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Declercq M, Treps L, Geldhof V, Conchinha NV, de Rooij LPMH, Subramanian A, Feyeux M, Cotinat M, Boeckx B, Vinckier S, Dupont L, Vermeulen F, Boon M, Proesmans M, Libbrecht L, Pirenne J, Monbaliu D, Jochmans I, Dewerchin M, Eelen G, Roskams T, Verleden S, Lambrechts D, Carmeliet P, Witters P. Single-cell RNA sequencing of cystic fibrosis liver disease explants reveals endothelial complement activation. Liver Int 2024; 44:2382-2395. [PMID: 38847551 DOI: 10.1111/liv.15963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/04/2024] [Accepted: 04/21/2024] [Indexed: 08/30/2024]
Abstract
BACKGROUND & AIMS Cystic fibrosis (CF) is considered a multisystemic disorder in which CF-associated liver disease (CFLD) is the third most common cause of mortality. Currently, no effective treatment is available for CFLD because its pathophysiology is still unclear. Interestingly, CFLD exhibits identical vascular characteristics as non-cirrhotic portal hypertension, recently classified as porto-sinusoidal vascular disorders (PSVD). METHODS Since endothelial cells (ECs) are an important component in PSVD, we performed single-cell RNA sequencing (scRNA-seq) on four explant livers from CFLD patients to identify differential endothelial characteristics which could contribute to the disease. We comprehensively characterized the endothelial compartment and compared it with publicly available scRNA-seq datasets from cirrhotic and healthy livers. Key gene signatures were validated ex vivo on patient tissues. RESULTS We found that ECs from CF liver explants are more closely related to healthy than cirrhotic patients. In CF patients we also discovered a distinct population of liver sinusoidal ECs-coined CF LSECs-upregulating genes involved in the complement cascade and coagulation. Finally, our immunostainings further validated the predominant periportal location of CF LSECs. CONCLUSIONS Our work showed novel aspects of human liver ECs at the single-cell level thereby supporting endothelial involvement in CFLD, and reinforcing the hypothesis that ECs could be a driver of PSVD. Therefore, considering the vascular compartment in CF and CFLD may help developing new therapeutic approaches for these diseases.
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Affiliation(s)
- Mathias Declercq
- Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Nantes Université, INSERM UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France
| | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Nadine V Conchinha
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Laura P M H de Rooij
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Abhishek Subramanian
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Telangana, India
| | - Magalie Feyeux
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, SFR Bonamy, Nantes, France
| | - Marine Cotinat
- Nantes Université, INSERM UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France
| | - Bram Boeckx
- Laboratory for Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lieven Dupont
- Department of Pneumology, UZ Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, Respiratory Diseases and Thoracic Surgery, KU Leuven, Leuven, Belgium
| | - Francois Vermeulen
- Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Flanders, Belgium
| | - Mieke Boon
- Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Flanders, Belgium
| | - Marijke Proesmans
- Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Flanders, Belgium
| | - Louis Libbrecht
- Department of Pathology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
- Department of Pathology, AZ Groeninge, Kortrijk, Belgium
- Laboratory of Hepatology, KU Leuven, Leuven, Belgium
| | - Jacques Pirenne
- Transplantation Research Group, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Abdominal Transplant Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Diethard Monbaliu
- Transplantation Research Group, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Abdominal Transplant Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Ina Jochmans
- Transplantation Research Group, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Abdominal Transplant Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Tania Roskams
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Stijn Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium
- Department of ASTARC, University of Antwerp, Wilrijk, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Peter Witters
- Department of Development and Regeneration, Woman and Child Unit, KU Leuven, Leuven, Belgium
- Department of Paediatrics and Metabolic Center, University Hospitals Leuven, Leuven, Belgium
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2
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García-Vega M, Llamas-Covarrubias MA, Loza M, Reséndiz-Sandoval M, Hinojosa-Trujillo D, Melgoza-González E, Valenzuela O, Mata-Haro V, Hernández-Oñate M, Soto-Gaxiola A, Chávez-Rueda K, Nakai K, Hernández J. Single-cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID-19. J Med Virol 2024; 96:e29851. [PMID: 39132689 DOI: 10.1002/jmv.29851] [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: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Here, we performed single-cell RNA sequencing of S1 and receptor binding domain protein-specific B cells from convalescent COVID-19 patients with different clinical manifestations. This study aimed to evaluate the role and developmental pathway of atypical memory B cells (MBCs) in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The results revealed a proinflammatory signature across B cell subsets associated with disease severity, as evidenced by the upregulation of genes such as GADD45B, MAP3K8, and NFKBIA in critical and severe individuals. Furthermore, the analysis of atypical MBCs suggested a developmental pathway similar to that of conventional MBCs through germinal centers, as indicated by the expression of several genes involved in germinal center processes, including CXCR4, CXCR5, BCL2, and MYC. Additionally, the upregulation of genes characteristic of the immune response in COVID-19, such as ZFP36 and DUSP1, suggested that the differentiation and activation of atypical MBCs may be influenced by exposure to SARS-CoV-2 and that these genes may contribute to the immune response for COVID-19 recovery. Our study contributes to a better understanding of atypical MBCs in COVID-19 and the role of other B cell subsets across different clinical manifestations.
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Affiliation(s)
- Melissa García-Vega
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | | | - Martin Loza
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Mónica Reséndiz-Sandoval
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Diana Hinojosa-Trujillo
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Edgar Melgoza-González
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Olivia Valenzuela
- Departamento de Ciencias Químico Biológicas, División de Ciencias Biológicas y de la Salud, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Verónica Mata-Haro
- Laboratorio de Microbiología e Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Miguel Hernández-Oñate
- CONAHCYT-Laboratorio de Fisiología y Biología Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Alan Soto-Gaxiola
- Hospital General del Estado de Sonora "Dr. Ernesto Ramos Bours", Secretaria de Salud del Estado de Sonora, Hermosillo, Sonora, Mexico
| | - Karina Chávez-Rueda
- Unidad de Investigación Médica en Inmunología, UMAE, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Jesús Hernández
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
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3
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Nardi C, Magnini A, Rastrelli V, Zantonelli G, Calistri L, Lorini C, Luzzi V, Gori L, Ciani L, Morecchiato F, Simonetti V, Peired AJ, Landini N, Cavigli E, Yang G, Guiot J, Tomassetti S, Colagrande S. Laboratory data and broncho-alveolar lavage on Covid-19 patients with no intensive care unit admission: Correlation with chest CT features and clinical outcomes. Medicine (Baltimore) 2024; 103:e39028. [PMID: 39029011 DOI: 10.1097/md.0000000000039028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/21/2024] Open
Abstract
Broncho-alveolar lavage (BAL) is indicated in cases of uncertain diagnosis but high suspicion of Sars-Cov-2 infection allowing to collect material for microbiological culture to define the presence of coinfection or super-infection. This prospective study investigated the correlation between chest computed tomography (CT) findings, Covid-19 Reporting and Data System score, and clinical outcomes in Coronavirus disease 2019 (Covid-19) patients who underwent BAL with the aim of predicting outcomes such as lung coinfection, respiratory failure, and hospitalization length based on chest CT abnormalities. Study population included 34 patients (range 38-90 years old; 20 males, 14 females) with a positive nucleic acid amplification test for Covid-19 infection, suitable BAL examination, and good quality chest CT scan in the absence of lung cancer history. Pulmonary coinfections were found in 20.6% of patients, predominantly caused by bacteria. Specific correlations were found between right middle lobe involvement and pulmonary co-infections. Severe lung injury (PaO2/FiO2 ratio of 100-200) was associated with substantial involvement of right middle, right upper, and left lower lobes. No significant correlation was found between chest CT findings and inflammatory markers (C-reactive protein, procalcitonin) or hospitalization length of stay. Specific chest CT patterns, especially in right middle lobe, could serve as indicators for the presence of co-infections and disease severity in noncritically ill Covid-19 patients, aiding clinicians in timely interventions and personalized treatment strategies.
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Affiliation(s)
- Cosimo Nardi
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence - Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Andrea Magnini
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence - Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Vieri Rastrelli
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence - Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Giulia Zantonelli
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence - Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Linda Calistri
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence - Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Chiara Lorini
- Department of Health Science, University of Florence, Florence, Italy
| | - Valentina Luzzi
- Department of Clinical and Experimental Medicine, Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | - Leonardo Gori
- Department of Clinical and Experimental Medicine, Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | - Luca Ciani
- Department of Clinical and Experimental Medicine, Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | - Fabio Morecchiato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | | | - Anna Julie Peired
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Nicholas Landini
- Department of Radiological, Oncological and Pathological Sciences, Policlinico Umberto I Hospital, "Sapienza" Rome University, Rome, Italy
| | - Edoardo Cavigli
- Department of Radiology, Careggi University Hospital, Florence, Italy
| | - Guang Yang
- Bioengineering Department and Imperial-X, Imperial College London, London, UK
| | - Julien Guiot
- Department of Respiratory Medicine, University Hospital of Liège, Liège, Belgium
| | - Sara Tomassetti
- Department of Clinical and Experimental Medicine, Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | - Stefano Colagrande
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence - Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
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4
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Xian SP, Li ZY, Li W, Yang PF, Huang SH, Liu Y, Tang L, Lai J, Zeng FM, He JZ, Liu Y. Spatial immune landscapes of SARS-CoV-2 gastrointestinal infection: macrophages contribute to local tissue inflammation and gastrointestinal symptoms. Front Cell Dev Biol 2024; 12:1375354. [PMID: 39100091 PMCID: PMC11295004 DOI: 10.3389/fcell.2024.1375354] [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: 01/23/2024] [Accepted: 07/02/2024] [Indexed: 08/06/2024] Open
Abstract
Background In some patients, persistent gastrointestinal symptoms like abdominal pain, nausea, and diarrhea occur as part of long COVID-19 syndrome following acute respiratory symptoms caused by SARS-CoV-2. However, the characteristics of immune cells in the gastrointestinal tract of COVID-19 patients and their association with these symptoms remain unclear. Methodology Data were collected from 95 COVID-19 patients. Among this cohort, 11 patients who exhibited gastrointestinal symptoms and underwent gastroscopy were selected. Using imaging mass cytometry, the gastrointestinal tissues of these patients were thoroughly analyzed to identify immune cell subgroups and investigate their spatial distribution. Results Significant acute inflammatory responses were found in the gastrointestinal tissues, particularly in the duodenum, of COVID-19 patients. These alterations included an increase in the levels of CD68+ macrophages and CD3+CD4+ T-cells, which was more pronounced in tissues with nucleocapsid protein (NP). The amount of CD68+ macrophages positively correlates with the number of CD3+CD4+ T-cells (R = 0.783, p < 0.001), additionally, spatial neighborhood analysis uncovered decreased interactions between CD68+ macrophages and multiple immune cells were noted in NP-positive tissues. Furthermore, weighted gene coexpression network analysis was employed to extract gene signatures related to clinical features and immune responses from the RNA-seq data derived from gastrointestinal tissues from COVID-19 patients, and we validated that the MEgreen module shown positive correlation with clinical parameter (i.e., Total bilirubin, ALT, AST) and macrophages (R = 0.84, p = 0.001), but negatively correlated with CD4+ T cells (R = -0.62, p = 0.004). By contrast, the MEblue module was inversely associated with macrophages and positively related with CD4+ T cells. Gene function enrichment analyses revealed that the MEgreen module is closely associated with biological processes such as immune response activation, signal transduction, and chemotaxis regulation, indicating its role in the gastrointestinal inflammatory response. Conclusion The findings of this study highlight the role of specific immune cell groups in the gastrointestinal inflammatory response in COVID-19 patients. Gene coexpression network analysis further emphasized the importance of the gene modules in gastrointestinal immune responses, providing potential molecular targets for the treatment of COVID-19-related gastrointestinal symptoms.
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Affiliation(s)
- Shi-Ping Xian
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zhan-Yu Li
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wei Li
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Peng-Fei Yang
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Shen-Hao Huang
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Ye Liu
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Lei Tang
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jun Lai
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Fa-Min Zeng
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jian-Zhong He
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Department of Ophthalmology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
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5
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Xu C, Wu J, Ye J, Si Y, Zhang J, Wu B, Pan L, Fu J, Ren Q, Xie S, Tang B, Xiao Y, Hong T. Multiomics integration-based immunological characterizations of adamantinomatous craniopharyngioma in relation to keratinization. Cell Death Dis 2024; 15:439. [PMID: 38906852 PMCID: PMC11192745 DOI: 10.1038/s41419-024-06840-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Although adamantinomatous craniopharyngioma (ACP) is a tumour with low histological malignancy, there are very few therapeutic options other than surgery. ACP has high histological complexity, and the unique features of the immunological microenvironment within ACP remain elusive. Further elucidation of the tumour microenvironment is particularly important to expand our knowledge of potential therapeutic targets. Here, we performed integrative analysis of 58,081 nuclei through single-nucleus RNA sequencing and spatial transcriptomics on ACP specimens to characterize the features and intercellular network within the microenvironment. The ACP environment is highly immunosuppressive with low levels of T-cell infiltration/cytotoxicity. Moreover, tumour-associated macrophages (TAMs), which originate from distinct sources, highly infiltrate the microenvironment. Using spatial transcriptomic data, we observed one kind of non-microglial derived TAM that highly expressed GPNMB close to the terminally differentiated epithelial cell characterized by RHCG, and this colocalization was verified by asmFISH. We also found the positive correlation of infiltration between these two cell types in datasets with larger cohort. According to intercellular communication analysis, we report a regulatory network that could facilitate the keratinization of RHCG+ epithelial cells, eventually causing tumour progression. Our findings provide a comprehensive analysis of the ACP immune microenvironment and reveal a potential therapeutic strategy base on interfering with these two types of cells.
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Affiliation(s)
- Chunming Xu
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jie Wu
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jiye Ye
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Yuancheng Si
- Department of Mathematics, University of Manchester, Manchester, UK
- The School of Economics, Fudan University, Shanghai, China
| | - Jinshi Zhang
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Bowen Wu
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Laisheng Pan
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jun Fu
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Quan Ren
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Shenhao Xie
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Bin Tang
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Yingqun Xiao
- Department of Pathology, Affiliated Infectious Disease Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Tao Hong
- Jiangxi Key Laboratory of Neurological Diseases, Department of Neurosurgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China.
