests that the MVA-S booster generates a robust and rapid antigen-specific immune response preventing virus infection. Notably, down-regulation of Atf3 and Zbtb16 genes in mice vaccinated with two doses of MVA-S may contribute to vaccine control of innate immune system and inflammation processes in the lungs during SARS-CoV-2 infection. This study shows host transcriptomic mechanisms likely involved in the MVA-S vaccine-mediated immune response against SARS-CoV-2 infection, which could help in improving vaccine dose assessment and developing novel, well-optimized SARS-CoV-2 vaccine candidates against prevalent or emerging VoCs.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Infectious Diseases Research Group (Genvip), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela (CHUS), Servicio Gallego de Salud (SERGAS), Santiago de Compostela, Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Guillermo Albericio
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Julián Montoto-Louzao
- Genetics, Vaccines and Infectious Diseases Research Group (Genvip), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela (CHUS), Servicio Gallego de Salud (SERGAS), Santiago de Compostela, Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Patricia Pérez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - David Astorgano
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infectious Diseases Research Group (Genvip), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infectious Diseases Research Group (Genvip), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Antonio Salas
- Genetics, Vaccines and Infectious Diseases Research Group (Genvip), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela (CHUS), Servicio Gallego de Salud (SERGAS), Santiago de Compostela, Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
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Earle K, Valero C, Conn DP, Vere G, Cook PC, Bromley MJ, Bowyer P, Gago S. Pathogenicity and virulence of Aspergillus fumigatus. Virulence 2023; 14:2172264. [PMID: 36752587 PMCID: PMC10732619 DOI: 10.1080/21505594.2023.2172264] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 02/09/2023] Open
Abstract
Pulmonary infections caused by the mould pathogen Aspergillus fumigatus are a major cause of morbidity and mortality globally. Compromised lung defences arising from immunosuppression, chronic respiratory conditions or more recently, concomitant viral or bacterial pulmonary infections are recognised risks factors for the development of pulmonary aspergillosis. In this review, we will summarise our current knowledge of the mechanistic basis of pulmonary aspergillosis with a focus on emerging at-risk populations.
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Affiliation(s)
- Kayleigh Earle
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Clara Valero
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Daniel P. Conn
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - George Vere
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Peter C. Cook
- MRC Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Michael J. Bromley
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Bowyer
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Sara Gago
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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10
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Li Y, Han L, Li P, Ge J, Xue Y, Chen L. Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks. BMC Genomics 2023; 24:619. [PMID: 37853311 PMCID: PMC10583333 DOI: 10.1186/s12864-023-09719-1] [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: 02/27/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
To explore the potential network markers and related signaling pathways of human B cells infected by COVID-19, we performed standardized integration and analysis of single-cell sequencing data to construct conditional cell-specific networks (CCSN) for each cell. Then the peripheral blood cells were clustered and annotated based on the conditional network degree matrix (CNDM) and gene expression matrix (GEM), respectively, and B cells were selected for further analysis. Besides, based on the CNDM of B cells, the hub genes and 'dark' genes (a gene has a significant difference between case and control samples not in a gene expression level but in a conditional network degree level) closely related to COVID-19 were revealed. Interestingly, some of the 'dark' genes and differential degree genes (DDGs) encoded key proteins in the JAK-STAT pathway, which had antiviral effects. The protein p21 encoded by the 'dark' gene CDKN1A was a key regulator for the COVID-19 infection-related signaling pathway. Elevated levels of proteins encoded by some DDGs were directly related to disease severity of patients with COVID-19. In short, the proteins encoded by 'dark' genes complement some missing links in COVID-19 and these signaling pathways played an important role in the growth and activation of B cells.
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Affiliation(s)
- Ying Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Liqin Han
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China
- Longmen Laboratory, Luoyang, 471003, Henan, China
| | - Peiluan Li
- School of Mathematics and Statistics, Henan University of Science and Technology, Luoyang, 471023, China.
- Longmen Laboratory, Luoyang, 471003, Henan, China.
| | - Jing Ge
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 201100, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310000, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201100, China.
- West China Biomedical Big Data Center, Med-X Center for Informatics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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11
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Burke B, Rocha SM, Zhan S, Eckley M, Reasoner C, Addetia A, Lewis J, Fagre A, Charley PA, Richt JA, Weiss SR, Tjalkens RB, Veesler D, Aboellail T, Schountz T. Regulatory T cell-like response to SARS-CoV-2 in Jamaican fruit bats (Artibeus jamaicensis) transduced with human ACE2. PLoS Pathog 2023; 19:e1011728. [PMID: 37856551 PMCID: PMC10617724 DOI: 10.1371/journal.ppat.1011728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 10/31/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Insectivorous Old World horseshoe bats (Rhinolophus spp.) are the likely source of the ancestral SARS-CoV-2 prior to its spillover into humans and causing the COVID-19 pandemic. Natural coronavirus infections of bats appear to be principally confined to the intestines, suggesting fecal-oral transmission; however, little is known about the biology of SARS-related coronaviruses in bats. Previous experimental challenges of Egyptian fruit bats (Rousettus aegyptiacus) resulted in limited infection restricted to the respiratory tract, whereas insectivorous North American big brown bats (Eptesicus fuscus) showed no evidence of infection. In the present study, we challenged Jamaican fruit bats (Artibeus jamaicensis) with SARS-CoV-2 to determine their susceptibility. Infection was confined to the intestine for only a few days with prominent viral nucleocapsid antigen in epithelial cells, and mononuclear cells of the lamina propria and Peyer's patches, but with no evidence of infection of other tissues; none of the bats showed visible signs of disease or seroconverted. Expression levels of ACE2 were low in the lungs, which may account for the lack of pulmonary infection. Bats were then intranasally inoculated with a replication-defective adenovirus encoding human ACE2 and 5 days later challenged with SARS-CoV-2. Viral antigen was prominent in lungs for up to 14 days, with loss of pulmonary cellularity during this time; however, the bats did not exhibit weight loss or visible signs of disease. From day 7, bats had low to moderate IgG antibody titers to spike protein by ELISA, and one bat on day 10 had low-titer neutralizing antibodies. CD4+ helper T cells became activated upon ex vivo recall stimulation with SARS-CoV-2 nucleocapsid peptide library and exhibited elevated mRNA expression of the regulatory T cell cytokines interleukin-10 and transforming growth factor-β, which may have limited inflammatory pathology. Collectively, these data show that Jamaican fruit bats are poorly susceptible to SARS-CoV-2 but that expression of human ACE2 in their lungs leads to robust infection and an adaptive immune response with low-titer antibodies and a regulatory T cell-like response that may explain the lack of prominent inflammation in the lungs. This model will allow for insight of how SARS-CoV-2 infects bats and how bat innate and adaptive immune responses engage the virus without overt clinical disease.
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Affiliation(s)
- Bradly Burke
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Savannah M. Rocha
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Shijun Zhan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Miles Eckley
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Clara Reasoner
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Juliette Lewis
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Anna Fagre
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Phillida A. Charley
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Juergen A. Richt
- Diagnostic Medicine/Pathobiology, Center of Excellence for Emerging and Zoonotic Animal Diseases, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronald B. Tjalkens
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Tawfik Aboellail
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Tony Schountz
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
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Stoian M, Roman A, Boeriu A, Onișor D, Bandila SR, Babă DF, Cocuz I, Niculescu R, Costan A, Laszlo SȘ, Corău D, Stoian A. Long-Term Radiological Pulmonary Changes in Mechanically Ventilated Patients with Respiratory Failure due to SARS-CoV-2 Infection. Biomedicines 2023; 11:2637. [PMID: 37893011 PMCID: PMC10604756 DOI: 10.3390/biomedicines11102637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
From the first reports of SARS-CoV-2, at the end of 2019 to the present, the global mortality associated with COVID-19 has reached 6,952,522 deaths as reported by the World Health Organization (WHO). Early intubation and mechanical ventilation can increase the survival rate of critically ill patients. This prospective study was carried out on 885 patients in the ICU of Mureș County Clinical Hospital, Romania. After applying inclusion and exclusion criteria, a total of 54 patients were included. Patients were monitored during hospitalization and at 6-month follow-up. We analyzed the relationship between invasive mechanical ventilation (IMV) and non-invasive mechanical ventilation (NIMV) and radiological changes on thoracic CT scans performed at 6-month follow-up and found no significant association. Regarding paraclinical analysis, there was a statistically significant association between patients grouped by IMV and ferritin level on day 1 of admission (p = 0.034), and between patients grouped by PaO2/FiO2 ratio with metabolic syndrome (p = 0.03) and the level of procalcitonin (p = 0.01). A significant proportion of patients with COVID-19 admitted to the ICU developed pulmonary fibrosis as observed at a 6-month evaluation. Patients with oxygen supplementation or mechanical ventilation require dynamic monitoring and radiological investigations, as there is a possibility of long-term pulmonary fibrosis that requires pharmacological interventions and finding new therapeutic alternatives.
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Affiliation(s)
- Mircea Stoian
- Department of Anesthesiology and Intensive Care, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540139 Targu Mures, Romania;
| | - Adina Roman
- Gastroenterology Department, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540142 Targu Mures, Romania; (A.B.); (D.O.)
| | - Alina Boeriu
- Gastroenterology Department, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540142 Targu Mures, Romania; (A.B.); (D.O.)
| | - Danusia Onișor
- Gastroenterology Department, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540142 Targu Mures, Romania; (A.B.); (D.O.)
| | - Sergio Rareș Bandila
- Orthopedic Surgery and Traumatology Service, Marina Baixa Hospital, Av. Alcade En Jaume Botella Mayor, 03570 Villajoyosa, Spain;
| | - Dragoș Florin Babă
- Department of Cell and Molecular Biology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540142 Targu Mures, Romania;
| | - Iuliu Cocuz
- Department of Pathophysiology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540136 Targu Mures, Romania; (I.C.); (R.N.); (A.S.)
| | - Raluca Niculescu
- Department of Pathophysiology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540136 Targu Mures, Romania; (I.C.); (R.N.); (A.S.)
| | - Anamaria Costan
- Faculty of Medicine, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540142 Targu Mures, Romania;
| | - Sergiu Ștefan Laszlo
- Intensive Care Unit, Mureș County Hospital, Street Gheorghe Marinescu no 1, 540136 Targu Mures, Romania;
| | - Dragoș Corău
- Intensive Care Unit, Mureș County Hospital, Street Gheorghe Marinescu no 1, 540136 Targu Mures, Romania;
| | - Adina Stoian
- Department of Pathophysiology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology of Târgu Mureș, 540136 Targu Mures, Romania; (I.C.); (R.N.); (A.S.)
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13
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Andalib KMS, Ahmed A, Habib A. Omics data analysis reveals common molecular basis of small cell lung cancer and COVID-19. J Biomol Struct Dyn 2023:1-16. [PMID: 37708006 DOI: 10.1080/07391102.2023.2257803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
The impact of COVID-19 infection on individuals with small cell lung cancer (SCLC) poses a serious threat. Unfortunately, the molecular basis of this severe comorbidity has yet to be elucidated. The present study addresses this gap utilizing publicly available omics data of COVID-19 and SCLC to explore the key molecules and associated pathways involved in the convergence of these diseases. Findings revealed 402 genes, that exhibited differential expression patterns in SCLC patients and also play a pivotal role in COVID-19 pathogenesis. Subsequent functional enrichment analyses identified relevant ontologies and pathways that are significantly associated with these genes, revealing important insights into their potential biological, molecular and cellular functions. The protein-protein interaction network, constructed under four combinatorial topological assessments, highlighted SMAD3, CAV1, PIK3R1, and FN1 as the primary components to this comorbidity. Our results suggest that these components significantly regulate this cross-talk triggering the PI3K-AKT and TGF-β signaling pathways. Lastly, this study made a multi-step computational attempt and identified corylifol A and ginkgetin from natural sources that can potentially inhibit these components. Therefore, the outcomes of this study offer novel perspectives on the common molecular mechanisms underlying SCLC and COVID-19 and present future opportunities for drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K M Salim Andalib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Asif Ahmed
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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14
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Duong-Quy S, Vo-Pham-Minh T, Tran-Xuan Q, Huynh-Anh T, Vo-Van T, Vu-Tran-Thien Q, Nguyen-Nhu V. Post-COVID-19 Pulmonary Fibrosis: Facts-Challenges and Futures: A Narrative Review. Pulm Ther 2023; 9:295-307. [PMID: 37209374 PMCID: PMC10199290 DOI: 10.1007/s41030-023-00226-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/19/2023] [Indexed: 05/22/2023] Open
Abstract
Patients with coronavirus disease 2019 (COVID-19) usually suffer from post-acute sequelae of coronavirus disease 2019 (PASC). Pulmonary fibrosis (PF) has the most significant long-term impact on patients' respiratory health, called post-COVID-19 pulmonary fibrosis (PC19-PF). PC19- PF can be caused by acute respiratory distress syndrome (ARDS) or pneumonia due to COVID-19. The risk factors of PC19-PF, such as older age, chronic comorbidities, the use of mechanical ventilation during the acute phase, and female sex, should be considered. Individuals with COVID-19 pneumonia symptoms lasting at least 12 weeks following diagnosis, including cough, dyspnea, exertional dyspnea, and poor saturation, accounted for nearly all disease occurrences. PC19-PF is characterized by persistent fibrotic tomographic sequelae associated with functional impairment throughout follow-up. Thus, clinical examination, radiology, pulmonary function tests, and pathological findings should be done to diagnose PC19-PF patients. PFT indicated persistent limitations in diffusion capacity and restrictive physiology, despite the absence of previous testing and inconsistency in the timeliness of assessments following acute illness. It has been hypothesized that PC19-PF patients may benefit from idiopathic pulmonary fibrosis treatment to prevent continued infection-related disorders, enhance the healing phase, and manage fibroproliferative processes. Immunomodulatory agents might reduce inflammation and the length of mechanical ventilation during the acute phase of COVID-19 infection, and the risk of the PC19-PF stage. Pulmonary rehabilitation, incorporating exercise training, physical education, and behavioral modifications, can improve the physical and psychological conditions of patients with PC19-PF.
