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Da Silva Filho J, Herder V, Gibbins MP, Dos Reis MF, Melo GC, Haley MJ, Judice CC, Val FFA, Borba M, Tavella TA, de Sousa Sampaio V, Attipa C, McMonagle F, Wright D, de Lacerda MVG, Costa FTM, Couper KN, Marcelo Monteiro W, de Lima Ferreira LC, Moxon CA, Palmarini M, Marti M. A spatially resolved single-cell lung atlas integrated with clinical and blood signatures distinguishes COVID-19 disease trajectories. Sci Transl Med 2024; 16:eadk9149. [PMID: 39259811 DOI: 10.1126/scitranslmed.adk9149] [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: 09/26/2023] [Revised: 02/15/2024] [Accepted: 08/05/2024] [Indexed: 09/13/2024]
Abstract
COVID-19 is characterized by a broad range of symptoms and disease trajectories. Understanding the correlation between clinical biomarkers and lung pathology during acute COVID-19 is necessary to understand its diverse pathogenesis and inform more effective treatments. Here, we present an integrated analysis of longitudinal clinical parameters, peripheral blood markers, and lung pathology in 142 Brazilian patients hospitalized with COVID-19. We identified core clinical and peripheral blood signatures differentiating disease progression between patients who recovered from severe disease compared with those who succumbed to the disease. Signatures were heterogeneous among fatal cases yet clustered into two patient groups: "early death" (<15 days until death) and "late death" (>15 days). Progression to early death was characterized systemically and in lung histopathological samples by rapid endothelial and myeloid activation and the presence of thrombi associated with SARS-CoV-2+ macrophages. In contrast, progression to late death was associated with fibrosis, apoptosis, and SARS-CoV-2+ epithelial cells in postmortem lung tissue. In late death cases, cytotoxicity, interferon, and T helper 17 (TH17) signatures were only detectable in the peripheral blood after 2 weeks of hospitalization. Progression to recovery was associated with higher lymphocyte counts, TH2 responses, and anti-inflammatory-mediated responses. By integrating antemortem longitudinal blood signatures and spatial single-cell lung signatures from postmortem lung samples, we defined clinical parameters that could be used to help predict COVID-19 outcomes.
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Affiliation(s)
- João Da Silva Filho
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Institute of Parasitology Zurich (IPZ), VetSuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matthew P Gibbins
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Institute of Parasitology Zurich (IPZ), VetSuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Monique Freire Dos Reis
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Brazil
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Federal University of Amazonas, Manaus, Brazil
- Amazonas Oncology Control Center Foundation, Manaus, Brazil
| | | | - Michael J Haley
- Department of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Carla Cristina Judice
- Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, Brazil
| | - Fernando Fonseca Almeida Val
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Mayla Borba
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Delphina Rinaldi Abdel Aziz Emergency Hospital (HPSDRA), Manaus, Brazil
| | - Tatyana Almeida Tavella
- Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, Brazil
- INSERM U1016, CNRS UMR8104, University of Paris Cité, Institut Cochin, Paris, France
| | | | - Charalampos Attipa
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fiona McMonagle
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Glasgow Imaging Facility/School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Derek Wright
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Marcus Vinicius Guimaraes de Lacerda
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
- Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- University of Texas Medical Branch, Galveston, TX, USA
| | | | - Kevin N Couper
- Department of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Wuelton Marcelo Monteiro
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, University of Amazonas State, Manaus, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Christopher Alan Moxon
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | | | - Matthias Marti
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Institute of Parasitology Zurich (IPZ), VetSuisse Faculty, University of Zurich, Zurich, Switzerland
