1
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Kenny G, Saini G, Gaillard CM, Negi R, Alalwan D, Garcia Leon A, McCann K, Tinago W, Kelly C, Cotter AG, de Barra E, Horgan M, Yousif O, Gautier V, Landay A, McAuley D, Feeney ER, O'Kane C, Mallon PWG. Early inflammatory profiles predict maximal disease severity in COVID-19: An unsupervised cluster analysis. Heliyon 2024; 10:e34694. [PMID: 39144942 PMCID: PMC11320140 DOI: 10.1016/j.heliyon.2024.e34694] [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: 03/14/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
Background The inflammatory changes that underlie the heterogeneous presentations of COVID-19 remain incompletely understood. In this study we aimed to identify inflammatory profiles that precede the development of severe COVID-19, that could serve as targets for optimised delivery of immunomodulatory therapies and provide insights for the development of new therapies. Methods We included individuals sampled <10 days from COVID-19 symptom onset, recruited from both inpatient and outpatient settings. We measured 61 biomarkers in plasma, including markers of innate immune and T cell activation, coagulation, tissue repair and lung injury. We used principal component analysis and hierarchical clustering to derive biomarker clusters, and ordinal logistic regression to explore associations between cluster membership and maximal disease severity, adjusting for known risk factors for severe COVID-19. Results In 312 individuals, median (IQR) 7 (4-9) days from symptom onset, we found four clusters. Cluster 1 was characterised by low overall inflammation, cluster 2 was characterised by higher levels of growth factors and markers of endothelial activation (EGF, VEGF, PDGF, TGFα, PAI-1 and p-selectin). Cluster 3 and 4 both had higher overall inflammation. Cluster 4 had the highest levels of most markers including markers of innate immune activation (IL6, procalcitonin, CRP, TNFα), and coagulation (D-dimer, TPO), in contrast cluster 3 had the highest levels of alveolar epithelial injury markers (RAGE, ST2), but relative downregulation of growth factors and endothelial activation markers, suggesting a dysfunctional inflammatory pattern. In unadjusted and adjusted analysis, compared to cluster 1, cluster 3 had the highest odds of progressing to more severe disease (unadjusted OR (95%CI) 9.02 (4.53-17.96), adjusted OR (95%CI) 6.02 (2.70-13.39)). Conclusion Early inflammatory profiles predicted subsequent maximal disease severity independent of risk factors for severe COVID-19. A cluster with downregulation of growth factors and endothelial activation markers, and early evidence of alveolar epithelial injury, had the highest risk of severe COVID-19.
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Affiliation(s)
- Grace Kenny
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
| | - Gurvin Saini
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Colette Marie Gaillard
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Riya Negi
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Dana Alalwan
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Alejandro Garcia Leon
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Kathleen McCann
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
| | - Willard Tinago
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Christine Kelly
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Aoife G. Cotter
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Eoghan de Barra
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Mary Horgan
- Department of Infectious Diseases, Cork University Hospital, Wilton, Cork, Ireland
| | - Obada Yousif
- Department of Endocrinology, Wexford General Hospital, Wexford, Ireland
| | - Virginie Gautier
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Alan Landay
- Department of Internal Medicine, Rush University, Chicago, IL, USA
| | | | - Eoin R. Feeney
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
| | | | - Patrick WG. Mallon
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
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2
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Kanth SM, Huapaya JA, Gairhe S, Wang H, Tian X, Demirkale CY, Hou C, Ma J, Kuhns DB, Fink DL, Malayeri A, Turkbey E, Harmon SA, Chen MY, Regenold D, Lynch NF, Ramelli S, Li W, Krack J, Kuruppu J, Lionakis MS, Strich JR, Davey R, Childs R, Chertow DS, Kovacs JA, Parizi PT, Suffredini AF. Longitudinal analysis of the lung proteome reveals persistent repair months after mild to moderate COVID-19. Cell Rep Med 2024; 5:101642. [PMID: 38981485 PMCID: PMC11293333 DOI: 10.1016/j.xcrm.2024.101642] [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: 01/23/2024] [Revised: 04/23/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024]
Abstract
In order to assess homeostatic mechanisms in the lung after COVID-19, changes in the protein signature of bronchoalveolar lavage from 45 patients with mild to moderate disease at three phases (acute, recovery, and convalescent) are evaluated over a year. During the acute phase, inflamed and uninflamed phenotypes are characterized by the expression of tissue repair and host defense response molecules. With recovery, inflammatory and fibrogenic mediators decline and clinical symptoms abate. However, at 9 months, quantified radiographic abnormalities resolve in the majority of patients, and yet compared to healthy persons, all showed ongoing activation of cellular repair processes and depression of the renin-kallikrein-kinin, coagulation, and complement systems. This dissociation of prolonged reparative processes from symptom and radiographic resolution suggests that occult ongoing disruption of the lung proteome is underrecognized and may be relevant to recovery from other serious viral pneumonias.
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Affiliation(s)
- Shreya M Kanth
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Julio A Huapaya
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Salina Gairhe
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Honghui Wang
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xin Tian
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cumhur Y Demirkale
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chunyan Hou
- Mass Spectrometry and Analytical Pharmacology Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Junfeng Ma
- Mass Spectrometry and Analytical Pharmacology Shared Resource, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Douglas B Kuhns
- Neutrophil Monitoring Lab, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Danielle L Fink
- Neutrophil Monitoring Lab, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Ashkan Malayeri
- Radiology and Imaging Sciences, Clinical Center (CC), National Institutes of Health, Bethesda, MD 20892, USA
| | - Evrim Turkbey
- Radiology and Imaging Sciences, Clinical Center (CC), National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie A Harmon
- Molecular Imaging Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcus Y Chen
- Cardiovascular Branch, National Institute of Heart, Lung, and Blood, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Regenold
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas F Lynch
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabrina Ramelli
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Willy Li
- Pharmacy Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Janell Krack
- Pharmacy Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Janaki Kuruppu
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey R Strich
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Davey
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Childs
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel S Chertow
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph A Kovacs
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Parizad Torabi- Parizi
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony F Suffredini
- Critical Care Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Gong Q, Fu M, Wang J, Zhao S, Wang H. Potential Immune-Inflammatory Proteome Biomarkers for Guiding the Treatment of Patients with Primary Acute Angle-Closure Glaucoma Caused by COVID-19. J Proteome Res 2024; 23:2587-2597. [PMID: 38836775 PMCID: PMC11232099 DOI: 10.1021/acs.jproteome.4c00325] [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: 04/16/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
Primary acute angle-closure glaucoma (PAACG) is a sight-threatening condition that can lead to blindness. With the increasing incidence of COVID-19, a multitude of people are experiencing acute vision loss and severe swelling of the eyes and head. These patients were then diagnosed with acute angle closure, with or without a history of PACG. However, the mechanism by which viral infection causes PACG has not been clarified. This is the first study to explore the specific inflammatory proteomic landscape in SARS-CoV-2-induced PAACG. The expression of 92 inflammation-related proteins in 19 aqueous humor samples from PAACGs or cataract patients was detected using the Olink Target 96 Inflammation Panel based on a highly sensitive and specific proximity extension assay technology. The results showed that 76 proteins were significantly more abundant in the PAACG group than in the cataract group. Notably, the top eight differentially expressed proteins were IL-8, MCP-1, TNFRSF9, DNER, CCL4, Flt3L, CXCL10, and CD40. Generally, immune markers are related to inflammation, macrophage activation, and viral infection, revealing the crucial role of macrophages in the occurrence of PAACGs caused by SARS-CoV-2.
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Affiliation(s)
- Qiaoyun Gong
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Mingshui Fu
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Jingyi Wang
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Shuzhi Zhao
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
| | - Haiyan Wang
- Department
of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai 200080, China
- National
Clinical Research Center for Eye Diseases, Shanghai 200080, China
- Shanghai
Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai
Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai
Engineering Center for Precise Diagnosis and Treatment of Eye Disease, Shanghai 200080, China
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4
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Li Y, Tao X, Ye S, Tai Q, You YA, Huang X, Liang M, Wang K, Wen H, You C, Zhang Y, Zhou X. A T-Cell-Derived 3-Gene Signature Distinguishes SARS-CoV-2 from Common Respiratory Viruses. Viruses 2024; 16:1029. [PMID: 39066192 PMCID: PMC11281602 DOI: 10.3390/v16071029] [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: 04/28/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Research on the host responses to respiratory viruses could help develop effective interventions and therapies against the current and future pandemics from the host perspective. To explore the pathogenesis that distinguishes SARS-CoV-2 infections from other respiratory viruses, we performed a multi-cohort analysis with integrated bioinformatics and machine learning. We collected 3730 blood samples from both asymptomatic and symptomatic individuals infected with SARS-CoV-2, seasonal human coronavirus (sHCoVs), influenza virus (IFV), respiratory syncytial virus (RSV), or human rhinovirus (HRV) across 15 cohorts. First, we identified an enhanced cellular immune response but limited interferon activities in SARS-CoV-2 infection, especially in asymptomatic cases. Second, we identified a SARS-CoV-2-specific 3-gene signature (CLSPN, RBBP6, CCDC91) that was predominantly expressed by T cells, could distinguish SARS-CoV-2 infection, including Omicron, from other common respiratory viruses regardless of symptoms, and was predictive of SARS-CoV-2 infection before detectable viral RNA on RT-PCR testing in a longitude follow-up study. Thereafter, a user-friendly online tool, based on datasets collected here, was developed for querying a gene of interest across multiple viral infections. Our results not only identify a unique host response to the viral pathogenesis in SARS-CoV-2 but also provide insights into developing effective tools against viral pandemics from the host perspective.
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Affiliation(s)
- Yang Li
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
| | - Xinya Tao
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
| | - Sheng Ye
- Chongqing Center for Disease Control and Prevention, Chongqing 400707, China;
| | - Qianchen Tai
- Department of Probability and Statistics, School of Mathematical Sciences, Peking University, Beijing 100091, China;
| | - Yu-Ang You
- Institute of Pharmaceutical Science, King’s College London, London WC2R 2LS, UK;
| | - Xinting Huang
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
| | - Mifang Liang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
| | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China;
| | - Haiyan Wen
- Chongqing International Travel Health Care Center, Chongqing 401120, China;
| | - Chong You
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
- Shanghai Institute for Mathematics and Interdisciplinary Sciences, Fudan University, Shanghai 200433, China
| | - Yan Zhang
- Sports & Medicine Integration Research Center (SMIRC), Capital University of Physical Education and Sports, Beijing 100088, China
| | - Xiaohua Zhou
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
- Department of Probability and Statistics, School of Mathematical Sciences, Peking University, Beijing 100091, China;
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5
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Zhou D, Zhao S, He K, Liu Q, Zhang F, Pu Z, Xiao L, Zhang L, Chen S, Qian X, Wu X, Shen Y, Yu L, Zhang H, Jin J, Xu M, Wang X, Zhu D, Xie Z, Xu X. Longitudinal dynamic single-cell mass cytometry analysis of peripheral blood mononuclear cells in COVID-19 patients within 6 months after viral RNA clearance. BMC Infect Dis 2024; 24:567. [PMID: 38844850 PMCID: PMC11157885 DOI: 10.1186/s12879-024-09464-0] [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: 09/09/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
This study investigates the longitudinal dynamic changes in immune cells in COVID-19 patients over an extended period after recovery, as well as the interplay between immune cells and antibodies. Leveraging single-cell mass spectrometry, we selected six COVID-19 patients and four healthy controls, dissecting the evolving landscape within six months post-viral RNA clearance, alongside the levels of anti-spike protein antibodies. The T cell immunophenotype ascertained via single-cell mass spectrometry underwent validation through flow cytometry in 37 samples. Our findings illuminate that CD8 + T cells, gamma-delta (gd) T cells, and NK cells witnessed an increase, in contrast to the reduction observed in monocytes, B cells, and double-negative T (DNT) cells over time. The proportion of monocytes remained significantly elevated in COVID-19 patients compared to controls even after six-month. Subpopulation-wise, an upsurge manifested within various T effector memory subsets, CD45RA + T effector memory, gdT, and NK cells, whereas declines marked the populations of DNT, naive and memory B cells, and classical as well as non-classical monocytes. Noteworthy associations surfaced between DNT, gdT, CD4 + T, NK cells, and the anti-S antibody titer. This study reveals the changes in peripheral blood mononuclear cells of COVID-19 patients within 6 months after viral RNA clearance and sheds light on the interactions between immune cells and antibodies. The findings from this research contribute to a better understanding of immune transformations during the recovery from COVID-19 and offer guidance for protective measures against reinfection in the context of viral variants.
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Affiliation(s)
- Diwenxin Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Shuai Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Keting He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Qiuhong Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Fen Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Zhangya Pu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Lanlan Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Lingjian Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Shangci Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Xiaohan Qian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Xiaoxin Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Yangfan Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Ling Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Huafen Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Jiandi Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Min Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Xiaoyan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Zhongyang Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China.
| | - Xiaowei Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China.
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6
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Starshinova A, Borozinets A, Kulpina A, Sereda V, Rubinstein A, Kudryavtsev I, Kudlay D. Bronchial Asthma and COVID-19: Etiology, Pathological Triggers, and Therapeutic Considerations. PATHOPHYSIOLOGY 2024; 31:269-287. [PMID: 38921725 PMCID: PMC11206645 DOI: 10.3390/pathophysiology31020020] [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: 02/24/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
Bronchial asthma (BA) continues to be a difficult disease to diagnose. Various factors have been described in the development of BA, but to date, there is no clear evidence for the etiology of this chronic disease. The emergence of COVID-19 has contributed to the pandemic course of asthma and immunologic features. However, there are no unambiguous data on asthma on the background and after COVID-19. There is correlation between various trigger factors that provoke the development of bronchial asthma. It is now obvious that the SARS-CoV-2 virus is one of the provoking factors. COVID-19 has affected the course of asthma. Currently, there is no clear understanding of whether asthma progresses during or after COVID-19 infection. According to the results of some studies, a significant difference was identified between the development of asthma in people after COVID-19. Mild asthma and moderate asthma do not increase the severity of COVID-19 infection. Nevertheless, oral steroid treatment and hospitalization for severe BA were associated with higher COVID-19 severity. The influence of SARS-CoV-2 infection is one of the protective factors. It causes the development of severe bronchial asthma. The accumulated experience with omalizumab in patients with severe asthma during COVID-19, who received omalizumab during the pandemic, has strongly suggested that continued treatment with omalizumab is safe and may help prevent the severe course of COVID-19. Targeted therapy for asthma with the use of omalizumab may also help to reduce severe asthma associated with COVID-19. However, further studies are needed to prove the effect of omalizumab. Data analysis should persist, based on the results of the course of asthma after COVID-19 with varying degrees of severity.