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Li X, Mi Z, Liu Z, Rong P. SARS-CoV-2: pathogenesis, therapeutics, variants, and vaccines. Front Microbiol 2024; 15:1334152. [PMID: 38939189 PMCID: PMC11208693 DOI: 10.3389/fmicb.2024.1334152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 with staggering economic fallout and human suffering. The unique structure of SARS-CoV-2 and its underlying pathogenic mechanism were responsible for the global pandemic. In addition to the direct damage caused by the virus, SARS-CoV-2 triggers an abnormal immune response leading to a cytokine storm, culminating in acute respiratory distress syndrome and other fatal diseases that pose a significant challenge to clinicians. Therefore, potential treatments should focus not only on eliminating the virus but also on alleviating or controlling acute immune/inflammatory responses. Current management strategies for COVID-19 include preventative measures and supportive care, while the role of the host immune/inflammatory response in disease progression has largely been overlooked. Understanding the interaction between SARS-CoV-2 and its receptors, as well as the underlying pathogenesis, has proven to be helpful for disease prevention, early recognition of disease progression, vaccine development, and interventions aimed at reducing immunopathology have been shown to reduce adverse clinical outcomes and improve prognosis. Moreover, several key mutations in the SARS-CoV-2 genome sequence result in an enhanced binding affinity to the host cell receptor, or produce immune escape, leading to either increased virus transmissibility or virulence of variants that carry these mutations. This review characterizes the structural features of SARS-CoV-2, its variants, and their interaction with the immune system, emphasizing the role of dysfunctional immune responses and cytokine storm in disease progression. Additionally, potential therapeutic options are reviewed, providing critical insights into disease management, exploring effective approaches to deal with the public health crises caused by SARS-CoV-2.
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Affiliation(s)
- Xi Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Mi
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhenguo Liu
- Department of Infectious Disease, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
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7
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Fan Y, Bian X, Meng X, Li L, Fu L, Zhang Y, Wang L, Zhang Y, Gao D, Guo X, Lammi MJ, Peng G, Sun S. Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration. Ann Rheum Dis 2024; 83:926-944. [PMID: 38325908 PMCID: PMC11187367 DOI: 10.1136/ard-2023-224420] [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: 05/11/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVES Single-cell and spatial transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome landscape and osteoarthritis (OA)-critical cell populations. METHODS Single-cell RNA sequencing and spatially resolved transcriptomic technology have been applied to characterise the cellular heterogeneity of human knee articular cartilage which were collected from 8 OA donors, and 3 non-OA control donors, and a total of 19 samples. The novel chondrocyte population and marker genes of interest were validated by immunohistochemistry staining, quantitative real-time PCR, etc. The OA-critical cell populations were validated through integrative analyses of publicly available bulk RNA sequencing data and large-scale genome-wide association studies. RESULTS We identified 33 cell population-specific marker genes that define 11 chondrocyte populations, including 9 known populations and 2 new populations, that is, pre-inflammatory chondrocyte population (preInfC) and inflammatory chondrocyte population (InfC). The novel findings that make this an important addition to the literature include: (1) the novel InfC activates the mediator MIF-CD74; (2) the prehypertrophic chondrocyte (preHTC) and hypertrophic chondrocyte (HTC) are potentially OA-critical cell populations; (3) most OA-associated differentially expressed genes reside in the articular surface and superficial zone; (4) the prefibrocartilage chondrocyte (preFC) population is a major contributor to the stratification of patients with OA, resulting in both an inflammatory-related subtype and a non-inflammatory-related subtype. CONCLUSIONS Our results highlight InfC, preHTC, preFC and HTC as potential cell populations to target for therapy. Also, we conclude that profiling of those cell populations in patients might be used to stratify patient populations for defining cohorts for clinical trials and precision medicine.
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Affiliation(s)
- Yue Fan
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, Shaanxi Province; Key Laboratory of Trace Elements and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xuzhao Bian
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xiaogao Meng
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Lei Li
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Laiyi Fu
- School of Automation Science and Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yanan Zhang
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Long Wang
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Center for Evidence-Based Medicine and Clinical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yan Zhang
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Department of Orthopaedics, Honghui Hospital, Xi'an, Shaanxi, China
| | - Dalong Gao
- Department of Orthopaedics, The Central Hospital of Xianyang, Xianyang, China
| | - Xiong Guo
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, Shaanxi Province; Key Laboratory of Trace Elements and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Mikko Juhani Lammi
- Department of Integrative Medical Biology, University of Umeå, Umeå, Sweden
| | - Guangdun Peng
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shiquan Sun
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, Shaanxi Province; Key Laboratory of Trace Elements and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Gonçalves SM, Pereira I, Feys S, Cunha C, Chamilos G, Hoenigl M, Wauters J, van de Veerdonk FL, Carvalho A. Integrating genetic and immune factors to uncover pathogenetic mechanisms of viral-associated pulmonary aspergillosis. mBio 2024; 15:e0198223. [PMID: 38651925 PMCID: PMC11237550 DOI: 10.1128/mbio.01982-23] [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] [Indexed: 04/25/2024] Open
Abstract
Invasive pulmonary aspergillosis is a severe fungal infection primarily affecting immunocompromised patients. Individuals with severe viral infections have recently been identified as vulnerable to developing invasive fungal infections. Both influenza-associated pulmonary aspergillosis (IAPA) and COVID-19-associated pulmonary aspergillosis (CAPA) are linked to high mortality rates, emphasizing the urgent need for an improved understanding of disease pathogenesis to unveil new molecular targets with diagnostic and therapeutic potential. The recent establishment of animal models replicating the co-infection context has offered crucial insights into the mechanisms that underlie susceptibility to disease. However, the development and progression of human viral-fungal co-infections exhibit a significant degree of interindividual variability, even among patients with similar clinical conditions. This observation implies a significant role for host genetics, but information regarding the genetic basis for viral-fungal co-infections is currently limited. In this review, we discuss how genetic factors known to affect either antiviral or antifungal immunity could potentially reveal pathogenetic mechanisms that predispose to IAPA or CAPA and influence the overall disease course. These insights are anticipated to foster further research in both pre-clinical models and human patients, aiming to elucidate the complex pathophysiology of viral-associated pulmonary aspergillosis and contributing to the identification of new diagnostic and therapeutic targets to improve the management of these co-infections.
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Affiliation(s)
- Samuel M Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Inês Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Simon Feys
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Georgios Chamilos
- Laboratory of Clinical Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Joost Wauters
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
- Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
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Doratt BM, Malherbe DC, Messaoudi I. Transcriptional and functional remodeling of lung-resident T cells and macrophages by Simian varicella virus infection. Front Immunol 2024; 15:1408212. [PMID: 38887303 PMCID: PMC11180879 DOI: 10.3389/fimmu.2024.1408212] [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: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 06/20/2024] Open
Abstract
Introduction Varicella zoster virus (VZV) causes varicella and can reactivate as herpes zoster, and both diseases present a significant burden worldwide. However, the mechanisms by which VZV establishes latency in the sensory ganglia and disseminates to these sites remain unclear. Methods We combined a single-cell sequencing approach and a well-established rhesus macaque experimental model using Simian varicella virus (SVV), which recapitulates the VZV infection in humans, to define the acute immune response to SVV in the lung as well as compare the transcriptome of infected and bystander lung-resident T cells and macrophages. Results and discussion Our analysis showed a decrease in the frequency of alveolar macrophages concomitant with an increase in that of infiltrating macrophages expressing antiviral genes as well as proliferating T cells, effector CD8 T cells, and T cells expressing granzyme A (GZMA) shortly after infection. Moreover, infected T cells harbored higher numbers of viral transcripts compared to infected macrophages. Furthermore, genes associated with cellular metabolism (glycolysis and oxidative phosphorylation) showed differential expression in infected cells, suggesting adaptations to support viral replication. Overall, these data suggest that SVV infection remodels the transcriptome of bystander and infected lung-resident T cells and macrophages.
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Affiliation(s)
| | | | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
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10
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Vazquez Guillamet MC, Vazquez Guillamet R, Rjob A, Reynolds D, Parikh B, Despotovic V, Byers DE, Ellebedy AH, Kollef MH, Mudd PA. Quantitative SARS-CoV-2 RT-PCR and Bronchoalveolar Cytokine Concentrations Redefine the COVID-19 Phenotypes in Critically Ill Patients. J Intensive Care Med 2024; 39:525-533. [PMID: 38629466 DOI: 10.1177/08850666231217707] [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] [Indexed: 05/14/2024]
Abstract
RATIONALE Recent studies suggest that both hypo- and hyperinflammatory acute respiratory distress syndrome (ARDS) phenotypes characterize severe COVID-19-related pneumonia. The role of lung Severe Acute Respiratory Syndrome - Coronavirus 2 (SARS-CoV-2) viral load in contributing to these phenotypes remains unknown. OBJECTIVES To redefine COVID-19 ARDS phenotypes when considering quantitative SARS-CoV-2 RT-PCR in the bronchoalveolar lavage of intubated patients. To compare the relevance of deep respiratory samples versus plasma in linking the immune response and the quantitative viral loads. METHODS Eligible subjects were adults diagnosed with COVID-19 ARDS who required mechanical ventilation and underwent bronchoscopy. We recorded the immune response in the bronchoalveolar lavage and plasma and the quantitative SARS-CoV-2 RT-PCR in the bronchoalveolar lavage. Hierarchical clustering on principal components was applied separately on the 2 compartments' datasets. Baseline characteristics were compared between clusters. MEASUREMENTS AND RESULTS Twenty subjects were enrolled between August 2020 and March 2021. Subjects underwent bronchoscopy on average 3.6 days after intubation. All subjects were treated with dexamethasone prior to bronchoscopy, 11 of 20 (55.6%) received remdesivir and 1 of 20 (5%) received tocilizumab. Adding viral load information to the classic 2-cluster model of ARDS revealed a new cluster characterized by hypoinflammatory responses and high viral load in 23.1% of the cohort. Hyperinflammatory ARDS was noted in 15.4% of subjects. Bronchoalveolar lavage clusters were more stable compared to plasma. CONCLUSIONS We identified a unique group of critically ill subjects with COVID-19 ARDS who exhibit hypoinflammatory responses but high viral loads in the lower airways. These clusters may warrant different treatment approaches to improve clinical outcomes.
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Affiliation(s)
- M Cristina Vazquez Guillamet
- Division of Infectious Diseases, Washington University in St. Louis, St. Louis, MO, USA
- Division of Pulmonary and Critical Care, Washington University in St. Louis, MO, USA
| | | | - Ashraf Rjob
- Department of Internal Medicine, Mountain View Regional Medical Center, Virginia, USA
| | - Daniel Reynolds
- Division of Pulmonary and Critical Care, Washington University in St. Louis, MO, USA
| | - Bijal Parikh
- Department of Pathology, Washington University in St. Louis, MO, USA
| | - Vladimir Despotovic
- Division of Pulmonary and Critical Care, Washington University in St. Louis, MO, USA
| | - Derek E Byers
- Division of Pulmonary and Critical Care, Washington University in St. Louis, MO, USA
| | - Ali H Ellebedy
- Department of Pathology, Washington University in St. Louis, MO, USA
| | - Marin H Kollef
- Division of Pulmonary and Critical Care, Washington University in St. Louis, MO, USA
| | - Philip A Mudd
- Department of Emergency Medicine, Washington University in St. Louis, MO, USA
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11
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Malireddi RKS, Sharma BR, Kanneganti TD. Innate Immunity in Protection and Pathogenesis During Coronavirus Infections and COVID-19. Annu Rev Immunol 2024; 42:615-645. [PMID: 38941608 DOI: 10.1146/annurev-immunol-083122-043545] [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] [Indexed: 06/30/2024]
Abstract
The COVID-19 pandemic was caused by the recently emerged β-coronavirus SARS-CoV-2. SARS-CoV-2 has had a catastrophic impact, resulting in nearly 7 million fatalities worldwide to date. The innate immune system is the first line of defense against infections, including the detection and response to SARS-CoV-2. Here, we discuss the innate immune mechanisms that sense coronaviruses, with a focus on SARS-CoV-2 infection and how these protective responses can become detrimental in severe cases of COVID-19, contributing to cytokine storm, inflammation, long-COVID, and other complications. We also highlight the complex cross talk among cytokines and the cellular components of the innate immune system, which can aid in viral clearance but also contribute to inflammatory cell death, cytokine storm, and organ damage in severe COVID-19 pathogenesis. Furthermore, we discuss how SARS-CoV-2 evades key protective innate immune mechanisms to enhance its virulence and pathogenicity, as well as how innate immunity can be therapeutically targeted as part of the vaccination and treatment strategy. Overall, we highlight how a comprehensive understanding of innate immune mechanisms has been crucial in the fight against SARS-CoV-2 infections and the development of novel host-directed immunotherapeutic strategies for various diseases.
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Affiliation(s)
- R K Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
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12
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Kircheis R. In Silico Analyses Indicate a Lower Potency for Dimerization of TLR4/MD-2 as the Reason for the Lower Pathogenicity of Omicron Compared to Wild-Type Virus and Earlier SARS-CoV-2 Variants. Int J Mol Sci 2024; 25:5451. [PMID: 38791489 PMCID: PMC11121871 DOI: 10.3390/ijms25105451] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The SARS-CoV-2 Omicron variants have replaced all earlier variants, due to increased infectivity and effective evasion from infection- and vaccination-induced neutralizing antibodies. Compared to earlier variants of concern (VoCs), the Omicron variants show high TMPRSS2-independent replication in the upper airway organs, but lower replication in the lungs and lower mortality rates. The shift in cellular tropism and towards lower pathogenicity of Omicron was hypothesized to correlate with a lower toll-like receptor (TLR) activation, although the underlying molecular mechanisms remained undefined. In silico analyses presented here indicate that the Omicron spike protein has a lower potency to induce dimerization of TLR4/MD-2 compared to wild type virus despite a comparable binding activity to TLR4. A model illustrating the molecular consequences of the different potencies of the Omicron spike protein vs. wild-type spike protein for TLR4 activation is presented. Further analyses indicate a clear tendency for decreasing TLR4 dimerization potential during SARS-CoV-2 evolution via Alpha to Gamma to Delta to Omicron variants.
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13
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Horvath L, Puschmann C, Scheiber A, Martowicz A, Sturm G, Trajanoski Z, Wolf D, Pircher A, Salcher S. Beyond binary: bridging neutrophil diversity to new therapeutic approaches in NSCLC. Trends Cancer 2024; 10:457-474. [PMID: 38360439 DOI: 10.1016/j.trecan.2024.01.010] [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: 11/03/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Neutrophils represent the most abundant myeloid cell subtype in the non-small-cell lung cancer (NSCLC) tumor microenvironment (TME). By anti- or protumor polarization, they impact multiple aspects of tumor biology and affect sensitivity to conventional therapies and immunotherapies. Single-cell RNA sequencing (scRNA-seq) analyses have unraveled an extensive neutrophil heterogeneity, helping our understanding of their pleiotropic role. In this review we summarize recent data and models on tumor-associated neutrophil (TAN) biology, focusing on the diversity that evolves in response to tumor-intrinsic cues. We categorize available transcriptomic profiles from different cancer entities into a defined set of neutrophil subclusters with distinct phenotypic properties, to step beyond the traditional binary N1/2 classification. Finally, we discuss potential ways to exploit these neutrophil states in the setting of anticancer therapy.