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Xu L, Yu D, Xu M, Liu Y, Yang LX, Zou QC, Feng XL, Li MH, Sheng N, Yao YG. Primate-specific BTN3A2 protects against SARS-CoV-2 infection by interacting with and reducing ACE2. EBioMedicine 2024; 107:105281. [PMID: 39142074 PMCID: PMC11367481 DOI: 10.1016/j.ebiom.2024.105281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is an immune-related disorder caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The complete pathogenesis of the virus remains to be determined. Unraveling the molecular mechanisms governing SARS-CoV-2 interactions with host cells is crucial for the formulation of effective prophylactic measures and the advancement of COVID-19 therapeutics. METHODS We analyzed human lung single-cell RNA sequencing dataset to discern the association of butyrophilin subfamily 3 member A2 (BTN3A2) expression with COVID-19. The BTN3A2 gene edited cell lines and transgenic mice were infected by live SARS-CoV-2 in a biosafety level 3 (BSL-3) laboratory. Immunoprecipitation, flow cytometry, biolayer interferometry and competition ELISA assays were performed in BTN3A2 gene edited cells. We performed quantitative real-time PCR, histological and/or immunohistochemical analyses for tissue samples from mice with or without SARS-CoV-2 infection. FINDINGS The BTN3A2 mRNA level was correlated with COVID-19 severity. BTN3A2 expression was predominantly identified in epithelial cells, elevated in pathological epithelial cells from COVID-19 patients and co-occurred with ACE2 expression in the same lung cell subtypes. BTN3A2 targeted the early stage of the viral life cycle by inhibiting SARS-CoV-2 attachment through interactions with the receptor-binding domain (RBD) of the Spike protein and ACE2. BTN3A2 inhibited ACE2-mediated SARS-CoV-2 infection by reducing ACE2 in vitro and in vivo. INTERPRETATION These results reveal a key role of BTN3A2 in the fight against COVID-19. Identifying potential monoclonal antibodies which mimic BTN3A2 may facilitate disruption of SARS-CoV-2 infection, providing a therapeutic avenue for COVID-19. FUNDING This study was supported by the National Natural Science Foundation of China (32070569, U1902215, and 32371017), the CAS "Light of West China" Program, and Yunnan Province (202305AH340006).
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Affiliation(s)
- Ling Xu
- Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China; Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China.
| | - Dandan Yu
- Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China; Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Min Xu
- Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yamin Liu
- Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Lu-Xiu Yang
- Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China
| | - Qing-Cui Zou
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Xiao-Li Feng
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Ming-Hua Li
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China
| | - Nengyin Sheng
- Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
| | - Yong-Gang Yao
- Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China; Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China; National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), National Resource Center for Non-Human Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650107, China.
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Vu Manh TP, Gouin C, De Wolf J, Jouneau L, Pascale F, Bevilacqua C, Ar Gouilh M, Da Costa B, Chevalier C, Glorion M, Hannouche L, Urien C, Estephan J, Magnan A, Le Guen M, Marquant Q, Descamps D, Dalod M, Schwartz-Cornil I, Sage E. SARS-CoV2 infection in whole lung primarily targets macrophages that display subset-specific responses. Cell Mol Life Sci 2024; 81:351. [PMID: 39147987 PMCID: PMC11335275 DOI: 10.1007/s00018-024-05322-z] [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: 05/22/2024] [Accepted: 06/05/2024] [Indexed: 08/17/2024]
Abstract
Deciphering the initial steps of SARS-CoV-2 infection, that influence COVID-19 outcomes, is challenging because animal models do not always reproduce human biological processes and in vitro systems do not recapitulate the histoarchitecture and cellular composition of respiratory tissues. To address this, we developed an innovative ex vivo model of whole human lung infection with SARS-CoV-2, leveraging a lung transplantation technique. Through single-cell RNA-seq, we identified that alveolar and monocyte-derived macrophages (AMs and MoMacs) were initial targets of the virus. Exposure of isolated lung AMs, MoMacs, classical monocytes and non-classical monocytes (ncMos) to SARS-CoV-2 variants revealed that while all subsets responded, MoMacs produced higher levels of inflammatory cytokines than AMs, and ncMos contributed the least. A Wuhan lineage appeared to be more potent than a D614G virus, in a dose-dependent manner. Amidst the ambiguity in the literature regarding the initial SARS-CoV-2 cell target, our study reveals that AMs and MoMacs are dominant primary entry points for the virus, and suggests that their responses may conduct subsequent injury, depending on their abundance, the viral strain and dose. Interfering on virus interaction with lung macrophages should be considered in prophylactic strategies.
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Affiliation(s)
- Thien-Phong Vu Manh
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13009, Marseille, France.