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Affiliation(s)
- Anna Starshinova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia;
| | - Anastasia Borozinets
- Medical Department, I.M. Sechenov First Moscow State Medical University, 197022 Moscow, Russia
| | - Anastasia Kulpina
- Medical Department, Saint Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia;
| | - Vitaliy Sereda
- Medical Department, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Artem Rubinstein
- Department of immunology, Institution of Experimental Medicine, 197376 St. Petersburg, Russia;
| | - Igor Kudryavtsev
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia;
- Department of immunology, Institution of Experimental Medicine, 197376 St. Petersburg, Russia;
| | - Dmitry Kudlay
- Institute of Immunology FMBA of Russia, 115478 Moscow, Russia;
- Department of Pharmacognosy and Industrial Pharmacy, Faculty of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
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7
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Armignacco R, Carlier N, Jouinot A, Birtolo MF, de Murat D, Tubach F, Hausfater P, Simon T, Gorochov G, Pourcher V, Beurton A, Goulet H, Manivet P, Bertherat J, Assié G. Whole blood transcriptome signature predicts severe forms of COVID-19: Results from the COVIDeF cohort study. Funct Integr Genomics 2024; 24:107. [PMID: 38772950 PMCID: PMC11108918 DOI: 10.1007/s10142-024-01359-2] [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: 02/26/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
COVID-19 is associated with heterogeneous outcome. Early identification of a severe progression of the disease is essential to properly manage the patients and improve their outcome. Biomarkers reflecting an increased inflammatory response, as well as individual features including advanced age, male gender, and pre-existing comorbidities, are risk factors of severe COVID-19. Yet, these features show limited accuracy for outcome prediction. The aim was to evaluate the prognostic value of whole blood transcriptome at an early stage of the disease. Blood transcriptome of patients with mild pneumonia was profiled. Patients with subsequent severe COVID-19 were compared to those with favourable outcome, and a molecular predictor based on gene expression was built. Unsupervised classification discriminated patients who would later develop a COVID-19-related severe pneumonia. The corresponding gene expression signature reflected the immune response to the viral infection dominated by a prominent type I interferon, with IFI27 among the most over-expressed genes. A 48-genes transcriptome signature predicting the risk of severe COVID-19 was built on a training cohort, then validated on an external independent cohort, showing an accuracy of 81% for predicting severe outcome. These results identify an early transcriptome signature of severe COVID-19 pneumonia, with a possible relevance to improve COVID-19 patient management.
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Affiliation(s)
- Roberta Armignacco
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France.
| | - Nicolas Carlier
- Service de Pneumologie, AP-HP, Hôpital Cochin, 75014, Paris, France
| | - Anne Jouinot
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France
- Service d'Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, 75014, Paris, France
| | | | - Daniel de Murat
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie Et de Santé Publique, AP-HP, 1901, F-75013, Paris, France
| | - Pierre Hausfater
- Emergency Department, APHP-Sorbonne Université, Hôpital Pitié-Salpêtrière, GRC-14 BIOSFAST, CIMI, UMR 1135, Sorbonne Université, Paris, France
| | - Tabassome Simon
- Service de Pharmacologie, Plateforme de Recherche Clinique URC-CRC-CRB de L'Est Parisien, Assistance Publique-Hôpitaux de Paris, Hôpital Saint Antoine, Sorbonne Université, Paris, France
| | - Guy Gorochov
- Centre d'Immunologie Et Des Maladies Infectieuses (CIMI), Department of Immunology, Sorbonne Université, Inserm, Hôpital Pitié Salpêtrière, Groupe Hospitalo-Universitaire Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Valérie Pourcher
- Department of Infectious Diseases, Hôpital Pitié Salpêtrière, Groupe Hospitalo-Universitaire Assistance Publique - Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Alexandra Beurton
- Service de Médecine Intensive Réanimation EOLE - Département R3S - Sorbonne, Université - Hôpital Universitaire Pitié - Salpêtrière - Assistance Publique Hôpitaux de Paris - 83 Boulevard de L'Hôpital, 75013, Paris, France
- UMRS 1158 Inserm-Sorbonne Université "Neurophysiologie Respiratoire Expérimentale Et Clinique'' Intensive Care Unit, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Hélène Goulet
- Emergency Department, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Philippe Manivet
- INSERM UMR 1141 "NeuroDiderot", Université Paris Cité, FHU I2-D2, Paris, France
- AP-HP, DMU BioGem, Centre de Ressources Biologiques Biobank Lariboisière/Saint Louis (BB-0033-00064), Hôpital Lariboisière, Paris, France
| | - Jérôme Bertherat
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France
- Service d'Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, 75014, Paris, France
| | - Guillaume Assié
- Université Paris Cité, CNRS UMR8104, INSERM U1016, Institut Cochin, F-75014, Paris, France.
- Service d'Endocrinologie, Center for Rare Adrenal Diseases, AP-HP, Hôpital Cochin, 75014, Paris, France.
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8
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Long MB, Howden AJM, Keir HR, Rollings CM, Giam YH, Pembridge T, Delgado L, Abo-Leyah H, Lloyd AF, Sollberger G, Hull R, Gilmour A, Hughes C, New BJM, Cassidy D, Shoemark A, Richardson H, Lamond AI, Cantrell DA, Chalmers JD, Brenes AJ. Extensive acute and sustained changes to neutrophil proteomes post-SARS-CoV-2 infection. Eur Respir J 2024; 63:2300787. [PMID: 38097207 PMCID: PMC10918319 DOI: 10.1183/13993003.00787-2023] [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: 05/14/2023] [Accepted: 11/23/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Neutrophils are important in the pathophysiology of coronavirus disease 2019 (COVID-19), but the molecular changes contributing to altered neutrophil phenotypes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not fully understood. We used quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes immediately following acute SARS-CoV-2 infection and during recovery. METHODS Prospective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May to December 2020). Patients were enrolled within 96 h of admission, with longitudinal sampling up to 29 days. Control groups comprised non-COVID-19 acute lower respiratory tract infection (LRTI) and age-matched noninfected controls. Neutrophils were isolated from peripheral blood and analysed using mass spectrometry. COVID-19 severity and recovery were defined using the World Health Organization ordinal scale. RESULTS Neutrophil proteomes from 84 COVID-19 patients were compared to those from 91 LRTI and 42 control participants. 5800 neutrophil proteins were identified, with >1700 proteins significantly changed in neutrophils from COVID-19 patients compared to noninfected controls. Neutrophils from COVID-19 patients initially all demonstrated a strong interferon signature, but this signature rapidly declined in patients with severe disease. Severe disease was associated with increased abundance of proteins involved in metabolism, immunosuppression and pattern recognition, while delayed recovery from COVID-19 was associated with decreased granule components and reduced abundance of metabolic proteins, chemokine and leukotriene receptors, integrins and inhibitory receptors. CONCLUSIONS SARS-CoV-2 infection results in the sustained presence of circulating neutrophils with distinct proteomes suggesting altered metabolic and immunosuppressive profiles and altered capacities to respond to migratory signals and cues from other immune cells, pathogens or cytokines.
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Affiliation(s)
- Merete B Long
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates equal contribution
| | - Andrew J M Howden
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates equal contribution
| | - Holly R Keir
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates equal contribution
| | - Christina M Rollings
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates equal contribution
| | - Yan Hui Giam
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Thomas Pembridge
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Lilia Delgado
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Hani Abo-Leyah
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Amy F Lloyd
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Gabriel Sollberger
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Rebecca Hull
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Amy Gilmour
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Chloe Hughes
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Benjamin J M New
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Diane Cassidy
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Amelia Shoemark
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Angus I Lamond
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Doreen A Cantrell
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates joint senior authorship
| | - Alejandro J Brenes
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates joint senior authorship
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9
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Takashima Y, Inaba T, Matsuyama T, Yoshii K, Tanaka M, Matsumoto K, Sudo K, Tokuda Y, Omi N, Nakano M, Nakaya T, Fujita N, Sotozono C, Sawa T, Tashiro K, Ohta B. Potential marker subset of blood-circulating cytokines on hematopoietic progenitor-to-Th1 pathway in COVID-19. Front Med (Lausanne) 2024; 11:1319980. [PMID: 38476443 PMCID: PMC10927758 DOI: 10.3389/fmed.2024.1319980] [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: 10/11/2023] [Accepted: 01/31/2024] [Indexed: 03/14/2024] Open
Abstract
In this study, we analyzed a relatively large subset of proteins, including 109 kinds of blood-circulating cytokines, and precisely described a cytokine storm in the expression level and the range of fluctuations during hospitalization for COVID-19. Of the proteins analyzed in COVID-19, approximately 70% were detected with Bonferroni-corrected significant differences in comparison with disease severity, clinical outcome, long-term hospitalization, and disease progression and recovery. Specifically, IP-10, sTNF-R1, sTNF-R2, sCD30, sCD163, HGF, SCYB16, IL-16, MIG, SDF-1, and fractalkine were found to be major components of the COVID-19 cytokine storm. Moreover, the 11 cytokines (i.e., SDF-1, SCYB16, sCD30, IL-11, IL-18, IL-8, IFN-γ, TNF-α, sTNF-R2, M-CSF, and I-309) were associated with the infection, mortality, disease progression and recovery, and long-term hospitalization. Increased expression of these cytokines could be explained in sequential pathways from hematopoietic progenitor cell differentiation to Th1-derived hyperinflammation in COVID-19, which might also develop a novel strategy for COVID-19 therapy with recombinant interleukins and anti-chemokine drugs.
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Affiliation(s)
- Yasuo Takashima
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tohru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tasuku Matsuyama
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kengo Yoshii
- Department of Mathematics and Statistics in Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masami Tanaka
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazumichi Matsumoto
- Faculty of Clinical Laboratory, University Hospital Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuki Sudo
- Department of Anesthesiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuichi Tokuda
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Natsue Omi
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naohisa Fujita
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Teiji Sawa
- Department of Anesthesiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- University Hospital Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Bon Ohta
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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10
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Chanda D, Del Rivero T, Ghimire R, More S, Mitrani MI, Bellio MA, Channappanavar R. Acellular Human Amniotic Fluid-Derived Extracellular Vesicles as Novel Anti-Inflammatory Therapeutics against SARS-CoV-2 Infection. Viruses 2024; 16:273. [PMID: 38400048 PMCID: PMC10892347 DOI: 10.3390/v16020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 is associated with acute respiratory distress syndrome (ARDS) and fatal pneumonia. Excessive inflammation caused by SARS-CoV-2 is the key driver of ARDS and lethal disease. Several FDA-approved drugs that suppress virus replication are in clinical use. However, despite strong evidence for the role of virus-induced inflammation in severe COVID-19, no effective anti-inflammatory drug is available to control fatal inflammation as well as efficiently clear the virus. Therefore, there is an urgent need to identify biologically derived immunomodulators that suppress inflammation and promote antiviral immunity. In this study, we evaluated acellular human amniotic fluid (acAF) containing extracellular vesicles (hAF-EVs) as a potential non-toxic and safe biologic for immunomodulation during COVID-19. Our in vitro results showed that acAF significantly reduced inflammatory cytokine production in TLR2/4/7 and SARS-CoV-2 structural protein-stimulated mouse macrophages. Importantly, an intraperitoneal administration of acAF reduced morbidity and mortality in SARS-CoV-2-infected mice. A detailed examination of SARS-CoV-2-infected lungs revealed that the increased protection in acAF-treated mice was associated with reduced viral titers and levels of inflammatory myeloid cell infiltration. Collectively, our results identify a novel biologic that has potential to suppress excessive inflammation and enhance survival following SARS-CoV-2 infection, highlighting the translational potential of acAF against COVID-19.
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Affiliation(s)
- Debarati Chanda
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
| | - Tania Del Rivero
- Organicell Regenerative Medicine, Davie, FL 33314, USA; (T.D.R.); (M.I.M.)
| | - Roshan Ghimire
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
| | - Maria Ines Mitrani
- Organicell Regenerative Medicine, Davie, FL 33314, USA; (T.D.R.); (M.I.M.)
| | - Michael A. Bellio
- Organicell Regenerative Medicine, Davie, FL 33314, USA; (T.D.R.); (M.I.M.)
| | - Rudragouda Channappanavar
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA; (D.C.); (R.G.); (S.M.)
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11
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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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12
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Augello M, Bono V, Rovito R, Tincati C, Bianchi S, Taramasso L, Di Biagio A, Callegaro A, Maggiolo F, Borghi E, Monforte AD, Marchetti G. Association between SARS-CoV-2 RNAemia, skewed T cell responses, inflammation, and severity in hospitalized COVID-19 people living with HIV. iScience 2024; 27:108673. [PMID: 38188525 PMCID: PMC10770729 DOI: 10.1016/j.isci.2023.108673] [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: 05/23/2023] [Revised: 10/31/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Severe COVID-19 outcomes have been reported in people living with HIV (PLWH), yet the underlying pathogenetic factors are largely unknown. We therefore aimed to assess SARS-CoV-2 RNAemia and plasma cytokines in PLWH hospitalized for COVID-19 pneumonia, exploring associations with magnitude and functionality of SARS-CoV-2-specific immune responses. Eighteen unvaccinated PLWH (16/18 on cART; median CD4 T cell count 361.5/μL; HIV-RNA<50 cp/mL in 15/18) and 18 age/sex-matched people without HIV were consecutively recruited at a median time of 10 days from symptoms onset. PLWH showed greater SARS-CoV-2 RNAemia, a distinct plasma cytokine profile, and worse respiratory function (lower PaO2/FiO2nadir), all correlating with skewed T cell responses (higher perforin production by cytotoxic T cells as well as fewer and less polyfunctional SARS-CoV-2-specific T cells), despite preserved humoral immunity. In conclusion, these data suggest a link between HIV-related T cell dysfunction and poor control over SARS-CoV-2 replication/dissemination that may in turn influence COVID-19 severity in PLWH.
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Affiliation(s)
- Matteo Augello
- Clinic of Infectious Diseases and Tropical Medicine, San Paolo Hospital, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Valeria Bono
- Clinic of Infectious Diseases and Tropical Medicine, San Paolo Hospital, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Roberta Rovito
- Clinic of Infectious Diseases and Tropical Medicine, San Paolo Hospital, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Camilla Tincati
- Clinic of Infectious Diseases and Tropical Medicine, San Paolo Hospital, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Silvia Bianchi
- Microbiology and Clinical Microbiology, Department of Health Sciences, University of Milan, Milan, Italy
| | - Lucia Taramasso
- Infectious Diseases Unit, San Martino Policlinico Hospital, Genoa, Italy
| | - Antonio Di Biagio
- Infectious Diseases Unit, San Martino Policlinico Hospital, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Annapaola Callegaro
- Biobank Unit and Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Franco Maggiolo
- Division of Infectious Diseases, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Elisa Borghi
- Microbiology and Clinical Microbiology, Department of Health Sciences, University of Milan, Milan, Italy
| | - Antonella d’Arminio Monforte
- Clinic of Infectious Diseases and Tropical Medicine, San Paolo Hospital, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases and Tropical Medicine, San Paolo Hospital, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
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13
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Lin QXX, Rajagopalan D, Gamage AM, Tan LM, Venkatesh PN, Chan WOY, Kumar D, Agrawal R, Chen Y, Fong SW, Singh A, Sun LJ, Tan SY, Chai LYA, Somani J, Lee B, Renia L, Ng LFP, Ramanathan K, Wang LF, Young B, Lye D, Singhal A, Prabhakar S. Longitudinal single cell atlas identifies complex temporal relationship between type I interferon response and COVID-19 severity. Nat Commun 2024; 15:567. [PMID: 38238298 PMCID: PMC10796319 DOI: 10.1038/s41467-023-44524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
Due to the paucity of longitudinal molecular studies of COVID-19, particularly those covering the early stages of infection (Days 1-8 symptom onset), our understanding of host response over the disease course is limited. We perform longitudinal single cell RNA-seq on 286 blood samples from 108 age- and sex-matched COVID-19 patients, including 73 with early samples. We examine discrete cell subtypes and continuous cell states longitudinally, and we identify upregulation of type I IFN-stimulated genes (ISGs) as the predominant early signature of subsequent worsening of symptoms, which we validate in an independent cohort and corroborate by plasma markers. However, ISG expression is dynamic in progressors, spiking early and then rapidly receding to the level of severity-matched non-progressors. In contrast, cross-sectional analysis shows that ISG expression is deficient and IFN suppressors such as SOCS3 are upregulated in severe and critical COVID-19. We validate the latter in four independent cohorts, and SOCS3 inhibition reduces SARS-CoV-2 replication in vitro. In summary, we identify complexity in type I IFN response to COVID-19, as well as a potential avenue for host-directed therapy.