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Affiliation(s)
- Lena Horvath
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Constanze Puschmann
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Alexandra Scheiber
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Agnieszka Martowicz
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria; Boehringer Ingelheim International Pharma GmbH & Co KG, Biberach, Germany
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Andreas Pircher
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Stefan Salcher
- Department of Hematology and Oncology, Internal Medicine V, Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck (MUI), Innsbruck, Austria.
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Zhuang Z, Zhuo J, Yuan Y, Chen Z, Zhang S, Zhu A, Zhao J, Zhao J. Harnessing T-Cells for Enhanced Vaccine Development against Viral Infections. Vaccines (Basel) 2024; 12:478. [PMID: 38793729 PMCID: PMC11125924 DOI: 10.3390/vaccines12050478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Despite significant strides in vaccine research and the availability of vaccines for many infectious diseases, the threat posed by both known and emerging infectious diseases persists. Moreover, breakthrough infections following vaccination remain a concern. Therefore, the development of novel vaccines is imperative. These vaccines must exhibit robust protective efficacy, broad-spectrum coverage, and long-lasting immunity. One promising avenue in vaccine development lies in leveraging T-cells, which play a crucial role in adaptive immunity and regulate immune responses during viral infections. T-cell recognition can target highly variable or conserved viral proteins, and memory T-cells offer the potential for durable immunity. Consequently, T-cell-based vaccines hold promise for advancing vaccine development efforts. This review delves into the latest research advancements in T-cell-based vaccines across various platforms and discusses the associated challenges.
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Affiliation(s)
- Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
| | - Jianfen Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Yaochang Yuan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510182, China; (Z.Z.); (J.Z.); (Y.Y.); (Z.C.); (S.Z.); (A.Z.); (J.Z.)
- Guangzhou National Laboratory, Guangzhou 510005, China
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15
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Zhou Z, Zeng X, Liao J, Dong X, Deng Y, Wang Y, Zhou M. Immune Characteristic Genes and Neutrophil Immune Transformation Studies in Severe COVID-19. Microorganisms 2024; 12:737. [PMID: 38674681 PMCID: PMC11052247 DOI: 10.3390/microorganisms12040737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/26/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
As a disease causing a global pandemic, the progression of symptoms to severe disease in patients with COVID-19 often has adverse outcomes, but research on the immunopathology of COVID-19 severe disease remains limited. In this study, we used mRNA-seq data from the peripheral blood of COVID-19 patients to identify six COVID-19 severe immune characteristic genes (FPR1, FCGR2A, TLR4, S100A12, CXCL1, and L TF), and found neutrophils to be the critical immune cells in COVID-19 severe disease. Subsequently, using scRNA-seq data from bronchoalveolar lavage fluid from COVID-19 patients, neutrophil subtypes highly expressing the S100A family were found to be located at the end of cellular differentiation and tended to release neutrophil extracellular traps. Finally, it was also found that alveolar macrophages, macrophages, and monocytes with a high expression of COVID-19 severe disease immune characteristic genes may influence neutrophils through intercellular ligand-receptor pairs to promote neutrophil extracellular trap release. This study provides immune characteristic genes, critical immune pathways, and immune cells in COVID-19 severe disease, explores intracellular immune transitions of critical immune cells and pit-induced intercellular communication of immune transitions, and provides new biomarkers and potential drug targets for the treatment of patients with COVID-19 severe disease.
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Affiliation(s)
| | | | | | | | | | - Yinghui Wang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (Z.Z.); (X.Z.); (J.L.); (X.D.); (Y.D.)
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (Z.Z.); (X.Z.); (J.L.); (X.D.); (Y.D.)
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Rai P, Marano JM, Kang L, Coutermarsh-Ott S, Daamen AR, Lipsky PE, Weger-Lucarelli J. Obesity fosters severe disease outcomes in a mouse model of coronavirus infection associated with transcriptomic abnormalities. J Med Virol 2024; 96:e29587. [PMID: 38587204 DOI: 10.1002/jmv.29587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Obesity has been identified as an independent risk factor for severe outcomes in humans with coronavirus disease 2019 (COVID-19) and other infectious diseases. Here, we established a mouse model of COVID-19 using the murine betacoronavirus, mouse hepatitis virus 1 (MHV-1). C57BL/6 and C3H/HeJ mice exposed to MHV-1 developed mild and severe disease, respectively. Obese C57BL/6 mice developed clinical manifestations similar to those of lean controls. In contrast, all obese C3H/HeJ mice succumbed by 8 days postinfection, compared to a 50% mortality rate in lean controls. Notably, both lean and obese C3H/HeJ mice exposed to MHV-1 developed lung lesions consistent with severe human COVID-19, with marked evidence of diffuse alveolar damage (DAD). To identify early predictive biomarkers of worsened disease outcomes in obese C3H/HeJ mice, we sequenced RNA from whole blood 2 days postinfection and assessed changes in gene and pathway expression. Many pathways uniquely altered in obese C3H/HeJ mice postinfection aligned with those found in humans with severe COVID-19. Furthermore, we observed altered gene expression related to the unfolded protein response and lipid metabolism in infected obese mice compared to their lean counterparts, suggesting a role in the severity of disease outcomes. This study presents a novel model for studying COVID-19 and elucidating the mechanisms underlying severe disease outcomes in obese and other hosts.
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Affiliation(s)
- Pallavi Rai
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
| | - Jeffrey M Marano
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, Virginia, USA
| | - Lin Kang
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Biomedical Affairs and Research, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
| | - Sheryl Coutermarsh-Ott
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
| | | | | | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
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17
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Kenney D, O’Connell AK, Tseng AE, Turcinovic J, Sheehan ML, Nitido AD, Montanaro P, Gertje HP, Ericsson M, Connor JH, Vrbanac V, Crossland NA, Harly C, Balazs AB, Douam F. Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583965. [PMID: 38496468 PMCID: PMC10942442 DOI: 10.1101/2024.03.08.583965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive. Using mice co-engrafted with a genetically matched human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral infection is rapidly cleared from fLX following a peak of viral replication. Acute replication results in the emergence of cell subsets enriched in viral RNA, including extravascular inflammatory monocytes (iMO) and macrophage-like T-cells, which dissipate upon infection resolution. iMO display robust antiviral responses, are transcriptomically unique among myeloid lineages, and their emergence associates with the recruitment of circulating CD4+ monocytes. Consistently, mice depleted for human CD4+ cells but not CD3+ T-cells failed to robustly clear infectious viruses and displayed signatures of chronic infection. Our findings uncover the transient differentiation of extravascular iMO from CD4+ monocytes as a major hallmark of SARS-CoV-2 infection resolution and open avenues for unravelling viral and host adaptations defining persistently active SARS-CoV-2 infection.
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Affiliation(s)
- Devin Kenney
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Anna E. Tseng
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meagan L. Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Paige Montanaro
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Hans P. Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - John H. Connor
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Nicholas A. Crossland
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Christelle Harly
- Université de Nantes, INSERM, CNRS, CRCINA, Nantes, France
- LabEx IGO ‘Immunotherapy, Graft, Oncology’, Nantes, France
- These authors contributed equally to the work
| | - Alejandro B. Balazs
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- These authors contributed equally to the work
- Lead contact
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18
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Feys S, Vanmassenhove S, Kraisin S, Yu K, Jacobs C, Boeckx B, Cambier S, Cunha C, Debaveye Y, Gonçalves SM, Hermans G, Humblet-Baron S, Jansen S, Lagrou K, Meersseman P, Neyts J, Peetermans M, Rocha-Pereira J, Schepers R, Spalart V, Starick MR, Thevissen K, Van Brussel T, Van Buyten T, Van Mol P, Vandenbriele C, Vanderbeke L, Wauters E, Wilmer A, Van Weyenbergh J, Van De Veerdonk FL, Carvalho A, Proost P, Martinod K, Lambrechts D, Wauters J. Lower respiratory tract single-cell RNA sequencing and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis: a single centre, retrospective, observational study. THE LANCET. MICROBE 2024; 5:e247-e260. [PMID: 38280387 DOI: 10.1016/s2666-5247(23)00368-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 01/29/2024]
Abstract
BACKGROUND COVID-19-associated pulmonary aspergillosis (CAPA) is a severe superinfection with the fungus Aspergillus affecting patients who are critically ill with COVID-19. The pathophysiology and the role of neutrophil extracellular traps (NETs) in this infection are largely unknown. We aimed to characterise the immune profile, with a focus on neutrophils and NET concentrations, of critically ill patients with COVID-19, with or without CAPA. METHODS We conducted a single-centre, retrospective, observational study in two patient cohorts, both recruited at University Hospitals Leuven, Belgium. We included adults aged 18 years or older who were admitted to the intensive care unit because of COVID-19 between March 31, 2020, and May 18, 2021, and who were included in the previous Contagious trial (NCT04327570). We investigated the immune cellular landscape of CAPA versus COVID-19 only by performing single-cell RNA sequencing (scRNA-seq) on bronchoalveolar lavage fluid. Bronchoalveolar lavage immune cell fractions were compared between patients with CAPA and patients with COVID-19 only. Additionally, we determined lower respiratory tract NET concentrations using biochemical assays in patients aged 18 years and older who were admitted to the intensive care unit because of severe COVID-19 between March 15, 2020, and Dec 31, 2021, for whom bronchoalveolar lavage was available in the hospital biobank. Bronchoalveolar lavage NET concentrations were compared between patients with CAPA and patients with COVID-19 only and integrated with existing data on immune mediators in bronchoalveolar lavage and 90-day mortality. FINDINGS We performed scRNA-seq of bronchoalveolar lavage on 43 samples from 39 patients, of whom 36 patients (30 male and six female; 14 with CAPA) were included in downstream analyses. We performed bronchoalveolar lavage NET analyses in 59 patients (46 male and 13 female), of whom 26 had CAPA. By scRNA-seq, patients with CAPA had significantly lower neutrophil fractions than patients with COVID-19 only (16% vs 33%; p=0·0020). The remaining neutrophils in patients with CAPA preferentially followed a hybrid maturation trajectory characterised by expression of genes linked to antigen presentation, with enhanced transcription of antifungal effector pathways. Patients with CAPA also showed depletion of mucosal-associated invariant T cells, reduced T helper 1 and T helper 17 differentiation, and transcriptional defects in specific aspects of antifungal immunity in macrophages and monocytes. We observed increased formation of NETs in patients with CAPA compared with patients with COVID-19 only (DNA complexed with citrullinated histone H3 median 15 898 ng/mL [IQR 4588-86 419] vs 7062 ng/mL [775-14 088]; p=0·042), thereby explaining decreased neutrophil fractions by scRNA-seq. Low bronchoalveolar lavage NET concentrations were associated with increased 90-day mortality in patients with CAPA. INTERPRETATION Qualitative and quantitative disturbances in monocyte, macrophage, B-cell, and T-cell populations could predispose patients with severe COVID-19 to develop CAPA. Hybrid neutrophils form a specialised response to CAPA, and an adequate neutrophil response to CAPA is a major determinant for survival in these patients. Therefore, measuring bronchoalveolar lavage NETs could have diagnostic and prognostic value in patients with CAPA. Clinicians should be wary of aspergillosis when using immunomodulatory therapy that might inhibit NETosis to treat patients with severe COVID-19. FUNDING Research Foundation Flanders, KU Leuven, UZ Leuven, VIB, the Fundação para a Ciência e a Tecnologia, the European Regional Development Fund, la Caixa Foundation, the Flemish Government, and Horizon 2020.
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Affiliation(s)
- Simon Feys
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium
| | - Sam Vanmassenhove
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sirima Kraisin
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Karen Yu
- Laboratory of Molecular Immunology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Cato Jacobs
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium
| | - Seppe Cambier
- Laboratory of Molecular Immunology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Yves Debaveye
- Department of Intensive Care Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Samuel M Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Greet Hermans
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stephanie Humblet-Baron
- Laboratory of Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Sander Jansen
- Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Philippe Meersseman
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marijke Peetermans
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium
| | - Joana Rocha-Pereira
- Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Rogier Schepers
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium
| | - Valérie Spalart
- Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium; Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Marick R Starick
- Laboratory of Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Thomas Van Brussel
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium
| | - Tina Van Buyten
- Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Pierre Van Mol
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium
| | - Christophe Vandenbriele
- Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium; Cardiology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Lore Vanderbeke
- Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Els Wauters
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium; Laboratory of Respiratory Diseases and Thoracic Surgery, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Alexander Wilmer
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium
| | - Johan Van Weyenbergh
- Laboratory of Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | | | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Paul Proost
- Laboratory of Molecular Immunology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Kimberly Martinod
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium
| | - Joost Wauters
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium.
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19
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Bao X, Li Q, Chen D, Dai X, Liu C, Tian W, Zhang H, Jin Y, Wang Y, Cheng J, Lai C, Ye C, Xin S, Li X, Su G, Ding Y, Xiong Y, Xie J, Tano V, Wang Y, Fu W, Deng S, Fang W, Sheng J, Ruan J, Zhao P. A multiomics analysis-assisted deep learning model identifies a macrophage-oriented module as a potential therapeutic target in colorectal cancer. Cell Rep Med 2024; 5:101399. [PMID: 38307032 PMCID: PMC10897549 DOI: 10.1016/j.xcrm.2024.101399] [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: 03/06/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/04/2024]
Abstract
Colorectal cancer (CRC) is a common malignancy involving multiple cellular components. The CRC tumor microenvironment (TME) has been characterized well at single-cell resolution. However, a spatial interaction map of the CRC TME is still elusive. Here, we integrate multiomics analyses and establish a spatial interaction map to improve the prognosis, prediction, and therapeutic development for CRC. We construct a CRC immune module (CCIM) that comprises FOLR2+ macrophages, exhausted CD8+ T cells, tolerant CD8+ T cells, exhausted CD4+ T cells, and regulatory T cells. Multiplex immunohistochemistry is performed to depict the CCIM. Based on this, we utilize advanced deep learning technology to establish a spatial interaction map and predict chemotherapy response. CCIM-Net is constructed, which demonstrates good predictive performance for chemotherapy response in both the training and testing cohorts. Lastly, targeting FOLR2+ macrophage therapeutics is used to disrupt the immunosuppressive CCIM and enhance the chemotherapy response in vivo.
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Affiliation(s)
- Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
| | - Qiong Li
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Dong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Xiaomeng Dai
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chuan Liu
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Weihong Tian
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yuzhi Jin
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yin Wang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chunyu Lai
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Chanqi Ye
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Shan Xin
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Xin Li
- Department of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ge Su
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Yangyang Xiong
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jindong Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Yanfang Wang
- Ludwig-Maximilians-Universität München (LMU), 80539 Munich, Germany
| | - Wenguang Fu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China
| | - Jianpeng Sheng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China; Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, China.
