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Gu J, Xu J, Jiao A, Cai N, Gu T, Wu P, Cheng X, Chen B, Chen Y, Liu X. Comprehensive analysis of single-cell transcriptomics and genetic factors reveals the mechanisms and preventive strategies for the progression from pulmonary fibrosis to lung cancer. Int Immunopharmacol 2024; 140:112803. [PMID: 39094357 DOI: 10.1016/j.intimp.2024.112803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/24/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Pulmonary fibrosis (PF) leads to excessive deposition of fibrous connective tissue in the lungs, increasing the risk of lung cancer due to the enhanced activity of fibroblasts (FBs). Fibroblast-mediated collagen fiber deposition creates a tumor-like microenvironment, laying the foundation for tumorigenesis. Clinically, numerous cases of lung cancer induced by pulmonary fibrosis have been observed. In recent years, the study of nucleotide point mutations, which provide more detailed insights than gene expression, has made significant advancements, offering new perspectives for clinical research. METHODS We initially employed Mendelian randomization to ascertain that the initial stage of lung cancer induced by PF belongs to small cell lung cancer (SCLC). Subsequently, pulmonary neuroendocrine cells (PNECs) were identified by using pseudo-time series analysis as cell clusters with carcinogenic potential. We categorized FBs into four groups according to their cellular metabolism, and then analyzed the cellular communication between FBs and PNECs, as well as changes in intracellular pathways of PNECs. Additionally, we examined the characteristic genome of FBs which is significantly associated with PF and investigated the impact of FBs on immune cells in the PF microenvironment. Finally, we explored strategies for preventing the progression from PF to lung cancer. RESULTS The genetic features of cells with carcinogenic potential in PF tissues were revealed, characterized by upregulation of Achaete-Scute Family BHLH Transcription Factor 1 (ASCL1), Homeobox B2 (HOXB2), Teashirt Zinc Finger Homeobox 2 (TSHZ2), Insulinoma-associated 1 (INSM1), and reduced activity of RE1 Silencing Transcription Factor (REST). FBs characterized by high glycolysis and low tricarboxylic acid (TCA) cycling played a key role in the progression of PF. The microenvironment of PF resembles the tumor microenvironment, providing a conducive immunosuppressive environment for the occurrence of cancer cells. In dendritic cells, rs9265808 is a susceptibility locus for progression from pulmonary fibrosis to lung cancer, mutations at this locus increase the expression of Complement Factor B (CFB), and excessive activation of the complement pathway is a crucial factor leading to lung cancer development in patients with pulmonary fibrosis. Ensuring adequate nutritional supply and physical function is one of the effective measures to prevent progression from pulmonary fibrosis to lung cancer. CONCLUSION CFB promotes lung cancer occurrence by inducing the accumulation and polarization of a large number of monocytes/macrophages in the lungs, driving disease progression by reducing the physical fitness of patients with pulmonary fibrosis.
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Affiliation(s)
- Jinghua Gu
- School of Life Sciences, Anhui Medical University, Hefei 230032, China; The First Clinical Medical College of Anhui Medical University, Hefei 230032, China; Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial Key Laboratory of Long Non-coding RNA and Cancer Metabolism, Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiansheng Xu
- The First Clinical Medical College of Anhui Medical University, Hefei 230032, China
| | - Annan Jiao
- The First Clinical Medical College of Anhui Medical University, Hefei 230032, China; The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Ningning Cai
- The First Clinical Medical College of Anhui Medical University, Hefei 230032, China
| | - Tianrui Gu
- School of Pharmacy, Zhejiang University, Hangzhou 310058, China
| | - Pengcheng Wu
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Xinyu Cheng
- School of Life Sciences, Anhui Medical University, Hefei 230032, China
| | - Bo Chen
- The First Clinical Medical College of Anhui Medical University, Hefei 230032, China; The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China.
| | - Yang Chen
- The First Clinical Medical College of Anhui Medical University, Hefei 230032, China; The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China.
| | - Xiaoying Liu
- School of Life Sciences, Anhui Medical University, Hefei 230032, China; Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial Key Laboratory of Long Non-coding RNA and Cancer Metabolism, Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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2
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Wang M, Zhang D, Lei T, Zhou Y, Qin H, Wu Y, Liu S, Zhang L, Jia K, Dong Y, Wang S, Li Y, Fan Y, Gui L, Dong Y, Zhang W, Li Z, Hou J. Interferon-responsive neutrophils and macrophages extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis. J Med Virol 2024; 96:e29889. [PMID: 39206862 DOI: 10.1002/jmv.29889] [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: 04/22/2024] [Revised: 07/24/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
The SARS-CoV-2 Omicron variant is characterized by its high transmissibility, which has caused a worldwide epidemiological event. Yet, it turns ominous once the disease progression degenerates into severe pneumonia and sepsis, presenting a horrendous lethality. To elucidate the alveolar immune or inflammatory landscapes of Omicron critical-ill patients, we performed single-cell RNA-sequencing (scRNA-seq) of bronchoalveolar lavage fluid (BALF) from the patients with critical pneumonia caused by Omicron infection, and analyzed the correlation between the clinical severity scores and different immune cell subpopulations. In the BALF of Omicron critical patients, the alveolar violent myeloid inflammatory environment was determined. ISG15+ neutrophils and CXCL10+ macrophages, both expressed the interferon-stimulated genes (ISGs), were negatively correlated with clinical pulmonary infection score, while septic CST7+ neutrophils and inflammatory VCAN+ macrophages were positively correlated with sequential organ failure assessment. The percentages of ISG15+ neutrophils were associated with more protective alveolar epithelial cells, and may reshape CD4+ T cells to the exhaustive phenotype, thus preventing immune injuries. The CXCL10+ macrophages may promote plasmablast/plasma cell survival and activation as well as the production of specific antibodies. As compared to the previous BALF scRNA-seq data from SARS-CoV-2 wild-type/Alpha critical patients, the subsets of neutrophils and macrophages with pro-inflammatory and immunoregulatory features presented obvious distinctions, suggesting an immune disparity in Omicron variants. Overall, this study provides a BALF single-cell atlas of Omicron critical patients, and suggests that alveolar interferon-responsive neutrophils and macrophages may extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis.
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Affiliation(s)
- Mu Wang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Dingji Zhang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ting Lei
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ye Zhou
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Hao Qin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Yanfeng Wu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Shuxun Liu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Liyuan Zhang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Kaiwei Jia
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yue Dong
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Suyuan Wang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yunhui Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yiwen Fan
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Liangchen Gui
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yuchao Dong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Zhixuan Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Jin Hou
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
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3
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Huang M, Mark A, Pham J, Vera K, Saravia-Butler AM, Beheshti A, Jiang Q, Fisch KM. RNA editing regulates host immune response and T cell homeostasis in SARS-CoV-2 infection. PLoS One 2024; 19:e0307450. [PMID: 39178184 PMCID: PMC11343423 DOI: 10.1371/journal.pone.0307450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/04/2024] [Indexed: 08/25/2024] Open
Abstract
Adenosine to inosine (A-to-I) RNA editing by ADAR1 has been implicated in maintaining self-tolerance, preventing autoimmunity, and mediating antiviral immunity. Foreign viral double-stranded RNA triggers rapid interferon response and activates ADAR1 in the host immune system. Emerging data points to a role of ADAR1 A-to-I editing in the inflammatory response associated with severe COVID-19 disease. We identify A-to-I editing events within human whole transcriptome data from SARS-CoV-2 infected individuals, non-infected individuals, and individuals with other viral illnesses from nasopharyngeal swabs. High levels of RNA editing in host cells are associated with low SARS-CoV-2 viral load (p = 9.27 E-06), suggesting an inhibitory effect of ADAR1 on viral infection. Additionally, we find differentially expressed genes associated with RNA-modifications and interferon response. Single cell RNA-sequencing analysis of SARS-CoV-2 infected nasopharyngeal swabs reveals that cytotoxic CD8 T cells upregulate ADAR1 in COVID-19 positive samples (p = 0.0269). We further reveal ADAR1 expression increases with CD4 and CD8 T cell activation, and knockdown of ADAR1 leads to apoptosis and aberrant IL-2 secretion. Together, our data suggests A-to-I RNA editing is required to maintain healthy homeostasis of activated T cells to combat SARS-CoV-2 infection.
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Affiliation(s)
- Molly Huang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Adam Mark
- Center for Computational Biology & Bioinformatics, University of California San Diego, La Jolla, California, United States of America
| | - Jessica Pham
- Division of Regenerative Medicine and Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Karina Vera
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Amanda M. Saravia-Butler
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, California, United States of America
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- COVID-19 International Research Team, Medford, Massachusetts, United States of America
| | - Qingfei Jiang
- Division of Regenerative Medicine and Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, California, United States of America
- Center for Computational Biology & Bioinformatics, University of California San Diego, La Jolla, California, United States of America
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4
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Israelow B, Iwasaki A. First encounter with SARS-CoV-2: immune portraits of COVID susceptibility. Nature 2024; 631:33-35. [PMID: 38898251 DOI: 10.1038/d41586-024-01644-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
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5
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Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L, Polanski K, Allen-Hyttinen J, Mehta P, Sumanaweera D, Boccacino JM, Sungnak W, Elmentaite R, Huang N, Mamanova L, Kapuge R, Bolt L, Prigmore E, Killingley B, Kalinova M, Mayer M, Boyers A, Mann A, Swadling L, Woodall MNJ, Ellis S, Smith CM, Teixeira VH, Janes SM, Chambers RC, Haniffa M, Catchpole A, Heyderman R, Noursadeghi M, Chain B, Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature 2024; 631:189-198. [PMID: 38898278 PMCID: PMC11222146 DOI: 10.1038/s41586-024-07575-x] [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: 02/24/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the dynamics of early cellular responses to this disease remains limited1. Here in our SARS-CoV-2 human challenge study, we used single-cell multi-omics profiling of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in seronegative individuals challenged with pre-Alpha SARS-CoV-2. Our analyses revealed rapid changes in cell-type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific time points and infection status. We observed that the interferon response in blood preceded the nasopharyngeal response. Moreover, nasopharyngeal immune infiltration occurred early in samples from individuals with only transient infection and later in samples from individuals with sustained infection. High expression of HLA-DQA2 before inoculation was associated with preventing sustained infection. Ciliated cells showed multiple immune responses and were most permissive for viral replication, whereas nasopharyngeal T cells and macrophages were infected non-productively. We resolved 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against infection.
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Affiliation(s)
- Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - David Scobie
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Helen R Wagstaffe
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | | | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | | | - Waradon Sungnak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Microbiology, Faculty of Science, and Integrative Computational BioScience Center, Mahidol University, Bangkok, Thailand
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Ensocell Therapeutics, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rakesh Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ben Killingley
- Department of Infectious Diseases, University College London Hospital, London, UK
| | | | | | | | | | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | | | - Samuel Ellis
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Vitor H Teixeira
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Robert Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Andreas Mayer
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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6
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Berger L, Wolf J, Kalbitz S, Kellner N, Lübbert C, Borte S. Comparative Analysis of Lymphocyte Populations in Post-COVID-19 Condition and COVID-19 Convalescent Individuals. Diagnostics (Basel) 2024; 14:1286. [PMID: 38928701 PMCID: PMC11202600 DOI: 10.3390/diagnostics14121286] [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: 05/06/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Reduced lymphocyte counts in peripheral blood are one of the most common observations in acute phases of viral infections. Although many studies have already examined the impact of immune (dys)regulation during SARS-CoV-2 infection, there are still uncertainties about the long-term consequences for lymphocyte homeostasis. Furthermore, as persistent cellular aberrations have been described following other viral infections, patients with "Post-COVID-19 Condition" (PCC) may present similarly. In order to investigate cellular changes in the adaptive immune system, we performed a retrospective analysis of flow cytometric data from lymphocyte subpopulations in 106 patients with confirmed SARS-CoV-2 infection who received medical care at our institution. The patients were divided into three groups according to the follow-up date; laboratory analyses of COVID-19 patients were compared with 28 unexposed healthy controls. Regarding B lymphocyte subsets, levels of IgA + CD27+, IgG + CD27+, IgM + CD27- and switched B cells were significantly reduced at the last follow-up compared to unexposed healthy controls (UHC). Of the 106 COVID-19 patients, 56 were clinically classified as featuring PCC. Significant differences between PCC and COVID-19 convalescents compared to UHC were observed in T helper cells and class-switched B cells. However, we did not detect specific or long-lasting immune cellular changes in PCC compared to the non-post-COVID-19 condition.