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Affiliation(s)
- Quy Xiao Xuan Lin
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Deepa Rajagopalan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Akshamal M Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Le Min Tan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Prasanna Nori Venkatesh
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Wharton O Y Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Dilip Kumar
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
| | - Ragini Agrawal
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Yao Chen
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Louisa J Sun
- Alexandra Hospital, Singapore, 159964, Singapore
| | - Seow-Yen Tan
- Changi General Hospital, Singapore, 529889, Singapore
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Kollengode Ramanathan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- National University Hospital, Singapore, 119074, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, 168753, Singapore
| | - Barnaby Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - David Lye
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Amit Singhal
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore.
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore.
| | - Shyam Prabhakar
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore.
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14
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Zivanovic N, Öner D, Abraham Y, McGinley J, Drysdale SB, Wildenbeest JG, Crabbe M, Vanhoof G, Thys K, Thwaites RS, Robinson H, Bont L, Openshaw PJM, Martinón‐Torres F, Pollard AJ, Aerssens J. Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus disease in infants. Clin Transl Med 2023; 13:e1507. [PMID: 38115705 PMCID: PMC10731116 DOI: 10.1002/ctm2.1507] [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: 07/10/2023] [Revised: 10/31/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023] Open
Abstract
Whereas most infants infected with respiratory syncytial virus (RSV) show no or only mild symptoms, an estimated 3 million children under five are hospitalized annually due to RSV disease. This study aimed to investigate biological mechanisms and associated biomarkers underlying RSV disease heterogeneity in young infants, enabling the potential to objectively categorize RSV-infected infants according to their medical needs. Immunophenotypic and functional profiling demonstrated the emergence of immature and progenitor-like neutrophils, proliferative monocytes (HLA-DRLow , Ki67+), impaired antigen-presenting function, downregulation of T cell response and low abundance of HLA-DRLow B cells in severe RSV disease. HLA-DRLow monocytes were found as a hallmark of RSV-infected infants requiring hospitalization. Complementary transcriptomics identified genes associated with disease severity and pointed to the emergency myelopoiesis response. These results shed new light on mechanisms underlying the pathogenesis and development of severe RSV disease and identified potential new candidate biomarkers for patient stratification.
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Affiliation(s)
- Nevena Zivanovic
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Deniz Öner
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Yann Abraham
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Joseph McGinley
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Simon B. Drysdale
- Centre for Neonatal and Paediatric Infection, Institute for Infection and Immunity, St George's, University of LondonLondonUK
| | - Joanne G. Wildenbeest
- Department of Pediatric Infectious Diseases and ImmunologyWilhelmina Children's Hospital, University Medical Center UtrechtUtrechtThe Netherlands
| | - Marjolein Crabbe
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Greet Vanhoof
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Kim Thys
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Ryan S. Thwaites
- Department of Respiratory MedicineNational Heart and Lung Institute, Imperial College LondonLondonUK
| | - Hannah Robinson
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Louis Bont
- Department of Pediatric Infectious Diseases and ImmunologyWilhelmina Children's Hospital, University Medical Center UtrechtUtrechtThe Netherlands
| | - Peter J. M. Openshaw
- Department of Respiratory MedicineNational Heart and Lung Institute, Imperial College LondonLondonUK
| | - Federico Martinón‐Torres
- Pediatrics DepartmentTranslational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de CompostelaGaliciaSpain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de CompostelaGaliciaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadridSpain
| | | | - Andrew J. Pollard
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Jeroen Aerssens
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
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15
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Weeratunga P, Denney L, Bull JA, Repapi E, Sergeant M, Etherington R, Vuppussetty C, Turner GDH, Clelland C, Woo J, Cross A, Issa F, de Andrea CE, Melero Bermejo I, Sims D, McGowan S, Zurke YX, Ahern DJ, Gamez EC, Whalley J, Richards D, Klenerman P, Monaco C, Udalova IA, Dong T, Antanaviciute A, Ogg G, Knight JC, Byrne HM, Taylor S, Ho LP. Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs. Nat Commun 2023; 14:7216. [PMID: 37940670 PMCID: PMC10632491 DOI: 10.1038/s41467-023-42421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we develop a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method reveals a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and CD8 T cells, is found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings offer further insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.
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Affiliation(s)
- Praveen Weeratunga
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Laura Denney
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joshua A Bull
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Emmanouela Repapi
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Martin Sergeant
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rachel Etherington
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chaitanya Vuppussetty
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gareth D H Turner
- Department of Cellular Pathology and Radcliffe Department of Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Colin Clelland
- Anatomic Pathology, Weill Cornell Medical College, Doha, Qatar
| | - Jeongmin Woo
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy Cross
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | | | - David Sims
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Simon McGowan
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David J Ahern
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Eddie C Gamez
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Justin Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Duncan Richards
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Diseases, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claudia Monaco
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Irina A Udalova
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Agne Antanaviciute
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Graham Ogg
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ling-Pei Ho
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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16
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Kusakabe T, Lin WY, Cheong JG, Singh G, Ravishankar A, Yeung ST, Mesko M, DeCelie MB, Carriche G, Zhao Z, Rand S, Doron I, Putzel GG, Worgall S, Cushing M, Westblade L, Inghirami G, Parkhurst CN, Guo CJ, Schotsaert M, García-Sastre A, Josefowicz SZ, Salvatore M, Iliev ID. Fungal microbiota sustains lasting immune activation of neutrophils and their progenitors in severe COVID-19. Nat Immunol 2023; 24:1879-1889. [PMID: 37872315 PMCID: PMC10805066 DOI: 10.1038/s41590-023-01637-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Gastrointestinal fungal dysbiosis is a hallmark of several diseases marked by systemic immune activation. Whether persistent pathobiont colonization during immune alterations and impaired gut barrier function has a durable impact on host immunity is unknown. We found that elevated levels of Candida albicans immunoglobulin G (IgG) antibodies marked patients with severe COVID-19 (sCOVID-19) who had intestinal Candida overgrowth, mycobiota dysbiosis and systemic neutrophilia. Analysis of hematopoietic stem cell progenitors in sCOVID-19 revealed transcriptional changes in antifungal immunity pathways and reprogramming of granulocyte myeloid progenitors (GMPs) for up to a year. Mice colonized with C. albicans patient isolates experienced increased lung neutrophilia and pulmonary NETosis during severe acute respiratory syndrome coronavirus-2 infection, which were partially resolved with antifungal treatment or by interleukin-6 receptor blockade. sCOVID-19 patients treated with tocilizumab experienced sustained reductions in C. albicans IgG antibodies titers and GMP transcriptional changes. These findings suggest that gut fungal pathobionts may contribute to immune activation during inflammatory diseases, offering potential mycobiota-immune therapeutic strategies for sCOVID-19 with prolonged symptoms.
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Affiliation(s)
- Takato Kusakabe
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Woan-Yu Lin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
| | - Jin-Gyu Cheong
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Stephen T Yeung
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- Department of Microbiology, New York University, Langone Health, New York City, NY, USA
| | - Marissa Mesko
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Meghan Bialt DeCelie
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Guilhermina Carriche
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Sophie Rand
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Itai Doron
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Gregory G Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Stefan Worgall
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pediatrics, Weill Cornell Medicine, New York City, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Christopher N Parkhurst
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Chun-Jun Guo
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York City, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai New York, New York City, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Steven Z Josefowicz
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Mirella Salvatore
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Iliyan D Iliev
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA.
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York City, NY, USA.
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17
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Drake KA, Talantov D, Tong GJ, Lin JT, Verheijden S, Katz S, Leung JM, Yuen B, Krishna V, Wu MJ, Sutherland AM, Short SA, Kheradpour P, Mumbach MR, Franz KM, Trifonov V, Lucas MV, Merson J, Kim CC. Multi-omic profiling reveals early immunological indicators for identifying COVID-19 Progressors. Clin Immunol 2023; 256:109808. [PMID: 37852344 DOI: 10.1016/j.clim.2023.109808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
We sought to better understand the immune response during the immediate post-diagnosis phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. In lymphocytes, the CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. These early stage observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19. BACKGROUND: Much of the literature on immune response post-SARS-CoV-2 infection has been in the acute and post-acute phases of infection. TRANSLATIONAL SIGNIFICANCE: We found differences at early time points of infection in approximately 160 participants. We compared multi-omic signatures in immune cells between individuals progressing to needing more significant medical intervention and non-progressors. We observed widespread evidence of a state of increased inflammation associated with progression, supported by a range of epigenomic, transcriptomic, and proteomic signatures. The signatures we identified support other findings at later time points and serve as the basis for prognostic biomarker development or to inform interventional strategies.
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Affiliation(s)
- Katherine A Drake
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Dimitri Talantov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Gary J Tong
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Jack T Lin
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Samuel Katz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Benjamin Yuen
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vinod Krishna
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Michelle J Wu
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Sarah A Short
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Pouya Kheradpour
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Maxwell R Mumbach
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Kate M Franz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vladimir Trifonov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Molly V Lucas
- Janssen Research & Development, LLC, NJ, United States of America
| | - James Merson
- Janssen Research & Development, LLC, San Francisco, CA, United States of America
| | - Charles C Kim
- Verily Life Sciences, South San Francisco, CA, United States of America.
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18
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Al-Zahrani MH, Alghamdi RA, Tarbiah NI, Alkhattabi NA, Joharjy HM, Khalifa RA. Role of CD27 and SAMHD1 and their genetic susceptibility to COVID-19. Saudi J Biol Sci 2023; 30:103821. [PMID: 38020556 PMCID: PMC10666556 DOI: 10.1016/j.sjbs.2023.103821] [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: 08/27/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 12/01/2023] Open
Abstract
SARS-CoV-2, which initiated the worldwide COVID-19 epidemic in 2019, has rapidly emerged and spread, resulting in significant public health challenges worldwide. The COVID-19 severity signs and their association with specific genes have been investigated to better comprehend this phenomenon. In this study, several genes were investigated to see whether they correspond with COVID-19 sickness severity. This research aims to determine and evaluate certain gene expression levels associated with the immune system, as these genes were reported to play important roles in immune control during the COVID-19 outbreak. We analyzed two immunity-linked genes: CD27 and SAMHD1 in COVID-19 patients' samples using RT-PCR, compared them to the samples from recovered, immunized, and healthy individuals. These data were examined to determine the potential relationships between clinical patterns, illness severity, and progression, and SARS-CoV-2 infection immunology. We observed that CD27 gene expression was higher in COVID-19 vaccinated and control groups, but lower in active and recovered COVID-19 patients. On the other hand, SAMHD1 gene expression was elevated in infected and recovered COVID-19 groups. According to our study, the proteins CD27 and SAMHD1 are essential for controlling the immunological response to COVID-19. Changes in their expression levels could increase the susceptibility of patients to severe complications associated with the disease. Therefore, the gene expression level of these proteins could serve as viable prognostic markers for COVID-19.
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Affiliation(s)
- Maryam H. Al-Zahrani
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rana A. Alghamdi
- Department of Chemistry, Sciences and Arts College, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Nesrin I. Tarbiah
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Nuha A. Alkhattabi
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Husam M. Joharjy
- Infection Control Department, King Abdulaziz Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | - Reham A. Khalifa
- Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, Cairo 11371, Egypt
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19
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Hakim AD, Awili M, O’Neal HR, Siddiqi O, Jaffrani N, Lee R, Overcash JS, Chauffe A, Hammond TC, Patel B, Waters M, Criner GJ, Pachori A, Junge G, Levitch R, Watts J, Koo P, Sengupta T, Yu L, Kiffe M, Pinck A, Stein RR, Bendrick-Peart J, Jenkins J, Rowlands M, Waldron-Lynch F, Matthews J. Efficacy and safety of MAS825 (anti-IL-1β/IL-18) in COVID-19 patients with pneumonia and impaired respiratory function. Clin Exp Immunol 2023; 213:265-275. [PMID: 37338154 PMCID: PMC10570997 DOI: 10.1093/cei/uxad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 03/02/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023] Open
Abstract
MAS825, a bispecific IL-1β/IL-18 monoclonal antibody, could improve clinical outcomes in COVID-19 pneumonia by reducing inflammasome-mediated inflammation. Hospitalized non-ventilated patients with COVID-19 pneumonia (n = 138) were randomized (1:1) to receive MAS825 (10 mg/kg single i.v.) or placebo in addition to standard of care (SoC). The primary endpoint was the composite Acute Physiology and Chronic Health Evaluation II (APACHE II) score on Day 15 or on the day of discharge (whichever was earlier) with worst-case imputation for death. Other study endpoints included safety, C-reactive protein (CRP), SARS-CoV-2 presence, and inflammatory markers. On Day 15, the APACHE II score was 14.5 ± 1.87 and 13.5 ± 1.8 in the MAS825 and placebo groups, respectively (P = 0.33). MAS825 + SoC led to 33% relative reduction in intensive care unit (ICU) admissions, ~1 day reduction in ICU stay, reduction in mean duration of oxygen support (13.5 versus 14.3 days), and earlier clearance of virus on Day 15 versus placebo + SoC group. On Day 15, compared with placebo group, patients treated with MAS825 + SoC showed a 51% decrease in CRP levels, 42% lower IL-6 levels, 19% decrease in neutrophil levels, and 16% lower interferon-γ levels, indicative of IL-1β and IL-18 pathway engagement. MAS825 + SoC did not improve APACHE II score in hospitalized patients with severe COVID-19 pneumonia; however, it inhibited relevant clinical and inflammatory pathway biomarkers and resulted in faster virus clearance versus placebo + SoC. MAS825 used in conjunction with SoC was well tolerated. None of the adverse events (AEs) or serious AEs were treatment-related.