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Affiliation(s)
- Sy Duong-Quy
- Clinical Research Unit, Lam Dong Medical College and Bio-Medical Research Centre, Dalat, Vietnam
- Immuno-Allergology Division, Hershey Medical Center, Penn State Medical College, State College, PA, USA
- Outpatient Department, Pham Ngoc Thach Medical University, Ho Chi Minh City, Vietnam
- Department of Respiratory Functional Exploration, University Medical Center, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thu Vo-Pham-Minh
- Department of Internal Medicine, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Quynh Tran-Xuan
- Department of Internal Medicine, Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Tuan Huynh-Anh
- Department of Respiratory Diseases, Hoan My Cuu Long Hospital, Can Tho, Vietnam
| | - Tinh Vo-Van
- Outpatient Department, Pham Ngoc Thach Medical University, Ho Chi Minh City, Vietnam
| | - Quan Vu-Tran-Thien
- Department of Respiratory Functional Exploration, University Medical Center, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vinh Nguyen-Nhu
- Department of Respiratory Functional Exploration, University Medical Center, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam.
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15
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Cambier S, Beretta F, Pörtner N, Metzemaekers M, de Carvalho AC, Martens E, Kaes J, Aelbrecht C, Jacobs C, Van Mol P, Wauters E, Meersseman P, Hermans G, Marques RE, Vanaudenaerde B, Vos R, Wauters J, Gouwy M, Proost P. Proteolytic inactivation of CXCL12 in the lungs and circulation of COVID-19 patients. Cell Mol Life Sci 2023; 80:234. [PMID: 37505242 PMCID: PMC11073220 DOI: 10.1007/s00018-023-04870-0] [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: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
The human chemokine stromal cell-derived factor-1 (SDF-1) or CXCL12 is involved in several homeostatic processes and pathologies through interaction with its cognate G protein-coupled receptor CXCR4. Recent research has shown that CXCL12 is present in the lungs and circulation of patients with coronavirus disease 2019 (COVID-19). However, the question whether the detected CXCL12 is bioactive was not addressed. Indeed, the activity of CXCL12 is regulated by NH2- and COOH-terminal post-translational proteolysis, which significantly impairs its biological activity. The aim of the present study was to characterize proteolytic processing of CXCL12 in broncho-alveolar lavage (BAL) fluid and blood plasma samples from critically ill COVID-19 patients. Therefore, we optimized immunosorbent tandem mass spectrometry proteoform analysis (ISTAMPA) for detection of CXCL12 proteoforms. In patient samples, this approach uncovered that CXCL12 is rapidly processed by site-specific NH2- and COOH-terminal proteolysis and ultimately degraded. This proteolytic inactivation occurred more rapidly in COVID-19 plasma than in COVID-19 BAL fluids, whereas BAL fluid samples from stable lung transplantation patients and the non-affected lung of lung cancer patients (control groups) hardly induced any processing of CXCL12. In COVID-19 BAL fluids with high proteolytic activity, processing occurred exclusively NH2-terminally and was predominantly mediated by neutrophil elastase. In low proteolytic activity BAL fluid and plasma samples, NH2- and COOH-terminal proteolysis by CD26 and carboxypeptidases were observed. Finally, protease inhibitors already approved for clinical use such as sitagliptin and sivelestat prevented CXCL12 processing and may therefore be of pharmacological interest to prolong CXCL12 half-life and biological activity in vivo.
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Affiliation(s)
- Seppe Cambier
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Fabio Beretta
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Noëmie Pörtner
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Mieke Metzemaekers
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Ana Carolina de Carvalho
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Erik Martens
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Janne Kaes
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Celine Aelbrecht
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Cato Jacobs
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Van Mol
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Els Wauters
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Meersseman
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Greet Hermans
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Bart Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Joost Wauters
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Mieke Gouwy
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium.
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16
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Wang P, Jin L, Zhang M, Wu Y, Duan Z, Guo Y, Wang C, Guo Y, Chen W, Liao Z, Wang Y, Lai R, Lee LP, Qin J. Blood-brain barrier injury and neuroinflammation induced by SARS-CoV-2 in a lung-brain microphysiological system. Nat Biomed Eng 2023:10.1038/s41551-023-01054-w. [PMID: 37349391 DOI: 10.1038/s41551-023-01054-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
In some patients, COVID-19 can trigger neurological symptoms with unclear pathogenesis. Here we describe a microphysiological system integrating alveolus and blood-brain barrier (BBB) tissue chips that recapitulates neuropathogenesis associated with infection by SARS-CoV-2. Direct exposure of the BBB chip to SARS-CoV-2 caused mild changes to the BBB, and infusion of medium from the infected alveolus chip led to more severe injuries on the BBB chip, including endothelial dysfunction, pericyte detachment and neuroinflammation. Transcriptomic analyses indicated downregulated expression of the actin cytoskeleton in brain endothelium and upregulated expression of inflammatory genes in glial cells. We also observed early cerebral microvascular damage following lung infection with a low viral load in the brains of transgenic mice expressing human angiotensin-converting enzyme 2. Our findings suggest that systemic inflammation is probably contributing to neuropathogenesis following SARS-CoV-2 infection, and that direct viral neural invasion might not be a prerequisite for this neuropathogenesis. Lung-brain microphysiological systems should aid the further understanding of the systemic effects and neurological complications of viral infection.
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Affiliation(s)
- Peng Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Science and Technology of China, Hefei, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China
| | - Lin Jin
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences-Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Min Zhang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunsong Wu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zilei Duan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences-Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yaqiong Guo
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Chaoming Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences-Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yingqi Guo
- Core Technology Facility of Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenwen Chen
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhiyi Liao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences-Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yaqing Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences-Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - Luke P Lee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA.
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Korea.
| | - Jianhua Qin
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- University of Science and Technology of China, Hefei, China.
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.
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Hossain MA, Sohel M, Sultana T, Hasan MI, Khan MS, Kibria KMK, Mahmud SMH, Rahman MH. Study of kaempferol in the treatment of COVID-19 combined with Chikungunya co-infection by network pharmacology and molecular docking technology. INFORMATICS IN MEDICINE UNLOCKED 2023; 40:101289. [PMID: 37346467 PMCID: PMC10264333 DOI: 10.1016/j.imu.2023.101289] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Chikungunya (CHIK) patients may be vulnerable to coronavirus disease (COVID-19). However, presently there are no anti-COVID-19/CHIK therapeutic alternatives available. The purpose of this research was to determine the pharmacological mechanism through which kaempferol functions in the treatment of COVID-19-associated CHIK co-infection. We have used a series of network pharmacology and computational analysis-based techniques to decipher and define the binding capacity, biological functions, pharmacological targets, and treatment processes in COVID-19-mediated CHIK co-infection. We identified key therapeutic targets for COVID-19/CHIK, including TP53, MAPK1, MAPK3, MAPK8, TNF, IL6 and NFKB1. Gene ontology, molecular and upstream pathway analysis of kaempferol against COVID-19 and CHIK showed that DEGs were confined mainly to the cytokine-mediated signalling pathway, MAP kinase activity, negative regulation of the apoptotic process, lipid and atherosclerosis, TNF signalling pathway, hepatitis B, toll-like receptor signaling, IL-17 and IL-18 signaling pathways. The study of the gene regulatory network revealed several significant TFs including KLF16, GATA2, YY1 and FOXC1 and miRNAs such as let-7b-5p, mir-16-5p, mir-34a-5p, and mir-155-5p that target differential-expressed genes (DEG). According to the molecular coupling results, kaempferol exhibited a high affinity for 5 receptor proteins (TP53, MAPK1, MAPK3, MAPK8, and TNF) compared to control inhibitors. In combination, our results identified significant targets and pharmacological mechanisms of kaempferol in the treatment of COVID-19/CHIK and recommended that core targets be used as potential biomarkers against COVID-19/CHIK viruses. Before conducting clinical studies for the intervention of COVID-19 and CHIK, kaempferol might be evaluated in wet lab tests at the molecular level.
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Affiliation(s)
- Md Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Md Sohel
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
- Department of Biochemistry and Molecular Biology, Primeasia University, Dhaka, Bangladesh
| | - Tayeba Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Md Imran Hasan
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Sharif Khan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - S M Hasan Mahmud
- Department of Computer Science, Faculty of Science and Technology, American International University-Bangladesh, Dhaka, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, 7003, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligent Research, Islamic University, Kushtia, 7003, Bangladesh
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18
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Onur MR, Özbay Y, İdilman İ, Karaosmanoğlu AD, Uysal Ramadan S, Barlık F, Aydın S, Odaman H, Altay C, Başara Akın I, Dicle O, Appak Ö, Gülpınar B, Erden A, Kula S, Gürsöy Çoruh A, Kuru Öz D, Kul M, Uzun Ç, Karavaş E, Levent A, Artaş H, Eryeşil H, Solmaz O, Öztürk Kaygusuz T, Faraşat M, Kale AB, Düzgün F, Pekindil G, Apaydın FD, Nass Duce M, Balcı Y, Esen K, Sağır Kahraman A, Karaca L, Maraş Özdemir Z, Kahraman B, Tosun M, Nural MS, Çamlıdağ İ, Onar MA, Ballı K, Güler E, Harman M, Elmas NZ, Öztürk C, Güngör Ö, Herek D, Yağcı AB, Erol C, Şeker M, İşlek İ, Can Y, Aslan S, Karadeniz Bilgili MY, Göncüoğlu A, Keleş H, Bekin Sarıkaya PZ, Bakır B, Dağoğlu Kartal MG, Durak G, Yücel Oğuzdoğan G, Alper F, Yalçın A, Gürel S, Alan B, Gündoğdu E, Aydın N, Cansu A, Civan Kuş C, Ofluoğlu Tuncer E, Pişkin FC, Çolakoğlu Er H, Değirmenci B, Özmen MN, Kantarcı M, Karçaaltıncaba M. Evaluation of abdominal computed tomography findings in patients with COVID-19: a multicenter study. Diagn Interv Radiol 2023; 29:414-427. [PMID: 36960669 PMCID: PMC10679620 DOI: 10.4274/dir.2022.221575] [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: 04/09/2022] [Accepted: 07/13/2022] [Indexed: 01/14/2023]
Abstract
PURPOSE To evaluate the frequency of abdominal computed tomography (CT) findings in patients with coronavirus disease-2019 (COVID-19) and interrogate the relationship between abdominal CT findings and patient demographic features, clinical findings, and laboratory test results as well as the CT atherosclerosis score in the abdominal aorta. METHODS This study was designed as a multicenter retrospective study. The abdominal CT findings of 1.181 patients with positive abdominal symptoms from 26 tertiary medical centers with a positive polymerase chain-reaction test for severe acute respiratory syndrome coronavirus 2 were reviewed. The frequency of ischemic and non-ischemic CT findings as well as the association between CT findings, clinical features, and abdominal aortic calcific atherosclerosis score (AA-CAS) were recorded. RESULTS Ischemic and non-ischemic abdominal CT findings were detected in 240 (20.3%) and 328 (27.7%) patients, respectively. In 147 patients (12.4%), intra-abdominal malignancy was present. The most frequent ischemic abdominal CT findings were bowel wall thickening (n = 120; 10.2%) and perivascular infiltration (n = 40; 3.4%). As for non-ischemic findings, colitis (n = 91; 7.7%) and small bowel inflammation (n = 73; 6.2%) constituted the most frequent disease processes. The duration of hospital stay was found to be higher in patients with abdominal CT findings than in patients without any positive findings (13.8 ± 13 vs. 10.4 ± 12.8 days, P < 0.001). The frequency of abdominal CT findings was significantly higher in patients who did not survive the infection than in patients who were discharged after recovery (41.7% vs. 27.4%, P < 0.001). Increased AA-CAS was found to be associated with a higher risk of ischemic conditions in abdominal CT examinations. CONCLUSION Abdominal symptoms in patients with COVID-19 are usually associated with positive CT findings. The presence of ischemic findings on CT correlates with poor COVID-19 outcomes. A high AA-CAS is associated with abdominal ischemic findings in patients with COVID-19.