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Affiliation(s)
- Luisa Berger
- Department of Infectious Diseases and Tropical Medicine, Hospital St. Georg, 04129 Leipzig, Germany
| | - Johannes Wolf
- Department of Laboratory Medicine, Hospital St. Georg, 04129 Leipzig, Germany
- ImmunoDeficiencyCenter Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, 04139 Leipzig, Germany
| | - Sven Kalbitz
- Department of Infectious Diseases and Tropical Medicine, Hospital St. Georg, 04129 Leipzig, Germany
| | - Nils Kellner
- Department of Infectious Diseases and Tropical Medicine, Hospital St. Georg, 04129 Leipzig, Germany
- ImmunoDeficiencyCenter Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, 04139 Leipzig, Germany
| | - Christoph Lübbert
- Department of Infectious Diseases and Tropical Medicine, Hospital St. Georg, 04129 Leipzig, Germany
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Leipzig University Medical Center, 04103 Leipzig, Germany
| | - Stephan Borte
- Department of Laboratory Medicine, Hospital St. Georg, 04129 Leipzig, Germany
- ImmunoDeficiencyCenter Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, 04139 Leipzig, Germany
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7
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Rosas-García J, Padilla-Zúñiga AJ, Ávila-Flores A, Gutiérrez-González LH, Mérida I, Santos-Mendoza T. Modeling of host PDZ-dependent interactions with SARS-CoV-2 Envelope protein and changes in PDZ proteins expression in macrophages and dendritic cells. J Leukoc Biol 2024:qiae118. [PMID: 38748862 DOI: 10.1093/jleuko/qiae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/16/2024] [Accepted: 05/01/2024] [Indexed: 07/10/2024] Open
Abstract
PDZ (PSD-95/Dlg/ZO-1) domain-containing proteins constitute a large family of scaffolds involved in a wide range of cellular tasks, and mainly studied in polarity functions. Diverse host PDZ proteins can be targeted by viral pathogens which express proteins containing PDZ-binding motifs (PDZbm). Previously, we have identified host PDZ-based interactions with the SARS-CoV-2 E protein (2E) in human monocytes. Here, we deepen the study of these interactions by docking and molecular dynamics analyses to identify the most favorable PDZ-PDZbm interaction of seven host PDZ proteins with the PDZbm of 2E. In addition, we analyzed changes in the expression of three of the PDZ proteins identified as 2E interactors in monocytes (syntenin, ZO-2, and IL-16), in human monocyte-derived macrophages (MΦ) and in dendritic cells (DCs) upon stimulation. Our results suggest that these PDZ proteins may have important functions in professional antigen-presenting cells (APCs), and their targeting by the PDZbm of 2E, a central virulence determinant of SARS-CoV-2, support the hypothesis that such PDZ-dependent interaction in immune cells may constitute a viral evasion mechanism. Inhibitor design based on the PDZbm of 2E in the development of drugs against a variety of diseases is discussed.
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Affiliation(s)
- Jorge Rosas-García
- Laboratory of Transcriptomics and Molecular Immunology. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Antonia Ávila-Flores
- Department of Immunology and Oncology, Spanish National Centre for Biotechnology. Madrid, Spain
| | - Luis Horacio Gutiérrez-González
- Laboratory of Transcriptomics and Molecular Immunology. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Isabel Mérida
- Department of Immunology and Oncology, Spanish National Centre for Biotechnology. Madrid, Spain
| | - Teresa Santos-Mendoza
- Laboratory of Transcriptomics and Molecular Immunology. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
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Taefehshokr N, Lac A, Vrieze AM, Dickson BH, Guo PN, Jung C, Blythe EN, Fink C, Aktar A, Dikeakos JD, Dekaban GA, Heit B. SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2. J Cell Sci 2024; 137:jcs262172. [PMID: 38682259 PMCID: PMC11166459 DOI: 10.1242/jcs.262172] [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: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
SARS-CoV-2 interferes with antigen presentation by downregulating major histocompatibility complex (MHC) II on antigen-presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen-presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. CIITA downregulation is independent of the proteolytic activity of NSP5, and rather, NSP5 delivers HDAC2 to the transcription factor IRF3 at an IRF-binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.
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Affiliation(s)
- Nima Taefehshokr
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Alex Lac
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Angela M. Vrieze
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Brandon H. Dickson
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Peter N. Guo
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Catherine Jung
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Eoin N. Blythe
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Corby Fink
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Amena Aktar
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Jimmy D. Dikeakos
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Gregory A. Dekaban
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Bryan Heit
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
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9
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Hamdorf M, Imhof T, Bailey-Elkin B, Betz J, Theobald SJ, Simonis A, Di Cristanziano V, Gieselmann L, Dewald F, Lehmann C, Augustin M, Klein F, Alejandre Alcazar MA, Rongisch R, Fabri M, Rybniker J, Goebel H, Stetefeld J, Brachvogel B, Cursiefen C, Koch M, Bock F. The unique ORF8 protein from SARS-CoV-2 binds to human dendritic cells and induces a hyper-inflammatory cytokine storm. J Mol Cell Biol 2024; 15:mjad062. [PMID: 37891014 PMCID: PMC11181941 DOI: 10.1093/jmcb/mjad062] [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: 07/04/2022] [Revised: 02/01/2023] [Accepted: 10/26/2023] [Indexed: 10/29/2023] Open
Abstract
The novel coronavirus pandemic, first reported in December 2019, was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 infection leads to a strong immune response and activation of antigen-presenting cells, which can elicit acute respiratory distress syndrome (ARDS) characterized by the rapid onset of widespread inflammation, the so-called cytokine storm. In response to viral infections, monocytes are recruited into the lung and subsequently differentiate into dendritic cells (DCs). DCs are critical players in the development of acute lung inflammation that causes ARDS. Here, we focus on the interaction of a specific SARS-CoV-2 open reading frame protein, ORF8, with DCs. We show that ORF8 binds to DCs, causes pre-maturation of differentiating DCs, and induces the secretion of multiple proinflammatory cytokines by these cells. In addition, we identified DC-SIGN as a possible interaction partner of ORF8 on DCs. Blockade of ORF8 leads to reduced production of IL-1β, IL-6, IL-12p70, TNF-α, MCP-1 (also named CCL2), and IL-10 by DCs. Therefore, a neutralizing antibody blocking the ORF8-mediated cytokine and chemokine response could be an improved therapeutic strategy against SARS-CoV-2.
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Affiliation(s)
- Matthias Hamdorf
- Cornea Lab Experimental Ophthalmology, Department of Ophthalmology, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA
| | - Thomas Imhof
- Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
- Institute for Experimental Dentistry and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Ben Bailey-Elkin
- Department of Microbiology, University of Manitoba, Winnipeg MB R3B 2E9 Manitoba, Canada
| | - Janina Betz
- Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
- Institute for Experimental Dentistry and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Alexander Simonis
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, 50935 Cologne, Germany
| | - Lutz Gieselmann
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, 50935 Cologne, Germany
| | - Felix Dewald
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, 50935 Cologne, Germany
| | - Clara Lehmann
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Max Augustin
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Miguel A Alejandre Alcazar
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Department of Children and Adolescent Medicine, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster Stress Responses in Aging-associated Diseases, 50931 Cologne, Germany
- Institute for Lung Health (ILH), Universities of Gießen and Marburg Lung Centre, Member of the German Center for Lung Research, 35392 Gießen, Germany
| | - Robert Rongisch
- Dermatology, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
| | - Mario Fabri
- Dermatology, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Heike Goebel
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
| | - Jörg Stetefeld
- Department of Microbiology, University of Manitoba, Winnipeg MB R3B 2E9 Manitoba, Canada
| | - Bent Brachvogel
- Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Claus Cursiefen
- Cornea Lab Experimental Ophthalmology, Department of Ophthalmology, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
- Institute for Experimental Dentistry and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Felix Bock
- Cornea Lab Experimental Ophthalmology, Department of Ophthalmology, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
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10
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Garcia G, Labrouche-Colomer S, Duvignaud A, Clequin E, Dussiau C, Trégouët DA, Malvy D, Prevel R, Zouine A, Pellegrin I, Goret J, Mamani-Matsuda M, Dewitte A, James C. Impaired balance between neutrophil extracellular trap formation and degradation by DNases in COVID-19 disease. J Transl Med 2024; 22:246. [PMID: 38454482 PMCID: PMC10919029 DOI: 10.1186/s12967-024-05044-7] [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: 12/14/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Thrombo-inflammation and neutrophil extracellular traps (NETs) are exacerbated in severe cases of COVID-19, potentially contributing to disease exacerbation. However, the mechanisms underpinning this dysregulation remain elusive. We hypothesised that lower DNase activity may be associated with higher NETosis and clinical worsening in patients with COVID-19. METHODS Biological samples were obtained from hospitalized patients (15 severe, 37 critical at sampling) and 93 non-severe ambulatory cases. Our aims were to compare NET biomarkers, functional DNase levels, and explore mechanisms driving any imbalance concerning disease severity. RESULTS Functional DNase levels were diminished in the most severe patients, paralleling an imbalance between NET markers and DNase activity. DNase1 antigen levels were higher in ambulatory cases but lower in severe patients. DNase1L3 antigen levels remained consistent across subgroups, not rising alongside NET markers. DNASE1 polymorphisms correlated with reduced DNase1 antigen levels. Moreover, a quantitative deficiency in plasmacytoid dendritic cells (pDCs), which primarily express DNase1L3, was observed in critical patients. Analysis of public single-cell RNAseq data revealed reduced DNase1L3 expression in pDCs from severe COVID-19 patient. CONCLUSION Severe and critical COVID-19 cases exhibited an imbalance between NET and DNase functional activity and quantity. Early identification of NETosis imbalance could guide targeted therapies against thrombo-inflammation in COVID-19-related sepsis, such as DNase administration, to avert clinical deterioration. TRIAL REGISTRATION COVERAGE trial (NCT04356495) and COLCOV19-BX study (NCT04332016).
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Affiliation(s)
- Geoffrey Garcia
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
| | - Sylvie Labrouche-Colomer
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France
| | - Alexandre Duvignaud
- Department of Infectious Diseases and Tropical Medicine, Hôpital Pellegrin, CHU Bordeaux, 33076, Bordeaux, France
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Etienne Clequin
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Anaesthesia and Intensive Care, Bordeaux University Hospital, 33600, Pessac, France
| | - Charles Dussiau
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France
| | - David-Alexandre Trégouët
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Denis Malvy
- Department of Infectious Diseases and Tropical Medicine, Hôpital Pellegrin, CHU Bordeaux, 33076, Bordeaux, France
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Renaud Prevel
- Medical Intensive Care Unit, Bordeaux University Hospital, 33000, Bordeaux, France
- Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM, UMR 1045, Bordeaux University, 33000, Bordeaux, France
| | - Atika Zouine
- CNRS, INSERM, TBM-Core, US5, UAR 3427, Flow Cytometry Facility, Bordeaux University, 33000, Bordeaux, France
| | - Isabelle Pellegrin
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Centre de Ressources Biologiques, Bordeaux University Hospital, 33000, Bordeaux, France
| | - Julien Goret
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
| | - Maria Mamani-Matsuda
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
| | - Antoine Dewitte
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Anaesthesia and Intensive Care, Bordeaux University Hospital, 33600, Pessac, France
| | - Chloe James
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France.
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France.
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11
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Massenet-Regad L, Soumelis V. ICELLNET v2: a versatile method for cell-cell communication analysis from human transcriptomic data. Bioinformatics 2024; 40:btae089. [PMID: 38490248 PMCID: PMC10955248 DOI: 10.1093/bioinformatics/btae089] [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: 11/09/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024] Open
Abstract
SUMMARY Several methods have been developed in the past years to infer cell-cell communication networks from transcriptomic data based on ligand and receptor expression. Among them, ICELLNET is one of the few approaches to consider the multiple subunits of ligands and receptors complexes to infer and quantify cell communication. In here, we present a major update of ICELLNET. As compared to its original implementation, we (i) drastically expanded the ICELLNET ligand-receptor database from 380 to 1669 biologically curated interactions, (ii) integrated important families of communication molecules involved in immune crosstalk, cell adhesion, and Wnt pathway, (iii) optimized ICELLNET framework for single-cell RNA sequencing data analyses, (iv) provided new visualizations of cell-cell communication results to facilitate prioritization and biological interpretation. This update will broaden the use of ICELLNET by the scientific community in different biological fields. AVAILABILITY AND IMPLEMENTATION ICELLNET package is implemented in R. Source code, documentation and tutorials are available on GitHub (https://github.com/soumelis-lab/ICELLNET).