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Affiliation(s)
- Alex D Hakim
- Providence Little Company of Mary Medical Center, Torrance, CA, USA
| | | | - Hollis R O’Neal
- Louisiana State University Health Sciences Center and Our Lady of the Lake Regional Medical Center, Baton Rouge, LA, USA
| | | | | | | | | | - Ann Chauffe
- Louisiana State University Health Sciences Center, Lafayette, LA, USA
| | | | - Bela Patel
- University of Texas McGovern Medical School, Houston, TX, US
| | | | - Gerard J Criner
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | | | | | | | | | - Philip Koo
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA
| | | | - Lili Yu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Michael Kiffe
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anne Pinck
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Richard R Stein
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Janet Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | - Jesse Matthews
- Hospital Medicine, St Charles Health System, Bend, OR, USA
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20
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Jackson WD, Giacomassi C, Ward S, Owen A, Luis TC, Spear S, Woollard KJ, Johansson C, Strid J, Botto M. TLR7 activation at epithelial barriers promotes emergency myelopoiesis and lung antiviral immunity. eLife 2023; 12:e85647. [PMID: 37566453 PMCID: PMC10465127 DOI: 10.7554/elife.85647] [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: 12/17/2022] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
Monocytes are heterogeneous innate effector leukocytes generated in the bone marrow and released into circulation in a CCR2-dependent manner. During infection or inflammation, myelopoiesis is modulated to rapidly meet the demand for more effector cells. Danger signals from peripheral tissues can influence this process. Herein we demonstrate that repetitive TLR7 stimulation via the epithelial barriers drove a potent emergency bone marrow monocyte response in mice. This process was unique to TLR7 activation and occurred independently of the canonical CCR2 and CX3CR1 axes or prototypical cytokines. The monocytes egressing the bone marrow had an immature Ly6C-high profile and differentiated into vascular Ly6C-low monocytes and tissue macrophages in multiple organs. They displayed a blunted cytokine response to further TLR7 stimulation and reduced lung viral load after RSV and influenza virus infection. These data provide insights into the emergency myelopoiesis likely to occur in response to the encounter of single-stranded RNA viruses at barrier sites.
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Affiliation(s)
- William D Jackson
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College LondonLondonUnited Kingdom
| | - Chiara Giacomassi
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College LondonLondonUnited Kingdom
| | - Sophie Ward
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College LondonLondonUnited Kingdom
| | - Amber Owen
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Tiago C Luis
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College LondonLondonUnited Kingdom
| | - Sarah Spear
- Division of Cancer, Department of Surgery and Cancer, Imperial College LondonLondonUnited Kingdom
| | - Kevin J Woollard
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College LondonLondonUnited Kingdom
| | - Cecilia Johansson
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Jessica Strid
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College LondonLondonUnited Kingdom
| | - Marina Botto
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College LondonLondonUnited Kingdom
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21
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Sulczewski FB, Maqueda-Alfaro RA, Alcántara-Hernández M, Perez OA, Saravanan S, Yun TJ, Seong D, Arroyo Hornero R, Raquer-McKay HM, Esteva E, Lanzar ZR, Leylek RA, Adams NM, Das A, Rahman AH, Gottfried-Blackmore A, Reizis B, Idoyaga J. Transitional dendritic cells are distinct from conventional DC2 precursors and mediate proinflammatory antiviral responses. Nat Immunol 2023; 24:1265-1280. [PMID: 37414907 PMCID: PMC10683792 DOI: 10.1038/s41590-023-01545-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 05/26/2023] [Indexed: 07/08/2023]
Abstract
High-dimensional approaches have revealed heterogeneity amongst dendritic cells (DCs), including a population of transitional DCs (tDCs) in mice and humans. However, the origin and relationship of tDCs to other DC subsets has been unclear. Here we show that tDCs are distinct from other well-characterized DCs and conventional DC precursors (pre-cDCs). We demonstrate that tDCs originate from bone marrow progenitors shared with plasmacytoid DCs (pDCs). In the periphery, tDCs contribute to the pool of ESAM+ type 2 DCs (DC2s), and these DC2s have pDC-related developmental features. Different from pre-cDCs, tDCs have less turnover, capture antigen, respond to stimuli and activate antigen-specific naïve T cells, all characteristics of differentiated DCs. Different from pDCs, viral sensing by tDCs results in IL-1β secretion and fatal immune pathology in a murine coronavirus model. Our findings suggest that tDCs are a distinct pDC-related subset with a DC2 differentiation potential and unique proinflammatory function during viral infections.
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Affiliation(s)
- Fernando Bandeira Sulczewski
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul A Maqueda-Alfaro
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Oriana A Perez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sanjana Saravanan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Tae Jin Yun
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - David Seong
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebeca Arroyo Hornero
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Hayley M Raquer-McKay
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Zachary R Lanzar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca A Leylek
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas M Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Annesa Das
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Adeeb H Rahman
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andres Gottfried-Blackmore
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Redwood City, CA, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
| | - Juliana Idoyaga
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA.
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22
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Colombo SAP, Brown SL, Hepworth MR, Hankinson J, Granato F, Kitchen SJ, Hussell T, Simpson A, Cook PC, MacDonald AS. Comparative phenotype of circulating versus tissue immune cells in human lung and blood compartments during health and disease. DISCOVERY IMMUNOLOGY 2023; 2:kyad009. [PMID: 37545765 PMCID: PMC10403752 DOI: 10.1093/discim/kyad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/31/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023]
Abstract
The lung is a dynamic mucosal surface constantly exposed to a variety of immunological challenges including harmless environmental antigens, pollutants, and potentially invasive microorganisms. Dysregulation of the immune system at this crucial site is associated with a range of chronic inflammatory conditions including asthma and Chronic Pulmonary Obstructive Disease (COPD). However, due to its relative inaccessibility, our fundamental understanding of the human lung immune compartment is limited. To address this, we performed flow cytometric immune phenotyping of human lung tissue and matched blood samples that were isolated from 115 donors undergoing lung tissue resection. We provide detailed characterization of the lung mononuclear phagocyte and T cell compartments, demonstrating clear phenotypic differences between lung tissue cells and those in peripheral circulation. Additionally, we show that CD103 expression demarcates pulmonary T cells that have undergone recent TCR and IL-7R signalling. Unexpectedly, we discovered that the immune landscape from asthmatic or COPD donors was broadly comparable to controls. Our data provide a much-needed expansion of our understanding of the pulmonary immune compartment in both health and disease.
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Affiliation(s)
- Stefano A P Colombo
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Sheila L Brown
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Matthew R Hepworth
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Jenny Hankinson
- Institute of Translational Genomics, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Felice Granato
- Department of Cardiothoracic Surgery, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Semra J Kitchen
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK
| | - Tracy Hussell
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Angela Simpson
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Peter C Cook
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, UK
| | - Andrew S MacDonald
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
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23
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Potts M, Fletcher-Etherington A, Nightingale K, Mescia F, Bergamaschi L, Calero-Nieto FJ, Antrobus R, Williamson J, Parsons H, Huttlin EL, Kingston N, Göttgens B, Bradley JR, Lehner PJ, Matheson NJ, Smith KGC, Wills MR, Lyons PA, Weekes MP. Proteomic analysis of circulating immune cells identifies cellular phenotypes associated with COVID-19 severity. Cell Rep 2023; 42:112613. [PMID: 37302069 PMCID: PMC10243220 DOI: 10.1016/j.celrep.2023.112613] [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: 11/15/2022] [Revised: 03/29/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
Certain serum proteins, including C-reactive protein (CRP) and D-dimer, have prognostic value in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nonetheless, these factors are non-specific, providing limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations that drive the pathogenesis of severe COVID-19. To identify cellular phenotypes associated with disease, we performed a comprehensive, unbiased analysis of total and plasma-membrane PBMC proteomes from 40 unvaccinated individuals with SARS-CoV-2, spanning the whole disease spectrum. Combined with RNA sequencing (RNA-seq) and flow cytometry from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing that immune-cell dysregulation progresses with increasing disease. The cell-surface proteins CEACAMs1, 6, and 8, CD177, CD63, and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3+CD4+CEACAM1/6/8+CD177+CD63+CD89+ and CD16+CEACAM1/6/8+ mononuclear cells. Utilization of these markers may facilitate real-time patient assessment by flow cytometry and identify immune populations that could be targeted to ameliorate immunopathology.
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Affiliation(s)
- Martin Potts
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alice Fletcher-Etherington
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Katie Nightingale
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Federica Mescia
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Laura Bergamaschi
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - James Williamson
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Harriet Parsons
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Berthold Göttgens
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 OAW, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Paul J Lehner
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Nicholas J Matheson
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; NHS Blood and Transplant, Cambridge CB2 0PT, UK
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Mark R Wills
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
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24
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Lin X, Chau C, Ma K, Huang Y, Ho JWK. DCATS: differential composition analysis for flexible single-cell experimental designs. Genome Biol 2023; 24:151. [PMID: 37365636 PMCID: PMC10294334 DOI: 10.1186/s13059-023-02980-3] [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: 03/21/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
Differential composition analysis - the identification of cell types that have statistically significant changes in abundance between multiple experimental conditions - is one of the most common tasks in single cell omic data analysis. However, it remains challenging to perform differential composition analysis in the presence of flexible experimental designs and uncertainty in cell type assignment. Here, we introduce a statistical model and an open source R package, DCATS, for differential composition analysis based on a beta-binomial regression framework that addresses these challenges. Our empirical evaluation shows that DCATS consistently maintains high sensitivity and specificity compared to state-of-the-art methods.
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Affiliation(s)
- Xinyi Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Chuen Chau
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kun Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Yuanhua Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Department of Statistics and Actuarial Science, Faculty of Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China.
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25
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Santopaolo M, Gregorova M, Hamilton F, Arnold D, Long A, Lacey A, Oliver E, Halliday A, Baum H, Hamilton K, Milligan R, Pearce O, Knezevic L, Morales Aza B, Milne A, Milodowski E, Jones E, Lazarus R, Goenka A, Finn A, Maskell N, Davidson AD, Gillespie K, Wooldridge L, Rivino L. Prolonged T-cell activation and long COVID symptoms independently associate with severe COVID-19 at 3 months. eLife 2023; 12:e85009. [PMID: 37310006 PMCID: PMC10319436 DOI: 10.7554/elife.85009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/11/2023] [Indexed: 06/14/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) causes immune perturbations which may persist long term, and patients frequently report ongoing symptoms for months after recovery. We assessed immune activation at 3-12 months post hospital admission in 187 samples from 63 patients with mild, moderate, or severe disease and investigated whether it associates with long COVID. At 3 months, patients with severe disease displayed persistent activation of CD4+ and CD8+ T-cells, based on expression of HLA-DR, CD38, Ki67, and granzyme B, and elevated plasma levels of interleukin-4 (IL-4), IL-7, IL-17, and tumor necrosis factor-alpha (TNF-α) compared to mild and/or moderate patients. Plasma from severe patients at 3 months caused T-cells from healthy donors to upregulate IL-15Rα, suggesting that plasma factors in severe patients may increase T-cell responsiveness to IL-15-driven bystander activation. Patients with severe disease reported a higher number of long COVID symptoms which did not however correlate with cellular immune activation/pro-inflammatory cytokines after adjusting for age, sex, and disease severity. Our data suggests that long COVID and persistent immune activation may correlate independently with severe disease.
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Affiliation(s)
- Marianna Santopaolo
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Michaela Gregorova
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Fergus Hamilton
- Academic Respiratory Unit, North Bristol NHS TrustBristolUnited Kingdom
| | - David Arnold
- Academic Respiratory Unit, North Bristol NHS TrustBristolUnited Kingdom
| | - Anna Long
- Diabetes and Metabolism, Bristol Medical School, University of BristolBristolUnited Kingdom
| | - Aurora Lacey
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Elizabeth Oliver
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Alice Halliday
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Holly Baum
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Kristy Hamilton
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Rachel Milligan
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Olivia Pearce
- Diabetes and Metabolism, Bristol Medical School, University of BristolBristolUnited Kingdom
| | - Lea Knezevic
- Bristol Veterinary School, University of BristolBristolUnited Kingdom
| | - Begonia Morales Aza
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Alice Milne
- Academic Respiratory Unit, North Bristol NHS TrustBristolUnited Kingdom
| | - Emily Milodowski
- Bristol Veterinary School, University of BristolBristolUnited Kingdom
| | - Eben Jones
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Rajeka Lazarus
- University Hospitals Bristol and Weston NHS Foundation TrustBristolUnited Kingdom
| | - Anu Goenka
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
- Department of Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for ChildrenBristolUnited Kingdom
| | - Adam Finn
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
- Department of Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for ChildrenBristolUnited Kingdom
- School of Population Health Sciences, University of BristolBristolUnited Kingdom
| | - Nicholas Maskell
- Academic Respiratory Unit, North Bristol NHS TrustBristolUnited Kingdom
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
| | - Kathleen Gillespie
- Diabetes and Metabolism, Bristol Medical School, University of BristolBristolUnited Kingdom
| | - Linda Wooldridge
- Bristol Veterinary School, University of BristolBristolUnited Kingdom
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of BristolBristolUnited Kingdom
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26
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Afewerki S, Stocco TD, Rosa da Silva AD, Aguiar Furtado AS, Fernandes de Sousa G, Ruiz-Esparza GU, Webster TJ, Marciano FR, Strømme M, Zhang YS, Lobo AO. In vitro high-content tissue models to address precision medicine challenges. Mol Aspects Med 2023; 91:101108. [PMID: 35987701 PMCID: PMC9384546 DOI: 10.1016/j.mam.2022.101108] [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: 04/08/2022] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023]
Abstract
The field of precision medicine allows for tailor-made treatments specific to a patient and thereby improve the efficiency and accuracy of disease prevention, diagnosis, and treatment and at the same time would reduce the cost, redundant treatment, and side effects of current treatments. Here, the combination of organ-on-a-chip and bioprinting into engineering high-content in vitro tissue models is envisioned to address some precision medicine challenges. This strategy could be employed to tackle the current coronavirus disease 2019 (COVID-19), which has made a significant impact and paradigm shift in our society. Nevertheless, despite that vaccines against COVID-19 have been successfully developed and vaccination programs are already being deployed worldwide, it will likely require some time before it is available to everyone. Furthermore, there are still some uncertainties and lack of a full understanding of the virus as demonstrated in the high number new mutations arising worldwide and reinfections of already vaccinated individuals. To this end, efficient diagnostic tools and treatments are still urgently needed. In this context, the convergence of bioprinting and organ-on-a-chip technologies, either used alone or in combination, could possibly function as a prominent tool in addressing the current pandemic. This could enable facile advances of important tools, diagnostics, and better physiologically representative in vitro models specific to individuals allowing for faster and more accurate screening of therapeutics evaluating their efficacy and toxicity. This review will cover such technological advances and highlight what is needed for the field to mature for tackling the various needs for current and future pandemics as well as their relevancy towards precision medicine.
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Affiliation(s)
- Samson Afewerki
- Division of Nanotechnology and Functional Materials, Department of Materials Science and Engineering, Ångström Laboratory, Uppsala University, BOX 35, 751 03, Uppsala, Sweden
| | - Thiago Domingues Stocco
- Bioengineering Program, Technological and Scientific Institute, Brazil University, 08230-030, São Paulo, SP, Brazil,Faculty of Medical Sciences, Unicamp - State University of Campinas, 13083-877, Campinas, SP, Brazil
| | | | - André Sales Aguiar Furtado
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil
| | - Gustavo Fernandes de Sousa
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil
| | - Guillermo U. Ruiz-Esparza
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA,Division of Health Sciences and Technology, Harvard University ‑ Massachusetts Institute of Technology, Boston, MA, 02115, USA
| | - Thomas J. Webster
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil,Hebei University of Technology, Tianjin, China
| | | | - Maria Strømme
- Division of Nanotechnology and Functional Materials, Department of Materials Science and Engineering, Ångström Laboratory, Uppsala University, BOX 35, 751 03, Uppsala, Sweden
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA; Division of Health Sciences and Technology, Harvard University ‑ Massachusetts Institute of Technology, Boston, MA, 02115, USA.
| | - Anderson Oliveira Lobo
- Interdisciplinary Laboratory for Advanced Materials, BioMatLab, Department of Materials Engineering, Federal University of Piauí (UFPI), Teresina, PI, Brazil.