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, China.
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20
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Tomassetti S, Ciani L, Luzzi V, Gori L, Trigiani M, Giuntoli L, Lavorini F, Poletti V, Ravaglia C, Torrego A, Maldonado F, Lentz R, Annunziato F, Maggi L, Rossolini GM, Pollini S, Para O, Ciurleo G, Casini A, Rasero L, Bartoloni A, Spinicci M, Munavvar M, Gasparini S, Comin C, Cerinic MM, Peired A, Henket M, Ernst B, Louis R, Corhay JL, Nardi C, Guiot J. Utility of bronchoalveolar lavage for COVID-19: a perspective from the Dragon consortium. Front Med (Lausanne) 2024; 11:1259570. [PMID: 38371516 PMCID: PMC10869531 DOI: 10.3389/fmed.2024.1259570] [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: 07/16/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
Diagnosing COVID-19 and treating its complications remains a challenge. This review reflects the perspective of some of the Dragon (IMI 2-call 21, #101005122) research consortium collaborators on the utility of bronchoalveolar lavage (BAL) in COVID-19. BAL has been proposed as a potentially useful diagnostic tool to increase COVID-19 diagnosis sensitivity. In both critically ill and non-critically ill COVID-19 patients, BAL has a relevant role in detecting other infections or supporting alternative diagnoses and can change management decisions in up to two-thirds of patients. BAL is used to guide steroid and immunosuppressive treatment and to narrow or discontinue antibiotic treatment, reducing the use of unnecessary broad antibiotics. Moreover, cellular analysis and novel multi-omics techniques on BAL are of critical importance for understanding the microenvironment and interaction between epithelial cells and immunity, revealing novel potential prognostic and therapeutic targets. The BAL technique has been described as safe for both patients and healthcare workers in more than a thousand procedures reported to date in the literature. Based on these preliminary studies, we recognize that BAL is a feasible procedure in COVID-19 known or suspected cases, useful to properly guide patient management, and has great potential for research.
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Affiliation(s)
- Sara Tomassetti
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Luca Ciani
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Valentina Luzzi
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Leonardo Gori
- Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Marco Trigiani
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Leonardo Giuntoli
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Federico Lavorini
- Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Venerino Poletti
- Department of Diseases of the Thorax, GB Morgagni Hospital, Forlì, Italy
| | - Claudia Ravaglia
- Department of Diseases of the Thorax, GB Morgagni Hospital, Forlì, Italy
| | - Alfons Torrego
- Respiratory Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Fabien Maldonado
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert Lentz
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Simona Pollini
- Department of Experimental Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Ombretta Para
- Internal Medicine Unit 1, AOU Careggi, Florence, Italy
| | - Greta Ciurleo
- Internal Medicine Unit 2, AOU Careggi, Florence, Italy
| | | | - Laura Rasero
- Department of Health Science, Clinical Innovations and Research Unit, Careggi University Hospital, Florence, Italy
| | - Alessandro Bartoloni
- Infectious and Tropical Diseases Unit, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Michele Spinicci
- Infectious and Tropical Diseases Unit, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mohammed Munavvar
- School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
- Department of Respiratory, Lancashire Teaching Hospital NHS Foundation Trust, Preston, United Kingdom
| | - Stefano Gasparini
- Interventional Pulmonology Unit, University Hospital Riuniti di Ancona, Ancona, Italy
| | - Camilla Comin
- Department of Experimental and Clinical Medicine Section of Surgery, Histopathology, and Molecular Pathology, University of Florence, Florence, Italy
| | - Marco Matucci Cerinic
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Anna Peired
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Monique Henket
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Benoit Ernst
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Renaud Louis
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Jean-louis Corhay
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Cosimo Nardi
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence, Florence, Italy
| | - Julien Guiot
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
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21
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Duan S, Li Q, Wang F, Kuang W, Dong Y, Liu D, Wang J, Li W, Chen Q, Zeng X, Li T. Single-Cell Transcriptomes and Immune Repertoires Reveal the Cell State and Molecular Changes in Pemphigus Vulgaris. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:375-388. [PMID: 38117802 DOI: 10.4049/jimmunol.2300312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/05/2023] [Indexed: 12/22/2023]
Abstract
The etiology and pathogenesis of pemphigus vulgaris (PV) entail intricate interactions between immune cells and epithelial cells. However, the specific subtypes of immune cells involved in PV, along with their respective roles, remain elusive. Likewise, the precise functions and mechanisms by which glucocorticoids affect cell types within the disease context require further elucidation. To address these knowledge gaps, we performed 5' single-cell RNA sequencing, combined with V(D)J enrichment on buccal mucosal lesions and peripheral blood samples from treatment-naive patients with PV, in conjunction with post-treatment peripheral blood samples obtained after oral prednisone treatment. Our findings suggest that the IL-1α signaling pathway, myeloid APCs, inflammatory CD8+ resident memory T cells, and dysfunctional CD4+ regulatory T cells are involved in the pathogenesis of PV. Part of these findings were validated by immunohistochemical assays and multiplex immunofluorescence assays. Furthermore, our results highlight the significant impact of prednisone treatment on monocytes and mucosal-associated invariant T cells while revealing a limited effect on CD4+ regulatory T cells. Additionally, we present the CDR3 amino acid sequence of BCR related to PV disease and investigate the characteristics of TCR/BCR clonotypes. In conclusion, our study provides a comprehensive understanding of PV, particularly focusing on the mucosal-dominant type, and sheds light on the effects of glucocorticoids within the PV context. These insights hold promise for the development of new therapeutic strategies in this autoimmune disorder.
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Affiliation(s)
- Shumin Duan
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Qionghua Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Fei Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Wenjing Kuang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yunmei Dong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Dan Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Jiongke Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Wei Li
- Department of Dermatology, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Xin Zeng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Taiwen Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
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22
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Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024; 42:293-304. [PMID: 37231261 PMCID: PMC10928517 DOI: 10.1038/s41587-023-01767-y] [Citation(s) in RCA: 226] [Impact Index Per Article: 226.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
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Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Madeline H Kowalski
- New York Genome Center, New York, NY, USA
- Institute for System Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Saket Choudhary
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Austin Hartman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Shaista Madad
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Carlos Fernandez-Granda
- Center for Data Science, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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23
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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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24
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Hou J, Wei Y, Zou J, Jaffery R, Sun L, Liang S, Zheng N, Guerrero AM, Egan NA, Bohat R, Chen S, Zheng C, Mao X, Yi SS, Chen K, McGrail DJ, Sahni N, Shi PY, Chen Y, Xie X, Peng W. Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection. Nat Commun 2024; 15:109. [PMID: 38168026 PMCID: PMC10761986 DOI: 10.1038/s41467-023-44175-1] [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: 08/03/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge gap, we perform a genome-wide CRISPR dropout screen and integrate analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-Seq, and host-virus proteins or protein/RNA interactome. This study uncovers many host factors that are currently underappreciated, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that modulate viral entry and/or replication. The cohesin complex is also identified as an anti-viral pathway, suggesting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discover another anti-viral regulator KLF5, a transcriptional factor involved in sphingolipid metabolism, which is up-regulated, and harbors genetic variations linked to COVID-19 patients with severe symptoms. Anti-viral effects of three identified candidates (DAZAP2/VTA1/KLF5) are confirmed individually. Molecular characterization of DAZAP2/VTA1/KLF5-knockout cells highlights the involvement of genes related to the coagulation system in determining the severity of COVID-19. Together, our results provide further resources for understanding the host anti-viral network during SARS-CoV-2 infection and may help develop new countermeasure strategies.
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Affiliation(s)
- Jiakai Hou
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Zou
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Roshni Jaffery
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Long Sun
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ningbo Zheng
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Ashley M Guerrero
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Nicholas A Egan
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Ritu Bohat
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Si Chen
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Caishang Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaobo Mao
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, and Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP) and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Nidhi Sahni
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology & Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Science, The University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Drug Discovery, The University of Texas Medical Branch, Galveston, TX, USA.
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Quantitative Sciences Program, MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, TX, USA.
| | - Xuping Xie
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Drug Discovery, The University of Texas Medical Branch, Galveston, TX, USA.
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.
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25
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van de Veerdonk FL. COVID-19 Pneumonia and Cytokine Storm Syndrome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1448:307-319. [PMID: 39117824 DOI: 10.1007/978-3-031-59815-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Virus-associated cytokine storm syndrome (CSS) has been recognized for a long time and the classic viruses associated are the herpes viruses EBV, CMV, and HHV-8 as described in chapters IVa,b. In addition, pandemic viruses such as influenza, SARS, and MERS can result in severe CSS that might ultimately lead to severe acute respiratory distress syndrome (ARDS) and death [1-3]. A new pandemic caused by SARS-CoV-2 that started in 2019 has defined another chapter in the virus-associated CSS. The clinical spectrum of SARS-CoV-2 infection has many faces. In most people, it will be asymptomatic, but it can also result in severe COVID-19 pneumonia, ARDS, and multiorgan failure depending on age, comorbidities, and immune status [4]. In addition, this pandemic has known many different stages and developed in a unique way in the first 2 years. It started in a setting where there was no immunity to the virus and after a year, highly effective vaccines were introduced and herd immunity built up over time. However, vaccine effectiveness was waning over time depending on multiple factors, and novel variant strains of the virus circulated across different areas in the world. Antiviral therapy was developed and introduced, and treatment changed from giving no immunomodulatory treatment, followed by the introduction of corticosteroids [5], and later the addition of more targeted strategies such as JAK inhibitors [6] and blocking IL-6 signaling [7]. Therefore, the scientific literature published on COVID-19 must be seen in the context of a highly dynamic and rapidly changing pandemic, making it difficult to compare results from early studies to more recent reports even within 2 years. Still, a lot has been learned over a very short period. It has become apparent that severe COVID-19 is predominantly a disease of immune dysregulation with components that can be defined as CSS. It has unique features and overlapping characteristics with other CSSs, and immunological treatment addressing the CSS has been extensively explored, which will be described here.
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26
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Lee PY. Monocytic Phagocytes in the Immunopathogenesis of Cytokine Storm Syndromes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1448:161-171. [PMID: 39117814 DOI: 10.1007/978-3-031-59815-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Cytokine storm syndromes (CSSs) are caused by a dysregulated host immune response to an inciting systemic inflammatory trigger. This maladaptive and harmful immune response culminates in collateral damage to host tissues resulting in life-threatening multisystem organ failure. Knowledge of the various immune cells that contribute to CSS pathogenesis has improved dramatically in the past decade. Monocytes, dendritic cells, and macrophages, collective known as monocytic phagocytes, are well-positioned within the immune system hierarchy to make key contributions to the initiation, propagation, and amplification of the hyperinflammatory response in CSS. The plasticity of monocytic phagocytes also makes them prime candidates for mediating immunoregulatory and tissue-healing functions in patients who recover from cytokine storm-mediated immunopathology. Therefore, approaches to manipulate the myriad functions of monocytic phagocytes may improve the clinical outcome of CSS.
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Affiliation(s)
- Pui Y Lee
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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27
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Yang F, Liu C, Li P, Wu A, Ma-Lauer Y, Zhang H, Su Z, Lu W, von Brunn A, Zhu D. Targeting Cyclophilin A and CD147 to Inhibit Replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and SARS-CoV-2-Induced Inflammation. Mol Pharmacol 2023; 104:239-254. [PMID: 37827578 DOI: 10.1124/molpharm.122.000587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/25/2023] [Accepted: 07/13/2023] [Indexed: 10/14/2023] Open
Abstract
Identification and development of effective therapeutics for coronavirus disease 2019 (COVID-19) are still urgently needed. The CD147-spike interaction is involved in the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 invasion process in addition to angiotensin-converting enzyme 2 (ACE2). Cyclophilin A (CyPA), the extracellular ligand of CD147, has been found to play a role in the infection and replication of coronaviruses. In this study, our results show that CyPA inhibitors such as cyclosporine A (CsA) and STG-175 can suppress the intracellular replication of SARS-CoV-2 by inhibiting the binding of CyPA to the SARS-CoV-2 nucleocapsid C-terminal domain (N-CTD), and the IC50 is 0.23 μM and 0.17 μM, respectively. Due to high homology, CsA also had inhibitory effects on SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), and the IC50 is 3.2 μM and 2.8 μM, respectively. Finally, we generated a formulation of phosphatidylserine (PS)-liposome-CsA for pulmonary drug delivery. These findings provide a scientific basis for identifying CyPA as a potential drug target for the treatment of COVID-19 as well as for the development of broad-spectrum inhibitors for coronavirus via targeting CyPA. Highlights: 1) SARS-CoV-2 infects cells via the binding of its S protein and CD147; 2) binding of SARS-CoV-2 N protein and CyPA is essential for viral replication; 3) CD147 and CyPA are potential therapeutic targets for SARS-CoV-2; and 4) CsA is a potential therapeutic strategy by interrupting CD147/CyPA interactions. SIGNIFICANCE STATEMENT: New severe acute respiratory syndrome coronavirus (SARS-CoV)-2 variants and other pathogenic coronaviruses (CoVs) are continually emerging, and new broad-spectrum anti-CoV therapy is urgently needed. We found that binding sites of cyclophilin A/cyclosporin A (CyPA/CsA) overlap with CyPA/N-CTD (nucleocapsid C-terminal domain), which shows the potential to target CyPA during SARS-CoV-2 infection. Here, we provide new evidence for targeting CyPA in the treatment of coronavirus disease 2019 (COVID-19) as well as the potential of developing CyPA inhibitors for broad-spectrum inhibition of CoVs.
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Affiliation(s)
- Fan Yang
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Chenglong Liu
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Pengyuan Li
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Aihua Wu
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Yue Ma-Lauer
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Hao Zhang
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Zhuang Su
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Wei Lu
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Albrecht von Brunn
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
| | - Di Zhu
- Department of Pharmacology, School of Pharmacy (F.Y., C.L.), Minhang Hospital and School of Pharmacy, State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Smart Drug Delivery Ministry of Education (A.W., W.L.), and Department of Pharmacology, School of Basic Medical Sciences (D.Z.), Fudan University, Shanghai, China; Max-von-Pettenkofer Institute, Ludwig-Maximilians-University of Munich and German Center for Infection Research, Munich, Germany (P.L., Y.M.-L., A.V.B.); Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, China (H.Z.); and S & T Global, Inc., Woburn, Massachusetts (Z.S.)