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Affiliation(s)
- Lucile Massenet-Regad
- Université Paris Cité, INSERM U976 HIPI, Paris, F-75010, France
- Université Paris-Saclay, Saint Aubin, F-91190, France
| | - Vassili Soumelis
- Université Paris Cité, INSERM U976 HIPI, Paris, F-75010, France
- Department of Immunology-Histocompatibility, Saint-Louis Hospital, AP-HP.Nord, Université Paris Cité, Paris 75010, France
- Owkin France, Paris 75010, France
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12
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Jogi HR, Smaraki N, Nayak SS, Rajawat D, Kamothi DJ, Panigrahi M. Single cell RNA-seq: a novel tool to unravel virus-host interplay. Virusdisease 2024; 35:41-54. [PMID: 38817399 PMCID: PMC11133279 DOI: 10.1007/s13337-024-00859-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/12/2024] [Indexed: 06/01/2024] Open
Abstract
Over the last decade, single cell RNA sequencing (scRNA-seq) technology has caught the momentum of being a vital revolutionary tool to unfold cellular heterogeneity by high resolution assessment. It evades the inadequacies of conventional sequencing technology which was able to detect only average expression level among cell populations. In the era of twenty-first century, several epidemic and pandemic viruses have emerged. Being an intracellular entity, viruses totally rely on host. Complex virus-host dynamics result when the virus tend to obtain factors from host cell required for its replication and establishment of infection. As a prevailing tool, scRNA-seq is able to understand virus-host interplay by comprehensive transcriptome profiling. Because of technological and methodological advancement, this technology is capable to recognize viral genome and host cell response heterogeneity. Further development in analytical methods with multiomics approach and increased availability of accessible scRNA-seq datasets will improve the understanding of viral pathogenesis that can be helpful for development of novel antiviral therapeutic strategies.
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Affiliation(s)
- Harsh Rajeshbhai Jogi
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Nabaneeta Smaraki
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Dhaval J. Kamothi
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
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13
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Chattopadhyay P, Mehta P, Soni J, Tardalkar K, Joshi M, Pandey R. Cell-specific housekeeping role of lncRNAs in COVID-19-infected and recovered patients. NAR Genom Bioinform 2024; 6:lqae023. [PMID: 38426128 PMCID: PMC10903533 DOI: 10.1093/nargab/lqae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
A plethora of studies have demonstrated the roles of lncRNAs in modulating disease severity and outcomes during infection. However, the spatio-temporal expression of these lncRNAs is poorly understood. In this study, we used single-cell RNA-seq to understand the spatio-temporal expression dynamics of lncRNAs across healthy, SARS-CoV-2-infected, and recovered individuals and their functional role in modulating the disease and recovery. We identified 203 differentially expressed lncRNAs, including cell type-specific ones like MALAT1, NEAT1, ZFAS1, SNHG7, SNHG8, and SNHG25 modulating immune function in classical monocyte, NK T, proliferating NK, plasmablast, naive, and activated B/T cells. Interestingly, we found invariant lncRNAs (no significant change in expression across conditions) regulating essential housekeeping functions (for example, HOTAIR, NRAV, SNHG27, SNHG28, and UCA1) in infected and recovered individuals. Despite similar repeat element abundance, variant lncRNAs displayed higher Alu content, suggesting increased interactions with proximal and distal genes, crucial for immune response modulation. The comparable repeat abundance but distinct expression levels of variant and invariant lncRNAs highlight the significance of investigating the regulatory mechanisms of invariant lncRNAs. Overall, this study offers new insights into the spatio-temporal expression patterns and functional roles of lncRNAs in SARS-CoV-2-infected and recovered individuals while highlighting the importance of invariant lncRNAs in the disease context.
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Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D.Y. Patil Education Society, Kadamwadi, Kolhapur-416003,Maharashtra, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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14
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Maino A, Amen A, Plumas J, Bouquet L, Deschamps M, Saas P, Chaperot L, Manches O. Development of a New Off-the-Shelf Plasmacytoid Dendritic Cell-Based Approach for the Expansion and Characterization of SARS-CoV-2-Specific T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:825-833. [PMID: 38214610 DOI: 10.4049/jimmunol.2300704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024]
Abstract
Global vaccination against COVID-19 has been widely successful; however, there is a need for complementary immunotherapies in severe forms of the disease and in immunocompromised patients. Cytotoxic CD8+ T cells have a crucial role in disease control, but their function can be dysregulated in severe forms of the disease. We report here a cell-based approach using a plasmacytoid dendritic cell line (PDC*line) to expand in vitro specific CD8+ responses against COVID-19 Ags. We tested the immunogenicity of eight HLA-A*02:01 restricted peptides derived from diverse SARS-Cov-2 proteins, selected by bioinformatics analyses in unexposed and convalescent donors. Higher ex vivo frequencies of specific T cells against these peptides were found in convalescent donors compared with unexposed donors, suggesting in situ T cell expansion upon viral infection. The peptide-loaded PDC*line induced robust CD8+ responses with total amplification rates that led up to a 198-fold increase in peptide-specific CD8+ T cell frequencies for a single donor. Of note, six of eight selected peptides provided significant amplifications, all of which were conserved between SARS-CoV variants and derived from the membrane, the spike protein, the nucleoprotein, and the ORF1ab. Amplified and cloned antiviral CD8+ T cells secreted IFN-γ upon peptide-specific activation. Furthermore, specific TCR sequences were identified for two highly immunogenic Ags. Hence, PDC*line represents an efficient platform to identify immunogenic viral targets for future immunotherapies.
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Affiliation(s)
- Anthony Maino
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Axelle Amen
- Laboratoire d'Immunologie, Centre Hospitalier Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, UMR 5075, Institut de Biologie Structurale, Grenoble, France
| | - Joël Plumas
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- PDC*line Pharma SAS, Grenoble, France
| | - Lucie Bouquet
- Université de Franche-Comté, Etablissement Français du Sang, INSERM, UMR RIGHT, Besançon, France
| | - Marina Deschamps
- Université de Franche-Comté, Etablissement Français du Sang, INSERM, UMR RIGHT, Besançon, France
| | - Philippe Saas
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Laurence Chaperot
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Olivier Manches
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
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15
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Jiang Y, Dai S, Pang R, Qin L, Zhang M, Liu H, Wang X, Zhang J, Peng G, Wang Y, Li W. Single-cell RNA sequencing reveals cell type-specific immune regulation associated with human neuromyelitis optica spectrum disorder. Front Immunol 2024; 15:1322125. [PMID: 38440735 PMCID: PMC10909925 DOI: 10.3389/fimmu.2024.1322125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction One rare type of autoimmune disease is called neuromyelitis optica spectrum disorder (NMOSD) and the peripheral immune characteristics of NMOSD remain unclear. Methods Here, single-cell RNA sequencing (scRNA-seq) is used to characterize peripheral blood mononuclear cells from individuals with NMOSD. Results The differentiation and activation of lymphocytes, expansion of myeloid cells, and an excessive inflammatory response in innate immunity are observed. Flow cytometry analyses confirm a significant increase in the percentage of plasma cells among B cells in NMOSD. NMOSD patients exhibit an elevated percentage of CD8+ T cells within the T cell population. Oligoclonal expansions of B cell receptors are observed after therapy. Additionally, individuals with NMOSD exhibit elevated expression of CXCL8, IL7, IL18, TNFSF13, IFNG, and NLRP3. Discussion Peripheral immune response high-dimensional single-cell profiling identifies immune cell subsets specific to a certain disease and identifies possible new targets for NMOSD.
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Affiliation(s)
- Yushu Jiang
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shuhua Dai
- Department of Neurology, Zhoukou Central Hospital, Zhoukou, Henan, China
| | - Rui Pang
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lingzhi Qin
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Milan Zhang
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Huiqin Liu
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaojuan Wang
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiewen Zhang
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Gongxin Peng
- Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yongchao Wang
- Department of Neurology, People’s Hospital of Yexian, Pingdingshan, Henan, China
| | - Wei Li
- Department of Neurology, Henan Joint International Research Laboratory Of Accurate Diagnosis, Treatment, Research And Development, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
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16
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Manfrini N, Notarbartolo S, Grifantini R, Pesce E. SARS-CoV-2: A Glance at the Innate Immune Response Elicited by Infection and Vaccination. Antibodies (Basel) 2024; 13:13. [PMID: 38390874 PMCID: PMC10885122 DOI: 10.3390/antib13010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to almost seven million deaths worldwide. SARS-CoV-2 causes infection through respiratory transmission and can occur either without any symptoms or with clinical manifestations which can be mild, severe or, in some cases, even fatal. Innate immunity provides the initial defense against the virus by sensing pathogen-associated molecular patterns and triggering signaling pathways that activate the antiviral and inflammatory responses, which limit viral replication and help the identification and removal of infected cells. However, temporally dysregulated and excessive activation of the innate immune response is deleterious for the host and associates with severe COVID-19. In addition to its defensive role, innate immunity is pivotal in priming the adaptive immune response and polarizing its effector function. This capacity is relevant in the context of both SARS-CoV-2 natural infection and COVID-19 vaccination. Here, we provide an overview of the current knowledge of the innate immune responses to SARS-CoV-2 infection and vaccination.
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Affiliation(s)
- Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Samuele Notarbartolo
- Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- CheckmAb Srl, 20122 Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
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17
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May L, Chu CF, Zielinski CE. Single-Cell RNA Sequencing Reveals HIF1A as a Severity-Sensitive Immunological Scar in Circulating Monocytes of Convalescent Comorbidity-Free COVID-19 Patients. Cells 2024; 13:300. [PMID: 38391913 PMCID: PMC10886588 DOI: 10.3390/cells13040300] [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: 12/22/2023] [Revised: 01/20/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is characterized by a wide range of clinical symptoms and a poorly predictable disease course. Although in-depth transcriptomic investigations of peripheral blood samples from COVID-19 patients have been performed, the detailed molecular mechanisms underlying an asymptomatic, mild or severe disease course, particularly in patients without relevant comorbidities, remain poorly understood. While previous studies have mainly focused on the cellular and molecular dissection of ongoing COVID-19, we set out to characterize transcriptomic immune cell dysregulation at the single-cell level at different time points in patients without comorbidities after disease resolution to identify signatures of different disease severities in convalescence. With single-cell RNA sequencing, we reveal a role for hypoxia-inducible factor 1-alpha (HIF1A) as a severity-sensitive long-term immunological scar in circulating monocytes of convalescent COVID-19 patients. Additionally, we show that circulating complexes formed by monocytes with either T cells or NK cells represent a characteristic cellular marker in convalescent COVID-19 patients irrespective of their preceding symptom severity. Together, these results provide cellular and molecular correlates of recovery from COVID-19 and could help in immune monitoring and in the design of new treatment strategies.
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Affiliation(s)
- Lilly May
- Leibniz Institute for Natural Products Research and Infection Biology, Department of Infection Immunology, 07745 Jena, Germany; (L.M.); (C.-F.C.)
- Center for Translational Cancer Research (TranslaTUM) & Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Chang-Feng Chu
- Leibniz Institute for Natural Products Research and Infection Biology, Department of Infection Immunology, 07745 Jena, Germany; (L.M.); (C.-F.C.)
- Center for Translational Cancer Research (TranslaTUM) & Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Christina E. Zielinski
- Leibniz Institute for Natural Products Research and Infection Biology, Department of Infection Immunology, 07745 Jena, Germany; (L.M.); (C.-F.C.)