| | - Carla Gouin
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Julien De Wolf
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, UVSQ, BREED, 78350, Jouy-en-Josas, France
| | - Florentina Pascale
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
| | - Claudia Bevilacqua
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Meriadeg Ar Gouilh
- Department of Virology, Univ Caen Normandie, Dynamicure INSERM UMR 1311, CHU Caen, 14000, Caen, France
| | - Bruno Da Costa
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | | | - Matthieu Glorion
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
| | - Laurent Hannouche
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13009, Marseille, France
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Céline Urien
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Jérôme Estephan
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Antoine Magnan
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Pulmonology, Foch Hospital, 92150, Suresnes, France
| | - Morgan Le Guen
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Anesthesiology, Foch Hospital, 92150, Suresnes, France
| | - Quentin Marquant
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Pulmonology, Foch Hospital, 92150, Suresnes, France
- Delegation to Clinical Research and Innovation, Foch Hospital, 92150, Suresnes, France
| | - Delphyne Descamps
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Marc Dalod
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13009, Marseille, France
| | | | - Edouard Sage
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
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Akkari L, Amit I, Bronte V, Fridlender ZG, Gabrilovich DI, Ginhoux F, Hedrick CC, Ostrand-Rosenberg S. Defining myeloid-derived suppressor cells. Nat Rev Immunol 2024:10.1038/s41577-024-01062-0. [PMID: 38969773 DOI: 10.1038/s41577-024-01062-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/07/2024]
Affiliation(s)
- Leila Akkari
- Division of Tumour Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | | | - Zvi G Fridlender
- Institute of Pulmonary Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | | | - Florent Ginhoux
- Gustave Roussy Cancer Campus, Villejuif, France.
- Paris-Saclay University, Paris, France.
| | - Catherine C Hedrick
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA.
- Georgia Cancer Center, Augusta University, Augusta, GA, USA.
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA.
| | - Suzanne Ostrand-Rosenberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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Xiong X, Zheng Z, Liu C, Wang X, Luo S, Xie Q, Liu Y, Chen Q, Zheng M. Unveiling the metabolic and coagulation disruptions in SARS-CoV-2-associated acute macular neuroretinopathy: A case-control study. J Med Virol 2024; 96:e29714. [PMID: 38837795 DOI: 10.1002/jmv.29714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/20/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
SARS-CoV-2 infection has been associated with the increased incidence of acute macular neuroretinopathy (AMN), an infrequent ocular disorder. However, the precise mechanisms underpinning AMN in the context of SARS-CoV-2 infection (AMN-SARS-CoV-2) remain elusive. In this case-control study, 14 patients diagnosed with AMN-SARS-CoV-2 between 2022/12 and 2023/3 were enrolled and compared with 14 SARS-CoV-2-infected individuals without AMN, who served as controls (SARS-CoV-2-no AMN). Metabolomic profiling using ultrahigh-performance liquid chromatography-online electrospray mass spectrometry revealed significant alterations in serum metabolites in AMN-SARS-CoV-2 patients. Coagulation abnormalities were observed in AMN-SARS-CoV-2 patients, and their relationship with metabolic disorders was studied. Finally, a predictive model for AMN-SARS-CoV-2 was established. Seventy-six upregulated and 42 downregulated metabolites were identified in AMN-SARS-CoV-2 cases. Notably, arginine metabolism within the urea cycle was significantly altered, evidenced by variations in ornithine, citrulline, l-proline, and ADAM levels, correlating with abnormal coagulation markers like platelet crit, fibrinogen degradation product, and fibrinogen. Additionally, increased arginase 1 (AGR1) activity within the urea cycle and reduced nitric oxide synthase activity were observed in AMN-SARS-CoV-2. The integration of urea cycle metabolite levels with coagulation parameters yielded a robust discriminatory model for AMN-SARS-CoV-2, as evidenced by an area under the curve of 0.96. The findings of the present study enhance our comprehension of the underlying metabolic mechanisms associated with AMN-SARS-CoV-2 and offer potential diagnostic markers for this uncommon ocular disorder within the context of SARS-CoV-2 infection.