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Morrell ED, Holton SE, Lawrance M, Orlov M, Franklin Z, Mitchem MA, DeBerg H, Gersuk VH, Garay A, Barnes E, Liu T, Peltan ID, Rogers A, Ziegler S, Wurfel MM, Mikacenic C. The transcriptional and phenotypic characteristics that define alveolar macrophage subsets in acute hypoxemic respiratory failure. Nat Commun 2023; 14:7443. [PMID: 37978185 PMCID: PMC10656558 DOI: 10.1038/s41467-023-43223-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
The transcriptional and phenotypic characteristics that define alveolar monocyte and macrophage subsets in acute hypoxemic respiratory failure (AHRF) are poorly understood. Here, we apply CITE-seq (single-cell RNA-sequencing and cell-surface protein quantification) to bronchoalveolar lavage and blood specimens longitudinally collected from participants with AHRF to identify alveolar myeloid subsets, and then validate their identity in an external cohort using flow cytometry. We identify alveolar myeloid subsets with transcriptional profiles that differ from other lung diseases as well as several subsets with similar transcriptional profiles as reported in healthy participants (Metallothionein) or patients with COVID-19 (CD163/LGMN). We use information from CITE-seq to determine cell-surface proteins that distinguish transcriptional subsets (CD14, CD163, CD123, CD71, CD48, CD86 and CD44). In the external cohort, we find a higher proportion of CD163/LGMN alveolar macrophages are associated with mortality in AHRF. We report a parsimonious set of cell-surface proteins that distinguish alveolar myeloid subsets using scalable approaches that can be applied to clinical cohorts.
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Affiliation(s)
- Eric D Morrell
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA.
| | - Sarah E Holton
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Matthew Lawrance
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Marika Orlov
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado, Aurora, CO, USA
| | - Zoie Franklin
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | | | - Hannah DeBerg
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Vivian H Gersuk
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Ashley Garay
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Elizabeth Barnes
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Ted Liu
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Ithan D Peltan
- Division of Pulmonary and Critical Care Medicine, Intermountain Health, Murray, UT, USA
| | - Angela Rogers
- Division of Pulmonary and Critical Care, Stanford University, Stanford, CA, USA
| | - Steven Ziegler
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Carmen Mikacenic
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA.
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29
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Al-Zahrani MH, Alghamdi RA, Tarbiah NI, Alkhattabi NA, Joharjy HM, Khalifa RA. Role of CD27 and SAMHD1 and their genetic susceptibility to COVID-19. Saudi J Biol Sci 2023; 30:103821. [PMID: 38020556 PMCID: PMC10666556 DOI: 10.1016/j.sjbs.2023.103821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 12/01/2023] Open
Abstract
SARS-CoV-2, which initiated the worldwide COVID-19 epidemic in 2019, has rapidly emerged and spread, resulting in significant public health challenges worldwide. The COVID-19 severity signs and their association with specific genes have been investigated to better comprehend this phenomenon. In this study, several genes were investigated to see whether they correspond with COVID-19 sickness severity. This research aims to determine and evaluate certain gene expression levels associated with the immune system, as these genes were reported to play important roles in immune control during the COVID-19 outbreak. We analyzed two immunity-linked genes: CD27 and SAMHD1 in COVID-19 patients' samples using RT-PCR, compared them to the samples from recovered, immunized, and healthy individuals. These data were examined to determine the potential relationships between clinical patterns, illness severity, and progression, and SARS-CoV-2 infection immunology. We observed that CD27 gene expression was higher in COVID-19 vaccinated and control groups, but lower in active and recovered COVID-19 patients. On the other hand, SAMHD1 gene expression was elevated in infected and recovered COVID-19 groups. According to our study, the proteins CD27 and SAMHD1 are essential for controlling the immunological response to COVID-19. Changes in their expression levels could increase the susceptibility of patients to severe complications associated with the disease. Therefore, the gene expression level of these proteins could serve as viable prognostic markers for COVID-19.
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Affiliation(s)
- Maryam H. Al-Zahrani
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rana A. Alghamdi
- Department of Chemistry, Sciences and Arts College, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Nesrin I. Tarbiah
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Nuha A. Alkhattabi
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Husam M. Joharjy
- Infection Control Department, King Abdulaziz Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | - Reham A. Khalifa
- Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, Cairo 11371, Egypt
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30
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Fu M, Shu S, Peng Z, Liu X, Chen X, Zeng Z, Yang Y, Cui H, Zhao R, Wang X, Du L, Wu M, Feng W, Song J. Single-Cell RNA Sequencing of Coronary Perivascular Adipose Tissue From End-Stage Heart Failure Patients Identifies SPP1+ Macrophage Subpopulation as a Target for Alleviating Fibrosis. Arterioscler Thromb Vasc Biol 2023; 43:2143-2164. [PMID: 37706320 PMCID: PMC10597444 DOI: 10.1161/atvbaha.123.319828] [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: 07/06/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Perivascular adipose tissue (PVAT) is vital for vascular homeostasis, and PVAT dysfunction is associated with increased atherosclerotic plaque burden. But the mechanisms underlining coronary PVAT dysfunction in coronary atherosclerosis remain elusive. METHODS We performed single-cell RNA sequencing of the stromal vascular fraction of coronary PVAT from 3 groups of heart transplant recipients with end-stage heart failure, including 3 patients with nonobstructive coronary atherosclerosis, 3 patients with obstructive coronary artery atherosclerosis, and 4 nonatherosclerosis control subjects. Bioinformatics was used to annotate the cellular populations, depict the cellular developmental trajectories and interactions, and explore the differences among 3 groups of coronary PVAT at the cellular and molecular levels. Pathological staining, quantitative real-time polymerase chain reaction, and in vitro studies were performed to validate the key findings. RESULTS Ten cell types were identified among 67 936 cells from human coronary PVAT. Several cellular subpopulations, including SPP1+ (secreted phosphoprotein 1) macrophages and profibrotic fibroadipogenic progenitor cells, were accumulated in PVAT surrounding atherosclerotic coronary arteries compared with nonatherosclerosis coronary arteries. The fibrosis percentage was increased in PVAT surrounding atherosclerotic coronary arteries, and it was positively associated with the grade of coronary artery stenosis. Cellular interaction analysis suggested OPN (osteopontin) secreted by SPP1+ macrophages interacted with CD44 (cluster of differentiation 44)/integrin on fibroadipogenic progenitor cells. Strikingly, correlation analyses uncovered that higher level of SPP1 in PVAT correlates with a more severe fibrosis degree and a higher coronary stenosis grade. In vitro studies showed that conditioned medium from atherosclerotic coronary PVAT promoted the migration and proliferation of fibroadipogenic progenitor cells, while such effect was prevented by blocking CD44 or integrin. CONCLUSIONS SPP1+ macrophages accumulated in the PVAT surrounding atherosclerotic coronary arteries, and they promoted the migration and proliferation of fibroadipogenic progenitor cells via OPN-CD44/integrin interaction and thus aggravated the fibrosis of coronary PVAT, which was positively correlated to the coronary stenosis burden. Therefore, SPP1+ macrophages in coronary PVAT may participate in the progression of coronary atherosclerosis.
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Affiliation(s)
- Mengxia Fu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Galactophore Department, Galactophore Center, Beijing Shijitan Hospital (M.F., M.W.), Capital Medical University, China
| | - Songren Shu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Zhiming Peng
- Department of Orthopedics, Peking Union Medical College Hospital (Z.P.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaorui Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Xiao Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Zhiwei Zeng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yicheng Yang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Cui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Ruojin Zhao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Xiaohu Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Leilei Du
- Laboratory of Cardiovascular Science, Beijing Clinical Research Institute, Beijing Friendship Hospital (L.D.), Capital Medical University, China
| | - Min Wu
- Galactophore Department, Galactophore Center, Beijing Shijitan Hospital (M.F., M.W.), Capital Medical University, China
| | - Wei Feng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases (W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases (W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, China (J.S.)
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31
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Diniz MO, Maini MK, Swadling L. T cell control of SARS-CoV-2: When, which, and where? Semin Immunol 2023; 70:101828. [PMID: 37651850 DOI: 10.1016/j.smim.2023.101828] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
Efficient immune protection against viruses such as SARS-CoV-2 requires the coordinated activity of innate immunity, B and T cells. Accumulating data point to a critical role for T cells not only in the clearance of established infection, but also for aborting viral replication independently of humoral immunity. Here we review the evidence supporting the contribution of antiviral T cells and consider which of their qualitative features favour efficient control of infection. We highlight how studies of SARS-CoV-2 and other coronaviridae in animals and humans have provided important lessons on the optimal timing (When), functionality and specificity (Which), and location (Where) of antiviral T cells. We discuss the clinical implications, particularly for the development of next-generation vaccines, and emphasise areas requiring further study.
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Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
| | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
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32
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Prieto-Villalobos J, Lucero CM, Rovegno M, Gómez GI, Retamal MA, Orellana JA. SARS-CoV-2 spike protein S1 activates Cx43 hemichannels and disturbs intracellular Ca 2+ dynamics. Biol Res 2023; 56:56. [PMID: 37876016 PMCID: PMC10598968 DOI: 10.1186/s40659-023-00468-9] [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: 06/14/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the ongoing coronavirus disease 2019 (COVID-19). An aspect of high uncertainty is whether the SARS-CoV-2 per se or the systemic inflammation induced by viral infection directly affects cellular function and survival in different tissues. It has been postulated that tissue dysfunction and damage observed in COVID-19 patients may rely on the direct effects of SARS-CoV-2 viral proteins. Previous evidence indicates that the human immunodeficiency virus and its envelope protein gp120 increase the activity of connexin 43 (Cx43) hemichannels with negative repercussions for cellular function and survival. Here, we evaluated whether the spike protein S1 of SARS-CoV-2 could impact the activity of Cx43 hemichannels. RESULTS We found that spike S1 time and dose-dependently increased the activity of Cx43 hemichannels in HeLa-Cx43 cells, as measured by dye uptake experiments. These responses were potentiated when the angiotensin-converting enzyme 2 (ACE2) was expressed in HeLa-Cx43 cells. Patch clamp experiments revealed that spike S1 increased unitary current events with conductances compatible with Cx43 hemichannels. In addition, Cx43 hemichannel opening evoked by spike S1 triggered the release of ATP and increased the [Ca2+]i dynamics elicited by ATP. CONCLUSIONS We hypothesize that Cx43 hemichannels could represent potential pharmacological targets for developing therapies to counteract SARS-CoV-2 infection and their long-term consequences.
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Affiliation(s)
- Juan Prieto-Villalobos
- Departamento de Neurología, Escuela de Medicina and Centro Interdisciplinario de Neurociencias, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Claudia M Lucero
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Santiago, Chile
| | - Maximiliano Rovegno
- Departamento de Medicina Intensiva, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo I Gómez
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Santiago, Chile
| | - Mauricio A Retamal
- Programa de Comunicación Celular en Cancer, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.
| | - Juan A Orellana
- Departamento de Neurología, Escuela de Medicina and Centro Interdisciplinario de Neurociencias, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile.
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33
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Malainou C, Abdin SM, Lachmann N, Matt U, Herold S. Alveolar macrophages in tissue homeostasis, inflammation, and infection: evolving concepts of therapeutic targeting. J Clin Invest 2023; 133:e170501. [PMID: 37781922 PMCID: PMC10541196 DOI: 10.1172/jci170501] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Alveolar macrophages (AMs) are the sentinel cells of the alveolar space, maintaining homeostasis, fending off pathogens, and controlling lung inflammation. During acute lung injury, AMs orchestrate the initiation and resolution of inflammation in order to ultimately restore homeostasis. This central role in acute lung inflammation makes AMs attractive targets for therapeutic interventions. Single-cell RNA-Seq and spatial omics approaches, together with methodological advances such as the generation of human macrophages from pluripotent stem cells, have increased understanding of the ontogeny, function, and plasticity of AMs during infectious and sterile lung inflammation, which could move the field closer to clinical application. However, proresolution phenotypes might conflict with proinflammatory and antibacterial responses. Therefore, therapeutic targeting of AMs at vulnerable time points over the course of infectious lung injury might harbor the risk of serious side effects, such as loss of antibacterial host defense capacity. Thus, the identification of key signaling hubs that determine functional fate decisions in AMs is of the utmost importance to harness their therapeutic potential.
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Affiliation(s)
- Christina Malainou
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health, Justus Liebig University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute, Giessen, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
| | - Shifaa M. Abdin
- German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Pediatric Pneumology, Allergology and Neonatology and
- REBIRTH Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Nico Lachmann
- German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Pediatric Pneumology, Allergology and Neonatology and
- REBIRTH Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- RESIST (Resolving Infection Susceptibility), Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Ulrich Matt
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health, Justus Liebig University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute, Giessen, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
| | - Susanne Herold
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health, Justus Liebig University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute, Giessen, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
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Yazici D, Cagan E, Tan G, Li M, Do E, Kucukkase OC, Simsek A, Kizmaz MA, Bozkurt T, Aydin T, Heider A, Rückert B, Brüggen MC, Dhir R, O'Mahony L, Akdis M, Nadeau KC, Budak F, Akdis CA, Ogulur I. Disrupted epithelial permeability as a predictor of severe COVID-19 development. Allergy 2023; 78:2644-2658. [PMID: 37422701 DOI: 10.1111/all.15800] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND An impaired epithelial barrier integrity in the gastrointestinal tract is important to the pathogenesis of many inflammatory diseases. Accordingly, we assessed the potential of biomarkers of epithelial barrier dysfunction as predictive of severe COVID-19. METHODS Levels of bacterial DNA and zonulin family peptides (ZFP) as markers of bacterial translocation and intestinal permeability and a total of 180 immune and inflammatory proteins were analyzed from the sera of 328 COVID-19 patients and 49 healthy controls. RESULTS Significantly high levels of circulating bacterial DNA were detected in severe COVID-19 cases. In mild COVID-19 cases, serum bacterial DNA levels were significantly lower than in healthy controls suggesting epithelial barrier tightness as a predictor of a mild disease course. COVID-19 patients were characterized by significantly elevated levels of circulating ZFP. We identified 36 proteins as potential early biomarkers of COVID-19, and six of them (AREG, AXIN1, CLEC4C, CXCL10, CXCL11, and TRANCE) correlated strongly with bacterial translocation and can be used to predict and discriminate severe cases from healthy controls and mild cases (area under the curve (AUC): 1 and 0.88, respectively). Proteomic analysis of the serum of 21 patients with moderate disease at admission which progressed to severe disease revealed 10 proteins associated with disease progression and mortality (AUC: 0.88), including CLEC7A, EIF4EBP1, TRANCE, CXCL10, HGF, KRT19, LAMP3, CKAP4, CXADR, and ITGB6. CONCLUSION Our results demonstrate that biomarkers of intact or defective epithelial barriers are associated with disease severity and can provide early information on the prediction at the time of hospital admission.