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Affiliation(s)
- Mehmet Ruhi Onur
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yakup Özbay
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - İlkay İdilman
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | | | - Selma Uysal Ramadan
- Clinic of Radiology, University of Health Sciences Turkey, Ankara Atatürk Sanatorium Training and Research Hospital, Ankara, Turkey
| | - Funda Barlık
- Department of Radiology, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Sonay Aydın
- Department of Radiology, Binali Yıldırım University Faculty of Medicine, Erzincan, Turkey
| | - Hüseyin Odaman
- Department of Radiology, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Canan Altay
- Department of Radiology, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Işıl Başara Akın
- Department of Radiology, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Oğuz Dicle
- Department of Radiology, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Özgür Appak
- Department of Medical Microbiology, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Başak Gülpınar
- Department of Radiology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Ayşe Erden
- Department of Radiology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Sezer Kula
- Department of Radiology, Ankara University Faculty of Medicine, Ankara, Turkey
| | | | - Diğdem Kuru Öz
- Department of Radiology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Melahat Kul
- Department of Radiology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Çağlar Uzun
- Department of Radiology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Erdal Karavaş
- Department of Radiology, Binali Yıldırım University Faculty of Medicine, Erzincan, Turkey
| | - Akın Levent
- Department of Radiology, Binali Yıldırım University Faculty of Medicine, Erzincan, Turkey
| | - Hakan Artaş
- Department of Radiology, Fırat University Faculty of Medicine, Elazığ, Turkey
| | - Hasan Eryeşil
- Department of Radiology, Fırat University Faculty of Medicine, Elazığ, Turkey
| | - Onur Solmaz
- Department of Radiology, Fırat University Faculty of Medicine, Elazığ, Turkey
| | - Türkkan Öztürk Kaygusuz
- Department of Infectious Diseases and Clinical Microbiology, Fırat University Faculty of Medicine, Elazığ, Turkey
| | - Mustafa Faraşat
- Department of Radiology, Celal Bayar University Faculty of Medicine, Manisa, Turkey
| | - Ahmet Burak Kale
- Department of Radiology, Celal Bayar University Faculty of Medicine, Manisa, Turkey
| | - Fatih Düzgün
- Department of Radiology, Celal Bayar University Faculty of Medicine, Manisa, Turkey
| | - Gökhan Pekindil
- Department of Radiology, Celal Bayar University Faculty of Medicine, Manisa, Turkey
| | - F. Demir Apaydın
- Department of Radiology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Meltem Nass Duce
- Department of Radiology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Yüksel Balcı
- Department of Radiology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Kaan Esen
- Department of Radiology, Mersin University Faculty of Medicine, Mersin, Turkey
| | | | - Leyla Karaca
- Department of Radiology, İnönü University Faculty of Medicine, Malatya, Turkey
| | | | - Bayram Kahraman
- Clinic of Radiology, Specialist Doctor Bayram Kahraman Radiology Clinic, Malatya, Turkey
| | - Mesude Tosun
- Department of Radiology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Mehmet Selim Nural
- Department of Radiology, Ondokuz Mayıs University Faculty of Medicine, Samsun, Turkey
| | - İlkay Çamlıdağ
- Department of Radiology, Ondokuz Mayıs University Faculty of Medicine, Samsun, Turkey
| | - Mustafa Arda Onar
- Department of Radiology, Ondokuz Mayıs University Faculty of Medicine, Samsun, Turkey
| | - Kaan Ballı
- Department of Radiology, Ege University Faculty of Medicine, İzmir, Turkey
| | - Ezgi Güler
- Department of Radiology, Ege University Faculty of Medicine, İzmir, Turkey
| | - Mustafa Harman
- Department of Radiology, Ege University Faculty of Medicine, İzmir, Turkey
| | - Nevra Zehra Elmas
- Department of Radiology, Ege University Faculty of Medicine, İzmir, Turkey
| | - Cansu Öztürk
- Clinic of Radiology, University of Health Sciences Turkey, Ankara Atatürk Sanatorium Training and Research Hospital, Ankara, Turkey
| | - Özlem Güngör
- Clinic of Radiology, University of Health Sciences Turkey, Ankara Atatürk Sanatorium Training and Research Hospital, Ankara, Turkey
| | - Duygu Herek
- Department of Radiology, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Ahmet Baki Yağcı
- Department of Radiology, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Cengiz Erol
- Department of Radiology, Medipol University Faculty of Medicine, İstanbul, Turkey
| | - Mehmet Şeker
- Department of Radiology, Medipol University Faculty of Medicine, İstanbul, Turkey
| | - İrem İşlek
- Department of Radiology, Medipol University Faculty of Medicine, İstanbul, Turkey
| | - Yusuf Can
- Department of Radiology, Medipol University Faculty of Medicine, İstanbul, Turkey
| | - Serdar Aslan
- Department of Radiology, Giresun University Faculty of Medicine, Giresun, Turkey
| | | | - Alper Göncüoğlu
- Department of Radiology, Kırıkkale University Faculty of Medicine, Kırıkkale, Turkey
| | - Hatice Keleş
- Department of Internal Medicine, Kırıkkale University Faculty of Medicine, Kırıkkale, Turkey
| | | | - Barış Bakır
- Department of Radiology, İstanbul University, İstanbul Faculty of Medicine, İstanbul, Turkey
| | | | - Görkem Durak
- Department of Radiology, İstanbul University, İstanbul Faculty of Medicine, İstanbul, Turkey
| | - Gülşen Yücel Oğuzdoğan
- Clinic of Radiology, University of Health Sciences Turkey, Başakşehir Çam and Sakura City Hospital, İstanbul, Turkey
| | - Fatih Alper
- Department of Radiology, Atatürk University Faculty of Medicine, Erzurum, Turkey
| | - Ahmet Yalçın
- Department of Radiology, Atatürk University Faculty of Medicine, Erzurum, Turkey
| | - Safiye Gürel
- Department of Radiology, Bolu Abant İzzet Baysal University Faculty of Medicine, Bolu, Turkey
| | - Bircan Alan
- Department of Radiology, Bolu Abant İzzet Baysal University Faculty of Medicine, Bolu, Turkey
| | - Elif Gündoğdu
- Department of Radiology, Eskişehir Osmangazi University Faculty of Medicine, Eskişehir, Turkey
| | - Nevin Aydın
- Department of Radiology, Eskişehir Osmangazi University Faculty of Medicine, Eskişehir, Turkey
| | - Ayşegül Cansu
- Department of Radiology, Karadeniz Technical University Faculty of Medicine, Trabzon, Turkey
| | - Ceyda Civan Kuş
- Clinic of Radiology, Marmara University Training and Research Hospital, İstanbul, Turkey
| | - Elif Ofluoğlu Tuncer
- Clinic of Radiology, University of Health Sciences Turkey, Sultan 2. Abdulhamid Han Training and Research Hospital, İstanbul, Turkey
| | - Ferhat Can Pişkin
- Department of Radiology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - Hale Çolakoğlu Er
- Department of Radiology, Ufuk University Faculty of Medicine, Ankara, Turkey
| | | | - Mustafa Nasuh Özmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Mecit Kantarcı
- Department of Radiology, Binali Yıldırım University Faculty of Medicine, Erzincan, Turkey
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Tian Z, Cen L. Interaction of Biochemical Processes between Chronic Obstructive Pulmonary Disease (COPD), Pulmonary Arterial Hypertension (PAH), and Coronavirus Disease 2019 (COVID-19). Pol J Microbiol 2023; 0:pjm-2023-015. [PMID: 37216361 DOI: 10.33073/pjm-2023-015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 05/24/2023] Open
Abstract
Both pulmonary arterial hypertension (PAH) and chronic obstructive pulmonary disease (COPD) are risk factors for coronavirus disease 2019 (COVID-19). Patients with lung injury and altered pulmonary vascular anatomy or function are more susceptible to infections. The purpose of the study is to ascertain whether individuals with COPD or PAH are affected synergistically by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Data sources for the construction of a protein-protein interaction (PPI) network and the identification of differentially expressed genes (DEGs) included three RNA-seq datasets from the GEO database (GSE147507, GSE106986, and GSE15197). Then, relationships between miRNAs, common DEGs, and transcription factor (TF) genes were discovered. Functional analysis using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other databases, as well as the forecasting of antiviral medications for COPD and PAH patients infected with SARS-CoV-2, were also performed. Eleven common DEGs were found in the three datasets, and their biological functions were primarily enriched in the control of protein modification processes, particularly phosphorylation. Growth factor receptor binding reflects molecular function. KEGG analysis indicated that co-DEGs mainly activate Ras, and PI3K-Akt signaling pathways and act on focal adhesions. NFKB1 interacted with HSA-miR-942 in the TF-miRNA-DEGs synergistic regulatory network. Acetaminophen is considered an effective drug candidate. There are some connections between COPD and PAH and the development of COVID-19. This research could aid in developing COVID-19 vaccines and medication candidates that would work well as COVID-19 therapies.
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20
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Xu Y, Ma Q, Ren J, Chen L, Guo W, Feng K, Zeng Z, Huang T, Cai Y. Using Machine Learning Methods in Identifying Genes Associated with COVID-19 in Cardiomyocytes and Cardiac Vascular Endothelial Cells. Life (Basel) 2023; 13:life13041011. [PMID: 37109540 PMCID: PMC10146712 DOI: 10.3390/life13041011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/02/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) not only causes respiratory system damage, but also imposes strain on the cardiovascular system. Vascular endothelial cells and cardiomyocytes play an important role in cardiac function. The aberrant expression of genes in vascular endothelial cells and cardiomyocytes can lead to cardiovascular diseases. In this study, we sought to explain the influence of respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the gene expression levels of vascular endothelial cells and cardiomyocytes. We designed an advanced machine learning-based workflow to analyze the gene expression profile data of vascular endothelial cells and cardiomyocytes from patients with COVID-19 and healthy controls. An incremental feature selection method with a decision tree was used in building efficient classifiers and summarizing quantitative classification genes and rules. Some key genes, such as MALAT1, MT-CO1, and CD36, were extracted, which exert important effects on cardiac function, from the gene expression matrix of 104,182 cardiomyocytes, including 12,007 cells from patients with COVID-19 and 92,175 cells from healthy controls, and 22,438 vascular endothelial cells, including 10,812 cells from patients with COVID-19 and 11,626 cells from healthy controls. The findings reported in this study may provide insights into the effect of COVID-19 on cardiac cells and further explain the pathogenesis of COVID-19, and they may facilitate the identification of potential therapeutic targets.
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Affiliation(s)
- Yaochen Xu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
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Salehi Z, Rasaee MJ. A Recombinant RBD-Based Phage Vaccine Report: A Solution to the Prevention of New Diseases? Vaccines (Basel) 2023; 11:vaccines11040833. [PMID: 37112745 PMCID: PMC10144462 DOI: 10.3390/vaccines11040833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The safety, inherent immunogenicity, stability, and low-cost production of bacteriophages make them an ideal platform for vaccine development. Most vaccination strategies against COVID-19 have targeted the spike protein of SARS-CoV-2 to generate neutralizing antibodies. P1, a truncated RBD-derived spike protein, has been shown to induce virus-neutralizing antibodies in preclinical studies. In this study, we first investigated whether recombinant phages displaying P1 on the M13 major protein could immunize mice against COVID-19, and second, whether inoculation with 50 µg of purified P1 in addition to the recombinant phages would stimulate the immune systems of the animals. The results showed that the mice that received recombinant phages were immunized against the phage particles, but did not have anti-P1 IgG. In contrast, compared with the negative control, the group that received a combination of P1 protein and recombinant phage was immunized against the P1 protein. In both groups, CD4+ and CD8+ T cells appeared in the lung tissue. These results suggest that the number of antigens on the phage body plays a crucial role in stimulating the immune system against the bacteriophage, although it is immunogenic enough to function as a phage vaccine.