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Pan H, He J, Yang Z, Yao X, Zhang H, Li R, Xiao Y, Zhao C, Jiang H, Liu Y, Li Z, Guo B, Zhang C, Li RZ, Liu L. Myricetin possesses the potency against SARS-CoV-2 infection through blocking viral-entry facilitators and suppressing inflammation in rats and mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154858. [PMID: 37224774 DOI: 10.1016/j.phymed.2023.154858] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/26/2023]
Abstract
BACKGROUND Myricetin (3,5,7-trihydroxy-2-(3,4,5-tri hydroxyphenyl)-4-benzopyrone) is a common flavonol extracted from many natural plants and Chinese herb medicines and has been demonstrated to have multiple pharmacological activities, such as anti-microbial, anti-thrombotic, neuroprotective, and anti-inflammatory effects. Previously, myricetin was reported to target Mpro and 3CL-Pro-enzymatic activity to SARS-CoV-2. However, the protective value of myricetin on SARS-Cov-2 infection through viral-entry facilitators has not yet been comprehensively understood. PURPOSE The aim of the current study was to evaluate the pharmacological efficacy and the mechanisms of action of myricetin against SARS-CoV-2 infection both in vitro and in vivo. METHODS The inhibitory effects of myricetin on SARS-CoV-2 infection and replication were assessed on Vero E6 cells. Molecular docking analysis and bilayer interferometry (BLI) assays, immunocytochemistry (ICC), and pseudoviruses assays were performed to evaluate the roles of myricetin in the intermolecular interaction between the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein and angiotensin-converting enzyme 2 (ACE2). The anti-inflammatory potency and mechanisms of myricetin were examined in THP1 macrophages in vitro, as well as in carrageenan-induced paw edema, delayed-type hypersensitivity (DTH) induced auricle edema, and LPS-induced acute lung injury (ALI) animal models. RESULTS The results showed that myricetin was able to inhibit binding between the RBD of the SARS-CoV-2 S protein and ACE2 through molecular docking analysis and BLI assay, demonstrating its potential as a viral-entry facilitator blocker. Myricetin could also significantly inhibit SASR-CoV-2 infection and replication in Vero E6 cells (EC50 55.18 μM), which was further validated with pseudoviruses containing the RBD (wild-type, N501Y, N439K, Y453F) and an S1 glycoprotein mutant (S-D614G). Moreover, myricetin exhibited a marked suppressive action on the receptor-interacting serine/threonine protein kinase 1 (RIPK1)-driven inflammation and NF-kappa B signaling in THP1 macrophages. In animal model studies, myricetin notably ameliorated carrageenan-induced paw edema in rats, DTH induced auricle edema in mice, and LPS-induced ALI in mice. CONCLUSION Our findings showed that myricetin inhibited HCoV-229E and SARS-CoV-2 replication in vitro, blocked SARS-CoV-2 virus entry facilitators and relieved inflammation through the RIPK1/NF-κB pathway, suggesting that this flavonol has the potential to be developed as a therapeutic agent against COVID-19.
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Affiliation(s)
- Hudan Pan
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, PR China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510000, PR China
| | - Jinlian He
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China
| | - Zifeng Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China; Guangzhou Laboratory, Guangzhou, Guangdong 510000, PR China; Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou, Guangdong 510000, PR China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China
| | - Han Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China; Guangzhou Laboratory, Guangzhou, Guangdong 510000, PR China
| | - Yao Xiao
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, PR China
| | - Caiping Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China
| | - Haiming Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China; Guangzhou Laboratory, Guangzhou, Guangdong 510000, PR China
| | - Yuntao Liu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, PR China
| | - Zhanguo Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China; Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing 100044, PR China
| | - Bin Guo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China; Guizhou University of Traditional Chinese Medicine, Guiyang 550025, PR China
| | - Chuanhai Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, PR China
| | - Run-Ze Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, PR China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510000, PR China.
| | - Liang Liu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, PR China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510000, PR China; Guangzhou Laboratory, Guangzhou, Guangdong 510000, PR China.
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28
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Scott NA, Pearmain L, Knight SB, Brand O, Morgan DJ, Jagger C, Harbach S, Khan S, Shuwa HA, Franklin M, Kästele V, Williams T, Prise I, McClure FA, Hackney P, Smith L, Menon M, Konkel JE, Lawless C, Wilson J, Mathioudakis AG, Stanel SC, Ustianowski A, Lindergard G, Brij S, Diar Bakerly N, Dark P, Brightling C, Rivera-Ortega P, Lord GM, Horsley A, Piper Hanley K, Felton T, Simpson A, Grainger JR, Hussell T, Mann ER. Monocyte migration profiles define disease severity in acute COVID-19 and unique features of long COVID. Eur Respir J 2023; 61:2202226. [PMID: 36922030 PMCID: PMC10040898 DOI: 10.1183/13993003.02226-2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 02/16/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND COVID-19 is associated with a dysregulated immune response but it is unclear how immune dysfunction contributes to the chronic morbidity persisting in many COVID-19 patients during convalescence (long COVID). METHODS We assessed phenotypical and functional changes of monocytes in COVID-19 patients during hospitalisation and up to 9 months of convalescence following COVID-19, respiratory syncytial virus or influenza A. Patients with progressive fibrosing interstitial lung disease were included as a positive control for severe, ongoing lung injury. RESULTS Monocyte alterations in acute COVID-19 patients included aberrant expression of leukocyte migration molecules, continuing into convalescence (n=142) and corresponding with specific symptoms of long COVID. Long COVID patients with unresolved lung injury, indicated by sustained shortness of breath and abnormal chest radiology, were defined by high monocyte expression of C-X-C motif chemokine receptor 6 (CXCR6) (p<0.0001) and adhesion molecule P-selectin glycoprotein ligand 1 (p<0.01), alongside preferential migration of monocytes towards the CXCR6 ligand C-X-C motif chemokine ligand 16 (CXCL16) (p<0.05), which is abundantly expressed in the lung. Monocyte CXCR6 and lung CXCL16 were heightened in patients with progressive fibrosing interstitial lung disease (p<0.001), confirming a role for the CXCR6-CXCL16 axis in ongoing lung injury. Conversely, monocytes from long COVID patients with ongoing fatigue exhibited a sustained reduction of the prostaglandin-generating enzyme cyclooxygenase 2 (p<0.01) and CXCR2 expression (p<0.05). These monocyte changes were not present in respiratory syncytial virus or influenza A convalescence. CONCLUSIONS Our data define unique monocyte signatures that define subgroups of long COVID patients, indicating a key role for monocyte migration in COVID-19 pathophysiology. Targeting these pathways may provide novel therapeutic opportunities in COVID-19 patients with persistent morbidity.
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Affiliation(s)
- Nicholas A Scott
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Equal contribution
| | - Laurence Pearmain
- North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Equal contribution
| | - Sean B Knight
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Department of Respiratory Medicine, Salford Royal NHS Foundation Trust, Manchester, UK
| | - Oliver Brand
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - David J Morgan
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Christopher Jagger
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Sarah Harbach
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Saba Khan
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Halima A Shuwa
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Miriam Franklin
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Verena Kästele
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Thomas Williams
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ian Prise
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Flora A McClure
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Pamela Hackney
- Research Innovation, Manchester University NHS Foundation Trust, Manchester, UK
| | - Lara Smith
- Research Innovation, Manchester University NHS Foundation Trust, Manchester, UK
| | - Madhvi Menon
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Joanne E Konkel
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Criag Lawless
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - James Wilson
- Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester, UK
- Department of Microbiology, Salford Royal NHS Foundation Trust, Manchester, UK
| | - Alexander G Mathioudakis
- North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital, Manchester, UK
| | - Stefan C Stanel
- North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital, Manchester, UK
| | - Andrew Ustianowski
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester, UK
| | - Gabriella Lindergard
- Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester, UK
| | - Seema Brij
- Department of Respiratory Medicine, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Nawar Diar Bakerly
- Department of Respiratory Medicine, Salford Royal NHS Foundation Trust, Manchester, UK
| | - Paul Dark
- Department of Respiratory Medicine, Salford Royal NHS Foundation Trust, Manchester, UK
| | - Christopher Brightling
- Department of Respiratory Sciences, Leicester NIHR BRC, University of Leicester, Leicester, UK
| | - Pilar Rivera-Ortega
- North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Graham M Lord
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Alex Horsley
- Division of Infection, Immunity and Respiratory Medicine, Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital, Manchester, UK
| | - Karen Piper Hanley
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Timothy Felton
- Division of Infection, Immunity and Respiratory Medicine, Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital, Manchester, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital, Manchester, UK
| | - John R Grainger
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Joint senior authors
| | - Tracy Hussell
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Joint senior authors
| | - Elizabeth R Mann
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Maternal and Fetal Health Centre, Division of Developmental Biology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Joint senior authors
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29
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Starikova EA, Rubinstein AA, Mammedova JT, Isakov DV, Kudryavtsev IV. Regulated Arginine Metabolism in Immunopathogenesis of a Wide Range of Diseases: Is There a Way to Pass between Scylla and Charybdis? Curr Issues Mol Biol 2023; 45:3525-3551. [PMID: 37185755 PMCID: PMC10137093 DOI: 10.3390/cimb45040231] [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: 03/29/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
More than a century has passed since arginine was discovered, but the metabolism of the amino acid never ceases to amaze researchers. Being a conditionally essential amino acid, arginine performs many important homeostatic functions in the body; it is involved in the regulation of the cardiovascular system and regeneration processes. In recent years, more and more facts have been accumulating that demonstrate a close relationship between arginine metabolic pathways and immune responses. This opens new opportunities for the development of original ways to treat diseases associated with suppressed or increased activity of the immune system. In this review, we analyze the literature describing the role of arginine metabolism in the immunopathogenesis of a wide range of diseases, and discuss arginine-dependent processes as a possible target for therapeutic approaches.
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Affiliation(s)
- Eleonora A Starikova
- Laboratory of Cellular Immunology, Department of Immunology, Institute of Experimental Medicine, Akademika Pavlova 12, 197376 Saint Petersburg, Russia
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L'va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Artem A Rubinstein
- Laboratory of Cellular Immunology, Department of Immunology, Institute of Experimental Medicine, Akademika Pavlova 12, 197376 Saint Petersburg, Russia
| | - Jennet T Mammedova
- Laboratory of General Immunology, Department of Immunology, Institute of Experimental Medicine, Akademika Pavlova 12, 197376 Saint Petersburg, Russia
| | - Dmitry V Isakov
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L'va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Igor V Kudryavtsev
- Laboratory of Cellular Immunology, Department of Immunology, Institute of Experimental Medicine, Akademika Pavlova 12, 197376 Saint Petersburg, Russia
- School of Biomedicine, Far Eastern Federal University, FEFU Campus, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia
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Park J, Dean LS, Jiyarom B, Gangcuangco LM, Shah P, Awamura T, Ching LL, Nerurkar VR, Chow DC, Igno F, Shikuma CM, Devendra G. Elevated circulating monocytes and monocyte activation in COVID-19 convalescent individuals. Front Immunol 2023; 14:1151780. [PMID: 37077911 PMCID: PMC10106598 DOI: 10.3389/fimmu.2023.1151780] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
Background Monocytes and macrophages play a pivotal role in inflammation during acute SARS-CoV-2 infection. However, their contribution to the development of post-acute sequelae of SARS-CoV-2 infection (PASC) are not fully elucidated. Methods A cross-sectional study was conducted comparing plasma cytokine and monocyte levels among three groups: participants with pulmonary PASC (PPASC) with a reduced predicted diffusing capacity for carbon monoxide [DLCOc, <80%; (PG)]; fully recovered from SARS-CoV-2 with no residual symptoms (recovered group, RG); and negative for SARS-CoV-2 (negative group, NG). The expressions of cytokines were measured in plasma of study cohort by Luminex assay. The percentages and numbers of monocyte subsets (classical, intermediate, and non-classical monocytes) and monocyte activation (defined by CD169 expression) were analyzed using flow cytometry analysis of peripheral blood mononuclear cells. Results Plasma IL-1Ra levels were elevated but FGF levels were reduced in PG compared to NG. Circulating monocytes and three subsets were significantly higher in PG and RG compared to NG. PG and RG exhibited higher levels of CD169+ monocyte counts and higher CD169 expression was detected in intermediate and non-classical monocytes from RG and PG than that found in NG. Further correlation analysis with CD169+ monocyte subsets revealed that CD169+ intermediate monocytes negatively correlated with DLCOc%, and CD169+ non-classical monocytes positively correlated with IL-1α, IL-1β, MIP-1α, Eotaxin, and IFN-γ. Conclusion This study present evidence that COVID convalescents exhibit monocyte alteration beyond the acute COVID-19 infection period even in convalescents with no residual symptoms. Further, the results suggest that monocyte alteration and increased activated monocyte subsets may impact pulmonary function in COVID-19 convalescents. This observation will aid in understanding the immunopathologic feature of pulmonary PASC development, resolution, and subsequent therapeutic interventions.
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Affiliation(s)
- Juwon Park
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Logan S. Dean
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Boonyanudh Jiyarom
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Louie Mar Gangcuangco
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Parthav Shah
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- John A. Burns School of Medicine, University of Hawai'i at Manoa, Honolulu, HI, United States
| | - Thomas Awamura
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Lauren L. Ching
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Vivek R. Nerurkar
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Dominic C. Chow
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Fritzie Igno
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
| | - Gehan Devendra
- Department of Medicine, John A. Burns School of Medicine, University of Hawai’i at Manoa, Honolulu, HI, United States
- Department of Pulmonary and Critical Care, Queen’s Medical Center, Honolulu, HI, United States
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Ye J, Shao X, Yang Y, Zhu F. Predicting the negative conversion time of nonsevere COVID-19 patients using machine learning methods. J Med Virol 2023; 95:e28747. [PMID: 37185847 DOI: 10.1002/jmv.28747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023]
Abstract
Based on the patient's clinical characteristics and laboratory indicators, different machine-learning methods were used to develop models for predicting the negative conversion time of nonsevere coronavirus disease 2019 (COVID-19) patients. A retrospective analysis was performed on 376 nonsevere COVID-19 patients admitted to Wuxi Fifth People's Hospital from May 2, 2022, to May 14, 2022. The patients were divided into training set (n = 309) and test set (n = 67). The clinical features and laboratory parameters of the patients were collected. In the training set, the least absolute shrinkage and selection operator (LASSO) was used to select predictive features and train six machine learning models: multiple linear regression (MLR), K-Nearest Neighbors Regression (KNNR), random forest regression (RFR), support vector machine regression (SVR), XGBoost regression (XGBR), and multilayer perceptron regression (MLPR). Seven best predictive features selected by LASSO included: age, gender, vaccination status, IgG, lymphocyte ratio, monocyte ratio, and lymphocyte count. The predictive performance of the models in the test set was MLPR > SVR > MLR > KNNR > XGBR > RFR, and MLPR had the strongest generalization performance, which is significantly better than SVR and MLR. In the MLPR model, vaccination status, IgG, lymphocyte count, and lymphocyte ratio were protective factors for negative conversion time; male gender, age, and monocyte ratio were risk factors. The top three features with the highest weights were vaccination status, gender, and IgG. Machine learning methods (especially MLPR) can effectively predict the negative conversion time of non-severe COVID-19 patients. It can help to rationally allocate limited medical resources and prevent disease transmission, especially during the Omicron pandemic.