- Center for Translational Cancer Research (TranslaTUM) & Institute of Virology, Technical University of Munich, 81675 Munich, Germany
- Department of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
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18
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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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Choi S, Lee J, Kim S, Lee YW, Kim GC, Hong SM, An SH, Noh H, Kim KE, On D, Lee SG, Jang HJ, Kim SH, Kim J, Seo JS, Kim JJ, Park IH, Oh J, Kim DJ, Yoon JH, Seok SH, Lee YJ, Kim SY, Kim YB, Hwang JY, Lee HJ, Kim HB, Park JW, Yun JW, Shin JS, Seo JY, Nam KT, Choi KS, Kwon HK, Lee HY, Kim JK, Seong JK. A longitudinal molecular and cellular lung atlas of lethal SARS-CoV-2 infection in K18-hACE2 transgenic mice. EBioMedicine 2024; 99:104932. [PMID: 38118400 PMCID: PMC10772566 DOI: 10.1016/j.ebiom.2023.104932] [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: 11/18/2022] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to approximately 500 million cases and 6 million deaths worldwide. Previous investigations into the pathophysiology of SARS-CoV-2 primarily focused on peripheral blood mononuclear cells from patients, lacking detailed mechanistic insights into the virus's impact on inflamed tissue. Existing animal models, such as hamster and ferret, do not faithfully replicate the severe SARS-CoV-2 infection seen in patients, underscoring the need for more relevant animal system-based research. METHODS In this study, we employed single-cell RNA sequencing (scRNA-seq) with lung tissues from K18-hACE2 transgenic (TG) mice during SARS-CoV-2 infection. This approach allowed for a comprehensive examination of the molecular and cellular responses to the virus in lung tissue. FINDINGS Upon SARS-CoV-2 infection, K18-hACE2 TG mice exhibited severe lung pathologies, including acute pneumonia, alveolar collapse, and immune cell infiltration. Through scRNA-seq, we identified 36 different types of cells dynamically orchestrating SARS-CoV-2-induced pathologies. Notably, SPP1+ macrophages in the myeloid compartment emerged as key drivers of severe lung inflammation and fibrosis in K18-hACE2 TG mice. Dynamic receptor-ligand interactions, involving various cell types such as immunological and bronchial cells, defined an enhanced TGFβ signaling pathway linked to delayed tissue regeneration, severe lung injury, and fibrotic processes. INTERPRETATION Our study provides a comprehensive understanding of SARS-CoV-2 pathogenesis in lung tissue, surpassing previous limitations in investigating inflamed tissues. The identified SPP1+ macrophages and the dysregulated TGFβ signaling pathway offer potential targets for therapeutic intervention. Insights from this research may contribute to the development of innovative diagnostics and therapies for COVID-19. FUNDING This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020M3A9I2109027, 2021R1A2C2004501).
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Affiliation(s)
- Seunghoon Choi
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Jusung Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Suhyeon Kim
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; BIO-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Youn Woo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Gi-Cheon Kim
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Seung-Min Hong
- Laboratory of Avian Diseases, BK21 Project for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Se-Hee An
- Laboratory of Avian Diseases, BK21 Project for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyuna Noh
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyung Eun Kim
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Dain On
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Gyu Lee
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Sung-Hee Kim
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jiseon Kim
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Seon Seo
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jeong Jin Kim
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - In Ho Park
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jooyeon Oh
- Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Da-Jung Kim
- Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jong-Hwi Yoon
- Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sang-Hyuk Seok
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24342, Republic of Korea
| | - Yu Jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24342, Republic of Korea
| | - Seo Yeon Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Young Been Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Ji-Yeon Hwang
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam 23620, Republic of Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 23620, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24342, Republic of Korea
| | - Jun-Won Yun
- Laboratory of Veterinary Toxicology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeon-Soo Shin
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jun-Young Seo
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ki Taek Nam
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, BK21 Project for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea.
| | - Ho-Keun Kwon
- Graduate School of Medical Science, BK21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 23488, Republic of Korea; Department of Nuclear Medicine, Seoul National University, College of Medicine, Seoul 03080, South Korea.
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea; Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Project for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; BIO-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea.
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20
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Pan J, Chang Z, Zhang X, Dong Q, Zhao H, Shi J, Wang G. Research progress of single-cell sequencing in tuberculosis. Front Immunol 2023; 14:1276194. [PMID: 37901241 PMCID: PMC10611525 DOI: 10.3389/fimmu.2023.1276194] [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: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Tuberculosis is a major infectious disease caused by Mycobacterium tuberculosis infection. The pathogenesis and immune mechanism of tuberculosis are not clear, and it is urgent to find new drugs, diagnosis, and treatment targets. A useful tool in the quest to reveal the enigmas related to Mycobacterium tuberculosis infection and disease is the single-cell sequencing technique. By clarifying cell heterogeneity, identifying pathogenic cell groups, and finding key gene targets, the map at the single cell level enables people to better understand the cell diversity of complex organisms and the immune state of hosts during infection. Here, we briefly reviewed the development of single-cell sequencing, and emphasized the different applications and limitations of various technologies. Single-cell sequencing has been widely used in the study of the pathogenesis and immune response of tuberculosis. We review these works summarizing the most influential findings. Combined with the multi-molecular level and multi-dimensional analysis, we aim to deeply understand the blank and potential future development of the research on Mycobacterium tuberculosis infection using single-cell sequencing technology.
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Affiliation(s)
| | | | | | | | | | - Jingwei Shi
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
| | - Guoqing Wang
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
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21
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Robertson SJ, Bedard O, McNally KL, Shaia C, Clancy CS, Lewis M, Broeckel RM, Chiramel AI, Shannon JG, Sturdevant GL, Rosenke R, Anzick SL, Forte E, Preuss C, Baker CN, Harder JM, Brunton C, Munger S, Bruno DP, Lack JB, Leung JM, Shamsaddini A, Gardina P, Sturdevant DE, Sun J, Martens C, Holland SM, Rosenthal NA, Best SM. Genetically diverse mouse models of SARS-CoV-2 infection reproduce clinical variation in type I interferon and cytokine responses in COVID-19. Nat Commun 2023; 14:4481. [PMID: 37491352 PMCID: PMC10368652 DOI: 10.1038/s41467-023-40076-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/05/2023] [Indexed: 07/27/2023] Open
Abstract
Inflammation in response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection drives severity of coronavirus disease 2019 (COVID-19) and is influenced by host genetics. To understand mechanisms of inflammation, animal models that reflect genetic diversity and clinical outcomes observed in humans are needed. We report a mouse panel comprising the genetically diverse Collaborative Cross (CC) founder strains crossed to human ACE2 transgenic mice (K18-hACE2) that confers susceptibility to SARS-CoV-2. Infection of CC x K18-hACE2 resulted in a spectrum of survival, viral replication kinetics, and immune profiles. Importantly, in contrast to the K18-hACE2 model, early type I interferon (IFN-I) and regulated proinflammatory responses were required for control of SARS-CoV-2 replication in PWK x K18-hACE2 mice that were highly resistant to disease. Thus, virus dynamics and inflammation observed in COVID-19 can be modeled in diverse mouse strains that provide a genetically tractable platform for understanding anti-coronavirus immunity.
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Affiliation(s)
- Shelly J Robertson
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | | | - Kristin L McNally
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Chad S Clancy
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Matthew Lewis
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Rebecca M Broeckel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Abhilash I Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Jeffrey G Shannon
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Gail L Sturdevant
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Sarah L Anzick
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Elvira Forte
- The Jackson Laboratory, Bar Harbor, ME, USA
- Springer Nature, New York, NY, USA
| | | | | | | | | | | | - Daniel P Bruno
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Justin B Lack
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jacqueline M Leung
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Amirhossein Shamsaddini
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Paul Gardina
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Daniel E Sturdevant
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jian Sun
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Craig Martens
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Steven M Holland
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Nadia A Rosenthal
- The Jackson Laboratory, Bar Harbor, ME, USA.
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA.
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA.
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22
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Lee YJ, Seok SH, Lee NY, Choi HJ, Lee YW, Chang HJ, Hwang JY, On DI, Noh HA, Lee SB, Kwon HK, Yun JW, Shin JS, Seo JY, Nam KT, Lee H, Lee HY, Park JW, Seong JK. Murine Coronavirus Disease 2019 Lethality Is Characterized by Lymphoid Depletion Associated with Suppressed Antigen-Presenting Cell Functionality. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:866-882. [PMID: 37024046 PMCID: PMC10073095 DOI: 10.1016/j.ajpath.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023]
Abstract
The disease severity of coronavirus disease 2019 (COVID-19) varies considerably from asymptomatic to serious, with fatal complications associated with dysregulation of innate and adaptive immunity. Lymphoid depletion in lymphoid tissues and lymphocytopenia have both been associated with poor disease outcomes in patients with COVID-19, but the mechanisms involved remain elusive. In this study, human angiotensin-converting enzyme 2 (hACE2) transgenic mouse models susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were used to investigate the characteristics and determinants of lethality associated with the lymphoid depletion observed in SARS-CoV-2 infection. The lethality of Wuhan SARS-CoV-2 infection in K18-hACE2 mice was characterized by severe lymphoid depletion and apoptosis in lymphoid tissues related to fatal neuroinvasion. The lymphoid depletion was associated with a decreased number of antigen-presenting cells (APCs) and their suppressed functionality below basal levels. Lymphoid depletion with reduced APC function was a specific feature observed in SARS-CoV-2 infection but not in influenza A infection and had the greatest prognostic value for disease severity in murine COVID-19. Comparison of transgenic mouse models resistant and susceptible to SARS-CoV-2 infection revealed that suppressed APC function could be determined by the hACE2 expression pattern and interferon-related signaling. Thus, we demonstrated that lymphoid depletion associated with suppressed APC function characterizes the lethality of COVID-19 mouse models. Our data also suggest a potential therapeutic approach to prevent the severe progression of COVID-19 by enhancing APC functionality.
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Affiliation(s)
- Yu Jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, ChunCheon, Republic of Korea
| | - Sang Hyeok Seok
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, ChunCheon, Republic of Korea
| | - Na Yun Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, ChunCheon, Republic of Korea
| | - Hee Jin Choi
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, ChunCheon, Republic of Korea
| | - Yoon Woo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Hee Jung Chang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Ji-Yeon Hwang
- Preclinical Research Center, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Da In On
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Republic of Korea
| | - Hyun Ah Noh
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Republic of Korea
| | - Su-Bin Lee
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ho-Keun Kwon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jun-Won Yun
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jeon-Soo Shin
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, Republic of Korea; Severance Biomedical Science Institute, and the Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jun-Young Seo
- Severance Biomedical Science Institute, and the Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, and the Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
| | - Ho Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, ChunCheon, Republic of Korea.
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Republic of Korea; Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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23
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Nakamura K, Dalal AR, Yokoyama N, Pedroza AJ, Kusadokoro S, Mitchel O, Gilles C, Masoudian B, Leipzig M, Casey KM, Hiesinger W, Uchida T, Fischbein MP. Lineage-Specific Induced Pluripotent Stem Cell-Derived Smooth Muscle Cell Modeling Predicts Integrin Alpha-V Antagonism Reduces Aortic Root Aneurysm Formation in Marfan Syndrome Mice. Arterioscler Thromb Vasc Biol 2023; 43:1134-1153. [PMID: 37078287 PMCID: PMC10330156 DOI: 10.1161/atvbaha.122.318448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND The role of increased smooth muscle cell (SMC) integrin αv signaling in Marfan syndrome (MFS) aortic aneurysm remains unclear. Herein, we examine the mechanism and potential efficacy of integrin αv blockade as a therapeutic strategy to reduce aneurysm progression in MFS. METHODS Induced pluripotent stem cells (iPSCs) were differentiated into aortic SMCs of the second heart field (SHF) and neural crest (NC) lineages, enabling in vitro modeling of MFS thoracic aortic aneurysms. The pathological role of integrin αv during aneurysm formation was confirmed by blockade of integrin αv with GLPG0187 in Fbn1C1039G/+ MFS mice. RESULTS iPSC-derived MFS SHF SMCs overexpress integrin αv relative to MFS NC and healthy control SHF cells. Furthermore, integrin αv downstream targets (FAK [focal adhesion kinase]/AktThr308/mTORC1 [mechanistic target of rapamycin complex 1]) were activated, especially in MFS SHF. Treatment of MFS SHF SMCs with GLPG0187 reduced p-FAK/p-AktThr308/mTORC1 activity back to control SHF levels. Functionally, MFS SHF SMCs had increased proliferation and migration compared to MFS NC SMCs and control SMCs, which normalized with GLPG0187 treatment. In the Fbn1C1039G/+ MFS mouse model, integrin αv, p-AktThr308, and downstream targets of mTORC1 proteins were elevated in the aortic root/ascending segment compared to littermate wild-type control. Mice treated with GLPG0187 (age 6-14 weeks) had reduced aneurysm growth, elastin fragmentation, and reduction of the FAK/AktThr308/mTORC1 pathway. GLPG0187 treatment reduced the amount and severity of SMC modulation assessed by single-cell RNA sequencing. CONCLUSIONS The integrin αv-FAK-AktThr308 signaling pathway is activated in iPSC SMCs from MFS patients, specifically from the SHF lineage. Mechanistically, this signaling pathway promotes SMC proliferation and migration in vitro. As biological proof of concept, GLPG0187 treatment slowed aneurysm growth and p-AktThr308 signaling in Fbn1C1039G/+ mice. Integrin αv blockade via GLPG0187 may be a promising therapeutic approach to inhibit MFS aneurysmal growth.