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Affiliation(s)
- Zahra Salehi
- Department of Medical Biotechnology, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Mohammad Javad Rasaee
- Department of Medical Biotechnology, Tarbiat Modares University, Tehran 1411713116, Iran
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Islam MA, Kibria MK, Hossen MB, Reza MS, Tasmia SA, Tuly KF, Mosharof MP, Kabir SR, Kabir MH, Mollah MNH. Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing. Sci Rep 2023; 13:4685. [PMID: 36949176 PMCID: PMC10031699 DOI: 10.1038/s41598-023-31276-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/09/2023] [Indexed: 03/24/2023] Open
Abstract
Some recent studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and idiopathic pulmonary fibrosis (IPF) disease might stimulate each other through the shared genes. Therefore, in this study, an attempt was made to explore common genomic biomarkers for SARS-CoV-2 infections and IPF disease highlighting their functions, pathways, regulators and associated drug molecules. At first, we identified 32 statistically significant common differentially expressed genes (cDEGs) between disease (SARS-CoV-2 and IPF) and control samples of RNA-Seq profiles by using a statistical r-package (edgeR). Then we detected 10 cDEGs (CXCR4, TNFAIP3, VCAM1, NLRP3, TNFAIP6, SELE, MX2, IRF4, UBD and CH25H) out of 32 as the common hub genes (cHubGs) by the protein-protein interaction (PPI) network analysis. The cHubGs regulatory network analysis detected few key TFs-proteins and miRNAs as the transcriptional and post-transcriptional regulators of cHubGs. The cDEGs-set enrichment analysis identified some crucial SARS-CoV-2 and IPF causing common molecular mechanisms including biological processes, molecular functions, cellular components and signaling pathways. Then, we suggested the cHubGs-guided top-ranked 10 candidate drug molecules (Tegobuvir, Nilotinib, Digoxin, Proscillaridin, Simeprevir, Sorafenib, Torin 2, Rapamycin, Vancomycin and Hesperidin) for the treatment against SARS-CoV-2 infections with IFP diseases as comorbidity. Finally, we investigated the resistance performance of our proposed drug molecules compare to the already published molecules, against the state-of-the-art alternatives publicly available top-ranked independent receptors by molecular docking analysis. Molecular docking results suggested that our proposed drug molecules would be more effective compare to the already published drug molecules. Thus, the findings of this study might be played a vital role for diagnosis and therapies of SARS-CoV-2 infections with IPF disease as comorbidity risk.
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Affiliation(s)
- Md Ariful Islam
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Kaderi Kibria
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Bayazid Hossen
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Selim Reza
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Samme Amena Tasmia
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Khanis Farhana Tuly
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Parvez Mosharof
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- School of Business, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Syed Rashel Kabir
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Hadiul Kabir
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Nurul Haque Mollah
- Bioinformatics Lab(Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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Liu JF, Peng WJ, Wu Y, Yang YH, Wu SF, Liu DP, Liu JN, Yang JT. Proteomic and phosphoproteomic characteristics of the cortex, hippocampus, thalamus, lung, and kidney in COVID-19-infected female K18-hACE2 mice. EBioMedicine 2023; 90:104518. [PMID: 36933413 PMCID: PMC10017276 DOI: 10.1016/j.ebiom.2023.104518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Neurological damage caused by coronavirus disease 2019 (COVID-19) has attracted increasing attention. Recently, through autopsies of patients with COVID-19, the direct identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in their central nervous system (CNS) has been reported, indicating that SARS-CoV-2 might directly attack the CNS. The need to prevent COVID-19-induced severe injuries and potential sequelae is urgent, requiring the elucidation of large-scale molecular mechanisms in vivo. METHODS In this study, we performed liquid chromatography-mass spectrometry-based proteomic and phosphoproteomic analyses of the cortex, hippocampus, thalamus, lungs, and kidneys of SARS-CoV-2-infected K18-hACE2 female mice. We then performed comprehensive bioinformatic analyses, including differential analyses, functional enrichment, and kinase prediction, to identify key molecules involved in COVID-19. FINDINGS We found that the cortex had higher viral loads than did the lungs, and the kidneys did not have SARS-COV-2. After SARS-CoV-2 infection, RIG-I-associated virus recognition, antigen processing and presentation, and complement and coagulation cascades were activated to different degrees in all five organs, especially the lungs. The infected cortex exhibited disorders of multiple organelles and biological processes, including dysregulated spliceosome, ribosome, peroxisome, proteasome, endosome, and mitochondrial oxidative respiratory chain. The hippocampus and thalamus had fewer disorders than did the cortex; however, hyperphosphorylation of Mapt/Tau, which may contribute to neurodegenerative diseases, such as Alzheimer's disease, was found in all three brain regions. Moreover, SARS-CoV-2-induced elevation of human angiotensin-converting enzyme 2 (hACE2) was observed in the lungs and kidneys, but not in the three brain regions. Although the virus was not detected, the kidneys expressed high levels of hACE2 and exhibited obvious functional dysregulation after infection. This indicates that SARS-CoV-2 can cause tissue infections or damage via complicated routes. Thus, the treatment of COVID-19 requires a multipronged approach. INTERPRETATION This study provides observations and in vivo datasets for COVID-19-associated proteomic and phosphoproteomic alterations in multiple organs, especially cerebral tissues, of K18-hACE2 mice. In mature drug databases, the differentially expressed proteins and predicted kinases in this study can be used as baits to identify candidate therapeutic drugs for COVID-19. This study can serve as a solid resource for the scientific community. The data in this manuscript will serve as a starting point for future research on COVID-19-associated encephalopathy. FUNDING This study was supported by grants from the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences, the National Natural Science Foundation of China, and the Natural Science Foundation of Beijing.
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Affiliation(s)
- Jiang-Feng Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wan-Jun Peng
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, CAMS and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Yue Wu
- School of Statistics and Data Science, Nankai University, Tianjin 300071, China
| | - Ye-Hong Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Song-Feng Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
| | - Jiang-Ning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, CAMS and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China.
| | - Jun-Tao Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
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Halsey G, Sinha D, Dhital S, Wang X, Vyavahare N. Role of elastic fiber degradation in disease pathogenesis. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166706. [PMID: 37001705 DOI: 10.1016/j.bbadis.2023.166706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
Elastin is a crucial extracellular matrix protein that provides structural integrity to tissues. Crosslinked elastin and associated microfibrils, named elastic fiber, contribute to biomechanics by providing the elasticity required for proper function. During aging and disease, elastic fiber can be progressively degraded and since there is little elastin synthesis in adults, degraded elastic fiber is not regenerated. There is substantial evidence linking loss or damage of elastic fibers to the clinical manifestation and pathogenesis of a variety of diseases. Disruption of elastic fiber networks by hereditary mutations, aging, or pathogenic stimuli results in systemic ailments associated with the production of elastin degradation products, inflammatory responses, and abnormal physiology. Due to its longevity, unique mechanical properties, and widespread distribution in the body, elastic fiber plays a central role in homeostasis of various physiological systems. While pathogenesis related to elastic fiber degradation has been more thoroughly studied in elastic fiber rich tissues such as the vasculature and the lungs, even tissues containing relatively small quantities of elastic fibers such as the eyes or joints may be severely impacted by elastin degradation. Elastic fiber degradation is a common observation in certain hereditary, age, and specific risk factor exposure induced diseases representing a converging point of pathological clinical phenotypes which may also help explain the appearance of co-morbidities. In this review, we will first cover the role of elastic fiber degradation in the manifestation of hereditary diseases then individually explore the structural role and degradation effects of elastic fibers in various tissues and organ systems. Overall, stabilizing elastic fiber structures and repairing lost elastin may be effective strategies to reverse the effects of these diseases.
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Affiliation(s)
- Gregory Halsey
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Dipasha Sinha
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Saphala Dhital
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Xiaoying Wang
- Department of Bioengineering, Clemson University, SC 29634, United States of America
| | - Naren Vyavahare
- Department of Bioengineering, Clemson University, SC 29634, United States of America.
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25
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Burke B, Rocha SM, Zhan S, Eckley M, Reasoner C, Addetia A, Lewis J, Fagre A, Charley P, Richt JA, Weiss SR, Tjalkens RB, Veesler D, Aboellail T, Schountz T. Regulatory T Cell-like Response to SARS-CoV-2 in Jamaican Fruit Bats ( Artibeus jamaicensis ) Transduced with Human ACE2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528205. [PMID: 36824814 PMCID: PMC9949052 DOI: 10.1101/2023.02.13.528205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Insectivorous Old World horseshoe bats ( Rhinolophus spp.) are the likely source of the ancestral SARS-CoV-2 prior to its spillover into humans and causing the COVID-19 pandemic. Natural coronavirus infections of bats appear to be principally confined to the intestines, suggesting fecal-oral transmission; however, little is known about the biology of SARS-related coronaviruses in bats. Previous experimental challenges of Egyptian fruit bats ( Rousettus aegyptiacus ) resulted in limited infection restricted to the respiratory tract, whereas insectivorous North American big brown bats ( Eptesicus fuscus ) showed no evidence of infection. In the present study, we challenged Jamaican fruit bats ( Artibeus jamaicensis ) with SARS-CoV-2 to determine their susceptibility. Infection was confined to the intestine for only a few days with prominent viral nucleocapsid antigen in epithelial cells, and mononuclear cells of the lamina propria and Peyer's patches, but with no evidence of infection of other tissues; none of the bats showed visible signs of disease or seroconverted. Expression levels of ACE2 were low in the lungs, which may account for the lack of pulmonary infection. Bats were then intranasally inoculated with a replication-defective adenovirus encoding human ACE2 and 5 days later challenged with SARS-CoV-2. Viral antigen was prominent in lungs for up to 14 days, with loss of pulmonary cellularity during this time; however, the bats did not exhibit weight loss or visible signs of disease. From day 7, bats had low to moderate IgG antibody titers to spike protein by ELISA, and one bat on day 10 had low-titer neutralizing antibodies. CD4 + helper T cells became activated upon ex vivo recall stimulation with SARS-CoV-2 nucleocapsid peptide library and exhibited elevated mRNA expression of the regulatory T cell cytokines interleukin-10 and transforming growth factor-β, which may have limited inflammatory pathology. Collectively, these data show that Jamaican fruit bats are poorly susceptibility to SARS-CoV-2 but that expression of human ACE2 in their lungs leads to robust infection and an adaptive immune response with low-titer antibodies and a regulatory T cell-like response that may explain the lack of prominent inflammation in the lungs. This model will allow for insight of how SARS-CoV-2 infects bats and how bat innate and adaptive immune responses engage the virus without overt clinical disease. Author Summary Bats are reservoir hosts of many viruses that infect humans, yet little is known about how they host these viruses, principally because of a lack of relevant and susceptible bat experimental infection models. Although SARS-CoV-2 originated in bats, no robust infection models of bats have been established. We determined that Jamaican fruit bats are poorly susceptible to SARS-CoV-2; however, their lungs can be transduced with human ACE2, which renders them susceptible to SARS-CoV-2. Despite robust infection of the lungs and diminishment of pulmonary cellularity, the bats showed no overt signs of disease and cleared the infection after two weeks. Despite clearance of infection, only low-titer antibody responses occurred and only a single bat made neutralizing antibody. Assessment of the CD4 + helper T cell response showed that activated cells expressed the regulatory T cell cytokines IL-10 and TGFβ that may have tempered pulmonary inflammation.