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Affiliation(s)
- Jiru Ye
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xiaonan Shao
- Department of Nuclear Medicine, The Third Affiliated Hospital of Soochow University, Institute of Clinical Translation of Nuclear Medicine and Molecular Imaging of Soochow University, Changzhou Clinical Medical Center, Changzhou, China
| | - Yong Yang
- Department of Pediatrics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Feng Zhu
- Department of Respiratory and Critical Care Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi Fifth People's Hospital, Wuxi, China
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Bodansky A, Vazquez SE, Chou J, Novak T, Al-Musa A, Young C, Newhams M, Kucukak S, Zambrano LD, Mitchell A, Wang CY, Moffitt K, Halasa NB, Loftis LL, Schwartz SP, Walker TC, Mack EH, Fitzgerald JC, Gertz SJ, Rowan CM, Irby K, Sanders RC, Kong M, Schuster JE, Staat MA, Zinter MS, Cvijanovich NZ, Tarquinio KM, Coates BM, Flori HR, Dahmer MK, Crandall H, Cullimore ML, Levy ER, Chatani B, Nofziger R, Geha RS, DeRisi J, Campbell AP, Anderson M, Randolph AG. NFKB2 haploinsufficiency identified via screening for IFN-α2 autoantibodies in children and adolescents hospitalized with SARS-CoV-2-related complications. J Allergy Clin Immunol 2023; 151:926-930.e2. [PMID: 36509151 PMCID: PMC9733962 DOI: 10.1016/j.jaci.2022.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Autoantibodies against type I IFNs occur in approximately 10% of adults with life-threatening coronavirus disease 2019 (COVID-19). The frequency of anti-IFN autoantibodies in children with severe sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is unknown. OBJECTIVE We quantified anti-type I IFN autoantibodies in a multicenter cohort of children with severe COVID-19, multisystem inflammatory syndrome in children (MIS-C), and mild SARS-CoV-2 infections. METHODS Circulating anti-IFN-α2 antibodies were measured by a radioligand binding assay. Whole-exome sequencing, RNA sequencing, and functional studies of peripheral blood mononuclear cells were used to study any patients with levels of anti-IFN-α2 autoantibodies exceeding the assay's positive control. RESULTS Among 168 patients with severe COVID-19, 199 with MIS-C, and 45 with mild SARS-CoV-2 infections, only 1 had high levels of anti-IFN-α2 antibodies. Anti-IFN-α2 autoantibodies were not detected in patients treated with intravenous immunoglobulin before sample collection. Whole-exome sequencing identified a missense variant in the ankyrin domain of NFKB2, encoding the p100 subunit of nuclear factor kappa-light-chain enhancer of activated B cells, aka NF-κB, essential for noncanonical NF-κB signaling. The patient's peripheral blood mononuclear cells exhibited impaired cleavage of p100 characteristic of NFKB2 haploinsufficiency, an inborn error of immunity with a high prevalence of autoimmunity. CONCLUSIONS High levels of anti-IFN-α2 autoantibodies in children and adolescents with MIS-C, severe COVID-19, and mild SARS-CoV-2 infections are rare but can occur in patients with inborn errors of immunity.
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Affiliation(s)
- Aaron Bodansky
- Department of Pediatric Critical Care Medicine, University of California, San Francisco, Calif
| | - Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, Calif; Diabetes Center, School of Medicine, University of California, San Francisco, Calif
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass; Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Mass.
| | - Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Mass; Department of Anesthesia, Harvard Medical School, Boston, Mass
| | - Amer Al-Musa
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Cameron Young
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Margaret Newhams
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Suden Kucukak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Laura D Zambrano
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Ga
| | - Anthea Mitchell
- Department of Biochemistry and Biophysics, University of California, San Francisco, Calif; Chan Zuckerberg Biohub, San Francisco, Calif
| | | | - Kristin Moffitt
- Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Mass; Division of Infectious Diseases, Boston Children's Hospital, Boston, Mass
| | - Natasha B Halasa
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tenn
| | - Laura L Loftis
- Section of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Stephanie P Schwartz
- Department of Pediatrics, University of North Carolina at Chapel Hill Children's Hospital, Chapel Hill, NC
| | - Tracie C Walker
- Department of Pediatrics, University of North Carolina at Chapel Hill Children's Hospital, Chapel Hill, NC
| | - Elizabeth H Mack
- Division of Pediatric Critical Care Medicine, Medical University of South Carolina, Charleston, SC
| | - Julie C Fitzgerald
- Department of Anesthesiology and Critical Care, Division of Critical Care, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Shira J Gertz
- Department of Pediatrics, Division of Pediatric Critical Care, Cooperman Barnabas Medical Center, Livingston, NJ
| | - Courtney M Rowan
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Indiana University School of Medicine, Riley Hospital for Children, Indianapolis, Ind
| | - Katherine Irby
- Section of Pediatric Critical Care, Department of Pediatrics, Arkansas Children's Hospital, Little Rock, Ark
| | - Ronald C Sanders
- Section of Pediatric Critical Care, Department of Pediatrics, Arkansas Children's Hospital, Little Rock, Ark
| | - Michele Kong
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Ala
| | - Jennifer E Schuster
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Mercy Kansas City, Kansas City, Mo
| | - Mary A Staat
- Department of Pediatrics, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Matt S Zinter
- Department of Pediatrics, Divisions of Critical Care and Bone Marrow Transplantation, University of California, San Francisco, Calif
| | - Natalie Z Cvijanovich
- Division of Critical Care Medicine, UCSF Benioff Children's Hospital, Oakland, Calif
| | - Keiko M Tarquinio
- Department of Pediatrics, Division of Critical Care Medicine, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Ga
| | - Bria M Coates
- Department of Pediatrics, Division of Critical Care Medicine, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Heidi R Flori
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Mott Children's Hospital and University of Michigan, Ann Arbor, Mich
| | - Mary K Dahmer
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Mott Children's Hospital and University of Michigan, Ann Arbor, Mich
| | - Hillary Crandall
- Department of Pediatrics, Division of Pediatric Critical Care, Primary Children's Hospital and University of Utah, Salt Lake City, Utah
| | - Melissa L Cullimore
- Department of Pediatrics, University of Nebraska Medical Center, College of Medicine, Children's Hospital and Medical Center, Omaha, Neb
| | - Emily R Levy
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Infectious Diseases, Division of Pediatric Critical Care Medicine, Mayo Clinic, Rochester, Minn
| | - Brandon Chatani
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, Fla
| | - Ryan Nofziger
- Department of Pediatrics, Division of Critical Care Medicine, Akron Children's Hospital, Akron, Ohio
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, Calif; Chan Zuckerberg Biohub, San Francisco, Calif
| | - Angela P Campbell
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Ga
| | - Mark Anderson
- Diabetes Center, School of Medicine, University of California, San Francisco, Calif
| | - Adrienne G Randolph
- Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, Mass; Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Mass; Department of Anesthesia, Harvard Medical School, Boston, Mass
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Grabherr S, Waltenspühl A, Büchler L, Lütge M, Cheng HW, Caviezel-Firner S, Ludewig B, Krebs P, Pikor NB. An Innate Checkpoint Determines Immune Dysregulation and Immunopathology during Pulmonary Murine Coronavirus Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:774-785. [PMID: 36715496 PMCID: PMC9986052 DOI: 10.4049/jimmunol.2200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/21/2022] [Indexed: 01/31/2023]
Abstract
Hallmarks of life-threatening, coronavirus-induced disease include dysregulated antiviral immunity and immunopathological tissue injury. Nevertheless, the sampling of symptomatic patients overlooks the initial inflammatory sequela culminating in severe coronavirus-induced disease, leaving a fundamental gap in our understanding of the early mechanisms regulating anticoronavirus immunity and preservation of tissue integrity. In this study, we delineate the innate regulators controlling pulmonary infection using a natural mouse coronavirus. Within hours of infection, the cellular landscape of the lung was transcriptionally remodeled altering host metabolism, protein synthesis, and macrophage maturation. Genetic perturbation revealed that these transcriptional programs were type I IFN dependent and critically controlled both host cell survival and viral spread. Unrestricted viral replication overshooting protective IFN responses culminated in increased IL-1β and alarmin production and triggered compensatory neutrophilia, interstitial inflammation, and vascular injury. Thus, type I IFNs critically regulate early viral burden, which serves as an innate checkpoint determining the trajectory of coronavirus dissemination and immunopathology.
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Affiliation(s)
- Sarah Grabherr
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Alexandra Waltenspühl
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Lorina Büchler
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Mechthild Lütge
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Hung-Wei Cheng
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Sonja Caviezel-Firner
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Burkhard Ludewig
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Natalia B. Pikor
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St. Gallen, Switzerland
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del Molino del Barrio I, Hayday TS, Laing AG, Hayday AC, Di Rosa F. COVID-19: Using high-throughput flow cytometry to dissect clinical heterogeneity. Cytometry A 2023; 103:117-126. [PMID: 34811890 PMCID: PMC9011838 DOI: 10.1002/cyto.a.24516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/18/2021] [Accepted: 11/11/2021] [Indexed: 12/22/2022]
Abstract
Here we consider how high-content flow cytometric methodology at appropriate scale and throughput rapidly provided meaningful biological data in our recent studies of COVID-19, which we discuss in the context of other similar investigations. In our work, high-throughput flow cytometry was instrumental to identify a consensus immune signature in COVID-19 patients, and to investigate the impact of SARS-CoV-2 exposure on patients with either solid or hematological cancers. We provide here some examples of our 'holistic' approach, in which flow cytometry data generated by lymphocyte and myelomonocyte panels were integrated with other analytical metrics, including SARS-CoV-2-specific serum antibody titers, plasma cytokine/chemokine levels, and in-depth clinical annotation. We report how selective differences between T cell subsets were revealed by a newly described flow cytometric TDS assay to distinguish actively cycling T cells in the peripheral blood. By such approaches, our and others' high-content flow cytometry studies collectively identified overt abnormalities and subtle but critical changes that discriminate the immuno-signature of COVID-19 patients from those of healthy donors and patients with non-COVID respiratory infections. Thereby, these studies offered several meaningful biomarkers of COVID-19 severity that have the potential to improve the management of patients and of hospital resources. In sum, flow cytometry provides an important means for rapidly obtaining data that can guide clinical decision-making without requiring highly expensive, sophisticated equipment, and/or "-omics" capabilities. We consider how this approach might be further developed.
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Affiliation(s)
- Irene del Molino del Barrio
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
- University College LondonLondonUK
- Cancer Research UK Cancer Immunotherapy AcceleratorLondonUK
| | - Thomas S. Hayday
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
| | - Adam G. Laing
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
| | - Adrian C. Hayday
- Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
- Cancer Research UK Cancer Immunotherapy AcceleratorLondonUK
- Immunosurveillance LaboratoryThe Francis Crick InstituteLondonUK
| | - Francesca Di Rosa
- Institute of Molecular Biology and PathologyNational Research Council of ItalyRomeItaly
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Falck-Jones S, Österberg B, Smed-Sörensen A. Respiratory and systemic monocytes, dendritic cells, and myeloid-derived suppressor cells in COVID-19: Implications for disease severity. J Intern Med 2023; 293:130-143. [PMID: 35996885 PMCID: PMC9538918 DOI: 10.1111/joim.13559] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Since the beginning of the SARS-CoV-2 pandemic in 2020, researchers worldwide have made efforts to understand the mechanisms behind the varying range of COVID-19 disease severity. Since the respiratory tract is the site of infection, and immune cells differ depending on their anatomical location, studying blood is not sufficient to understand the full immunopathogenesis in patients with COVID-19. It is becoming increasingly clear that monocytes, dendritic cells (DCs), and monocytic myeloid-derived suppressor cells (M-MDSCs) are involved in the immunopathology of COVID-19 and may play important roles in determining disease severity. Patients with mild COVID-19 display an early antiviral (interferon) response in the nasopharynx, expansion of activated intermediate monocytes, and low levels of M-MDSCs in blood. In contrast, patients with severe COVID-19 seem to lack an early efficient induction of interferons, and skew towards a more suppressive response in blood. This is characterized by downregulation of activation markers and decreased functional capacity of blood monocytes and DCs, reduced circulating DCs, and increased levels of HLA-DRlo CD14+ M-MDSCs. These suppressive characteristics could potentially contribute to delayed T-cell responses in severe COVID-19 cases. In contrast, airways of patients with severe COVID-19 display hyperinflammation with elevated levels of inflammatory monocytes and monocyte-derived macrophages, and reduced levels of tissue-resident alveolar macrophages. These monocyte-derived cells contribute to excess inflammation by producing cytokines and chemokines. Here, we review the current knowledge on the role of monocytes, DCs, and M-MDSCs in COVID-19 and how alterations and the anatomical distribution of these cell populations may relate to disease severity.
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Affiliation(s)
- Sara Falck-Jones
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Björn Österberg
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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36
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Cross AR, de Andrea CE, Villalba-Esparza M, Landecho MF, Cerundolo L, Weeratunga P, Etherington RE, Denney L, Ogg G, Ho LP, Roberts IS, Hester J, Klenerman P, Melero I, Sansom SN, Issa F. Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury. JCI Insight 2023; 8:e157837. [PMID: 36472908 PMCID: PMC9977306 DOI: 10.1172/jci.insight.157837] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Severe lung damage resulting from COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways, and genes present across the spectrum of histopathological damage in COVID-19-affected lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from 46 areas of interest covering more than 62,000 cells within well-preserved lung samples from 3 patients. Despite substantial interpatient heterogeneity, we discovered evidence for a common immune-cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines, including CXCL9, CXCL10, and CXCL11, which are known to promote the recruitment of CXCR3+ immune cells. The TNF superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were consistently upregulated in the areas with severe tissue damage. We used published spatial and single-cell SARS-CoV-2 data sets to validate our findings in the lung tissue from additional cohorts of patients with COVID-19. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies.