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Affiliation(s)
- Ken Nakamura
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Alex R. Dalal
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Nobu Yokoyama
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Albert J. Pedroza
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Sho Kusadokoro
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Olivia Mitchel
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Casey Gilles
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Bahar Masoudian
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Matthew Leipzig
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Kerriann M. Casey
- Department of Comparative Medicine, Stanford University School of Medicine. Stanford CA, USA
| | - William Hiesinger
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
| | - Tetsuro Uchida
- Second Department of Surgery, Yamagata University Faculty of Medicine. Yamagata, Japan
| | - Michael P. Fischbein
- Department of Cardiothoracic Surgery, Stanford University School of Medicine. Stanford CA, USA
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24
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Prebensen C, Lefol Y, Myhre PL, Lüders T, Jonassen C, Blomfeldt A, Omland T, Nilsen H, Berdal JE. Longitudinal whole blood transcriptomic analysis characterizes neutrophil activation and interferon signaling in moderate and severe COVID-19. Sci Rep 2023; 13:10368. [PMID: 37365222 PMCID: PMC10293211 DOI: 10.1038/s41598-023-37606-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/24/2023] [Indexed: 06/28/2023] Open
Abstract
A maladaptive inflammatory response has been implicated in the pathogenesis of severe COVID-19. This study aimed to characterize the temporal dynamics of this response and investigate whether severe disease is associated with distinct gene expression patterns. We performed microarray analysis of serial whole blood RNA samples from 17 patients with severe COVID-19, 15 patients with moderate disease and 11 healthy controls. All study subjects were unvaccinated. We assessed whole blood gene expression patterns by differential gene expression analysis, gene set enrichment, two clustering methods and estimated relative leukocyte abundance using CIBERSORT. Neutrophils, platelets, cytokine signaling, and the coagulation system were activated in COVID-19, and this broad immune activation was more pronounced in severe vs. moderate disease. We observed two different trajectories of neutrophil-associated genes, indicating the emergence of a more immature neutrophil phenotype over time. Interferon-associated genes were strongly enriched in early COVID-19 before falling markedly, with modest severity-associated differences in trajectory. In conclusion, COVID-19 necessitating hospitalization is associated with a broad inflammatory response, which is more pronounced in severe disease. Our data suggest a progressively more immature circulating neutrophil phenotype over time. Interferon signaling is enriched in COVID-19 but does not seem to drive severe disease.
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Affiliation(s)
- Christian Prebensen
- Department of Infectious Diseases, Oslo University Hospital, Kirkeveien 166, 0450, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Yohan Lefol
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Peder L Myhre
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Cardiology, Akershus University Hospital, Lørenskog, Norway
| | - Torben Lüders
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | | | - Anita Blomfeldt
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Torbjørn Omland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Cardiology, Akershus University Hospital, Lørenskog, Norway
| | - Hilde Nilsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Jan-Erik Berdal
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Infectious Diseases, Akershus University Hospital, Lørenskog, Norway
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25
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Edahiro R, Shirai Y, Takeshima Y, Sakakibara S, Yamaguchi Y, Murakami T, Morita T, Kato Y, Liu YC, Motooka D, Naito Y, Takuwa A, Sugihara F, Tanaka K, Wing JB, Sonehara K, Tomofuji Y, Namkoong H, Tanaka H, Lee H, Fukunaga K, Hirata H, Takeda Y, Okuzaki D, Kumanogoh A, Okada Y. Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity. Nat Genet 2023; 55:753-767. [PMID: 37095364 PMCID: PMC10181941 DOI: 10.1038/s41588-023-01375-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/15/2023] [Indexed: 04/26/2023]
Abstract
Mechanisms underpinning the dysfunctional immune response in severe acute respiratory syndrome coronavirus 2 infection are elusive. We analyzed single-cell transcriptomes and T and B cell receptors (BCR) of >895,000 peripheral blood mononuclear cells from 73 coronavirus disease 2019 (COVID-19) patients and 75 healthy controls of Japanese ancestry with host genetic data. COVID-19 patients showed a low fraction of nonclassical monocytes (ncMono). We report downregulated cell transitions from classical monocytes to ncMono in COVID-19 with reduced CXCL10 expression in ncMono in severe disease. Cell-cell communication analysis inferred decreased cellular interactions involving ncMono in severe COVID-19. Clonal expansions of BCR were evident in the plasmablasts of patients. Putative disease genes identified by COVID-19 genome-wide association study showed cell type-specific expressions in monocytes and dendritic cells. A COVID-19-associated risk variant at the IFNAR2 locus (rs13050728) had context-specific and monocyte-specific expression quantitative trait loci effects. Our study highlights biological and host genetic involvement of innate immune cells in COVID-19 severity.
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Affiliation(s)
- Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Yusuke Takeshima
- Laboratory of Experimental Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yuta Yamaguchi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Teruaki Murakami
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Yasuhiro Kato
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Yu-Chen Liu
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Yoko Naito
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Ayako Takuwa
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kentaro Tanaka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - James B Wing
- Laboratory of Human Immunology (Single Cell Immunology), Immunology Frontier Research Center, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Hiromu Tanaka
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Ho Lee
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
- Japan Agency for Medical Research and Development - Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Japan Agency for Medical Research and Development - Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Osaka, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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26
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Wang X, Guan F, Miller H, Byazrova MG, Cndotti F, Benlagha K, Camara NOS, Lei J, Filatov A, Liu C. The role of dendritic cells in COVID-19 infection. Emerg Microbes Infect 2023; 12:2195019. [PMID: 36946172 PMCID: PMC10171120 DOI: 10.1080/22221751.2023.2195019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The persistent pandemic of coronavirus disease in 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) currently poses a major infectious threat to public health around the world. COVID-19 is an infectious disease characterized by strong induction of inflammatory cytokines, progressive lung inflammation, and potential multiple organ dysfunction. SARS-CoV-2 infection is closely related to the innate immune system and adaptive immune system. Dendritic cells (DCs), as a "bridge" connecting innate immunity and adaptive immunity, play many important roles in viral diseases. In this review, we will pay special attention to the possible mechanism of dendritic cells in human viral transmission and clinical progression of diseases, as well as the reduction and dysfunction of DCs in severe SARS-CoV-2 infection, so as to understand the mechanism and immunological characteristics of SARS-CoV-2 infection.
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Affiliation(s)
- Xuying Wang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
- Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
| | - Heather Miller
- Cytek Biosciences, R&D Clinical Reagents, Fremont, CA, United States
| | - Maria G Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522, Moscow, Russia
| | - Fabio Cndotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kamel Benlagha
- Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Niels Olsen Saraiva Camara
- Laboratory of Human Immunology, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo - SP, Brazil
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
| | - Alexander Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, 115522, Moscow, Russia
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, Hubei, China
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27
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Aghamiri SS, Puniya BL, Amin R, Helikar T. A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery. Front Immunol 2023; 14:1112985. [PMID: 36993954 PMCID: PMC10040975 DOI: 10.3389/fimmu.2023.1112985] [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: 11/30/2022] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells (APCs) with the unique ability to mediate inflammatory responses of the immune system. Given the critical role of DCs in shaping immunity, they present an attractive avenue as a therapeutic target to program the immune system and reverse immune disease disorders. To ensure appropriate immune response, DCs utilize intricate and complex molecular and cellular interactions that converge into a seamless phenotype. Computational models open novel frontiers in research by integrating large-scale interaction to interrogate the influence of complex biological behavior across scales. The ability to model large biological networks will likely pave the way to understanding any complex system in more approachable ways. We developed a logical and predictive model of DC function that integrates the heterogeneity of DCs population, APC function, and cell-cell interaction, spanning molecular to population levels. Our logical model consists of 281 components that connect environmental stimuli with various layers of the cell compartments, including the plasma membrane, cytoplasm, and nucleus to represent the dynamic processes within and outside the DC, such as signaling pathways and cell-cell interactions. We also provided three sample use cases to apply the model in the context of studying cell dynamics and disease environments. First, we characterized the DC response to Sars-CoV-2 and influenza co-infection by in-silico experiments and analyzed the activity level of 107 molecules that play a role in this co-infection. The second example presents simulations to predict the crosstalk between DCs and T cells in a cancer microenvironment. Finally, for the third example, we used the Kyoto Encyclopedia of Genes and Genomes enrichment analysis against the model's components to identify 45 diseases and 24 molecular pathways that the DC model can address. This study presents a resource to decode the complex dynamics underlying DC-derived APC communication and provides a platform for researchers to perform in-silico experiments on human DC for vaccine design, drug discovery, and immunotherapies.
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Affiliation(s)
| | | | - Rada Amin
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
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28
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Li J, Huang F, Ma Q, Guo W, Feng K, Huang T, Cai YD. Identification of genes related to immune enhancement caused by heterologous ChAdOx1-BNT162b2 vaccines in lymphocytes at single-cell resolution with machine learning methods. Front Immunol 2023; 14:1131051. [PMID: 36936955 PMCID: PMC10017451 DOI: 10.3389/fimmu.2023.1131051] [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: 12/30/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The widely used ChAdOx1 nCoV-19 (ChAd) vector and BNT162b2 (BNT) mRNA vaccines have been shown to induce robust immune responses. Recent studies demonstrated that the immune responses of people who received one dose of ChAdOx1 and one dose of BNT were better than those of people who received vaccines with two homologous ChAdOx1 or two BNT doses. However, how heterologous vaccines function has not been extensively investigated. In this study, single-cell RNA sequencing data from three classes of samples: volunteers vaccinated with heterologous ChAdOx1-BNT and volunteers vaccinated with homologous ChAd-ChAd and BNT-BNT vaccinations after 7 days were divided into three types of immune cells (3654 B, 8212 CD4+ T, and 5608 CD8+ T cells). To identify differences in gene expression in various cell types induced by vaccines administered through different vaccination strategies, multiple advanced feature selection methods (max-relevance and min-redundancy, Monte Carlo feature selection, least absolute shrinkage and selection operator, light gradient boosting machine, and permutation feature importance) and classification algorithms (decision tree and random forest) were integrated into a computational framework. Feature selection methods were in charge of analyzing the importance of gene features, yielding multiple gene lists. These lists were fed into incremental feature selection, incorporating decision tree and random forest, to extract essential genes, classification rules and build efficient classifiers. Highly ranked genes include PLCG2, whose differential expression is important to the B cell immune pathway and is positively correlated with immune cells, such as CD8+ T cells, and B2M, which is associated with thymic T cell differentiation. This study gave an important contribution to the mechanistic explanation of results showing the stronger immune response of a heterologous ChAdOx1-BNT vaccination schedule than two doses of either BNT or ChAdOx1, offering a theoretical foundation for vaccine modification.
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Affiliation(s)
- Jing Li
- School of Computer Science, Baicheng Normal University, Baicheng, Jilin, China
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai, China
| | - QingLan Ma
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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29
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Lopardo V, Montella F, Esposito RM, Zannella C, Aliberti SM, Capunzo M, Franci G, Puca AA, Ciaglia E. SARS-CoV-2 Lysate Stimulation Impairs the Release of Platelet-like Particles and Megakaryopoiesis in the MEG-01 Cell Line. Int J Mol Sci 2023; 24:4723. [PMID: 36902151 PMCID: PMC10003077 DOI: 10.3390/ijms24054723] [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: 12/06/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
SARS-CoV-2 infection causes a considerable inflammatory response coupled with impaired platelet reactivity, which can lead to platelet disorders recognized as negative prognostic factors in COVID-19 patients. The virus may cause thrombocytopenia or thrombocytosis during the different disease stages by destroying or activating platelets and influencing platelet production. While it is known that several viruses can impair megakaryopoiesis by generating an improper production and activation of platelets, the potential involvement of SARS-CoV-2 in affecting megakaryopoiesis is poorly understood. To this purpose, we explored, in vitro, the impact of SARS-CoV-2 stimulation in the MEG-01 cell line, a human megakaryoblastic leukemia cell line, considering its spontaneous capacity of releasing platelet-like particles (PLPs). We interrogated the effect of heat-inactivated SARS-CoV-2 lysate in the release of PLPs and activation from MEG-01, the signaling pathway influenced by SARS-CoV-2, and the functional effect on macrophagic skewing. The results highlight the potential influence of SARS-CoV-2 in the early stages of megakaryopoiesis by enhancing the production and activation of platelets, very likely due to the impairment of STATs signaling and AMPK activity. Overall, these findings provide new insight into the role of SARS-CoV-2 in affecting megakaryocyte-platelet compartment, possibly unlocking another avenue by which SARS-CoV-2 moves.