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Fu J, Yang Q, Luo Y, Zhang S, Tang J, Zhang Y, Zhang H, Xu H, Zhu F. Label-free proteome quantification and evaluation. Brief Bioinform 2023; 24:6833644. [PMID: 36403090 DOI: 10.1093/bib/bbac477] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/24/2022] [Accepted: 10/08/2022] [Indexed: 11/21/2022] Open
Abstract
The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on >3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Song Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Tang
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hanxiang Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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Macedo-da-Silva J, Rosa-Fernandes L, Gomes VDM, Santiago VF, Santos DM, Molnar CMS, Barboza BR, de Souza EE, Marques RF, Boscardin SB, Durigon EL, Marinho CRF, Wrenger C, Marie SKN, Palmisano G. Protein Arginylation Is Regulated during SARS-CoV-2 Infection. Viruses 2023; 15:v15020290. [PMID: 36851505 PMCID: PMC9964439 DOI: 10.3390/v15020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In 2019, the world witnessed the onset of an unprecedented pandemic. By February 2022, the infection by SARS-CoV-2 has already been responsible for the death of more than 5 million people worldwide. Recently, we and other groups discovered that SARS-CoV-2 infection induces ER stress and activation of the unfolded protein response (UPR) pathway. Degradation of misfolded/unfolded proteins is an essential element of proteostasis and occurs mainly in lysosomes or proteasomes. The N-terminal arginylation of proteins is characterized as an inducer of ubiquitination and proteasomal degradation by the N-degron pathway. RESULTS The role of protein arginylation during SARS-CoV-2 infection was elucidated. Protein arginylation was studied in Vero CCL-81, macrophage-like THP1, and Calu-3 cells infected at different times. A reanalysis of in vivo and in vitro public omics data combined with immunoblotting was performed to measure levels of arginyl-tRNA-protein transferase (ATE1) and its substrates. Dysregulation of the N-degron pathway was specifically identified during coronavirus infections compared to other respiratory viruses. We demonstrated that during SARS-CoV-2 infection, there is an increase in ATE1 expression in Calu-3 and Vero CCL-81 cells. On the other hand, infected macrophages showed no enzyme regulation. ATE1 and protein arginylation was variant-dependent, as shown using P1 and P2 viral variants and HEK 293T cells transfection with the spike protein and receptor-binding domains (RBD). In addition, we report that ATE1 inhibitors, tannic acid and merbromine (MER) reduce viral load. This finding was confirmed in ATE1-silenced cells. CONCLUSIONS We demonstrate that ATE1 is increased during SARS-CoV-2 infection and its inhibition has potential therapeutic value.
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Affiliation(s)
- Janaina Macedo-da-Silva
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Vinicius de Morais Gomes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Deivid Martins Santos
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | | | - Bruno Rafael Barboza
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Edmarcia Elisa de Souza
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Rodolfo Ferreira Marques
- Laboratory of Antigen Targeting for Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Silvia Beatriz Boscardin
- Laboratory of Antigen Targeting for Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Edison Luiz Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo 05508-000, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo 05508-000, Brazil
- School of Natural Sciences, Macquarie University, Sydney 2109, Australia
- Correspondence: or ; Tel.: +55-11-99920-8662
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COVID-19-associated monocytic encephalitis (CAME): histological and proteomic evidence from autopsy. Signal Transduct Target Ther 2023; 8:24. [PMID: 36609561 PMCID: PMC9816522 DOI: 10.1038/s41392-022-01291-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Severe neurological symptoms are associated with Coronavirus disease 2019 (COVID-19). However, the morphologic features, pathological nature and their potential mechanisms in patient brains have not been revealed despite evidence of neurotropic infection. In this study, neuropathological damages and infiltrating inflammatory cells were quantitatively evaluated by immunohistochemical staining, ultrastructural examination under electron microscopy, and an image threshold method, in postmortem brains from nine critically ill COVID-19 patients and nine age-matched cadavers of healthy individuals. Differentially expressed proteins were identified by quantitative proteomic assays. Histopathological findings included neurophagocytosis, microglia nodules, satellite phenomena, extensive edema, focal hemorrhage, and infarction, as well as infiltrating mononuclear cells. Immunostaining of COVID-19 brains revealed extensive activation of both microglia and astrocytes, severe damage of the blood-brain barrier (BBB) and various degrees of perivascular infiltration by predominantly CD14+/CD16+/CD141+/CCR7+/CD11c+ monocytes and occasionally CD4+/CD8+ T lymphocytes. Quantitative proteomic assays combined with bioinformatics analysis identified upregulated proteins predominantly involved in immune responses, autophagy and cellular metabolism in COVID-19 patient brains compared with control brains. Proteins involved in brain development, neuroprotection, and extracellular matrix proteins of the basement membrane were downregulated, potentially caused by the activation of transforming growth factor β receptor and vascular endothelial growth factor signaling pathways. Thus, our results define histopathological and molecular profiles of COVID-19-associated monocytic encephalitis (CAME) and suggest potential therapeutic targets.
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Huang JJ, Wang CW, Liu Y, Zhang YY, Yang NB, Yu YC, Jiang Q, Song QF, Qian GQ. Role of the extracellular matrix in COVID-19. World J Clin Cases 2023; 11:73-83. [PMID: 36687194 PMCID: PMC9846981 DOI: 10.12998/wjcc.v11.i1.73] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
An outbreak of coronavirus disease 2019 (COVID-19) has spread globally, with over 500 million cases and 6 million deaths to date. COVID-19 is associated with a systemic inflammatory response and abnormalities of the extracellular matrix (ECM), which is also involved in inflammatory storms. Upon viral infection, ECM proteins are involved in the recruitment of inflammatory cells and interference with target organ metabolism, including in the lungs. Additionally, serum biomarkers of ECM turnover are associated with the severity of COVID-19 and may serve as potential targets. Consequently, understanding the expression and function of ECM, particularly of the lung, during severe acute respiratory syndrome of the coronavirus 2 infection would provide valuable insights into the mechanisms of COVID-19 progression. In this review, we summarize the current findings on ECM, such as hyaluronic acid, matrix metalloproteinases, and collagen, which are linked to the severity and inflammation of COVID-19. Some drugs targeting the extracellular surface have been effective. In the future, these ECM findings could provide novel perspectives on the pathogenesis and treatment of COVID-19.
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Affiliation(s)
- Jia-Jia Huang
- School of Medicine, Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Chu-Wen Wang
- School of Medicine, Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Ying Liu
- School of Medicine, Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Ying-Ying Zhang
- School of Medicine, Ningbo University, Ningbo 315000, Zhejiang Province, China
| | - Nai-Bin Yang
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China
| | - Yu-Chun Yu
- Department of Endocrinology, Ningbo Ninth Hospital, Ningbo 315000, Zhejiang Province, China
| | - Qi Jiang
- Department of Digestive, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China
| | - Qi-Fa Song
- Medical Data Center, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China
| | - Guo-Qing Qian
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo 315000, Zhejiang Province, China
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Pathogenetic Mechanisms of Liver-Associated Injuries, Management, and Current Challenges in COVID-19 Patients. Biomolecules 2023; 13:biom13010099. [PMID: 36671484 PMCID: PMC9855873 DOI: 10.3390/biom13010099] [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: 11/11/2022] [Revised: 11/28/2022] [Accepted: 12/10/2022] [Indexed: 01/06/2023] Open
Abstract
The global outbreak of COVID-19 possesses serious challenges and adverse impacts for patients with progression of chronic liver disease and has become a major threat to public health. COVID-19 patients have a high risk of lung injury and multiorgan dysfunction that remains a major challenge to hepatology. COVID-19 patients and those with liver injury exhibit clinical manifestations, including elevation in ALT, AST, GGT, bilirubin, TNF-α, and IL-6 and reduction in the levels of CD4 and CD8. Liver injury in COVID-19 patients is induced through multiple factors, including a direct attack of SARS-CoV-2 on liver hepatocytes, hypoxia reperfusion dysfunction, cytokine release syndrome, drug-induced hepatotoxicity caused by lopinavir and ritonavir, immune-mediated inflammation, renin-angiotensin system, and coagulopathy. Cellular and molecular mechanisms underlying liver dysfunction are not fully understood in severe COVID-19 attacks. High mortality and the development of chronic liver diseases such as cirrhosis, alcoholic liver disease, autoimmune hepatitis, nonalcoholic fatty liver disease, and hepatocellular carcinoma are also associated with patients with liver damage. COVID-19 patients with preexisting or developing liver disease should be managed. They often need hospitalization and medication, especially in conjunction with liver transplants. In the present review, we highlight the attack of SARS-CoV-2 on liver hepatocytes by exploring the cellular and molecular events underlying the pathophysiological mechanisms in COVID-19 patients with liver injury. We also discuss the development of chronic liver diseases during the progression of SARS-CoV-2 replication. Lastly, we explore management principles in COVID-19 patients with liver injury and liver transplantation.
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Aktar S, Amin S. SARS-CoV-2 mediated dysregulation in cell signaling events drives the severity of COVID-19. Virus Res 2023; 323:198962. [PMID: 36209917 PMCID: PMC9536871 DOI: 10.1016/j.virusres.2022.198962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 01/25/2023]
Abstract
A balance in immune response against an unfamiliar pathogen is crucial to eliminate the infection. A cascade of cell signaling events is immediately activated upon sensing the presence of SARS-CoV-2 by cellular toll like receptors in a natural host response manner against the invading virus. The ultimate aim of such innate immune signaling pathways is to provide a required level of protection to our bodies by interfering with the invader. However, if there is any loss in such balance, an impairment in immune system emerge that fails to control the regulated transcription and translation of signaling components. Consequently, excessive level of proinflammatory mediators release into the circulatory systems that ultimately cause "cytokine storm" and COVID-19 pathological syndromes. The limited production of interferons (IFNs), while excessive yield of pro-inflammatory cytokines followed by SARS-CoV-2 infection suggests an abnormal cell signaling event and explains the reasons of increased immunopathology and severity in COVID-19.
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Affiliation(s)
- Salma Aktar
- Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh.
| | - Saiful Amin
- Chittagong Medical University, Chattogram, Bangladesh
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Zuliani-Alvarez L, Piccinini AM. A virological view of tenascin-C in infection. Am J Physiol Cell Physiol 2023; 324:C1-C9. [PMID: 36458980 PMCID: PMC9762962 DOI: 10.1152/ajpcell.00333.2022] [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] [Indexed: 12/03/2022]
Abstract
Tenascin-C is a large extracellular matrix glycoprotein with complex, not yet fully unveiled roles. Its context- and structure-dependent modus operandi renders tenascin-C a puzzling protein. Since its discovery ∼40 years ago, research into tenascin-C biology continues to reveal novel functions, the most recent of all being its immunomodulatory activity, especially its role in infection, which is just now beginning to emerge. Here, we explore the role of tenascin-C in the immune response to viruses, including SARS-CoV-2 and HIV-1. Recently, tenascin-C has emerged as a biomarker of disease severity during COVID-19 and other viral infections, and we highlight relevant RNA sequencing and proteomic analyses that suggest a correlation between tenascin-C levels and disease severity. Finally, we ask what the function of this protein during viral replication is and propose tenascin-C as an intercellular signal of inflammation shuttled to distal sites via exosomes, a player in the repair and remodeling of infected and damaged tissues during severe infectious disease, as well as a ligand for specific pathogens with distinct implications for the host.
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Affiliation(s)
- Lorena Zuliani-Alvarez
- 1QBI Coronavirus Research Group, San Francisco, California,2Quantitative Biosciences Institute, University of California, San Francisco, California,3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
| | - Anna M. Piccinini
- 4School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
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Li C, Li Y, Zhang H, Zhuo Y, Zhang L, Yang L, Gao Q, Tu Z, Shao R, Wang Y, Zhang J, Cui L, Zhang S. Xuanfei Baidu Decoction suppresses complement overactivation and ameliorates IgG immune complex-induced acute lung injury by inhibiting JAK2/STAT3/SOCS3 and NF-κB signaling pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 109:154551. [PMID: 36610119 PMCID: PMC9678227 DOI: 10.1016/j.phymed.2022.154551] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/19/2022] [Accepted: 11/14/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND The significant clinical efficacy of Xuanfei Baidu Decoction (XFBD) is proven in the treatment of patients with coronavirus disease 2019 (COVID-19) in China. However, the mechanisms of XFBD against acute lung injury (ALI) are still poorly understood. METHODS In vivo, the mouse model of ALI was induced by IgG immune complexes (IgG-IC), and then XFBD (4g/kg, 8g/kg) were administered by gavage respectively. 24 h after inducing ALI, the lungs were collected for histological and molecular analysis. In vitro, alveolar macrophages inflammation models induced by IgG-IC were performed and treated with different dosage of XFBD-containing serum to investigate the protective role and molecular mechanisms of XFBD. RESULTS The results revealed that XFBD mitigated lung injury and significantly downregulated the production of pro-inflammatory mediators in lung tissues and macrophages upon IgG-IC stimulation. Notably, XFBD attenuated C3a and C5a generation, inhibited the expression of C3aR and C5aR and suppressed the activation of JAK2/STAT3/SOCS3 and NF-κB signaling pathway in lung tissues and macrophages induced by IgG-IC. Moreover, in vitro experiments, we verified that Colivelin TFA (CAF, STAT3 activator) and C5a treatment markedly elevated the IgG-IC-triggered inflammatory responses in macrophages and XFBD weakened the effects of CAF or C5a. CONCLUSION XFBD suppressed complement overactivation and ameliorated IgG immune complex-induced acute lung injury by inhibiting JAK2/STAT3/SOCS3 and NF-κB signaling pathway. These data contribute to understanding the mechanisms of XFBD in COVID-19 treatment.