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Affiliation(s)
- Duygu Yazici
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Eren Cagan
- Department of Immunology, Bursa Uludag University School of Medicine, Bursa, Turkey
- Department of Pediatric Infectious Diseases, Bursa Yuksek Ihtisas Training and Research Hospital, University of Health Sciences, Bursa, Turkey
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Manru Li
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Evan Do
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
| | - Ozan C Kucukkase
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Abdurrahman Simsek
- Department of Immunology, Bursa Uludag University School of Medicine, Bursa, Turkey
| | - Muhammed Ali Kizmaz
- Department of Immunology, Bursa Uludag University School of Medicine, Bursa, Turkey
| | - Tugce Bozkurt
- Department of Immunology, Bursa Uludag University School of Medicine, Bursa, Turkey
| | - Tamer Aydin
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Anja Heider
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Beate Rückert
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Marie-Charlotte Brüggen
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Raja Dhir
- SEED Inc. Co., Los Angeles, California, USA
| | - Liam O'Mahony
- Department of Medicine and School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Mubeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Kari C Nadeau
- Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Ferah Budak
- Department of Immunology, Bursa Uludag University School of Medicine, Bursa, Turkey
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Ismail Ogulur
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
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Fernández-Rojas MA, Ávila G, Romero-Valdovinos M, Plett-Torres T, Salazar AM, Sordo M, Chávez-Vargas M, Coeto Ángeles CJ, Cruz-Rivera M, Santiago-Olivares C, Ramírez Hinojosa JP, Maravilla P, Flisser A, Ostrosky-Wegman P, Mendlovic F. Elevated Levels of Cytotoxicity, Cytokines, and Anti-SARS-CoV-2 Antibodies in Mild Cases of COVID-19. Viral Immunol 2023; 36:550-561. [PMID: 37603294 DOI: 10.1089/vim.2023.0012] [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] [Indexed: 08/22/2023] Open
Abstract
Current evidence shows higher production of cytokines and antibodies against severe acute respiratory coronavirus 2 (SARS-CoV-2) in severe and critical cases of Coronavirus Disease 2019 (COVID-19) in comparison with patients with moderate or mild disease. A recent hypothesis proposes an important role of genotoxicity and cytotoxicity in the induction of the cytokine storm observed in some patients at later stages of the disease. Interestingly, in this study, we report significantly higher levels of interleukin (IL)-1β, IL-6, MCP-1, and IL-4 cytokines in mild COVID-19 patients versus severe cases, as well as a high frequency of karyorrhexis (median [Me] = 364 vs. 20 cells) and karyolysis (Me = 266 vs. 52 cells) in the mucosal epithelial cells of both groups of patients compared with uninfected individuals. Although we observed higher levels of anti-SARS-CoV-2 IgM and IgG antibodies in COVID-19 patients, IgM antibodies were significantly higher only in mild cases, for the N and the S viral antigens. High levels of IgG antibodies were observed in both mild and severe cases. Our results showed elevated concentrations of proinflammatory and anti-inflammatory cytokines in mild cases, which may reflect an active innate immune response and could be related to the higher IgM and IgG antibody levels found in those patients. In addition, we found that SARS-CoV-2 infection induces cytotoxic damage in the oral mucosa, highlighting the importance of studying the genotoxic and cytotoxic events induced by infection and its role in the pathophysiology of COVID-19.
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Affiliation(s)
- Miguel A Fernández-Rojas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Guillermina Ávila
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Mirza Romero-Valdovinos
- Hospital General "Dr. Manuel Gea González", SSA. Calzada de Tlalpan 4800, Col Seccion XVI, Mexico City, Mexico
| | - Tanya Plett-Torres
- Plan de Estudios Combinados en Medicina, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ana María Salazar
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico
| | - Monserrat Sordo
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico
| | - Mariana Chávez-Vargas
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Cesar Josué Coeto Ángeles
- Hospital General "Dr. Manuel Gea González", SSA. Calzada de Tlalpan 4800, Col Seccion XVI, Mexico City, Mexico
| | - Mayra Cruz-Rivera
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Carlos Santiago-Olivares
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Juan Pablo Ramírez Hinojosa
- Hospital General "Dr. Manuel Gea González", SSA. Calzada de Tlalpan 4800, Col Seccion XVI, Mexico City, Mexico
| | - Pablo Maravilla
- Hospital General "Dr. Manuel Gea González", SSA. Calzada de Tlalpan 4800, Col Seccion XVI, Mexico City, Mexico
| | - Ana Flisser
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Patricia Ostrosky-Wegman
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico
| | - Fela Mendlovic
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
- Facultad de Ciencias de la Salud, Universidad Anáhuac México Norte, Huixquilucan, Mexico State, Mexico
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36
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Shafqat A, Omer MH, Albalkhi I, Alabdul Razzak G, Abdulkader H, Abdul Rab S, Sabbah BN, Alkattan K, Yaqinuddin A. Neutrophil extracellular traps and long COVID. Front Immunol 2023; 14:1254310. [PMID: 37828990 PMCID: PMC10565006 DOI: 10.3389/fimmu.2023.1254310] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
Post-acute COVID-19 sequelae, commonly known as long COVID, encompasses a range of systemic symptoms experienced by a significant number of COVID-19 survivors. The underlying pathophysiology of long COVID has become a topic of intense research discussion. While chronic inflammation in long COVID has received considerable attention, the role of neutrophils, which are the most abundant of all immune cells and primary responders to inflammation, has been unfortunately overlooked, perhaps due to their short lifespan. In this review, we discuss the emerging role of neutrophil extracellular traps (NETs) in the persistent inflammatory response observed in long COVID patients. We present early evidence linking the persistence of NETs to pulmonary fibrosis, cardiovascular abnormalities, and neurological dysfunction in long COVID. Several uncertainties require investigation in future studies. These include the mechanisms by which SARS-CoV-2 brings about sustained neutrophil activation phenotypes after infection resolution; whether the heterogeneity of neutrophils seen in acute SARS-CoV-2 infection persists into the chronic phase; whether the presence of autoantibodies in long COVID can induce NETs and protect them from degradation; whether NETs exert differential, organ-specific effects; specifically which NET components contribute to organ-specific pathologies, such as pulmonary fibrosis; and whether senescent cells can drive NET formation through their pro-inflammatory secretome in long COVID. Answering these questions may pave the way for the development of clinically applicable strategies targeting NETs, providing relief for this emerging health crisis.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | | | | | | | | | | | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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37
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Wang Y, Gao T, Li W, Tai C, Xie Y, Chen D, Liu S, Huang F, Wang W, Chen Y, Wang B. Engineered clinical-grade mesenchymal stromal cells combating SARS-CoV-2 omicron variants by secreting effective neutralizing antibodies. Cell Biosci 2023; 13:160. [PMID: 37653459 PMCID: PMC10470189 DOI: 10.1186/s13578-023-01099-z] [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: 04/04/2023] [Accepted: 07/30/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND The emergence of SARS-CoV-2 becomes life-threatening for the older and immunocompromised individuals, whereas limited treatment is available on these populations. Mesenchymal stromal cells (MSCs) have been reported to be useful in SARS-CoV-2 treatment and reduce SARS-CoV-2-related sequelae. RESULTS In this study, we developed an autonomous cellular machine to secret neutralizing antibody in vivo constantly based on the clinical-grade MSCs, to combat SARS-CoV-2 infections. First, various modified recombinant plasmids were constructed and transfected into clinical-grade MSCs by electroporation, for assembly and expression of neutralizing anti-SARS-CoV-2 antibodies. Second, the stable antibody secreting MSCs clones were screened through pseudovirus neutralization assay. Finally, we investigated the pharmacokinetics and biodistribution of neutralizing antibody secreted by engineered MSCs in vivo. The stable clinical-grade MSCs clones, expressing XGv347-10 and LY-CoV1404-5 neutralizing antibodies, exhibited their feasibility and protective efficacy against SARS-CoV-2 infection. Transplanted engineered clinical-grade MSCs effectively delivered the SARS-CoV-2 antibodies to the lung, and the immune hyperresponsiveness caused by COVID-19 was coordinated by MSC clones through inhibiting the differentiation of CD4 + T cells into Th1 and Th17 subpopulations. CONCLUSIONS Our data suggested that engineered clinical-grade MSCs secreting effective neutralizing antibodies as cellular production machines had the potential to combat SARS-CoV-2 infection, which provided a new avenue for effectively treating the older and immunocompromised COVID-19 patients.
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Affiliation(s)
- Yanning Wang
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - Tianyun Gao
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - WanTing Li
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Xuzhou Medical University, Nanjing, 21000, China
| | - Chenxu Tai
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - Yuanyuan Xie
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - Dong Chen
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - Shuo Liu
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - Feifei Huang
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - Wenqing Wang
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, 21000, China.
| | - Bin Wang
- Clinical Stem Cell Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210000, China.
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38
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Baird S, Ashley CL, Marsh‐Wakefield F, Alca S, Ashhurst TM, Ferguson AL, Lukeman H, Counoupas C, Post JJ, Konecny P, Bartlett A, Martinello M, Bull RA, Lloyd A, Grey A, Hutchings O, Palendira U, Britton WJ, Steain M, Triccas JA. A unique cytotoxic CD4 + T cell-signature defines critical COVID-19. Clin Transl Immunology 2023; 12:e1463. [PMID: 37645435 PMCID: PMC10461786 DOI: 10.1002/cti2.1463] [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: 03/21/2023] [Revised: 06/04/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
Objectives SARS-CoV-2 infection causes a spectrum of clinical disease presentation, ranging from asymptomatic to fatal. While neutralising antibody (NAb) responses correlate with protection against symptomatic and severe infection, the contribution of the T-cell response to disease resolution or progression is still unclear. As newly emerging variants of concern have the capacity to partially escape NAb responses, defining the contribution of individual T-cell subsets to disease outcome is imperative to inform the development of next-generation COVID-19 vaccines. Methods Immunophenotyping of T-cell responses in unvaccinated individuals was performed, representing the full spectrum of COVID-19 clinical presentation. Computational and manual analyses were used to identify T-cell populations associated with distinct disease states. Results Critical SARS-CoV-2 infection was characterised by an increase in activated and cytotoxic CD4+ lymphocytes (CTL). These CD4+ CTLs were largely absent in asymptomatic to severe disease states. In contrast, non-critical COVID-19 was associated with high frequencies of naïve T cells and lack of activation marker expression. Conclusion Highly activated and cytotoxic CD4+ T-cell responses may contribute to cell-mediated host tissue damage and progression of COVID-19. Induction of these potentially detrimental T-cell responses should be considered when developing and implementing effective COVID-19 control strategies.
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Affiliation(s)
- Sarah Baird
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Caroline L Ashley
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Felix Marsh‐Wakefield
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
- Human Cancer and Viral Immunology LaboratoryThe University of SydneyCamperdownNSWAustralia
| | - Sibel Alca
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Thomas M Ashhurst
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Sydney Cytometry Core Research FacilityCharles Perkins Centre, Centenary Institute and The University of SydneyCamperdownNSWAustralia
| | - Angela L Ferguson
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
| | - Hannah Lukeman
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Claudio Counoupas
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Tuberculosis Research ProgramCentenary InstituteSydneyNSWAustralia
| | - Jeffrey J Post
- Prince of Wales Clinical SchoolUNSWSydneyNSWAustralia
- School of Clinical Medicine, Medicine & HealthUNSWSydneyNSWAustralia
| | - Pamela Konecny
- Prince of Wales Clinical SchoolUNSWSydneyNSWAustralia
- St George HospitalSydneyNSWAustralia
| | - Adam Bartlett
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
- Sydney Children's HospitalSydneyNSWAustralia
| | | | - Rowena A Bull
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
| | - Andrew Lloyd
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
| | - Alice Grey
- RPA Virtual Hospital, Sydney Local Health DistrictSydneyNSWAustralia
| | - Owen Hutchings
- RPA Virtual Hospital, Sydney Local Health DistrictSydneyNSWAustralia
| | - Umaimainthan Palendira
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
| | - Warwick J Britton
- Tuberculosis Research ProgramCentenary InstituteSydneyNSWAustralia
- Department of Clinical ImmunologyRoyal Prince Alfred HospitalCamperdownNSWAustralia
| | - Megan Steain
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - James A Triccas
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
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Li J, Zhang K, Zhang Y, Gu Z, Huang C. Neutrophils in COVID-19: recent insights and advances. Virol J 2023; 20:169. [PMID: 37533131 PMCID: PMC10398943 DOI: 10.1186/s12985-023-02116-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an acute respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can lead to acute respiratory distress syndrome (ARDS), multi-organ failure and death, posing significant threat to human health. Studies have found that pathological mechanisms, such as cytokine storms caused by uncontrolled innate immune system activation, release of damage-associated molecular patterns during tissue injury and a high incidence of thrombotic events, are associated with the function and dysfunction of neutrophils. Specifically, the increased formation of low-density neutrophils (LDNs) and neutrophil extracellular traps (NETs) has been shown to be closely linked with the severity and poor prognosis in patients with COVID-19. Our work focuses on understanding the increased number, abnormal activation, lung tissue infiltration, and elevated neutrophil-to-lymphocyte ratio in the pathogenesis of COVID-19. We also explore the involvement of NETs and LDNs in disease progression and thrombosis formation, along with potential therapeutic strategies targeting neutrophil and NETs formation.
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Affiliation(s)
- Jiayu Li
- Department of Infectious Diseases, Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Kegong Zhang
- Department of Infectious Diseases, Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Ye Zhang
- Department of Infectious Diseases, Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Ziyang Gu
- Department of Infectious Diseases, Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China
| | - Changxing Huang
- Department of Infectious Diseases, Second Affiliated Hospital of Air Force Military Medical University, Xi'an, 710038, China.