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Affiliation(s)
- Valentina Lopardo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
| | - Francesco Montella
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
| | - Roberta Maria Esposito
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
| | - Carla Zannella
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Silvana Mirella Aliberti
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
| | - Mario Capunzo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Annibale Alessandro Puca
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
- Cardiovascular Research Unit, IRCCS MultiMedica, 20138 Milan, Italy
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Via Salvatore Allende, 84081 Baronissi, Italy
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30
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Winheim E, Eser T, Deák F, Ahmed MIM, Baranov O, Rinke L, Eisenächer K, Santos-Peral A, Karimzadeh H, Pritsch M, Scherer C, Muenchhoff M, Hellmuth JC, von Bergwelt-Baildon M, Olbrich L, Hoelscher M, Wieser A, Kroidl I, Rothenfusser S, Geldmacher C, Krug AB. Distinct and dynamic activation profiles of circulating dendritic cells and monocytes in mild COVID-19 and after yellow fever vaccination. Eur J Immunol 2023; 53:e2250090. [PMID: 36404054 DOI: 10.1002/eji.202250090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
Dysregulation of the myeloid cell compartment is a feature of severe disease in hospitalized COVID-19 patients. Here, we investigated the response of circulating dendritic cell (DC) and monocyte subpopulations in SARS-CoV-2 infected outpatients with mild disease and compared it to the response of healthy individuals to yellow fever vaccine virus YF17D as a model of a well-coordinated response to viral infection. In SARS-CoV-2-infected outpatients circulating DCs were persistently reduced for several weeks whereas after YF17D vaccination DC numbers were decreased temporarily and rapidly replenished by increased proliferation until 14 days after vaccination. The majority of COVID-19 outpatients showed high expression of CD86 and PD-L1 in monocytes and DCs early on, resembling the dynamic after YF17D vaccination. In a subgroup of patients, low CD86 and high PD-L1 expression were detected in monocytes and DCs coinciding with symptoms, higher age, and lower lymphocyte counts. This phenotype was similar to that observed in severely ill COVID-19 patients, but less pronounced. Thus, prolonged reduction and dysregulated activation of blood DCs and monocytes were seen in a subgroup of symptomatic non-hospitalized COVID-19 patients while a transient coordinated activation was characteristic for the majority of patients with mild COVID-19 and the response to YF17D vaccination.
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Affiliation(s)
- Elena Winheim
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Munich, Germany
| | - Tabea Eser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Flora Deák
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Mohamed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Olga Baranov
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Linus Rinke
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Munich, Germany
| | - Katharina Eisenächer
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Munich, Germany
| | - Antonio Santos-Peral
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Unit Clinical Pharmacology (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Hadi Karimzadeh
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Unit Clinical Pharmacology (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Michael Pritsch
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Unit Clinical Pharmacology (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
| | - Maximilian Muenchhoff
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine & Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Munich, Germany
| | - Johannes C Hellmuth
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Michael von Bergwelt-Baildon
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Simon Rothenfusser
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
- Unit Clinical Pharmacology (EKLiP), Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Anne B Krug
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Munich, Germany
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Mudi PK, Mahanty AK, Kotakonda M, Prasad S, Bhattacharyya S, Biswas B. A benzimidazole scaffold as a promising inhibitor against SARS-CoV-2. J Biomol Struct Dyn 2023; 41:1798-1810. [PMID: 35000553 DOI: 10.1080/07391102.2021.2024448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The manuscript reports the green-chemical synthesis of a new diindole-substituted benzimidazole compound, B1 through a straightforward route in coupling between indolyl-3-carboxaldehyde and o-phenylenediamine in water medium under the aerobic condition at 75 ºC. The single crystal X-ray structural analysis of B1 suggests that the disubstituted benzimidazole compound crystallizes in a monoclinic system and the indole groups exist in a perpendicular fashion with respect to benzimidazole moiety. The SARS-CoV-2 screening activity has been studied against 1 × 10e4 VeroE6 cells in a dose-dependent manner following Hoechst 33342 and nucleocapsid staining activity with respect to remdesivir. The compound exhibits 92.4% cell viability for 30 h and 35.1% inhibition against VeroE6 cells at non-cytotoxic concentration. Molecular docking studies predict high binding propensities of B1 with the main protease (Mpro) and non-structural (nsp2 and nsp7-nsp8) proteins of SARS-CoV-2 through a number of non-covalent interactions. Molecular dynamics (MD) simulation analysis for 100 ns confirms the formation of stable conformations of B1-docked proteins with significant changes of binding energy, attributing the potential inhibition properties of the synthetic benzimidazole scaffold against SARS-CoV-2. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prafullya Kumar Mudi
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | - Ayan Kumar Mahanty
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | | | - Sunnapu Prasad
- Department of Pharmaceutical Chemistry, Sri Ramakrishna Institute of Paramedical Science, Coimbatore, India
| | - Subires Bhattacharyya
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
| | - Bhaskar Biswas
- Department of Chemistry, Department of Biotechnology, University of North Bengal, Darjeeling, India
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Islam MS, Wang Z, Abdel-Mohsen M, Chen X, Montaner LJ. Tissue injury and leukocyte changes in post-acute sequelae of SARS-CoV-2: review of 2833 post-acute patient outcomes per immune dysregulation and microbial translocation in long COVID. J Leukoc Biol 2023; 113:236-254. [PMID: 36807444 DOI: 10.1093/jleuko/qiac001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 01/18/2023] Open
Abstract
A significant number of persons with coronavirus disease 2019 (COVID-19) experience persistent, recurrent, or new symptoms several months after the acute stage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This phenomenon, termed post-acute sequelae of SARS-CoV-2 (PASC) or long COVID, is associated with high viral titers during acute infection, a persistently hyperactivated immune system, tissue injury by NETosis-induced micro-thrombofibrosis (NETinjury), microbial translocation, complement deposition, fibrotic macrophages, the presence of autoantibodies, and lymphopenic immune environments. Here, we review the current literature on the immunological imbalances that occur during PASC. Specifically, we focus on data supporting common immunopathogenesis and tissue injury mechanisms shared across this highly heterogenous disorder, including NETosis, coagulopathy, and fibrosis. Mechanisms include changes in leukocyte subsets/functions, fibroblast activation, cytokine imbalances, lower cortisol, autoantibodies, co-pathogen reactivation, and residual immune activation driven by persistent viral antigens and/or microbial translocation. Taken together, we develop the premise that SARS-CoV-2 infection results in PASC as a consequence of acute and/or persistent single or multiple organ injury mediated by PASC determinants to include the degree of host responses (inflammation, NETinjury), residual viral antigen (persistent antigen), and exogenous factors (microbial translocation). Determinants of PASC may be amplified by comorbidities, age, and sex.
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Affiliation(s)
- Md Sahidul Islam
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, Avenida da Universidade, Taipa 999078, University of Macau, Macau S.A.R., China
| | - Zhaoxiong Wang
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, Avenida da Universidade, Taipa 999078, University of Macau, Macau S.A.R., China
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, United States
| | - Xin Chen
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, Avenida da Universidade, Taipa 999078, University of Macau, Macau S.A.R., China.,Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa 999078, Macau S.A.R., China.,MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida da Universidade, Taipa 999078, Macau S.A.R., China.,Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Research Building N22, University of Macau, Avenida da Universidade, Taipa 999078, Macau S.A.R., China
| | - Luis J Montaner
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, United States
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33
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Severe COVID-19 patients have impaired plasmacytoid dendritic cell-mediated control of SARS-CoV-2. Nat Commun 2023; 14:694. [PMID: 36755036 PMCID: PMC9907212 DOI: 10.1038/s41467-023-36140-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/18/2023] [Indexed: 02/10/2023] Open
Abstract
Type I and III interferons (IFN-I/λ) are important antiviral mediators against SARS-CoV-2 infection. Here, we demonstrate that plasmacytoid dendritic cells (pDC) are the predominant IFN-I/λ source following their sensing of SARS-CoV-2-infected cells. Mechanistically, this short-range sensing by pDCs requires sustained integrin-mediated cell adhesion with infected cells. In turn, pDCs restrict viral spread by an IFN-I/λ response directed toward SARS-CoV-2-infected cells. This specialized function enables pDCs to efficiently turn-off viral replication, likely via a local response at the contact site with infected cells. By exploring the pDC response in SARS-CoV-2 patients, we further demonstrate that pDC responsiveness inversely correlates with the severity of the disease. The pDC response is particularly impaired in severe COVID-19 patients. Overall, we propose that pDC activation is essential to control SARS-CoV-2-infection. Failure to develop this response could be important to understand severe cases of COVID-19.
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Kashima Y, Mizutani T, Nakayama-Hosoya K, Moriyama S, Matsumura T, Yoshimura Y, Sasaki H, Horiuchi H, Miyata N, Miyazaki K, Tachikawa N, Takahashi Y, Suzuki T, Sugano S, Matano T, Kawana-Tachikawa A, Suzuki Y. Multimodal single-cell analyses of peripheral blood mononuclear cells of COVID-19 patients in Japan. Sci Rep 2023; 13:1935. [PMID: 36732528 PMCID: PMC9893982 DOI: 10.1038/s41598-023-28696-9] [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: 09/06/2022] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 continues to spread worldwide. Patients with COVID-19 show distinct clinical symptoms. Although many studies have reported various causes for the diversity of symptoms, the underlying mechanisms are not fully understood. Peripheral blood mononuclear cells from COVID-19 patients were collected longitudinally, and single-cell transcriptome and T cell receptor repertoire analysis was performed. Comparison of molecular features and patients' clinical information revealed that the proportions of cells present, and gene expression profiles differed significantly between mild and severe cases; although even among severe cases, substantial differences were observed among the patients. In one severely-infected elderly patient, an effective antibody response seemed to have failed, which may have caused prolonged viral clearance. Naïve T cell depletion, low T cell receptor repertoire diversity, and aberrant hyperactivation of most immune cell subsets were observed during the acute phase in this patient. Through this study, we provided a better understanding of the diversity of immune landscapes and responses. The information obtained from this study can help medical professionals develop personalized optimal clinical treatment strategies for COVID-19.
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Affiliation(s)
- Yukie Kashima
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Taketoshi Mizutani
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | | | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Matsumura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiro Yoshimura
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Hiroaki Sasaki
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Hiroshi Horiuchi
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Nobuyuki Miyata
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Kazuhito Miyazaki
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Natsuo Tachikawa
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sumio Sugano
- Institute of Kashiwa-No-Ha Omics Gate, Kashiwa, Chiba, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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Miao G, Chen Z, Cao H, Wu W, Chu X, Liu H, Zhang L, Zhu H, Cai H, Lu X, Shi J, Liu Y, Feng T. From Immunogen to COVID-19 vaccines: Prospects for the post-pandemic era. Biomed Pharmacother 2023; 158:114208. [PMID: 36800265 PMCID: PMC9805901 DOI: 10.1016/j.biopha.2022.114208] [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: 11/30/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
The COVID-19 pandemic has affected millions of people and posed an unprecedented burden on healthcare systems and economies worldwide since the outbreak of the COVID-19. A considerable number of nations have investigated COVID-19 and proposed a series of prevention and treatment strategies thus far. The pandemic prevention strategies implemented in China have suggested that the spread of COVID-19 can be effectively reduced by restricting large-scale gathering, developing community-scale nucleic acid testing, and conducting epidemiological investigations, whereas sporadic cases have always been identified in numerous places. Currently, there is still no decisive therapy for COVID-19 or related complications. The development of COVID-19 vaccines has raised the hope for mitigating this pandemic based on the intercross immunity induced by COVID-19. Thus far, several types of COVID-19 vaccines have been developed and released to into financial markets. From the perspective of vaccine use in globe, COVID-19 vaccines are beneficial to mitigate the pandemic, whereas the relative adverse events have been reported progressively. This is a review about the development, challenges and prospects of COVID-19 vaccines, and it can provide more insights into all aspects of the vaccines.