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Affiliation(s)
- Caixia Li
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
| | - Yuhong Li
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Han Zhang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yuzhen Zhuo
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
| | - Lanqiu Zhang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
| | - Lei Yang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
| | - Qiaoying Gao
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
| | - Zhengwei Tu
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
| | - Rui Shao
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yu Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Junhua Zhang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Lihua Cui
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China.
| | - Shukun Zhang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Integrated Traditional Chinese and Western Medicine Hospital, Tianjin Nankai Hospital; Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China.
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Rizvi ZA, Babele P, Madan U, Sadhu S, Tripathy MR, Goswami S, Mani S, Dikshit M, Awasthi A. Pharmacological potential of Withania somnifera (L.) Dunal and Tinospora cordifolia (Willd.) Miers on the experimental models of COVID-19, T cell differentiation, and neutrophil functions. Front Immunol 2023; 14:1138215. [PMID: 36960064 PMCID: PMC10028191 DOI: 10.3389/fimmu.2023.1138215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Cytokine release syndrome (CRS) due to severe acute respiratory coronavirus-2 (SARS-CoV-2) infection leads to life-threatening pneumonia which has been associated with coronavirus disease (COVID-19) pathologies. Centuries-old Asian traditional medicines such as Withania somnifera (L.) Dunal (WS) and Tinospora cordifolia (Willd.) Miers (TC) possess potent immunomodulatory effects and were used by the AYUSH ministry, in India during the COVID-19 pandemic. In the present study, we investigated WS and TC's anti-viral and immunomodulatory efficacy at the human equivalent doses using suitable in vitro and in vivo models. While both WS and TC showed immuno-modulatory potential, WS showed robust protection against loss in body weight, viral load, and pulmonary pathology in the hamster model of SARS-CoV2. In vitro pretreatment of mice and human neutrophils with WS and TC had no adverse effect on PMA, calcium ionophore, and TRLM-induced ROS generation, phagocytosis, bactericidal activity, and NETs formation. Interestingly, WS significantly suppressed the pro-inflammatory cytokines-induced Th1, Th2, and Th17 differentiation. We also used hACE2 transgenic mice to further investigate the efficacy of WS against acute SARS-CoV2 infection. Prophylactic treatment of WS in the hACE2 mice model showed significant protection against body weight loss, inflammation, and the lung viral load. The results obtained indicate that WS promoted the immunosuppressive environment in the hamster and hACE2 transgenic mice models and limited the worsening of the disease by reducing inflammation, suggesting that WS might be useful against other acute viral infections. The present study thus provides pre-clinical efficacy data to demonstrate a robust protective effect of WS against COVID-19 through its broader immunomodulatory activity.
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Affiliation(s)
- Zaigham Abbas Rizvi
- Immuno-biology Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- *Correspondence: Amit Awasthi, ; Madhu Dikshit, ; ; Zaigham Abbas Rizvi,
| | - Prabhakar Babele
- NCD, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Upasna Madan
- Immuno-biology Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Srikanth Sadhu
- Immuno-biology Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Manas Ranjan Tripathy
- Immuno-biology Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Sandeep Goswami
- Immuno-biology Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Shailendra Mani
- NCD, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Madhu Dikshit
- NCD, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, Faridabad, Haryana, India
- Pharmacology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- *Correspondence: Amit Awasthi, ; Madhu Dikshit, ; ; Zaigham Abbas Rizvi,
| | - Amit Awasthi
- Immuno-biology Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Immunology-Core Lab, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, Faridabad, Haryana, India
- *Correspondence: Amit Awasthi, ; Madhu Dikshit, ; ; Zaigham Abbas Rizvi,
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Gindlhuber J, Tomin T, Wiesenhofer F, Zacharias M, Liesinger L, Demichev V, Kratochwill K, Gorkiewicz G, Schittmayer M, Birner-Gruenberger R. Proteomic profiling of end-stage COVID-19 lung biopsies. Clin Proteomics 2022; 19:46. [PMID: 36526981 PMCID: PMC9758034 DOI: 10.1186/s12014-022-09386-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The outbreak of a novel coronavirus (SARS-CoV-2) in 2019 led to a worldwide pandemic, which remains an integral part of our lives to this day. Coronavirus disease (COVID-19) is a flu like condition, often accompanied by high fever and respiratory distress. In some cases, conjointly with other co-morbidities, COVID-19 can become severe, leading to lung arrest and even death. Although well-known from a clinical standpoint, the mechanistic understanding of lethal COVID-19 is still rudimentary. Studying the pathology and changes on a molecular level associated with the resulting COVID-19 disease is impeded by the highly infectious nature of the virus and the concomitant sampling challenges. We were able to procure COVID-19 post-mortem lung tissue specimens by our collaboration with the BSL-3 laboratory of the Biobanking and BioMolecular resources Research Infrastructure Austria which we subjected to state-of-the-art quantitative proteomic analysis to better understand the pulmonary manifestations of lethal COVID-19. Lung tissue samples from age-matched non-COVID-19 patients who died within the same period were used as controls. Samples were subjected to parallel accumulation-serial fragmentation combined with data-independent acquisition (diaPASEF) on a timsTOF Pro and obtained raw data was processed using DIA-NN software. Here we report that terminal COVID-19 patients display an increase in inflammation, acute immune response and blood clot formation (with concomitant triggering of fibrinolysis). Furthermore, we describe that COVID-19 diseased lungs undergo severe extracellular matrix restructuring, which was corroborated on the histopathological level. However, although undergoing an injury, diseased lungs seem to have impaired proliferative and tissue repair signalling, with several key kinase-mediated signalling pathways being less active. This might provide a mechanistic link to post-acute sequelae of COVID-19 (PASC; "Long COVID"). Overall, we emphasize the importance of histopathological patient stratification when interpreting molecular COVID-19 data.
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Affiliation(s)
- Juergen Gindlhuber
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Tamara Tomin
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Vienna, Austria
| | - Florian Wiesenhofer
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Martin Zacharias
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Laura Liesinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Vadim Demichev
- Institute of Biochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Klaus Kratochwill
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Gregor Gorkiewicz
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Vienna, Austria.
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria.
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Vienna, Austria.
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Kamalabadi M, Ghoorchian A, Derakhshandeh K, Gholyaf M, Ravan M. Design and Fabrication of a Gas Sensor Based on a Polypyrrole/Silver Nanoparticle Film for the Detection of Ammonia in Exhaled Breath of COVID-19 Patients Suffering from Acute Kidney Injury. Anal Chem 2022; 94:16290-16298. [DOI: 10.1021/acs.analchem.2c02760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Mahdie Kamalabadi
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
- Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
| | - Arash Ghoorchian
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
- Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
| | - Katayoun Derakhshandeh
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
- Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
| | - Mahmoud Gholyaf
- Urology & Nephrology Research Center, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
| | - Maryam Ravan
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran
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More TH, Mozafari B, Märtens A, Herr C, Lepper PM, Danziger G, Volk T, Hoersch S, Krawczyk M, Guenther K, Hiller K, Bals R. Plasma Metabolome Alterations Discriminate between COVID-19 and Non-COVID-19 Pneumonia. Metabolites 2022; 12:1058. [PMID: 36355140 PMCID: PMC9693035 DOI: 10.3390/metabo12111058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 03/10/2024] Open
Abstract
Pneumonia is a common cause of morbidity and mortality and is most often caused by bacterial pathogens. COVID-19 is characterized by lung infection with potential progressive organ failure. The systemic consequences of both disease on the systemic blood metabolome are not fully understood. The aim of this study was to compare the blood metabolome of both diseases and we hypothesize that plasma metabolomics may help to identify the systemic effects of these diseases. Therefore, we profiled the plasma metabolome of 43 cases of COVID-19 pneumonia, 23 cases of non-COVID-19 pneumonia, and 26 controls using a non-targeted approach. Metabolic alterations differentiating the three groups were detected, with specific metabolic changes distinguishing the two types of pneumonia groups. A comparison of venous and arterial blood plasma samples from the same subjects revealed the distinct metabolic effects of pulmonary pneumonia. In addition, a machine learning signature of four metabolites was predictive of the disease outcome of COVID-19 subjects with an area under the curve (AUC) of 86 ± 10 %. Overall, the results of this study uncover systemic metabolic changes that could be linked to the etiology of COVID-19 pneumonia and non-COVID-19 pneumonia.
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Affiliation(s)
- Tushar H. More
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Bahareh Mozafari
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Andre Märtens
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Christian Herr
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Philipp M. Lepper
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Guy Danziger
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Thomas Volk
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Saarland University, 66421 Homburg, Germany
| | - Sabrina Hoersch
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Saarland University, 66421 Homburg, Germany
| | - Marcin Krawczyk
- Department of Internal Medicine II-Gastroenterology, Saarland University, 66421 Homburg, Germany
| | - Katharina Guenther
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Robert Bals
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, 66421 Homburg, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
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Hou N, Wang L, Li M, Xie B, He L, Guo M, Liu S, Wang M, Zhang R, Wang K. Do COVID-19 CT features vary between patients from within and outside mainland China? Findings from a meta-analysis. Front Public Health 2022; 10:939095. [PMID: 36311632 PMCID: PMC9616120 DOI: 10.3389/fpubh.2022.939095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 07/25/2022] [Indexed: 01/25/2023] Open
Abstract
Background Chest computerized tomography (CT) plays an important role in detecting patients with suspected coronavirus disease 2019 (COVID-19), however, there are no systematic summaries on whether the chest CT findings of patients within mainland China are applicable to those found in patients outside. Methods Relevant studies were retrieved comprehensively by searching PubMed, Embase, and Cochrane Library databases before 15 April 2022. Quality assessment of diagnostic accuracy studies (QUADAS) was used to evaluate the quality of the included studies, which were divided into two groups according to whether they were in mainland China or outside. Data on diagnostic performance, unilateral or bilateral lung involvement, and typical chest CT imaging appearances were extracted, and then, meta-analyses were performed with R software to compare the CT features of COVID-19 pneumonia between patients from within and outside mainland China. Results Of the 8,258 studies screened, 19 studies with 3,400 patients in mainland China and 14 studies with 554 outside mainland China were included. Overall, the risk of quality assessment and publication bias was low. The diagnostic value of chest CT is similar between patients from within and outside mainland China (93, 91%). The pooled incidence of unilateral lung involvement (15, 7%), the crazy-paving sign (31, 21%), mixed ground-glass opacities (GGO) and consolidations (51, 35%), air bronchogram (44, 25%), vascular engorgement (59, 33%), bronchial wall thickening (19, 12%), and septal thickening (39, 26%) in patients from mainland China were significantly higher than those from outside; however, the incidence rates of bilateral lung involvement (75, 84%), GGO (78, 87%), consolidations (45, 58%), nodules (12, 17%), and pleural effusion (9, 15%) were significantly lower. Conclusion Considering that the chest CT features of patients in mainland China may not reflect those of the patients abroad, radiologists and clinicians should be familiar with various CT presentations suggestive of COVID-19 in different regions.
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Affiliation(s)
- Nianzong Hou
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai, China,Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Lin Wang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Mingzhe Li
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Bing Xie
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Lu He
- Department of Urology, Dongfeng Hospital, Hubei University of Medicine, Shiyan, China
| | - Mingyu Guo
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Shuo Liu
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Meiyu Wang
- Department of Cardiology, The People's Hospital of Zhangdian District, Zibo, China
| | - Rumin Zhang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Kai Wang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China,*Correspondence: Kai Wang
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Li P, Liu Y, Cheng Z, Yu X, Li Y. COVID-19-associated liver injury: Clinical characteristics, pathophysiological mechanisms and treatment management. Biomed Pharmacother 2022; 154:113568. [PMID: 36029543 PMCID: PMC9381432 DOI: 10.1016/j.biopha.2022.113568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has become a global epidemic and poses a major threat to public health. In addition to COVID-19 manifesting as a respiratory disease, patients with severe disease also have complications in extrapulmonary organs, including liver damage. Abnormal liver function is relatively common in COVID-19 patients; its clinical manifestations can range from an asymptomatic elevation of liver enzymes to decompensated hepatic function, and liver injury is more prevalent in severe and critical patients. Liver injury in COVID-19 patients is a comprehensive effect mediated by multiple factors, including liver damage directly caused by SARS-CoV-2, drug-induced liver damage, hypoxia reperfusion dysfunction, immune stress and inflammatory factor storms. Patients with chronic liver disease (especially alcohol-related liver disease, nonalcoholic fatty liver disease, cirrhosis and hepatocellular carcinoma) are at increased risk of severe disease and death after infection with SARS-CoV-2, and COVID-19 aggravates liver damage in patients with chronic liver disease. This article reviews the latest SARS-CoV-2 reports, focusing on the liver damage caused by COVID-19 and the underlying mechanism, and expounds on the risk, treatment and vaccine safety of SARS-CoV-2 in patients with chronic liver disease and liver transplantation.