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Affiliation(s)
- Amy R. Cross
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Manuel F. Landecho
- Department of Internal Medicine, and
- Department of Immunology and Immunotherapy, Clínica de la Universidad de Navarra, Pamplona, Spain
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Praveen Weeratunga
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Rachel E. Etherington
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura Denney
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ling-Pei Ho
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ian S.D. Roberts
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joanna Hester
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ignacio Melero
- Department of Immunology and Immunotherapy, Clínica de la Universidad de Navarra, Pamplona, Spain
- CIBERONC, Madrid, Spain
- Center for Applied Medical Research, Pamplona, Spain
| | - Stephen N. Sansom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
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Arguinchona LM, Zagona-Prizio C, Joyce ME, Chan ED, Maloney JP. Microvascular significance of TGF-β axis activation in COVID-19. Front Cardiovasc Med 2023; 9:1054690. [PMID: 36684608 PMCID: PMC9852847 DOI: 10.3389/fcvm.2022.1054690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/09/2022] [Indexed: 01/09/2023] Open
Abstract
As 2023 approaches, the COVID-19 pandemic has killed millions. While vaccines have been a crucial intervention, only a few effective medications exist for prevention and treatment of COVID-19 in breakthrough cases or in unvaccinated or immunocompromised patients. SARS-CoV-2 displays early and unusual features of micro-thrombosis and immune dysregulation that target endothelial beds of the lungs, skin, and other organs. Notably, anticoagulation improves outcomes in some COVID-19 patients. The protein transforming growth factor-beta (TGF-β1) has constitutive roles in maintaining a healthy microvasculature through its roles in regulating inflammation, clotting, and wound healing. However, after infection (including viral infection) TGF-β1 activation may augment coagulation, cause immune dysregulation, and direct a path toward tissue fibrosis. Dysregulation of TGF-β signaling in immune cells and its localization in areas of microvascular injury are now well-described in COVID-19, and such events may contribute to the acute respiratory distress syndrome and skin micro-thrombosis outcomes frequently seen in severe COVID-19. The high concentration of TGF-β in platelets and in other cells within microvascular thrombi, its ability to activate the clotting cascade and dysregulate immune pathways, and its pro-fibrotic properties all contribute to a unique milieu in the COVID-19 microvasculature. This unique environment allows for propagation of microvascular clotting and immune dysregulation. In this review we summarize the physiological functions of TGF-β and detail the evidence for its effects on the microvasculature in COVID-19. In addition, we explore the potential role of existing TGF-β inhibitors for the prevention and treatment of COVID-19 associated microvascular thrombosis and immune dysregulation.
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Affiliation(s)
- Lauren M. Arguinchona
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Caterina Zagona-Prizio
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Megan E. Joyce
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Edward D. Chan
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States,National Jewish Health, Denver, CO, United States
| | - James P. Maloney
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,*Correspondence: James P. Maloney,
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COVID-19 Heart Lesions in Children: Clinical, Diagnostic and Immunological Changes. Int J Mol Sci 2023; 24:ijms24021147. [PMID: 36674665 PMCID: PMC9866514 DOI: 10.3390/ijms24021147] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
In the beginning of COVID-19, the proportion of confirmed cases in the pediatric population was relatively small and there was an opinion that children often had a mild or asymptomatic course of infection. Our understanding of the immune response, diagnosis and treatment of COVID-19 is highly oriented towards the adult population. At the same time, despite the fact that COVID-19 in children usually occurs in a mild form, there is an incomplete understanding of the course as an acute infection and its subsequent manifestations such as Long-COVID-19 or Post-COVID-19, PASC in the pediatric population, correlations with comorbidities and immunological changes. In mild COVID-19 in childhood, some authors explain the absence of population decreasing T and B lymphocytes. Regardless of the patient's condition, they can have the second phase, related to the exacerbation of inflammation in the heart tissue even if the viral infection was completely eliminated-post infectious myocarditis. Mechanism of myocardial dysfunction development in MIS-C are not fully understood. It is known that various immunocompetent cells, including both resident inflammatory cells of peripheral tissues (for example macrophages, dendritic cells, resident memory T-lymphocytes and so on) and also circulating in the peripheral blood immune cells play an important role in the immunopathogenesis of myocarditis. It is expected that hyperproduction of interferons and the enhanced cytokine response of T cells 1 and 2 types contribute to dysfunction of the myocardium. However, the role of Th1 in the pathogenesis of myocarditis remains highly controversial. At the same time, the clinical manifestations and mechanisms of damage, including the heart, both against the background and after COVID-19, in children differ from adults. Further studies are needed to evaluate whether transient or persistent cardiac complications are associated with long-term adverse cardiac events.
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39
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Affiliation(s)
- Adrian Liston
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
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40
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Patra T, Ray R. Bystander effect of SARS-CoV-2 spike protein on human monocytic THP-1 cell activation and initiation of prothrombogenic stimulus representing severe COVID-19. J Inflamm (Lond) 2022; 19:28. [PMID: 36585712 PMCID: PMC9801152 DOI: 10.1186/s12950-022-00325-8] [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: 05/17/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Hypercoagulable state and thromboembolic complications are potential life-threatening events in COVID-19 patients. Our previous studies demonstrated that SARS-CoV-2 infection as well as viral spike protein expressed epithelial cells exhibit senescence with the release of inflammatory molecules, including alarmins. FINDINGS We observed extracellular alarmins present in the culture media of SARS-CoV-2 spike expressing cells activate human THP-1 monocytes to secrete pro-inflammatory cytokines to a significant level. The release of THP-1 derived pro-inflammatory cytokine signature correlated with the serum of acute COVID-19 patient, but not in post-COVID-19 state. Our study suggested that the alarmins secreted by spike expressing cells, initiated phagocytosis property of THP-1 cells. The phagocytic monocytes secreted complement component C5a and generated an autocrine signal via C5aR1 receptor. The C5a-C5aR1 signal induced formation of monocyte mediated extracellular trap resulted in the generation of a prothrombogenic stimulus with activating platelets and increased tissue factor activity. We also observed an enhanced C5a level, platelet activating factor, and high tissue factor activity in the serum of acute COVID-19 patients, but not in recovered patients. CONCLUSION Our present study demonstrated that SARS-CoV-2 spike protein modulates monocyte responses in a paracrine manner for prothrombogenic stimulus by the generation of C5a complement component.
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Affiliation(s)
- Tapas Patra
- Departments of Internal Medicine, Division of Infectious Diseases, Allergy & Immunology, Edward A. Doisy Research Center, 1100 South Grand Blvd, MO 63104 Saint Louis, USA
| | - Ranjit Ray
- Departments of Internal Medicine, Division of Infectious Diseases, Allergy & Immunology, Edward A. Doisy Research Center, 1100 South Grand Blvd, MO 63104 Saint Louis, USA ,grid.262962.b0000 0004 1936 9342Molecular Microbiology & Immunology, Saint Louis University, 63104 Saint Louis, Missouri, MO USA
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41
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Gisby JS, Buang NB, Papadaki A, Clarke CL, Malik TH, Medjeral-Thomas N, Pinheiro D, Mortimer PM, Lewis S, Sandhu E, McAdoo SP, Prendecki MF, Willicombe M, Pickering MC, Botto M, Thomas DC, Peters JE. Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence. Nat Commun 2022; 13:7775. [PMID: 36522333 PMCID: PMC9753891 DOI: 10.1038/s41467-022-35454-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. We observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.
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Affiliation(s)
- Jack S Gisby
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Norzawani B Buang
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Artemis Papadaki
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Candice L Clarke
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Talat H Malik
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Nicholas Medjeral-Thomas
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Damiola Pinheiro
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Paige M Mortimer
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Shanice Lewis
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Eleanor Sandhu
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Stephen P McAdoo
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Maria F Prendecki
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Matthew C Pickering
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Marina Botto
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - David C Thomas
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK.
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK.
| | - James E Peters
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK.
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The Association of Low CD4 Expression on Monocytes and Low CD8+ T-Cell Count at Hospital Admission Predicts the Need for Mechanical Ventilation in Patients With COVID-19 Pneumonia: A Prospective Monocentric Cohort Study. Crit Care Explor 2022; 4:e0810. [PMID: 36518218 PMCID: PMC9742091 DOI: 10.1097/cce.0000000000000810] [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] [Indexed: 12/12/2022] Open
Abstract
To identify COVID-19-associated immunophenotyping patterns at hospital admission and to determine if some patterns could predict the need for mechanical ventilation (MV). DESIGN Prospective observational monocentric cohort study. SETTING A university-affiliated hospital in Marseille, France. PATIENTS Thirty patients presenting with laboratory-confirmed COVID-19 pneumonia were enrolled within the first 48 hours of hospital admission and compared with 18 healthy controls. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Whole-blood leukocytes were immunophenotyped with a rapid and simplified one-step flow cytometry method. Thirty-eight immune and five laboratory parameters were compared first between COVID-19 patients and controls and then between the COVID-19 patients who received or not MV during their stays. The variables that significantly discriminated MV from non-MV patients in univariate analysis were entered into a multiple stepwise logistic regression analysis. The COVID-19 patients were predominantly male (87%), aged 61 years (50-71 yr), and 93% received early corticosteroid therapy. Sixteen patients (53%) were managed with noninvasive respiratory support, and 14 (47%) required MV. Compared with controls, COVID-19 patients were characterized by an immune signature featuring: 1) decreased HLA-DR expression on monocytes; 2) reduced basophils, eosinophils, T-cells, NK cells, and nonclassical monocyte count; and 3) up regulation of CD169 on monocytes, CD64 on neutrophils, the adhesion/migration markers (CD62L and CD11b), and the checkpoint inhibitor CD274 on myeloid cells. Among the COVID-19 patients, those who received MV had lower level of CD4 and HLA-DR on monocytes, lower CD8+ T-cell count, and higher lactate dehydrogenase at hospital admission. In multivariate analysis, only CD4 on monocytes (p = 0.032) and CD8+ T-cell count (p = 0.026) were associated with MV requirement. The model combining these two variables provided an area under curve of 0.97 (95% CI, 0.83-0.99). CONCLUSIONS The association of low CD4 on monocytes and low CD8+ T-cell count at hospital admission was highly predictive of the need for MV in hospitalized patients with COVID-19 pneumonia.
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Jackson H, Rivero Calle I, Broderick C, Habgood-Coote D, D’Souza G, Nichols S, Vito O, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Barreiro-de Acosta M, Cunnington AJ, Herberg JA, Wright VJ, Gómez-Carballa A, Salas A, Levin M, Martinon-Torres F, Kaforou M, Jackson H, Calle IR, Habgood-Coote D, D’Souza G, Nichols S, Gómez-Rial J, Cunnington AJ, Herberg JA, Wright VJ, Gómez-Carballa A, Salas A, Levin M, Martinon-Torres F, Kaforou M, Antonio AG, Julián ÁE, Antonio AL, Gema BC, Xabier BP, Miriam BG, María Victoria CG, Miriam CL, Amparo CN, Mónica CP, José Javier CA, María José CT, Ana Isabel DU, Blanca DE, María Jesús DS, Cristina FP, Juan FV, Cristóbal GR, José Luis GA, Luisa GV, Elena GV, Alberto GC, José GR, Francisco Javier GB, Beatriz GL, Pilar LI, Beatriz LM, Marta LF, Montserrat LF, Ana LL, Federico MT, De la Cruz Daniel N, Eloína NM, Juan Bautista OD, Jacobo PS, María PN, del Molino Bernal Marisa P, Hugo PF, Lidia PR, Sara P, Manuel PR, Antonio PR, Gloria María PH, Teresa QV, Lorenzo RC, Patricia RC, Susana RG, Sara RV, Vanessa RB, Irene RC, Carmen RV, Nuria RN, Carmen RTS, Eva SP, José Miguel SO, Carla SV, Sonia SF, Pablo SS, Manuel TM, Rocío TP, Mercedes TC, Luis VC, Pablo VG, Soledad VIM, Sandra VL, Rocio FI, Iria BR, Cristina CS. Characterisation of the blood RNA host response underpinning severity in COVID-19 patients. Sci Rep 2022; 12:12216. [PMID: 35844004 PMCID: PMC9288817 DOI: 10.1038/s41598-022-15547-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/24/2022] [Indexed: 01/08/2023] Open
Abstract
Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups. Increasing COVID-19 severity was characterised by an abundance of inflammatory immune response genes and pathways, including many related to neutrophils and macrophages, in addition to an upregulation of immunoglobulin genes. In this study, for the first time, we show how immunomodulatory treatments commonly administered to COVID-19 patients greatly alter the transcriptome. Our insights into COVID-19 severity reveal the role of immune dysregulation in the progression to severe disease and highlight the need for further research exploring the interplay between SARS-CoV-2 and the inflammatory immune response.
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Ruenjaiman V, Sodsai P, Kueanjinda P, Bunrasmee W, Klinchanhom S, Reantragoon R, Tunvirachaisakul C, Manothummetha K, Mejun N, Liengswangwong K, Torvorapanit P, Paitoonpong L, Putcharoen O, Palaga T, Hirankarn N, Mittrakulkij C, Chiewbangyang F, Kaewsrihawong J, Sanpakit J, Kulkiatprasert K, Munkong K, Keawthawon N, Wattanakul N, Limchanachon N, Roopsuwankun N, Chaosuwannakij N, Larpanekanan P, Pitakkitnukun P, Homswad P, Ratanapraisorn S, Atchariyapakorn S, Vongphanich S, Jessadapornchai S, Avihingsanon T, Piyasathapornpong T. Impact of SARS-CoV-2 infection on the profiles and responses of innate immune cells after recovery. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:993-1004. [PMID: 36220753 PMCID: PMC9519362 DOI: 10.1016/j.jmii.2022.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/30/2022] [Accepted: 09/24/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUNDS SARS-CoV-2 infection results in a broad spectrum of clinical outcomes, ranging from asymptomatic to severe symptoms and death. Most COVID-19 pathogenesis is associated with hyperinflammatory conditions driven primarily by myeloid cell lineages. The long-term effects of SARS-CoV-2 infection post recovery include various symptoms. METHODS We performed a longitudinal study of the innate immune profiles 1 and 3 months after recovery in the Thai cohort by comparing patients with mild, moderate, and severe clinical symptoms using peripheral blood mononuclear cells (n = 62). RESULTS Significant increases in the frequencies of monocytes compared to controls and NK cells compared to mild and moderate patients were observed in severe patients 1-3 months post recovery. Increased polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) were observed in all recovered patients, even after 3 months. Increased IL-6 and TNFα levels in monocytes were observed 1 month after recovery in response to lipopolysaccharide (LPS) stimulation, while decreased CD86 and HLA-DR levels were observed regardless of stimulation. A multiplex analysis of serum cytokines performed at 1 month revealed that most innate cytokines, except for TNFα, IL4/IL-13 (Th2) and IFNγ (Th1), were elevated in recovered patients in a severity-dependent manner. Finally, the myelopoiesis cytokines G-CSF and GM-CSF were higher in all patient groups. Increased monocytes and IL-6- and TNFα-producing cells were significantly associated with long COVID-19 symptoms. CONCLUSIONS These results reveal that COVID-19 infection influences the frequencies and functions of innate immune cells for up to 3 months after recovery, which may potentially lead to some of the long COVID symptoms.
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Affiliation(s)
- Vichaya Ruenjaiman
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand,Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pimpayao Sodsai
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand,Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand
| | - Patipark Kueanjinda
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand,Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand
| | - Worawan Bunrasmee
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand,Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand
| | - Siriwan Klinchanhom
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand,Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rangsima Reantragoon
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand,Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Kasama Manothummetha
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nuthchaya Mejun
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kaewkwan Liengswangwong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pattama Torvorapanit
- Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand,Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Leilani Paitoonpong
- Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand,Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Opass Putcharoen
- Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand,Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand,Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand,Corresponding author. Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nattiya Hirankarn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand,Center of Excellence in Immunology and Immune-Mediated Diseases Chulalongkorn University, Bangkok, 10330, Thailand
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Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines. Genome Med 2022; 14:134. [PMID: 36443794 PMCID: PMC9706884 DOI: 10.1186/s13073-022-01137-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. METHODS In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14 + CD15- monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. RESULTS We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. CONCLUSION Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the release of aberrant immature monocytes, increased systemic levels of pro-inflammatory cytokines, and changes in immune cell crosstalk in these patients.