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40
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Philippot Q, Fekkar A, Gervais A, Le Voyer T, Boers LS, Conil C, Bizien L, de Brabander J, Duitman JW, Romano A, Rosain J, Blaize M, Migaud M, Jeljeli M, Hammadi B, Desmons A, Marchal A, Mayaux J, Zhang Q, Jouanguy E, Borie R, Crestani B, Luyt CE, Adle-Biassette H, Sene D, Megarbane B, Cobat A, Bastard P, Bos LDJ, Casanova JL, Puel A. Autoantibodies Neutralizing Type I IFNs in the Bronchoalveolar Lavage of at Least 10% of Patients During Life-Threatening COVID-19 Pneumonia. J Clin Immunol 2023; 43:1093-1103. [PMID: 37209324 PMCID: PMC10199445 DOI: 10.1007/s10875-023-01512-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023]
Abstract
Autoantibodies (auto-Abs) neutralizing type I interferons (IFNs) are found in the blood of at least 15% of unvaccinated patients with life-threatening COVID-19 pneumonia. We report here the presence of auto-Abs neutralizing type I IFNs in the bronchoalveolar lavage (BAL) of 54 of the 415 unvaccinated patients (13%) with life-threatening COVID-19 pneumonia tested. The 54 individuals with neutralizing auto-Abs in the BAL included 45 (11%) with auto-Abs against IFN-α2, 37 (9%) with auto-Abs against IFN-ω, 54 (13%) with auto-Abs against IFN-α2 and/or ω, and five (1%) with auto-Abs against IFN-β, including three (0.7%) with auto-Abs neutralizing IFN-α2, IFN-ω, and IFN-β, and two (0.5%) with auto-Abs neutralizing IFN-α2 and IFN-β. Auto-Abs against IFN-α2 also neutralize the other 12 subtypes of IFN-α. Paired plasma samples were available for 95 patients. All seven patients with paired samples who had detectable auto-Abs in BAL also had detectable auto-Abs in plasma, and one patient had auto-Abs detectable only in blood. Auto-Abs neutralizing type I IFNs are, therefore, present in the alveolar space of at least 10% of patients with life-threatening COVID-19 pneumonia. These findings suggest that these auto-Abs impair type I IFN immunity in the lower respiratory tract, thereby contributing to hypoxemic COVID-19 pneumonia.
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Affiliation(s)
- Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France.
- Imagine Institute, Université Paris Cité, Paris, EU, France.
| | - Arnaud Fekkar
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
- AP-HP, Groupe Hospitalier La Pitié-Salpêtrière, Service de Parasitologie Mycologie, Paris, EU, France
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Leonoor S Boers
- Amsterdam UMC, University of Amsterdam, Intensive Care Medicine, Meibergdreef 9, Amsterdam, EU, The Netherlands
| | - Clément Conil
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Justin de Brabander
- Center for Experimental Molecular Medicine, Amsterdam UMC, Amsterdam, EU, Netherlands
| | - Jan Willem Duitman
- Amsterdam UMC, Location AMC, Department of Pulmonary Medicine, University of Amsterdam, 1105 AZ, Amsterdam, EU, The Netherlands
- Amsterdam UMC, Department of Experimental Immunology, Location University of Amsterdam, 1105 AZ, Amsterdam, EU, The Netherlands
- Amsterdam Infection & Immunity, Inflammatory Diseases, 1105 AZ, Amsterdam, EU, The Netherlands
| | - Alessia Romano
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Marion Blaize
- AP-HP, Groupe Hospitalier La Pitié-Salpêtrière, Service de Parasitologie Mycologie, Paris, EU, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Maxime Jeljeli
- Département 3I « Infection, Immunité Et Inflammation », Institut Cochin, INSERM U1016, Université Paris Cité, Paris, EU, France
- Faculté de Médecine, AP-HP-Centre Université de Paris, Hôpital Cochin, Service d'Immunologie Biologique, Université Paris Cité, Paris, EU, France
| | - Boualem Hammadi
- General Chemistry Laboratory, Department of Clinical Chemistry, APHP, Necker Hospital for Sick Children, Paris, EU, France
| | - Aurore Desmons
- Clinical Metabolomic Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine (CRSA), Saint Antoine Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP Sorbonne Université), Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
| | - Julien Mayaux
- INSERM, UMRS1158 Neurophysiologie Respiratoire Expérimentale et Clinique, Sorbonne Université, Paris, EU, France
- Site Pitié-Salpêtrière, Service de Pneumologie, Médecine Intensive et Réanimation, Département R3S, Hôpital Pitié-Salpêtrière, AP-HP, Sorbonne Université, Paris, EU, France
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Raphael Borie
- Service de Pneumologie A Hôpital Bichat, APHP, Paris, EU, France
- Inserm, PHERE, Université Paris Cité, 75018, Paris, EU, France
| | - Bruno Crestani
- Service de Pneumologie A Hôpital Bichat, APHP, Paris, EU, France
- Inserm, PHERE, Université Paris Cité, 75018, Paris, EU, France
| | - Charles Edouard Luyt
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, AP-HP, Hôpital Pitié-Salpêtrière, Paris, EU, France
- Inserm, Institute of Cardiometabolism and Nutrition (ICAN), Sorbonne Université, Paris, EU, France
| | - Homa Adle-Biassette
- AP-HP, Hôpital Lariboisière, Service Anatomie Pathologique and Université de Paris, Paris, EU, France
- Inserm, NeuroDiderot, Paris, EU, France
| | - Damien Sene
- Internal Medicine Department, AP-HP, Lariboisière Hospital, Paris, EU, France
- Université Paris Cité, Paris, EU, France
| | - Bruno Megarbane
- Department of Medical and Toxicological Critical Care, APHP, Lariboisière Hospital, Paris, EU, France
- INSERM UMRS-1144, Paris-University, Paris, EU, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Lieuwe D J Bos
- Amsterdam UMC, University of Amsterdam, Intensive Care Medicine, Meibergdreef 9, Amsterdam, EU, The Netherlands
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, EU, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute for Genetic Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 24 Boulevard du Montparnasse 75015, EU, Paris, France
- Imagine Institute, Université Paris Cité, Paris, EU, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
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41
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Marino G, Zhang B, Schmitz A, Schwensen HV, Reinert LS, Paludan SR. STING is redundant for host defense and pathology of COVID-19-like disease in mice. Life Sci Alliance 2023; 6:e202301997. [PMID: 37277149 PMCID: PMC10241217 DOI: 10.26508/lsa.202301997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
Critical COVID-19 is characterized by lack of early type I interferon-mediated host defense and subsequent hyper-inflammation in the lungs. Aberrant activation of macrophages and neutrophils has been reported to lead to excessive activation of innate immunological pathways. It has recently been suggested that the DNA-sensing cGAS-STING pathway drives pathology in the SARS-CoV-2-infected lungs, but mechanistic understanding from in vivo models is needed. Here, we tested whether STING is involved in COVID-19-like disease using the K18-hACE2 mouse model. We report that disease development after SARS-CoV-2 infection is unaltered in STING-deficient K18-hACE2 mice. In agreement with this, STING deficiency did not affect control of viral replication or production of interferons and inflammatory cytokines. This was accompanied by comparable profiles of infiltrating immune cells into the lungs of infected mice. These data do not support a role for STING in COVID-19 pathology and calls for further investigation into the pathogenesis of critical COVID-19.
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Affiliation(s)
- Giorgia Marino
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Baocun Zhang
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Hanna Vf Schwensen
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Line S Reinert
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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Cambier S, Beretta F, Pörtner N, Metzemaekers M, de Carvalho AC, Martens E, Kaes J, Aelbrecht C, Jacobs C, Van Mol P, Wauters E, Meersseman P, Hermans G, Marques RE, Vanaudenaerde B, Vos R, Wauters J, Gouwy M, Proost P. Proteolytic inactivation of CXCL12 in the lungs and circulation of COVID-19 patients. Cell Mol Life Sci 2023; 80:234. [PMID: 37505242 PMCID: PMC11073220 DOI: 10.1007/s00018-023-04870-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
The human chemokine stromal cell-derived factor-1 (SDF-1) or CXCL12 is involved in several homeostatic processes and pathologies through interaction with its cognate G protein-coupled receptor CXCR4. Recent research has shown that CXCL12 is present in the lungs and circulation of patients with coronavirus disease 2019 (COVID-19). However, the question whether the detected CXCL12 is bioactive was not addressed. Indeed, the activity of CXCL12 is regulated by NH2- and COOH-terminal post-translational proteolysis, which significantly impairs its biological activity. The aim of the present study was to characterize proteolytic processing of CXCL12 in broncho-alveolar lavage (BAL) fluid and blood plasma samples from critically ill COVID-19 patients. Therefore, we optimized immunosorbent tandem mass spectrometry proteoform analysis (ISTAMPA) for detection of CXCL12 proteoforms. In patient samples, this approach uncovered that CXCL12 is rapidly processed by site-specific NH2- and COOH-terminal proteolysis and ultimately degraded. This proteolytic inactivation occurred more rapidly in COVID-19 plasma than in COVID-19 BAL fluids, whereas BAL fluid samples from stable lung transplantation patients and the non-affected lung of lung cancer patients (control groups) hardly induced any processing of CXCL12. In COVID-19 BAL fluids with high proteolytic activity, processing occurred exclusively NH2-terminally and was predominantly mediated by neutrophil elastase. In low proteolytic activity BAL fluid and plasma samples, NH2- and COOH-terminal proteolysis by CD26 and carboxypeptidases were observed. Finally, protease inhibitors already approved for clinical use such as sitagliptin and sivelestat prevented CXCL12 processing and may therefore be of pharmacological interest to prolong CXCL12 half-life and biological activity in vivo.
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Affiliation(s)
- Seppe Cambier
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Fabio Beretta
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Noëmie Pörtner
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Mieke Metzemaekers
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Ana Carolina de Carvalho
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Erik Martens
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Janne Kaes
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Celine Aelbrecht
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Cato Jacobs
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Van Mol
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Els Wauters
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Meersseman
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Greet Hermans
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Bart Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Joost Wauters
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Mieke Gouwy
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Rega - Herestraat 49, Box 1042, 3000, Leuven, Belgium.
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Lamarthée B, Callemeyn J, Van Herck Y, Antoranz A, Anglicheau D, Boada P, Becker JU, Debyser T, De Smet F, De Vusser K, Eloudzeri M, Franken A, Gwinner W, Koshy P, Kuypers D, Lambrechts D, Marquet P, Mathias V, Rabant M, Sarwal MM, Senev A, Sigdel TK, Sprangers B, Thaunat O, Tinel C, Van Brussel T, Van Craenenbroeck A, Van Loon E, Vaulet T, Bosisio F, Naesens M. Transcriptional and spatial profiling of the kidney allograft unravels a central role for FcyRIII+ innate immune cells in rejection. Nat Commun 2023; 14:4359. [PMID: 37468466 DOI: 10.1038/s41467-023-39859-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 06/28/2023] [Indexed: 07/21/2023] Open
Abstract
Rejection remains the main cause of premature graft loss after kidney transplantation, despite the use of potent immunosuppression. This highlights the need to better understand the composition and the cell-to-cell interactions of the alloreactive inflammatory infiltrate. Here, we performed droplet-based single-cell RNA sequencing of 35,152 transcriptomes from 16 kidney transplant biopsies with varying phenotypes and severities of rejection and without rejection, and identified cell-type specific gene expression signatures for deconvolution of bulk tissue. A specific association was identified between recipient-derived FCGR3A+ monocytes, FCGR3A+ NK cells and the severity of intragraft inflammation. Activated FCGR3A+ monocytes overexpressed CD47 and LILR genes and increased paracrine signaling pathways promoting T cell infiltration. FCGR3A+ NK cells overexpressed FCRL3, suggesting that antibody-dependent cytotoxicity is a central mechanism of NK-cell mediated graft injury. Multiplexed immunofluorescence using 38 markers on 18 independent biopsy slides confirmed this role of FcγRIII+ NK and FcγRIII+ nonclassical monocytes in antibody-mediated rejection, with specificity to the glomerular area. These results highlight the central involvement of innate immune cells in the pathogenesis of allograft rejection and identify several potential therapeutic targets that might improve allograft longevity.
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Affiliation(s)
- Baptiste Lamarthée
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Université de Franche-Comté, UBFC, EFS, Inserm UMR RIGHT, Besançon, France
| | - Jasper Callemeyn
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Yannick Van Herck
- Department of Oncology, Laboratory for Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Dany Anglicheau
- Department of Nephrology and Kidney Transplantation, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, Inserm U1151, Necker Enfants-Malades Institute, Paris, France
| | - Patrick Boada
- Division of Multi-Organ Transplantation, Department of Surgery, UCSF, 513 Parnassus, San Francisco, CA, USA
| | - Jan Ulrich Becker
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Tim Debyser
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Katrien De Vusser
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Maëva Eloudzeri
- Université Paris Cité, Inserm U1151, Necker Enfants-Malades Institute, Paris, France
| | - Amelie Franken
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Human Genetics, Laboratory of Translational Genetics, KU Leuven, Leuven, Belgium
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Priyanka Koshy
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Human Genetics, Laboratory of Translational Genetics, KU Leuven, Leuven, Belgium
| | - Pierre Marquet
- Department of Pharmacology and Transplantation, University of Limoges, Inserm U1248, Limoges University Hospital, Limoges, France
| | - Virginie Mathias
- EFS, HLA Laboratory, Décines, France
- Université Claude Bernard Lyon I, Inserm U1111, CNRS UMR5308, CIRI, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Marion Rabant
- Université Paris Cité, Inserm U1151, Necker Enfants-Malades Institute, Paris, France
- Department of Pathology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Minnie M Sarwal
- Division of Multi-Organ Transplantation, Department of Surgery, UCSF, 513 Parnassus, San Francisco, CA, USA
| | - Aleksandar Senev
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Histocompatibility and Immunogenetics Laboratory, Red Cross-Flanders, Mechelen, Belgium
| | - Tara K Sigdel
- Division of Multi-Organ Transplantation, Department of Surgery, UCSF, 513 Parnassus, San Francisco, CA, USA
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Olivier Thaunat
- Université Claude Bernard Lyon I, Inserm U1111, CNRS UMR5308, CIRI, Ecole Normale Supérieure de Lyon, Lyon, France
- Hospices Civils de Lyon, Edouard Herriot Hospital, Department of Transplantation, Nephrology and Clinical Immunology, Lyon, France
| | - Claire Tinel
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Université de Franche-Comté, UBFC, EFS, Inserm UMR RIGHT, Besançon, France
- Department of Nephrology and Kidney Transplantation, Dijon Hospital, Dijon, France
| | - Thomas Van Brussel
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Human Genetics, Laboratory of Translational Genetics, KU Leuven, Leuven, Belgium
| | - Amaryllis Van Craenenbroeck
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Thibaut Vaulet
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Francesca Bosisio
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium.
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium.
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Song L, Sun X, Qi T, Yang J. Mixed model-based deconvolution of cell-state abundances (MeDuSA) along a one-dimensional trajectory. NATURE COMPUTATIONAL SCIENCE 2023; 3:630-643. [PMID: 38177744 PMCID: PMC10766563 DOI: 10.1038/s43588-023-00487-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/13/2023] [Indexed: 01/06/2024]
Abstract
Deconvoluting cell-state abundances from bulk RNA-sequencing data can add considerable value to existing data, but achieving fine-resolution and high-accuracy deconvolution remains a challenge. Here we introduce MeDuSA, a mixed model-based method that leverages single-cell RNA-sequencing data as a reference to estimate cell-state abundances along a one-dimensional trajectory in bulk RNA-sequencing data. The advantage of MeDuSA lies primarily in estimating cell abundance in each state while fitting the remaining cells of the same type individually as random effects. Extensive simulations and real-data benchmark analyses demonstrate that MeDuSA greatly improves the estimation accuracy over existing methods for one-dimensional trajectories. Applying MeDuSA to cohort-level RNA-sequencing datasets reveals associations of cell-state abundances with disease or treatment conditions and cell-state-dependent genetic control of transcription. Our study provides a high-accuracy and fine-resolution method for cell-state deconvolution along a one-dimensional trajectory and demonstrates its utility in characterizing the dynamics of cell states in various biological processes.