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Affiliation(s)
- Penghui Li
- Center for Health Research, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Liu
- Center for Health Research, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ziqi Cheng
- Center for Health Research, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaorui Yu
- Center for Health Research, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yinxiong Li
- Center for Health Research, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; State Key Laboratory of Respiratory Disease, Guangzhou, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China.
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Alnamshan MM. Potential histopathological and immunological effects of SARS-CoV-2 on the liver. BRAZ J BIOL 2022; 82:e262008. [PMID: 36074418 DOI: 10.1590/1519-6984.262008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022] Open
Abstract
The coronavirus disease outbreak of 2019 (COVID-19) poses a serious threat to public health worldwide. Lung injury is the most common complication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. However, other organs, including the liver, can also be affected. Currently, there is limited evidence that liver impairment is associated with severe SARS-CoV-2 infection. Clinicians will need to determine whether liver injury is caused by an underlying liver condition, COVID-19 therapy, the virus directly, or immune-mediated inflammation or represents a complicated disease course in the context of COVID-19. To address the scarcity of data on histopathological changes and immunological effects on the liver with COVID-19 positivity, we analyze and summarize recent findings. We searched PubMed, Medline, Google Scholar, Science Direct, Scopus, and Web of Science databases up to December 1, 2021, identifying published studies with the search terms "Histopathology in COVID-19," "COVID-19," "Pathological changes in liver in COVID-19," "Liver pathology in COVID-19," "immunological effects in liver in COVID-19," and "SARS-CoV-2." This concise review will aid clinicians and researchers in better understanding the tissue histopathology and immunological consequences of SARS-CoV-2 on the liver, enabling improved care planning and avoiding future dangers.
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Affiliation(s)
- M M Alnamshan
- Imam Abdulrahman Bin Faisal University, College of Science, Department of Biology, Dammam, Saudi Arabia
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Wybranowski T, Pyskir J, Bosek M, Napiórkowska M, Cyrankiewicz M, Ziomkowska B, Pilaczyńska-Cemel M, Pyskir M, Rogańska M, Kruszewski S, Przybylski G. The Mortality Risk and Pulmonary Fibrosis Investigated by Time-Resolved Fluorescence Spectroscopy from Plasma in COVID-19 Patients. J Clin Med 2022; 11:jcm11175081. [PMID: 36079011 PMCID: PMC9457233 DOI: 10.3390/jcm11175081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/10/2022] [Accepted: 08/26/2022] [Indexed: 01/18/2023] Open
Abstract
A method of rapidly pointing out the risk of developing persistent pulmonary fibrosis from a sample of blood is extraordinarily needed for diagnosis, prediction of death, and post-infection prognosis assessment. Collagen scar formation has been found to play an important role in the lung remodeling following SARS-CoV-2 infection. For this reason, the concentration of collagen degradation products in plasma may reflect the process of lung remodeling and determine the extent of fibrosis. According to our previously published results of an in vitro study, an increase in the concentration of type III collagen degradation products in plasma resulted in a decrease in the fluorescence lifetime of plasma at a wavelength of 450 nm. The aim of this study was to use time-resolved fluorescence spectroscopy to assess pulmonary fibrosis, and to find out if the lifetime of plasma fluorescence is shortened in patients with COVID-19. The presented study is thus far the only one to explore the fluorescence lifetime of plasma in patients with COVID-19 and pulmonary fibrosis. The time-resolved spectrometer Life Spec II with the sub-nanosecond pulsed 360 nm EPLED® diode was used in order to measure the fluorescence lifetime of plasma. The survival analysis showed that COVID-19 mortality was associated with a decreased mean fluorescence lifetime of plasma. The AUC of mean fluorescence lifetime in predicting death was 0.853 (95% CI 0.735−0.972, p < 0.001) with a cut-off value of 7 ns, and with 62% sensitivity and 100% specificity. We observed a significant decrease in the mean fluorescence lifetime in COVID-19 non-survivors (p < 0.001), in bacterial pneumonia patients without COVID-19 (p < 0.001), and in patients diagnosed with idiopathic pulmonary fibrosis (p < 0.001), relative to healthy subjects. Furthermore, these results suggest that the development of pulmonary fibrosis may be a real and serious problem in former COVID-19 patients in the future. A reduction in the mean fluorescence lifetime of plasma was observed in many patients 6 months after discharge. On the basis of these data, it can be concluded that a decrease in the mean fluorescence lifetime of plasma at 450 nm may be a risk factor for mortality, and probably also for pulmonary fibrosis in hospitalized COVID-19 patients.
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Affiliation(s)
- Tomasz Wybranowski
- Biophysics Department, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Jerzy Pyskir
- Biophysics Department, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Maciej Bosek
- Biophysics Department, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Marta Napiórkowska
- Biophysics Department, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Michał Cyrankiewicz
- Biophysics Department, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Blanka Ziomkowska
- Biophysics Department, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Marta Pilaczyńska-Cemel
- Department of Lung Diseases, Neoplasms and Tuberculosis, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Małgorzata Pyskir
- Department of Rehabilitation, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Milena Rogańska
- Department of Lung Diseases, Neoplasms and Tuberculosis, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Stefan Kruszewski
- Biophysics Department, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
| | - Grzegorz Przybylski
- Department of Lung Diseases, Neoplasms and Tuberculosis, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-067 Bydgoszcz, Poland
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Zhang N, Wang S, Wong CC. Proteomics research of SARS-CoV-2 and COVID-19 disease. MEDICAL REVIEW (BERLIN, GERMANY) 2022; 2:427-445. [PMID: 37724330 PMCID: PMC10388787 DOI: 10.1515/mr-2022-0016] [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: 06/05/2022] [Accepted: 07/06/2022] [Indexed: 09/20/2023]
Abstract
Currently, coronavirus disease 2019 (COVID-19) is still spreading in a global scale, exerting a massive health and socioeconomic crisis. Deep insights into the molecular functions of the viral proteins and the pathogenesis of this infectious disease are urgently needed. In this review, we comprehensively describe the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and summarize their protein interaction map with host cells. In the protein interaction network between the virus and the host, a total of 787 host prey proteins that appeared in at least two studies or were verified by co-immunoprecipitation experiments. Together with 29 viral proteins, a network of 1762 proximal interactions were observed. We also review the proteomics results of COVID-19 patients and proved that SARS-CoV-2 hijacked the host's translation system, post-translation modification system, and energy supply system via viral proteins, resulting in various immune disorders, multiple cardiomyopathies, and cholesterol metabolism diseases.
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Affiliation(s)
- Nan Zhang
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Siyuan Wang
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Catherine C.L. Wong
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, P. R. China
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Gutman H, Aftalion M, Melamed S, Politi B, Nevo R, Havusha-Laufer S, Achdout H, Gur D, Israely T, Dachir S, Mamroud E, Sagi I, Vagima Y. Matrix Metalloproteinases Expression Is Associated with SARS-CoV-2-Induced Lung Pathology and Extracellular-Matrix Remodeling in K18-hACE2 Mice. Viruses 2022; 14:1627. [PMID: 35893698 PMCID: PMC9332556 DOI: 10.3390/v14081627] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 infection induced lung inflammation characterized by cytokine storm and fulminant immune response of both resident and migrated immune cells, accelerating alveolar damage. In this work we identified members of the matrix metalloprotease (MMPs) family associated with lung extra-cellular matrix (ECM) destruction using K18-hACE2-transgenic mice (K18-hACE2) infected intranasally with SARS-CoV-2. Five days post infection, the lungs exhibited overall alveolar damage of epithelial cells and massive leukocytes infiltration. A substantial pulmonary increase in MMP8, MMP9, and MMP14 in the lungs post SARS-CoV-2 infection was associated with degradation of ECM components including collagen, laminin, and proteoglycans. The process of tissue damage and ECM degradation during SARS-CoV-2 lung infection is suggested to be associated with activity of members of the MMPs family, which in turn may be used as a therapeutic intervention.
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Affiliation(s)
- Hila Gutman
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
- Department of Biological Regulation, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
- Department of Biomolecular Sciences, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Moshe Aftalion
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Sharon Melamed
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Boaz Politi
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Reinat Nevo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Sapir Havusha-Laufer
- Department of Biological Regulation, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Hagit Achdout
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - David Gur
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Tomer Israely
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Shlomit Dachir
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Emanuelle Mamroud
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Yaron Vagima
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
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44
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Considerations for Novel COVID-19 Mucosal Vaccine Development. Vaccines (Basel) 2022; 10:vaccines10081173. [PMID: 35893822 PMCID: PMC9329946 DOI: 10.3390/vaccines10081173] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Mucosal surfaces are the first contact sites of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Most SARS-CoV-2 vaccines induce specific IgG responses but provide limited mucosal immunity. Cytokine B-cell activation factor (BAFF) and A proliferation-inducing ligand (APRIL) in the tumor necrosis factor (TNF) superfamily play key immunological functions during B cell development and antibody production. Furthermore, homeostatic chemokines, such as C-X-C motif chemokine ligand 13 (CXCL13), chemokine (C–C motif) ligand 19 (CCL19), and CCL21, can induce B- and T-cell responses to infection and promote the formation of inducible bronchus-associated lymphoid tissues (iBALT), where specific local immune responses and memory cells are generated. We reviewed the role of BAFF, APRIL, CXCL13, CCL19, and CCL21 in the activation of local B-cell responses and antibody production, and the formation of iBALT in the lung following viral respiratory infections. We speculate that mucosal vaccines may offer more efficient protection against SARS-CoV-2 infection than systematic vaccines and hypothesize that a novel SARS-CoV-2 mRNA mucosal vaccine using BAFF/APRIL or CXCL13 as immunostimulants combined with the spike protein-encoding mRNA may enhance the efficiency of the local immune response and prevent the early stages of SARS-CoV-2 replication and the rapid viral clearance from the airways.
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45
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Al-Mustanjid M, Mahmud SMH, Akter F, Rahman MS, Hossen MS, Rahman MH, Moni MA. Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. INFORMATICS IN MEDICINE UNLOCKED 2022; 32:101003. [PMID: 35818398 PMCID: PMC9259025 DOI: 10.1016/j.imu.2022.101003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating since 2019, and its global dominance is rising. Evidences suggest the respiratory illness SARS-CoV-2 has a sensitive affect on causing organ damage and other complications to the patients with autoimmune diseases (AD), posing a significant risk factor. The genetic interrelationships and molecular appearances between SARS-CoV-2 and AD are yet unknown. We carried out the transcriptomic analytical framework to delve into the SARS-CoV-2 impacts on AD progression. We analyzed both gene expression microarray and RNA-Seq datasets from SARS-CoV-2 and AD affected tissues. With neighborhood-based benchmarks and multilevel network topology, we obtained dysfunctional signaling and ontological pathways, gene disease (diseasesome) association network and protein-protein interaction network (PPIN), uncovered essential shared infection recurrence connectivities with biological insights underlying between SARS-CoV-2 and AD. We found a total of 77, 21, 9, 54 common DEGs for SARS-CoV-2 and inflammatory bowel disorder (IBD), SARS-CoV-2 and rheumatoid arthritis (RA), SARS-CoV-2 and systemic lupus erythematosus (SLE) and SARS-CoV-2 and type 1 diabetes (T1D). The enclosure of these common DEGs with bimolecular networks revealed 10 hub proteins (FYN, VEGFA, CTNNB1, KDR, STAT1, B2M, CD3G, ITGAV, TGFB3). Drugs such as amlodipine besylate, vorinostat, methylprednisolone, and disulfiram have been identified as a common ground between SARS-CoV-2 and AD from drug repurposing investigation which will stimulate the optimal selection of medications in the battle against this ongoing pandemic triggered by COVID-19.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - S M Hasan Mahmud
- Department of Computer Science, American International University-Bangladesh, Dhaka, 1229, Bangladesh
| | - Farzana Akter
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Shazzadur Rahman
- Department of Computer Science & Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Sajid Hossen
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia-7003, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science and Engineering, Pabna Science & Technology University, Pabna, 6600, Bangladesh
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46
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Gene Networks of Hyperglycemia, Diabetic Complications, and Human Proteins Targeted by SARS-CoV-2: What Is the Molecular Basis for Comorbidity? Int J Mol Sci 2022; 23:ijms23137247. [PMID: 35806251 PMCID: PMC9266766 DOI: 10.3390/ijms23137247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
People with diabetes are more likely to have severe COVID-19 compared to the general population. Moreover, diabetes and COVID-19 demonstrate a certain parallelism in the mechanisms and organ damage. In this work, we applied bioinformatics analysis of associative molecular networks to identify key molecules and pathophysiological processes that determine SARS-CoV-2-induced disorders in patients with diabetes. Using text-mining-based approaches and ANDSystem as a bioinformatics tool, we reconstructed and matched networks related to hyperglycemia, diabetic complications, insulin resistance, and beta cell dysfunction with networks of SARS-CoV-2-targeted proteins. The latter included SARS-CoV-2 entry receptors (ACE2 and DPP4), SARS-CoV-2 entry associated proteases (TMPRSS2, CTSB, and CTSL), and 332 human intracellular proteins interacting with SARS-CoV-2. A number of genes/proteins targeted by SARS-CoV-2 (ACE2, BRD2, COMT, CTSB, CTSL, DNMT1, DPP4, ERP44, F2RL1, GDF15, GPX1, HDAC2, HMOX1, HYOU1, IDE, LOX, NUTF2, PCNT, PLAT, RAB10, RHOA, SCARB1, and SELENOS) were found in the networks of vascular diabetic complications and insulin resistance. According to the Gene Ontology enrichment analysis, the defined molecules are involved in the response to hypoxia, reactive oxygen species metabolism, immune and inflammatory response, regulation of angiogenesis, platelet degranulation, and other processes. The results expand the understanding of the molecular basis of diabetes and COVID-19 comorbidity.