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Malik SA, Modarage K, Goggolidou P. A systematic review assessing the effectiveness of COVID-19 mRNA vaccines in chronic kidney disease (CKD) individuals. F1000Res 2022; 11:909. [PMID: 36531259 PMCID: PMC9732501 DOI: 10.12688/f1000research.122820.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Background: SARS-CoV-2 is a coronavirus that has rapidly spread across the world with a detrimental effect on the global population. Several reports have highlighted an increased mortality rate and a higher severity of COVID-19 infection in chronic kidney disease (CKD) individuals. Upon the development of various SARS-CoV-2 vaccines, mRNA vaccines including BNT162b2 and mRNA-1273 were deemed safe, with a high efficacy in preventing COVID-19 in the general population. This review investigates whether SARS-CoV-2 mRNA vaccines are as effective in triggering an immune response in Dialysis Patients (DPs) and Kidney Transplant Recipients (KTRs) and if a third dose is required in this population. Methods: A systematic search employing the PRISMA criteria was conducted in several major databases, with the data being extracted from publications for the period January 2021 to May 2022 (PROSPERO: CRD42022338514, June 15, 2022). Results: 80 studies were included in this analysis with a total cohort number of 15,059 participants. Overall, 85.29% (OR = 17.08, 95% CI = 15.84-18.42, I 2 = 98%) and 41.06% (OR = 0.52, 95% CI = 0.48-0.5, I 2 = 95%) of DPs and KTRs included in this review showed positive seroconversion after two doses of either mRNA vaccine, respectively. A total 76% (OR = 6.53, 95% CI = 5.63-7.5, I 2 = 96%) of the cohort given a third dose of an mRNA vaccine demonstrated positive seroconversion, with 61.86% (OR = 2.31, 95% CI = 1.95-2.75 I 2 = 95%) of the cohort that was assessed for a cellular response displaying a positive response. Conclusions: This data emphasises a reduced incidence of a positive immune response in DPs and KTRs compared to healthy controls, albeit a better response in DPs than when compared to KTRs alone was observed. A third dose appears to increase the occurrence of an immune response in the overall DP/KTR cohort.
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Affiliation(s)
- Soniya A. Malik
- Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY, UK
| | - Kavindiya Modarage
- Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY, UK
| | - Paraskevi Goggolidou
- Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY, UK,
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George PM, Reed A, Desai SR, Devaraj A, Faiez TS, Laverty S, Kanwal A, Esneau C, Liu MKC, Kamal F, Man WDC, Kaul S, Singh S, Lamb G, Faizi FK, Schuliga M, Read J, Burgoyne T, Pinto AL, Micallef J, Bauwens E, Candiracci J, Bougoussa M, Herzog M, Raman L, Ahmetaj-Shala B, Turville S, Aggarwal A, Farne HA, Dalla Pria A, Aswani AD, Patella F, Borek WE, Mitchell JA, Bartlett NW, Dokal A, Xu XN, Kelleher P, Shah A, Singanayagam A. A persistent neutrophil-associated immune signature characterizes post-COVID-19 pulmonary sequelae. Sci Transl Med 2022; 14:eabo5795. [PMID: 36383686 DOI: 10.1126/scitranslmed.abo5795] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Interstitial lung disease and associated fibrosis occur in a proportion of individuals who have recovered from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through unknown mechanisms. We studied individuals with severe coronavirus disease 2019 (COVID-19) after recovery from acute illness. Individuals with evidence of interstitial lung changes at 3 to 6 months after recovery had an up-regulated neutrophil-associated immune signature including increased chemokines, proteases, and markers of neutrophil extracellular traps that were detectable in the blood. Similar pathways were enriched in the upper airway with a concomitant increase in antiviral type I interferon signaling. Interaction analysis of the peripheral phosphoproteome identified enriched kinases critical for neutrophil inflammatory pathways. Evaluation of these individuals at 12 months after recovery indicated that a subset of the individuals had not yet achieved full normalization of radiological and functional changes. These data provide insight into mechanisms driving development of pulmonary sequelae during and after COVID-19 and provide a rational basis for development of targeted approaches to prevent long-term complications.
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Affiliation(s)
- Peter M George
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Anna Reed
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Sujal R Desai
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Anand Devaraj
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Tasnim Shahridan Faiez
- Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Sarah Laverty
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Amama Kanwal
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Camille Esneau
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Michael K C Liu
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | | | - William D-C Man
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
- Faculty of Life Sciences and Medicine, King's College London, London WC2R 2LS, UK
| | - Sundeep Kaul
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Suveer Singh
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Georgia Lamb
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Fatima K Faizi
- Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Michael Schuliga
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jane Read
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Thomas Burgoyne
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Andreia L Pinto
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Jake Micallef
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Emilie Bauwens
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Julie Candiracci
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Mhammed Bougoussa
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Marielle Herzog
- Belgian Volition SRL, 22 rue Phocas Lejeune, Parc Scientifique Créalys, Isnes 5032, Belgium
| | - Lavanya Raman
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | - Stuart Turville
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hugo A Farne
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
- Chest and Allergy Department, St Mary's Hospital, Imperial College NHS Trust, London W2 1NY, UK
| | - Alessia Dalla Pria
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
- Department of HIV and Genitourinary Medicine, Chelsea and Westminster NHS Foundation Trust, London SW10 9NH, UK
| | - Andrew D Aswani
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London SE1 7EH, UK
- Santersus AG, Buckhauserstrasse 34, Zurich 8048, Switzerland
| | - Francesca Patella
- Kinomica Ltd, Biohub, Alderley Park, Alderley Edge, Macclesfield, Cheshire SK10 4TG, UK
| | - Weronika E Borek
- Kinomica Ltd, Biohub, Alderley Park, Alderley Edge, Macclesfield, Cheshire SK10 4TG, UK
| | - Jane A Mitchell
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Nathan W Bartlett
- Faculty of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Arran Dokal
- Kinomica Ltd, Biohub, Alderley Park, Alderley Edge, Macclesfield, Cheshire SK10 4TG, UK
| | - Xiao-Ning Xu
- Section of Virology, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Peter Kelleher
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- Department of HIV and Genitourinary Medicine, Chelsea and Westminster NHS Foundation Trust, London SW10 9NH, UK
- Immunology of Infection Section, Department of Infectious Disease, Imperial College London, London W2 1PG, UK
- Department of Infection and Immunity Sciences, North West London Pathology NHS Trust, London W2 1NY, UK
| | - Anand Shah
- Royal Brompton and Harefield Clinical Group, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
- MRC Centre of Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Aran Singanayagam
- Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
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Saifi MA, Bansod S, Godugu C. COVID-19 and fibrosis: Mechanisms, clinical relevance, and future perspectives. Drug Discov Today 2022; 27:103345. [PMID: 36075378 PMCID: PMC9444298 DOI: 10.1016/j.drudis.2022.103345] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/19/2022] [Accepted: 09/01/2022] [Indexed: 01/08/2023]
Abstract
Coronavirus 2019 (COVID-19), caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has had significant impacts worldwide since its emergence in December, 2019. Despite a high recovery rate, there is a growing concern over its residual, long-term effects. However, because of a lack of long-term data, we are still far from establishing a consensus on post-COVID-19 complications. The deposition of excessive extracellular matrix (ECM), known as fibrosis, has been observed in numerous survivors of COVID-19. Given the exceptionally high number of individuals affected, there is an urgent need to address the emergence of fibrosis post-COVID-19. In this review, we discuss the clinical relevance of COVID-19-associated fibrosis, the current status of antifibrotic agents, novel antifibrotic targets, and challenges to its management.
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Affiliation(s)
- Mohd Aslam Saifi
- Department of Biological Sciences (Regulatory Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500 037, India
| | - Sapana Bansod
- Department of Internal Medicine, Oncology Division, Washington University, School of Medicine, St Louis, MO 63110, USA
| | - Chandraiah Godugu
- Department of Biological Sciences (Regulatory Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500 037, India.
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Pandori WJ, Padgett LE, Alimadadi A, Gutierrez NA, Araujo DJ, Huh CJ, Olingy CE, Dinh HQ, Wu R, Vijayanand P, Chee SJ, Ottensmeier CH, Hedrick CC. Single-cell immune profiling reveals long-term changes in myeloid cells and identifies a novel subset of CD9 + monocytes associated with COVID-19 hospitalization. J Leukoc Biol 2022; 112:1053-1063. [PMID: 35866369 PMCID: PMC9350203 DOI: 10.1002/jlb.4cova0122-076r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/16/2022] [Accepted: 05/11/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in severe immune dysfunction, hospitalization, and death. Many patients also develop long-COVID-19, experiencing symptoms months after infection. Although significant progress has been made in understanding the immune response to acute SARS-CoV-2 infection, gaps remain in our knowledge of how innate immunity influences disease kinetics and severity. We hypothesized that cytometry by time-of-flight analysis of PBMCs from healthy and infected subjects would identify novel cell surface markers and innate immune cell subsets associated with COVID-19 severity. In this pursuit, we identified monocyte and dendritic cell subsets that changed in frequency during acute SARS-CoV-2 infection and correlated with clinical parameters of disease severity. Subsets of nonclassical monocytes decreased in frequency in hospitalized subjects, yet increased in the most severe patients and positively correlated with clinical values associated with worse disease severity. CD9, CD163, PDL1, and PDL2 expression significantly increased in hospitalized subjects, and CD9 and 6-Sulfo LacNac emerged as the markers that best distinguished monocyte subsets amongst all subjects. CD9+ monocytes remained elevated, whereas nonclassical monocytes remained decreased, in the blood of hospitalized subjects at 3-4 months postinfection. Finally, we found that CD9+ monocytes functionally released more IL-8 and MCP-1 after LPS stimulation. This study identifies new monocyte subsets present in the blood of COVID-19 patients that correlate with disease severity, and links CD9+ monocytes to COVID-19 progression.
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Affiliation(s)
- William J. Pandori
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Lindsey E. Padgett
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Ahmad Alimadadi
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Norma A. Gutierrez
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Daniel J. Araujo
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Christine J. Huh
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Claire E. Olingy
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Huy Q. Dinh
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Runpei Wu
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Pandurangan Vijayanand
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Serena J. Chee
- Institute of Systems, Molecular and Integrative Biology (ISMIB)University of LiverpoolLiverpoolUK
| | - Christian H. Ottensmeier
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
- Institute of Systems, Molecular and Integrative Biology (ISMIB)University of LiverpoolLiverpoolUK
| | - Catherine C. Hedrick
- Center for Autoimmunity and InflammationLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
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Kudryavtsev IV, Arsentieva NA, Korobova ZR, Isakov DV, Rubinstein AA, Batsunov OK, Khamitova IV, Kuznetsova RN, Savin TV, Akisheva TV, Stanevich OV, Lebedeva AA, Vorobyov EA, Vorobyova SV, Kulikov AN, Sharapova MA, Pevtsov DE, Totolian AA. Heterogenous CD8+ T Cell Maturation and 'Polarization' in Acute and Convalescent COVID-19 Patients. Viruses 2022; 14:1906. [PMID: 36146713 PMCID: PMC9504186 DOI: 10.3390/v14091906] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The adaptive antiviral immune response requires interaction between CD8+ T cells, dendritic cells, and Th1 cells for controlling SARS-CoV-2 infection, but the data regarding the role of CD8+ T cells in the acute phase of COVID-19 and post-COVID-19 syndrome are still limited. METHODS . Peripheral blood samples collected from patients with acute COVID-19 (n = 71), convalescent subjects bearing serum SARS-CoV-2 N-protein-specific IgG antibodies (n = 51), and healthy volunteers with no detectable antibodies to any SARS-CoV-2 proteins (HC, n = 46) were analyzed using 10-color flow cytometry. RESULTS Patients with acute COVID-19 vs. HC and COVID-19 convalescents showed decreased absolute numbers of CD8+ T cells, whereas the frequency of CM and TEMRA CD8+ T cells in acute COVID-19 vs. HC was elevated. COVID-19 convalescents vs. HC had increased naïve and CM cells, whereas TEMRA cells were decreased compared to HC. Cell-surface CD57 was highly expressed by the majority of CD8+ T cells subsets during acute COVID-19, but convalescents had increased CD57 on 'naïve', CM, EM4, and pE1 2-3 months post-symptom onset. CXCR5 expression was altered in acute and convalescent COVID-19 subjects, whereas the frequencies of CXCR3+ and CCR4+ cells were decreased in both patient groups vs. HC. COVID-19 convalescents had increased CCR6-expressing CD8+ T cells. Moreover, CXCR3+CCR6- Tc1 cells were decreased in patients with acute COVID-19 and COVID-19 convalescents, whereas Tc2 and Tc17 levels were increased compared to HC. Finally, IL-27 negatively correlated with the CCR6+ cells in acute COVID-19 patients. CONCLUSIONS We described an abnormal CD8+ T cell profile in COVID-19 convalescents, which resulted in lower frequencies of effector subsets (TEMRA and Tc1), higher senescent state (upregulated CD57 on 'naïve' and memory cells), and higher frequencies of CD8+ T cell subsets expressing lung tissue and mucosal tissue homing molecules (Tc2, Tc17, and Tc17.1). Thus, our data indicate that COVID-19 can impact the long-term CD8+ T cell immune response.
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Affiliation(s)
- Igor V. Kudryavtsev
- Institute of Experimental Medicine, Akademika Pavlova 12, 197376 Saint Petersburg, Russia
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Natalia A. Arsentieva
- Laboratory of Immunology, Saint Petersburg Pasteur Institute, Mira 14, 197101 Saint Petersburg, Russia
| | - Zoia R. Korobova
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
- Laboratory of Immunology, Saint Petersburg Pasteur Institute, Mira 14, 197101 Saint Petersburg, Russia
| | - Dmitry V. Isakov
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Artem A. Rubinstein
- Institute of Experimental Medicine, Akademika Pavlova 12, 197376 Saint Petersburg, Russia
| | - Oleg K. Batsunov
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
- Laboratory of Immunology, Saint Petersburg Pasteur Institute, Mira 14, 197101 Saint Petersburg, Russia
| | - Irina V. Khamitova
- Laboratory of Immunology, Saint Petersburg Pasteur Institute, Mira 14, 197101 Saint Petersburg, Russia
| | - Raisa N. Kuznetsova
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
- Laboratory of Immunology, Saint Petersburg Pasteur Institute, Mira 14, 197101 Saint Petersburg, Russia
| | - Tikhon V. Savin
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
- Laboratory of Immunology, Saint Petersburg Pasteur Institute, Mira 14, 197101 Saint Petersburg, Russia
| | - Tatiana V. Akisheva
- Institute of Experimental Medicine, Akademika Pavlova 12, 197376 Saint Petersburg, Russia
| | - Oksana V. Stanevich
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
- Smorodintsev Research Institute of Influenza, Prof. Popov St. 15/17, 197376 Saint Petersburg, Russia
| | - Aleksandra A. Lebedeva
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Evgeny A. Vorobyov
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Snejana V. Vorobyova
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Alexander N. Kulikov
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Maria A. Sharapova
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Dmitrii E. Pevtsov
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
| | - Areg A. Totolian
- Medical Faculty, First Saint Petersburg State I. Pavlov Medical University, L’va Tolstogo St. 6-8, 197022 Saint Petersburg, Russia
- Laboratory of Immunology, Saint Petersburg Pasteur Institute, Mira 14, 197101 Saint Petersburg, Russia
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