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Affiliation(s)
- Ganggang Miao
- Department of General Surgery, The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, China,Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiqiang Chen
- Department of Nuclear Medicine, The First Affiliated Hospital of Suzhou University, Suzhou, China
| | - Hengsong Cao
- Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, China
| | - Wenhao Wu
- Department of Clinical Medicine, Nanjing Medical University The First School of Clinical Medicine, Nanjing, China
| | - Xi Chu
- Department of Radiology, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing, China
| | - Hanyuan Liu
- Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, China
| | - Leyao Zhang
- Department of Clinical Medicine, Nanjing Medical University The First School of Clinical Medicine, Nanjing, China
| | - Hongfei Zhu
- Department of Clinical Medicine, Nanjing Medical University The First School of Clinical Medicine, Nanjing, China
| | - Hongzhou Cai
- Department of Urology, Jiangsu Cancer Hospital &The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Xiaolan Lu
- Department of Clinical laboratory, Canglang Hospital of Suzhou, Suzhou, China.
| | - Junfeng Shi
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China; Department of Molecular and Celluar Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
| | - Yuan Liu
- Department of Infectious Disease,The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Tingting Feng
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China.
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Hopkins FR, Govender M, Svanberg C, Nordgren J, Waller H, Nilsdotter-Augustinsson Å, Henningsson AJ, Hagbom M, Sjöwall J, Nyström S, Larsson M. Major alterations to monocyte and dendritic cell subsets lasting more than 6 months after hospitalization for COVID-19. Front Immunol 2023; 13:1082912. [PMID: 36685582 PMCID: PMC9846644 DOI: 10.3389/fimmu.2022.1082912] [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: 10/28/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction After more than two years the Coronavirus disease-19 (COVID-19) pandemic continues to burden healthcare systems and economies worldwide, and it is evident that the effects on the immune system can persist for months post-infection. The activity of myeloid cells such as monocytes and dendritic cells (DC) is essential for correct mobilization of the innate and adaptive responses to a pathogen. Impaired levels and responses of monocytes and DC to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is likely to be a driving force behind the immune dysregulation that characterizes severe COVID-19. Methods Here, we followed a cohort of COVID-19 patients hospitalized during the early waves of the pandemic for 6-7 months. The levels and phenotypes of circulating monocyte and DC subsets were assessed to determine both the early and long-term effects of the SARS-CoV-2 infection. Results We found increased monocyte levels that persisted for 6-7 months, mostly attributed to elevated levels of classical monocytes. Myeloid derived suppressor cells were also elevated over this period. While most DC subsets recovered from an initial decrease, we found elevated levels of cDC2/cDC3 at the 6-7 month timepoint. Analysis of functional markers on monocytes and DC revealed sustained reduction in program death ligand 1 (PD-L1) expression but increased CD86 expression across almost all cell types examined. Finally, C-reactive protein (CRP) correlated positively to the levels of intermediate monocytes and negatively to the recovery of DC subsets. Conclusion By exploring the myeloid compartments, we show here that alterations in the immune landscape remain more than 6 months after severe COVID-19, which could be indicative of ongoing healing and/or persistence of viral antigens.
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Affiliation(s)
- Francis R. Hopkins
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Melissa Govender
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Cecilia Svanberg
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johan Nordgren
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Hjalmar Waller
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Linköping University, Linköping, Sweden
| | - Anna J. Henningsson
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine in Jönköping, Ryhov County Hospital, Jönköping, Sweden
| | - Marie Hagbom
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johanna Sjöwall
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Linköping University, Linköping, Sweden
| | - Sofia Nyström
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Linköping University, Linköping, Sweden
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. Single-cell RNA-seq methods to interrogate virus-host interactions. Semin Immunopathol 2023; 45:71-89. [PMID: 36414692 PMCID: PMC9684776 DOI: 10.1007/s00281-022-00972-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aaron J Wilk
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Madeline J Lee
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Purvesh Khatri
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Medicine, Center for Biomedical Informatics Research, Stanford, CA, USA.
- Inflammatix, Inc., Sunnyvale, CA, 94085, USA.
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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Arish M, Qian W, Narasimhan H, Sun J. COVID-19 immunopathology: From acute diseases to chronic sequelae. J Med Virol 2023; 95:e28122. [PMID: 36056655 PMCID: PMC9537925 DOI: 10.1002/jmv.28122] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 01/17/2023]
Abstract
The clinical manifestation of coronavirus disease 2019 (COVID-19) mainly targets the lung as a primary affected organ, which is also a critical site of immune cell activation by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, recent reports also suggest the involvement of extrapulmonary tissues in COVID-19 pathology. The interplay of both innate and adaptive immune responses is key to COVID-19 management. As a result, a robust innate immune response provides the first line of defense, concomitantly, adaptive immunity neutralizes the infection and builds memory for long-term protection. However, dysregulated immunity, both innate and adaptive, can skew towards immunopathology both in acute and chronic cases. Here we have summarized some of the recent findings that provide critical insight into the immunopathology caused by SARS-CoV-2, in acute and post-acute cases. Finally, we further discuss some of the immunomodulatory drugs in preclinical and clinical trials for dampening the immunopathology caused by COVID-19.
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Affiliation(s)
- Mohd Arish
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Wei Qian
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Harish Narasimhan
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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Maher AK, Burnham KL, Jones EM, Tan MMH, Saputil RC, Baillon L, Selck C, Giang N, Argüello R, Pillay C, Thorley E, Short CE, Quinlan R, Barclay WS, Cooper N, Taylor GP, Davenport EE, Dominguez-Villar M. Transcriptional reprogramming from innate immune functions to a pro-thrombotic signature by monocytes in COVID-19. Nat Commun 2022; 13:7947. [PMID: 36572683 PMCID: PMC9791976 DOI: 10.1038/s41467-022-35638-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/14/2022] [Indexed: 12/27/2022] Open
Abstract
Although alterations in myeloid cells have been observed in COVID-19, the specific underlying mechanisms are not completely understood. Here, we examine the function of classical CD14+ monocytes in patients with mild and moderate COVID-19 during the acute phase of infection and in healthy individuals. Monocytes from COVID-19 patients display altered expression of cell surface receptors and a dysfunctional metabolic profile that distinguish them from healthy monocytes. Secondary pathogen sensing ex vivo leads to defects in pro-inflammatory cytokine and type-I IFN production in moderate COVID-19 cases, together with defects in glycolysis. COVID-19 monocytes switch their gene expression profile from canonical innate immune to pro-thrombotic signatures and are functionally pro-thrombotic, both at baseline and following ex vivo stimulation with SARS-CoV-2. Transcriptionally, COVID-19 monocytes are characterized by enrichment of pathways involved in hemostasis, immunothrombosis, platelet aggregation and other accessory pathways to platelet activation and clot formation. These results identify a potential mechanism by which monocyte dysfunction may contribute to COVID-19 pathology.
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Affiliation(s)
- Allison K Maher
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emma M Jones
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Michelle M H Tan
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Rocel C Saputil
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Claudia Selck
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Nicolas Giang
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Rafael Argüello
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Clio Pillay
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Emma Thorley
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Charlotte-Eve Short
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Rachael Quinlan
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Nichola Cooper
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
| | - Graham P Taylor
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Emma E Davenport
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Godoy-Tena G, Barmada A, Morante-Palacios O, de la Calle-Fabregat C, Martins-Ferreira R, Ferreté-Bonastre AG, Ciudad L, Ruiz-Sanmartín A, Martínez-Gallo M, Ferrer R, Ruiz-Rodriguez JC, Rodríguez-Ubreva J, Vento-Tormo R, Ballestar E. 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: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Anis Barmada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1RQ, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Octavio Morante-Palacios
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Carlos de la Calle-Fabregat
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Anna G Ferreté-Bonastre
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartín
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), 08035, Barcelona, Spain
| | - Ricard Ferrer
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Intensive Care Department, Vall d'Hebron University Hospital, Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1RQ, UK
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241, China.
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Mortezaee K, Majidpoor J. Cellular immune states in SARS-CoV-2-induced disease. Front Immunol 2022; 13:1016304. [PMID: 36505442 PMCID: PMC9726761 DOI: 10.3389/fimmu.2022.1016304] [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: 08/10/2022] [Accepted: 10/31/2022] [Indexed: 11/24/2022] Open
Abstract
The general immune state plays important roles against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Cells of the immune system are encountering rapid changes during the acute phase of SARS-CoV-2-induced disease. Reduced fraction of functional CD8+ T cells, disrupted cross-talking between CD8+ T cells with dendritic cells (DCs), and impaired immunological T-cell memory, along with the higher presence of hyperactive neutrophils, high expansion of myeloid-derived suppressor cells (MDSCs) and non-classical monocytes, and attenuated cytotoxic capacity of natural killer (NK) cells, are all indicative of low efficient immunity against viral surge within the body. Immune state and responses from pro- or anti-inflammatory cells of the immune system to SARS-CoV-2 are discussed in this review. We also suggest some strategies to enhance the power of immune system against SARS-CoV-2-induced disease.
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Affiliation(s)
- Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran,*Correspondence: Keywan Mortezaee, ;
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
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42
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Zhu Q, Xu Y, Wang T, Xie F. Innate and adaptive immune response in SARS-CoV-2 infection-Current perspectives. Front Immunol 2022; 13:1053437. [PMID: 36505489 PMCID: PMC9727711 DOI: 10.3389/fimmu.2022.1053437] [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: 09/25/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has been a global pandemic, caused by a novel coronavirus strain with strong infectivity, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the in-depth research, the close relationship between COVID-19 and immune system has been dug out. During the infection, macrophages, dendritic cells, natural killer cells, CD8+ T cells, Th1, Th17, Tfh cells and effector B cells are all involved in the anti-SARS-CoV-2 responses, however, the dysfunctional immune responses will ultimately lead to the excessive inflammation, acute lung injury, even other organ failure. Thus, a detailed understanding of pertinent immune response during COVID-19 will provide insights in predicting disease outcomes and developing appropriate therapeutic approaches. In this review, we mainly clarify the role of immune cells in COVID-19 and the target-vaccine development and treatment.
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Affiliation(s)
- Qiugang Zhu
- Department of Laboratory Medicine, Shangyu People’s Hospital of Shaoxing, Shaoxing, China
| | - Yan Xu
- Department of Respiratory Medicine, Shangyu People’s Hospital of Shaoxing, Shaoxing, China
| | - Ting Wang
- Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Feiting Xie
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Feiting Xie,
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Ma Q, Ma W, Song TZ, Wu Z, Liu Z, Hu Z, Han JB, Xu L, Zeng B, Wang B, Sun Y, Yu DD, Wu Q, Yao YG, Zheng YT, Wang X. Single-nucleus transcriptomic profiling of multiple organs in a rhesus macaque model of SARS-CoV-2 infection. Zool Res 2022; 43:1041-1062. [PMID: 36349357 PMCID: PMC9700497 DOI: 10.24272/j.issn.2095-8137.2022.443] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/09/2022] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs. However, cellular and molecular understanding of SARS-CoV-2 infection-associated pathology and immune defense features in different organs remains incomplete. Here, we profiled approximately 77 000 single-nucleus transcriptomes of the lung, liver, kidney, and cerebral cortex in rhesus macaques ( Macaca mulatta) infected with SARS-CoV-2 and healthy controls. Integrated analysis of the multi-organ dataset suggested that the liver harbored the strongest global transcriptional alterations. We observed prominent impairment in lung epithelial cells, especially in AT2 and ciliated cells, and evident signs of fibrosis in fibroblasts. These lung injury characteristics are similar to those reported in patients with coronavirus disease 2019 (COVID-19). Furthermore, we found suppressed MHC class I/II molecular activity in the lung, inflammatory response in the liver, and activation of the kynurenine pathway, which induced the development of an immunosuppressive microenvironment. Analysis of the kidney dataset highlighted tropism of tubule cells to SARS-CoV-2, and we found membranous nephropathy (an autoimmune disease) caused by podocyte dysregulation. In addition, we identified the pathological states of astrocytes and oligodendrocytes in the cerebral cortex, providing molecular insights into COVID-19-related neurological implications. Overall, our multi-organ single-nucleus transcriptomic survey of SARS-CoV-2-infected rhesus macaques broadens our understanding of disease features and antiviral immune defects caused by SARS-CoV-2 infection, which may facilitate the development of therapeutic interventions for COVID-19.