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Affiliation(s)
- Liyang Song
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Xiwei Sun
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ting Qi
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
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45
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Cheon IS, Son YM, Sun J. Tissue-resident memory T cells and lung immunopathology. Immunol Rev 2023; 316:63-83. [PMID: 37014096 PMCID: PMC10524334 DOI: 10.1111/imr.13201] [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: 01/13/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
Abstract
Rapid reaction to microbes invading mucosal tissues is key to protect the host against disease. Respiratory tissue-resident memory T (TRM ) cells provide superior immunity against pathogen infection and/or re-infection, due to their presence at the site of pathogen entry. However, there has been emerging evidence that exuberant TRM -cell responses contribute to the development of various chronic respiratory conditions including pulmonary sequelae post-acute viral infections. In this review, we have described the characteristics of respiratory TRM cells and processes underlying their development and maintenance. We have reviewed TRM -cell protective functions against various respiratory pathogens as well as their pathological activities in chronic lung conditions including post-viral pulmonary sequelae. Furthermore, we have discussed potential mechanisms regulating the pathological activity of TRM cells and proposed therapeutic strategies to alleviate TRM -cell-mediated lung immunopathology. We hope that this review provides insights toward the development of future vaccines or interventions that can harness the superior protective abilities of TRM cells, while minimizing the potential for immunopathology, a particularly important topic in the era of coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- In Su Cheon
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Young Min Son
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Gyeonggi-do, Republic of Korea 17546
| | - Jie Sun
- Carter Immunology Center, 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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46
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Deng CH, Li TQ, Zhang W, Zhao Q, Wang Y. Targeting Inflammasome Activation in Viral Infection: A Therapeutic Solution? Viruses 2023; 15:1451. [PMID: 37515138 PMCID: PMC10384481 DOI: 10.3390/v15071451] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Inflammasome activation is exclusively involved in sensing activation of innate immunity and inflammatory response during viral infection. Accumulating evidence suggests that the manipulation of inflammasome assembly or its interaction with viral proteins are critical factors in viral pathogenesis. Results from pilot clinical trials show encouraging results of NLRP3 inflammasome suppression in reducing mortality and morbidity in SARS-CoV-2-infected patients. In this article, we summarize the up-to-date understanding of inflammasomes, including NLRP3, AIM2, NLRP1, NLRP6, and NLRC4 in various viral infections, with particular focus on RNA viruses such as SARS-CoV-2, HIV, IAV, and Zika virus and DNA viruses such as herpes simplex virus 1. We also discuss the current achievement of the mechanisms involved in viral infection-induced inflammatory response, host defense, and possible therapeutic solutions.
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Affiliation(s)
- Chuan-Han Deng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao 999078, China
| | - Tian-Qi Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao 999078, China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Av. Wai Long, Taipa, Macao 999078, China
| | - Qi Zhao
- Cancer Centre, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida da Universidade, Taipa, Macao 999078, China
| | - Ying Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Avenida da Universidade, Taipa, Macao 999078, China
- Department of Pharmaceutical Sciences, Faculty of Health Science, University of Macau, Avenida da Universidade, Taipa, Macao 999078, China
- Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510632, China
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47
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Huijghebaert S, Parviz S, Rabago D, Baxter A, Chatterjee U, Khan FR, Fabbris C, Poulas K, Hsu S. Saline nasal irrigation and gargling in COVID-19: a multidisciplinary review of effects on viral load, mucosal dynamics, and patient outcomes. Front Public Health 2023; 11:1161881. [PMID: 37397736 PMCID: PMC10312243 DOI: 10.3389/fpubh.2023.1161881] [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: 02/08/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
With unrelenting SARS-CoV-2 variants, additional COVID-19 mitigation strategies are needed. Oral and nasal saline irrigation (SI) is a traditional approach for respiratory infections/diseases. As a multidisciplinary network with expertise/experience with saline, we conducted a narrative review to examine mechanisms of action and clinical outcomes associated with nasal SI, gargling, spray, or nebulization in COVID-19. SI was found to reduce SARS-CoV-2 nasopharyngeal loads and hasten viral clearance. Other mechanisms may involve inhibition of viral replication, bioaerosol reduction, improved mucociliary clearance, modulation of ENaC, and neutrophil responses. Prophylaxis was documented adjunctive to personal protective equipment. COVID-19 patients experienced significant symptom relief, while overall data suggest lower hospitalization risk. We found no harm and hence recommend SI use, as safe, inexpensive, and easy-to-use hygiene measure, complementary to hand washing or mask-wearing. In view of mainly small studies, large well-controlled or surveillance studies can help to further validate the outcomes and to implement its use.
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Affiliation(s)
| | - Shehzad Parviz
- Medstar Health, Brooke Grove Rehabilitation Village, Sandy Spring, MD, United States
- Infectious Disease, Adventist Healthcare, White Oak Medical Center, Silver Spring, MD, United States
| | - David Rabago
- Departments of Family and Community Medicine and Public Health Sciences, Penn State College of Medicine, Pennsylvania, PA, United States
| | - Amy Baxter
- Department of Emergency Medicine, Augusta University, Augusta, GA, United States
| | - Uday Chatterjee
- Department of Paediatric Surgery, Park Medical Research and Welfare Society, Kolkata, West Bengal, India
| | - Farhan R. Khan
- Department of Surgery, Aga Khan University, Karachi, Pakistan
| | | | | | - Stephen Hsu
- Department of Oral Biology, Augusta University, Augusta, GA, United States
- Department of Oral Health and Diagnostic Sciences, Augusta University, Augusta, GA, United States
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48
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Olivier T, Blomet J, Desmecht D. Central role of lung macrophages in SARS-CoV-2 physiopathology: a cross-model single-cell RNA-seq perspective. Front Immunol 2023; 14:1197588. [PMID: 37350967 PMCID: PMC10282834 DOI: 10.3389/fimmu.2023.1197588] [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: 03/31/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023] Open
Abstract
Cytokine storms are considered a driving factor in coronavirus disease 2019 (COVID-19) severity. However, the triggering and resolution of this cytokine production, as well as the link between this phenomenon and infected cells, are still poorly understood. In this study, a cross-species scRNA-seq analysis showed that cytokine-producing macrophages together with pneumocytes were found to be the main contributors of viral transcripts in both Syrian hamsters and African green monkeys. Whatever the cell type, viral read-bearing cells show an apoptotic phenotype. A comparison of SARS-CoV-2 entry receptor candidates showed that Fc receptors are better correlated with infected cells than ACE2, NRP1, or AXL. Although both species show similar interferon responses, differences in adaptive immunity were highlighted. Lastly, Fc receptor and cytokine upregulation in M1 macrophages was found to correlate with a comprehensive interferon response. Based on these results, we propose a model in which lung macrophages play a central role in COVID-19 severity through antibody-dependent enhancement.
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Affiliation(s)
- Thibaut Olivier
- GAS Department, Prevor Research Laboratories, Valmondois, France
- Department of Pathology, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
| | - Joël Blomet
- GAS Department, Prevor Research Laboratories, Valmondois, France
| | - Daniel Desmecht
- Department of Pathology, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
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49
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Van de Sande B, Lee JS, Mutasa-Gottgens E, Naughton B, Bacon W, Manning J, Wang Y, Pollard J, Mendez M, Hill J, Kumar N, Cao X, Chen X, Khaladkar M, Wen J, Leach A, Ferran E. Applications of single-cell RNA sequencing in drug discovery and development. Nat Rev Drug Discov 2023; 22:496-520. [PMID: 37117846 PMCID: PMC10141847 DOI: 10.1038/s41573-023-00688-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 04/30/2023]
Abstract
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods, together with associated computational tools and the growing availability of public data resources, are transforming drug discovery and development. New opportunities are emerging in target identification owing to improved disease understanding through cell subtyping, and highly multiplexed functional genomics screens incorporating scRNA-seq are enhancing target credentialling and prioritization. ScRNA-seq is also aiding the selection of relevant preclinical disease models and providing new insights into drug mechanisms of action. In clinical development, scRNA-seq can inform decision-making via improved biomarker identification for patient stratification and more precise monitoring of drug response and disease progression. Here, we illustrate how scRNA-seq methods are being applied in key steps in drug discovery and development, and discuss ongoing challenges for their implementation in the pharmaceutical industry.
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Affiliation(s)
| | | | | | - Bart Naughton
- Computational Neurobiology, Eisai, Cambridge, MA, USA
| | - Wendi Bacon
- EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
- The Open University, Milton Keynes, UK
| | | | - Yong Wang
- Precision Bioinformatics, Prometheus Biosciences, San Diego, CA, USA
| | | | - Melissa Mendez
- Genomic Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Jon Hill
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Namit Kumar
- Informatics & Predictive Sciences, Bristol Myers Squibb, San Diego, CA, USA
| | - Xiaohong Cao
- Genomic Research Center, AbbVie Inc., Cambridge, MA, USA
| | - Xiao Chen
- Magnet Biomedicine, Cambridge, MA, USA
| | - Mugdha Khaladkar
- Human Genetics and Computational Biology, GlaxoSmithKline, Collegeville, PA, USA
| | - Ji Wen
- Oncology Research and Development Unit, Pfizer, La Jolla, CA, USA
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50
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Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med 2023; 29:1563-1577. [PMID: 37291214 PMCID: PMC10287567 DOI: 10.1038/s41591-023-02327-2] [Citation(s) in RCA: 128] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/30/2023] [Indexed: 06/10/2023]
Abstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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Grants
- P50 AR080612 NIAMS NIH HHS
- R01 HL153375 NHLBI NIH HHS
- R01 HL127349 NHLBI NIH HHS
- U54 HL165443 NHLBI NIH HHS
- P01 HL107202 NHLBI NIH HHS
- U01 HL148856 NHLBI NIH HHS
- R21 HL156124 NHLBI NIH HHS
- U54 AG075931 NIA NIH HHS
- Wellcome Trust
- R01 HL146557 NHLBI NIH HHS
- R01 HL123766 NHLBI NIH HHS
- U01 HL148861 NHLBI NIH HHS
- R01 HL141852 NHLBI NIH HHS
- R01 ES034350 NIEHS NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 HL126176 NHLBI NIH HHS
- R21 HL161760 NHLBI NIH HHS
- R01 HL145372 NHLBI NIH HHS
- P01 AG049665 NIA NIH HHS
- K12 HD105271 NICHD NIH HHS
- U19 AI135964 NIAID NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 HL142568 NHLBI NIH HHS
- R01 HL153312 NHLBI NIH HHS
- U54 AG079754 NIA NIH HHS
- R56 HL157632 NHLBI NIH HHS
- R01 HL158139 NHLBI NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL153045 NHLBI NIH HHS
- U54 HL145608 NHLBI NIH HHS
- P50 AR060780 NIAMS NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL146519 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R01 HL068702 NHLBI NIH HHS
- U01 HL145567 NHLBI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- MR/R015635/1 Medical Research Council
- R01 MD010443 NIMHD NIH HHS
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” NIH 1U54HL145608-01 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- ESPOD fellowship of EMBL-EBI and Sanger Institute
- 3IA Cote d’Azur PhD program
- The Ministry of Economic Affairs and Climate Policy by means of the PPP
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Joachim Herz Stiftung (Joachim Herz Foundation)
- P50 AR060780-06A1
- University College London, Birkbeck MRC Doctoral Training Programme
- Jikei University School of Medicine (Jikei University)
- 5R01HL14254903, 4UH3CA25513503
- R01HL127349, R01HL141852, U01HL145567 and CZI
- MRC Clinician Scientist Fellowship (MR/W00111X/1)
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” 2R01HL068702
- R01 HL135156, R01 MD010443, R01 HL128439, P01 HL132821, P01 HL107202, R01 HL117004, and DOD Grant W81WH-16-2-0018
- HL142568 and HL14507 from the NHLBI
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”, 2R01HL068702
- Wellcome (WT211276/Z/18/Z) Sanger core grant WT206194 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- R21HL156124, R56HL157632, and R21HL161760
- CZI, 5U01HL148856
- CZI, 5U01HL148856, R01 HL153045
- U.S. Department of Defense (United States Department of Defense)
- The National Institute of Health R01HL145372
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- Conseil Départemental des Alpes Maritimes
- Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR SAHARRA (ANR-19-CE14–0027), ANR-19-P3IA-0002–3IA, the National Infrastructure France Génomique (ANR-10-INBS-09-03), PPIA 4D-OMICS (21-ESRE-0052), and the Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”.
- Wellcome Trust (Wellcome)
- Sanger core grant WT206194 Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- Doris Duke Charitable Foundation (DDCF)
- The National Institute of Health R01HL145372 Department of Defense W81XWH-19-1-0416
- The National Institute of Health R01HL146557 and R01HL153375 and funds from Chan Zuckerberg Initiative - Human Lung Cell Atlas-pilot award
- 1U54HL145608-01
- CZI Deep Visual Proteomics
- 1U54HL145608-01, U01HL148861-03
- 1) the Chan Zuckerberg Initiative, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”; 2) R01 HL153312; 3) U19 AI135964; 4) P01 AG049665
- Netherlands Lung Foundation project nos. 5.1.14.020 and 4.1.18.226, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”
- grant number 2019-002438 from the Chan Zuckerberg Foundation, by the Helmholtz Association’s Initiative and Networking Fund through Helmholtz AI [ZT-I-PF-5-01] and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells)
- 1 U01 HL14555-01, R01 HL123766-04
- NIH U54 AG075931, 5R01 HL146519
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Affiliation(s)
- Lisa Sikkema
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ciro Ramírez-Suástegui
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Daniel C Strobl
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tessa E Gillett
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Luke Zappia
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | | | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Yuge Ji
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Meshal Ansari
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Leonie Apperloo
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christophe Bécavin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Antoine Collin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Aurore C A Gay
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Janine Gote-Schniering
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Baharak Hooshiar Kashani
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Kemal Inecik
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theodore S Kapellos
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Tessa M Kole
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sylvie Leroy
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Christoph H Mayr
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | | | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Carlo De Donno
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Leander Dony
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | | | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Ni Huang
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ignacio L Ibarra
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Preetish Kadur Lakshminarasimha Murthy
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mohammad Lotfollahi
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carlos Talavera-López
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
| | - Kyle J Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kaylee B Worlock
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Tushar J Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marko Z Nikolic
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Falk
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Dana Pe'er
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
| | - Sara A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Malte D Luecken
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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