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Dubuc I, Prunier J, Lacasse É, Gravel A, Puhm F, Allaeys I, Archambault AS, Gudimard L, Villano R, Droit A, Flamand N, Boilard É, Flamand L. Cytokines and Lipid Mediators of Inflammation in Lungs of SARS-CoV-2 Infected Mice. Front Immunol 2022; 13:893792. [PMID: 35812400 PMCID: PMC9264370 DOI: 10.3389/fimmu.2022.893792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/26/2022] [Indexed: 12/25/2022] Open
Abstract
Coronavirus disease 19 (COVID-19) is the clinical manifestation of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection. A hallmark of COVID-19 is a lung inflammation characterized by an abundant leukocyte infiltrate, elevated levels of cytokines/chemokines, lipid mediators of inflammation (LMI) and microthrombotic events. Animal models are useful for understanding the pathophysiological events leading to COVID-19. One such animal model is the K18-ACE2 transgenic mice. Despite their importance in inflammation, the study of LMI in lung of SARS-CoV-2 infected K18-ACE2 mice has yet to be studied to our knowledge. Using tandem mass spectrometry, the lung lipidome at different time points of infection was analyzed. Significantly increased LMI included N-oleoyl-serine, N-linoleoyl-glycine, N-oleoyl-alanine, 1/2-linoleoyl-glycerol, 1/2-docosahexaenoyl-glycerol and 12-hydroxy-eicosapenatenoic acid. The levels of prostaglandin (PG) E1, PGF2α, stearoyl-ethanolamide and linoleoyl-ethanolamide were found to be significantly reduced relative to mock-infected mice. Other LMI were present at similar levels (or undetected) in both uninfected and infected mouse lungs. In parallel to LMI measures, transcriptomic and cytokine/chemokine profiling were performed. Viral replication was robust with maximal lung viral loads detected on days 2-3 post-infection. Lung histology revealed leukocyte infiltration starting on day 3 post-infection, which correlated with the presence of high concentrations of several chemokines/cytokines. At early times post-infection, the plasma of infected mice contained highly elevated concentration of D-dimers suggestive of blood clot formation/dissolution. In support, the presence of blood clots in the lung vasculature was observed during infection. RNA-Seq analysis of lung tissues indicate that SARS-CoV-2 infection results in the progressive modulation of several hundred genes, including several inflammatory mediators and genes related to the interferons. Analysis of the lung lipidome indicated modest, yet significant modulation of a minority of lipids. In summary, our study suggests that SARS-CoV-2 infection in humans and mice share common features, such as elevated levels of chemokines in lungs, leukocyte infiltration and increased levels of circulating D-dimers. However, the K18-ACE2 mouse model highlight major differences in terms of LMI being produced in response to SARS-CoV-2 infection. The potential reasons and impact of these differences on the pathology and therapeutic strategies to be employed to treat severe COVID-19 are discussed.
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Affiliation(s)
- Isabelle Dubuc
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
| | - Julien Prunier
- Division endocrinologie et néphrologie, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
| | - Émile Lacasse
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
| | - Annie Gravel
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
| | - Florian Puhm
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
- Centre de Recherche Arthrite, Université Laval, Québec City, QC, Canada
| | - Isabelle Allaeys
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
- Centre de Recherche Arthrite, Université Laval, Québec City, QC, Canada
| | - Anne-Sophie Archambault
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Département de médecine, Faculté de médecine, Université Laval, Québec City, QC, Canada
| | - Leslie Gudimard
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
| | - Rosaria Villano
- Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Pozzuoli, Italy
| | - Arnaud Droit
- Division endocrinologie et néphrologie, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
| | - Nicolas Flamand
- Centre de Recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Département de médecine, Faculté de médecine, Université Laval, Québec City, QC, Canada
| | - Éric Boilard
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
- Centre de Recherche Arthrite, Université Laval, Québec City, QC, Canada
- Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City, QC, Canada
| | - Louis Flamand
- Division des maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec City, QC, Canada
- Centre de Recherche Arthrite, Université Laval, Québec City, QC, Canada
- Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City, QC, Canada
- *Correspondence: Louis Flamand,
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Bruiners N, Guerrini V, Ukey R, Dikdan RJ, Yang JH, Mishra PK, Onyuka A, Handler D, Vieth J, Carayannopoulos M, Guo S, Pollen M, Pinter A, Tyagi S, Feingold D, Philipp C, Libutti SK, Gennaro ML. Longitudinal Analysis of Biologic Correlates of COVID-19 Resolution: Case Report. Front Med (Lausanne) 2022; 9:915367. [PMID: 35783607 PMCID: PMC9240225 DOI: 10.3389/fmed.2022.915367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
While the biomarkers of COVID-19 severity have been thoroughly investigated, the key biological dynamics associated with COVID-19 resolution are still insufficiently understood. We report a case of full resolution of severe COVID-19 due to convalescent plasma transfusion. Following transfusion, the patient showed fever remission, improved respiratory status, and rapidly decreased viral burden in respiratory fluids and SARS-CoV-2 RNAemia. Longitudinal unbiased proteomic analysis of plasma and single-cell transcriptomics of peripheral blood cells conducted prior to and at multiple times after convalescent plasma transfusion identified the key biological processes associated with the transition from severe disease to disease-free state. These included (i) temporally ordered upward and downward changes in plasma proteins reestablishing homeostasis and (ii) post-transfusion disappearance of a subset of monocytes characterized by hyperactivated Interferon responses and decreased TNF-α signaling. Monitoring specific dysfunctional myeloid cell subsets in peripheral blood may provide prognostic keys in COVID-19.
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Affiliation(s)
- Natalie Bruiners
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Valentina Guerrini
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Rahul Ukey
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
| | - Ryan J. Dikdan
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
| | - Jason H. Yang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, United States
- Center for Emerging and Re-emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Pankaj Kumar Mishra
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
| | - Alberta Onyuka
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Deborah Handler
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Joshua Vieth
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Mary Carayannopoulos
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Shuang Guo
- Division of Hematology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Maressa Pollen
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Abraham Pinter
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Sanjay Tyagi
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Daniel Feingold
- Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Claire Philipp
- Division of Hematology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Steven K. Libutti
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
- *Correspondence: Steven K. Libutti
| | - Maria Laura Gennaro
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, United States
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, United States
- Maria Laura Gennaro
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49
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Leng L, Ma J, Zhang PP, Xu SC, Li X, Jin Y, Cai J, Tang R, Zhao L, He ZC, Li MS, Zhang H, Zhou LR, Wu ZH, Li TR, Zhu YP, Wang YJ, Wu HB, Ping YF, Yao XH, Zhu CH, Guo HT, Tan LY, Liang ZY, Bian XW, Zhang SY. Spatial region-resolved proteome map reveals mechanism of COVID-19-associated heart injury. Cell Rep 2022; 39:110955. [PMID: 35679865 PMCID: PMC9135696 DOI: 10.1016/j.celrep.2022.110955] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/28/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022] Open
Abstract
Direct myocardial and vascular injuries due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection-driven inflammation is the leading cause of acute cardiac injury associated with coronavirus disease 2019 (COVID-19). However, in-depth knowledge of the injury characteristics of the heart affected by inflammation is lacking. In this study, using a quantitative spatial proteomics strategy that combines comparative anatomy, laser-capture microdissection, and histological examination, we establish a region-resolved proteome map of the myocardia and microvessels with obvious inflammatory cells from hearts of patients with COVID-19. A series of molecular dysfunctions of myocardia and microvessels is observed in different cardiac regions. The myocardia and microvessels of the left atrial are the most susceptible to virus infection and inflammatory storm, suggesting more attention should be paid to the lesion and treatment of these two parts. These results can guide in improving clinical treatments for cardiovascular diseases associated with COVID-19.
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Affiliation(s)
- Ling Leng
- Stem Cell and Regenerative Medicine Lab, Department of Medical Science Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Pei-Pei Zhang
- Department of Pathology, The First Hospital Affiliated to University of Science and Technology of China (USTC), Intelligent Pathology Institute, Division of Life Sciences and Medicine, USTC, Hefei, Anhui 230036, China; Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China; Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Si-Chi Xu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiao Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ye Jin
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jun Cai
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Rui Tang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China
| | - Lei Zhao
- Department of Pathology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhi-Cheng He
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China
| | - Man-Sheng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Liang-Rui Zhou
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhi-Hong Wu
- Stem Cell and Regenerative Medicine Lab, Department of Medical Science Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Tian-Ran Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China
| | - Yun-Ping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Basic Medical School, Anhui Medical University, Anhui 230032, China
| | - Yu-Jie Wang
- Stem Cell and Regenerative Medicine Lab, Department of Medical Science Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Hai-Bo Wu
- Department of Pathology, The First Hospital Affiliated to University of Science and Technology of China (USTC), Intelligent Pathology Institute, Division of Life Sciences and Medicine, USTC, Hefei, Anhui 230036, China
| | - Yi-Fang Ping
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China
| | - Xiao-Hong Yao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China
| | - Chu-Hong Zhu
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hai-Tao Guo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China
| | - Le-Yong Tan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China
| | - Zhi-Yong Liang
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Xiu-Wu Bian
- Department of Pathology, The First Hospital Affiliated to University of Science and Technology of China (USTC), Intelligent Pathology Institute, Division of Life Sciences and Medicine, USTC, Hefei, Anhui 230036, China; Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing 400038, China.
| | - Shu-Yang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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50
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Fava VM, Bourgey M, Nawarathna PM, Orlova M, Cassart P, Vinh DC, Cheng MP, Bourque G, Schurr E, Langlais D. A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19. SCIENCE ADVANCES 2022; 8:eabm2510. [PMID: 35648852 PMCID: PMC9159580 DOI: 10.1126/sciadv.abm2510] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Despite the availability of highly efficacious vaccines, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lacks effective drug treatment, which results in a high rate of mortality. To address this therapeutic shortcoming, we applied a systems biology approach to the study of patients hospitalized with severe COVID. We show that, at the time of hospital admission, patients who were equivalent on the clinical ordinal scale displayed significant differential monocyte epigenetic and transcriptomic attributes between those who would survive and those who would succumb to COVID-19. We identified messenger RNA metabolism, RNA splicing, and interferon signaling pathways as key host responses overactivated by patients who would not survive. Those pathways are prime drug targets to reduce mortality of critically ill patients with COVID-19, leading us to identify tacrolimus, zotatifin, and nintedanib as three strong candidates for treatment of severely ill patients at the time of hospital admission.
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Affiliation(s)
- Vinicius M. Fava
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Pubudu M. Nawarathna
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Marianna Orlova
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Pauline Cassart
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
| | - Donald C. Vinh
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Infectious Diseases and Division of Medical Microbiology, McGill University Health Center, McGill University, Montreal, QC, Canada
| | - Matthew Pellan Cheng
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Infectious Diseases and Division of Medical Microbiology, McGill University Health Center, McGill University, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- McGill International TB Centre, McGill University, Montreal, QC, Canada
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
- Corresponding author. (D.L.); (E.S.)
| | - David Langlais
- Department for Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
- Corresponding author. (D.L.); (E.S.)
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