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Affiliation(s)
- Qiang Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenji Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tian-Zhang Song
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Zhaobo Wu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zeyuan Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenxiang Hu
- LivzonBio, Inc., Zhuhai, Guangdong 519045, China
| | - Jian-Bao Han
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Bo Zeng
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Yinuo Sun
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan-Dan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China. E-mail:
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China. E-mail:
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
- Advanced Innovation Center for Human Brain Protection, Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China. E-mail:
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Tizazu AM, Mengist HM, Demeke G. Aging, inflammaging and immunosenescence as risk factors of severe COVID-19. Immun Ageing 2022; 19:53. [PMID: 36369012 PMCID: PMC9650172 DOI: 10.1186/s12979-022-00309-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a respiratory infectious disease caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by having a heterogeneous disease course, ranging from asymptomatic and mild symptoms to more severe and critical cases. In most cases the severity of COVID-19 is related to host factors, especially deregulation of the immune response in patients. Even if COVID-19 indiscriminately affects individuals of different age group, ethnicity and economic status; most severe cases and disproportional mortality occur in elderly individuals. This point out that aging is one risk factor for unfavourable clinical outcomes among COVID-19 patients. The biology of aging is a complex process; Aging can alter the structure and function of cells, tissues, and organs resulting in impaired response to stress. Alongside with other systems, the immune system is also affected with the aging process. Immunosenescence is an age associated change in the immune system that affects the overall response to immunological challenges in the elderly. Similarly, apart from the normal inflammatory process, aging is associated with a low grade, sterile, chronic inflammation which is termed as inflammaging. We hypothesized that inflammaging and immunosenescence could play an important role in SARS-CoV-2 pathogenesis and poor recovery from COVID-19 in elderly individuals. This review summarizes the changes in the immune system with age and how these changes play part in the pathogenesis of SARS-CoV-2 and clinical outcome of COVID-19 which could add to the understanding of age associated targeted immunotherapy in the elderly.
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Affiliation(s)
- Anteneh Mehari Tizazu
- Department of Microbiology, Parasitology and Immunology, School of Medicine, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia.
| | - Hylemariam Mihiretie Mengist
- Department of Medical Laboratory Science, College of Medicine and Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Gebreselassie Demeke
- Department of Medical Laboratory Science, College of Medicine and Health Science, Debre Markos University, Debre Markos, Ethiopia
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Tardiveau C, Monneret G, Lukaszewicz AC, Cheynet V, Cerrato E, Imhoff K, Peronnet E, Bodinier M, Kreitmann L, Blein S, Llitjos JF, Conti F, Gossez M, Buisson M, Yonis H, Cour M, Argaud L, Delignette MC, Wallet F, Dailler F, Monard C, Brengel-Pesce K, Venet F. A 9-mRNA signature measured from whole blood by a prototype PCR panel predicts 28-day mortality upon admission of critically ill COVID-19 patients. Front Immunol 2022; 13:1022750. [DOI: 10.3389/fimmu.2022.1022750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Immune responses affiliated with COVID-19 severity have been characterized and associated with deleterious outcomes. These approaches were mainly based on research tools not usable in routine clinical practice at the bedside. We observed that a multiplex transcriptomic panel prototype termed Immune Profiling Panel (IPP) could capture the dysregulation of immune responses of ICU COVID-19 patients at admission. Nine transcripts were associated with mortality in univariate analysis and this 9-mRNA signature remained significantly associated with mortality in a multivariate analysis that included age, SOFA and Charlson scores. Using a machine learning model with these 9 mRNA, we could predict the 28-day survival status with an Area Under the Receiver Operating Curve (AUROC) of 0.764. Interestingly, adding patients’ age to the model resulted in increased performance to predict the 28-day mortality (AUROC reaching 0.839). This prototype IPP demonstrated that such a tool, upon clinical/analytical validation and clearance by regulatory agencies could be used in clinical routine settings to quickly identify patients with higher risk of death requiring thus early aggressive intensive care.
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Chaisawangwong W, Wang H, Kouo T, Salathe SF, Isser A, Bieler JG, Zhang ML, Livingston NK, Li S, Horowitz JJ, Samet RE, Zyskind I, Rosenberg AZ, Schneck JP. Cross-reactivity of SARS-CoV-2- and influenza A-specific T cells in individuals exposed to SARS-CoV-2. JCI Insight 2022; 7:e158308. [PMID: 36134660 PMCID: PMC9675569 DOI: 10.1172/jci.insight.158308] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Cross-reactive immunity between SARS-CoV-2 and other related coronaviruses has been well-documented, and it may play a role in preventing severe COVID-19. Epidemiological studies early in the pandemic showed a geographical association between high influenza vaccination rates and lower incidence of SARS-CoV-2 infection. We, therefore, analyzed whether exposure to influenza A virus (IAV) antigens could influence the T cell repertoire in response to SARS-CoV-2, indicating a heterologous immune response between these 2 unrelated viruses. Using artificial antigen-presenting cells (aAPCs) combined with real-time reverse-transcription PCR (RT-qPCR), we developed a sensitive assay to quickly screen for antigen-specific T cell responses and detected a significant correlation between responses to SARS-CoV-2 epitopes and IAV dominant epitope (M158-66). Further analysis showed that some COVID-19 convalescent donors exhibited both T cell receptor (TCR) specificity and functional cytokine responses to multiple SARS-CoV-2 epitopes and M158-66. Utilizing an aAPC-based stimulation/expansion assay, we detected cross-reactive T cells with specificity to SARS-CoV-2 and IAV. In addition, TCR sequencing of the cross-reactive and IAV-specific T cells revealed similarities between the TCR repertoires of the two populations. These results indicate that heterologous immunity shaped by our exposure to other unrelated endemic viruses may affect our immune response to novel viruses such as SARS-CoV-2.
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Affiliation(s)
| | - Hanzhi Wang
- Department of Biomedical Engineering, Whiting School of Engineering
| | - Theodore Kouo
- Department of Pediatrics, Division of Emergency Medicine
| | | | - Ariel Isser
- Department of Biomedical Engineering, School of Medicine, and
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Maya L. Zhang
- Department of Biomedical Engineering, Whiting School of Engineering
| | | | - Shuyi Li
- Department of Pathology, School of Medicine
| | | | - Ron E. Samet
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York, New York, USA; Maimonides Medical Center, New York, New York, USA
| | | | - Jonathan P. Schneck
- Department of Pathology, School of Medicine
- Department of Biomedical Engineering, School of Medicine, and
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Institute for Nanobiotechnology and
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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47
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Single-Cell Gene Expression Analysis Revealed Immune Cell Signatures of Delta COVID-19. Cells 2022; 11:cells11192950. [PMID: 36230912 PMCID: PMC9563974 DOI: 10.3390/cells11192950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/04/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is accompanied by a cytokine storm with the release of many proinflammatory factors and development of respiratory syndrome. Several SARS-CoV-2 lineages have been identified, and the Delta variant (B.1.617), linked with high mortality risk, has become dominant in many countries. Understanding the immune responses associated with COVID-19 lineages may therefore aid the development of therapeutic and diagnostic strategies. Multiple single-cell gene expression studies revealed innate and adaptive immunological factors and pathways correlated with COVID-19 severity. Additional investigations covering host–pathogen response characteristics for infection caused by different lineages are required. Here, we performed single-cell transcriptome profiling of blood mononuclear cells from the individuals with different severity of the COVID-19 and virus lineages to uncover variant specific molecular factors associated with immunity. We identified significant changes in lymphoid and myeloid cells. Our study highlights that an abundant population of monocytes with specific gene expression signatures accompanies Delta lineage of SARS-CoV-2 and contributes to COVID-19 pathogenesis inferring immune components for targeted therapy.
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Bencze D, Fekete T, Pázmándi K. Correlation between Type I Interferon Associated Factors and COVID-19 Severity. Int J Mol Sci 2022; 23:ijms231810968. [PMID: 36142877 PMCID: PMC9506204 DOI: 10.3390/ijms231810968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
Antiviral type I interferons (IFN) produced in the early phase of viral infections effectively inhibit viral replication, prevent virus-mediated tissue damages and promote innate and adaptive immune responses that are all essential to the successful elimination of viruses. As professional type I IFN producing cells, plasmacytoid dendritic cells (pDC) have the ability to rapidly produce waste amounts of type I IFNs. Therefore, their low frequency, dysfunction or decreased capacity to produce type I IFNs might increase the risk of severe viral infections. In accordance with that, declined pDC numbers and delayed or inadequate type I IFN responses could be observed in patients with severe coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as compared to individuals with mild or no symptoms. Thus, besides chronic diseases, all those conditions, which negatively affect the antiviral IFN responses lengthen the list of risk factors for severe COVID-19. In the current review, we would like to briefly discuss the role and dysregulation of pDC/type I IFN axis in COVID-19, and introduce those type I IFN-dependent factors, which account for an increased risk of COVID-19 severity and thus are responsible for the different magnitude of individual immune responses to SARS-CoV-2.
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Affiliation(s)
- Dóra Bencze
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
| | - Tünde Fekete
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
| | - Kitti Pázmándi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
- Correspondence: ; Tel./Fax: +36-52-417-159
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49
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Iba T, Levi M, Thachil J, Levy JH. Disseminated Intravascular Coagulation: The Past, Present, and Future Considerations. Semin Thromb Hemost 2022; 48:978-987. [PMID: 36100234 DOI: 10.1055/s-0042-1756300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Disseminated intravascular coagulation (DIC) has been understood as a consumptive coagulopathy. However, impaired hemostasis is a component of DIC that occurs in a progressive manner. The critical concept of DIC is systemic activation of coagulation with vascular endothelial damage. DIC is the dynamic coagulation/fibrinolysis disorder that can proceed from compensated to decompensated phases, and is not simply impaired hemostasis, a misunderstanding that continues to evoke confusion among clinicians. DIC is a critical step of disease progression that is important to monitor over time. Impaired microcirculation and subsequent organ failure due to pathologic microthrombi formation are the pathophysiologies in sepsis-associated DIC. Impaired hemostasis due to coagulation factor depletion from hemodilution, shock, and hyperfibrinolysis occurs in trauma-associated DIC. Overt-DIC diagnostic criteria have been used clinically for more than 20 years but may not be adequate to detect the compensated phase of DIC, and due to different underlying causes, there is no "one-size-fits-all criteria." Individualized criteria for heterogeneous conditions continue to be proposed to facilitate the diagnosis. We believe that future research will provide therapeutics using new diagnostic criteria. Finally, DIC is also classified as either acute or chronic, and acute DIC results from progressive coagulation activation over a short time and requires urgent management. In this review, we examine the advances in research for DIC.
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Affiliation(s)
- Toshiaki Iba
- Department of Emergency and Disaster Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Marcel Levi
- Department of Vascular Medicine, Amsterdam University Medical Center, Amsterdam, The Netherlands.,Department of Medicine, Cardiometabolic Programme-NIHR UCLH/UCL BRC, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Jecko Thachil
- Department of Haematology, Manchester Royal Infirmary, Manchester, United Kingdom
| | - Jerrold H Levy
- Department of Anesthesiology, Critical Care, and Surgery, Duke University School of Medicine, Durham, North Carolina
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50
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Liu W, Jia J, Dai Y, Chen W, Pei G, Yan Q, Zhao Z. Delineating COVID-19 immunological features using single-cell RNA sequencing. Innovation (N Y) 2022; 3:100289. [PMID: 35879967 PMCID: PMC9299978 DOI: 10.1016/j.xinn.2022.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/16/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the molecular mechanisms of coronavirus disease 2019 (COVID-19) pathogenesis and immune response is vital for developing therapies. Single-cell RNA sequencing has been applied to delineate the cellular heterogeneity of the host response toward COVID-19 in multiple tissues and organs. Here, we review the applications and findings from over 80 original COVID-19 single-cell RNA sequencing studies as well as many secondary analysis studies. We describe that single-cell RNA sequencing reveals multiple features of COVID-19 patients with different severity, including cell populations with proportional alteration, COVID-19-induced genes and pathways, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in single cells, and adaptation of immune repertoire. We also collect published single-cell RNA sequencing datasets from original studies. Finally, we discuss the limitations in current studies and perspectives for future advance.
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Affiliation(s)
- Wendao Liu
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Johnathan Jia
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wenhao Chen
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Qiheng Yan
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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