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Affiliation(s)
- Xiaojing Xiong
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng Zheng
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunlin Liu
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinyu Wang
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuai Luo
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinqin Xie
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Liu
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qingwei Chen
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of General Practice, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Minming Zheng
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Ophthalmology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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6
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Monneret G, Voirin N, Richard JC, Cour M, Rimmelé T, Garnier L, Yonis H, Coudereau R, Gossez M, Malcus C, Wallet F, Delignette MC, Dailler F, Buisson M, Argaud L, Lukaszewicz AC, Venet F. Monitoring monocyte HLA-DR expression and CD4 + T lymphocyte count in dexamethasone-treated severe COVID-19 patients. Ann Intensive Care 2024; 14:76. [PMID: 38762684 PMCID: PMC11102415 DOI: 10.1186/s13613-024-01310-5] [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: 12/18/2023] [Accepted: 05/12/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND A 10-day dexamethasone regimen has emerged as the internationally adopted standard-of-care for severe COVID-19 patients. However, the immune response triggered by SARS-CoV-2 infection remains a complex and dynamic phenomenon, leading to various immune profiles and trajectories. The immune status of severe COVID-19 patients following complete dexamethasone treatment has yet to be thoroughly documented. RESULTS To analyze monocyte HLA-DR expression (mHLA-DR) and CD4 + T lymphocyte count (CD4) in critically ill COVID-19 patients after a dexamethasone course and evaluate their association with 28-day ICU mortality, adult COVID-19 patients (n = 176) with an ICU length of stay of at least 10 days and under dexamethasone treatment were included. Associations between each biomarker value (or in combination) measured at day 10 after ICU admission and 28-day mortality in ICU were evaluated. At day 10, the majority of patients presented decreased values of both parameters. A significant association between low mHLA-DR and 28-day mortality was observed. This association remained significant in a multivariate analysis including age, comorbidities or pre-existing immunosuppression (adjusted Hazard ratio (aHR) = 2.86 [1.30-6.32], p = 0.009). Similar results were obtained with decreased CD4 + T cell count (aHR = 2.10 [1.09-4.04], p = 0.027). When combining these biomarkers, patients with both decreased mHLA-DR and low CD4 presented with an independent and significant elevated risk of 28-day mortality (i.e., 60%, aHR = 4.83 (1.72-13.57), p = 0.001). CONCLUSIONS By using standardized immunomonitoring tools available in clinical practice, it is possible to identify a subgroup of patients at high risk of mortality at the end of a 10-day dexamethasone treatment. This emphasizes the significance of integrating immune monitoring into the surveillance of intensive care patients in order to guide further immumodulation approaches.
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Affiliation(s)
- Guillaume Monneret
- Immunology Laboratory, Hospices Civils de Lyon, Edouard Herriot Hospital, 5 Place d'Arsonval, 69437, Lyon, France.
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression", Joint Research Unit HCL-bioMérieux, (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), 69003, Lyon, France.
| | | | - Jean-Christophe Richard
- Medical Intensive Care Department, Hospices Civils de Lyon, Croix-Rousse University Hospital, 69004, Lyon, France
| | - Martin Cour
- Medical Intensive Care Department, Hospices Civils de Lyon, Edouard Herriot Hospital, 69437, Lyon, France
| | - Thomas Rimmelé
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression", Joint Research Unit HCL-bioMérieux, (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), 69003, Lyon, France
- Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, 69437, Lyon, France
| | - Lorna Garnier
- Immunology Laboratory, Hospices Civils de Lyon, Lyon-Sud University Hospital, 69495, Pierre Bénite, France
| | - Hodane Yonis
- Medical Intensive Care Department, Hospices Civils de Lyon, Croix-Rousse University Hospital, 69004, Lyon, France
| | - Remy Coudereau
- Immunology Laboratory, Hospices Civils de Lyon, Edouard Herriot Hospital, 5 Place d'Arsonval, 69437, Lyon, France
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression", Joint Research Unit HCL-bioMérieux, (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), 69003, Lyon, France
| | - Morgane Gossez
- Immunology Laboratory, Hospices Civils de Lyon, Edouard Herriot Hospital, 5 Place d'Arsonval, 69437, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude, Bernard-Lyon 1, Lyon, France
| | - Christophe Malcus
- Immunology Laboratory, Hospices Civils de Lyon, Edouard Herriot Hospital, 5 Place d'Arsonval, 69437, Lyon, France
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression", Joint Research Unit HCL-bioMérieux, (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), 69003, Lyon, France
| | - Florent Wallet
- Intensive Care Department, Hospices Civils de Lyon, Lyon-Sud University Hospital, 69495, Pierre-Bénite, France
| | - Marie-Charlotte Delignette
- Anesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Croix-Rousse University Hospital, 69004, Lyon, France
| | - Frederic Dailler
- Neurological Anesthesiology and Intensive Care Department, Hospices Civils de Lyon, Pierre Wertheimer Hospital, Lyon, France
| | - Marielle Buisson
- Centre d'Investigation Clinique de Lyon (CIC 1407 Inserm), Hospices Civils de Lyon, Lyon, France
| | - Laurent Argaud
- Medical Intensive Care Department, Hospices Civils de Lyon, Croix-Rousse University Hospital, 69004, Lyon, France
| | - Anne-Claire Lukaszewicz
- EA 7426 "Pathophysiology of Injury-Induced Immunosuppression", Joint Research Unit HCL-bioMérieux, (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon - bioMérieux), 69003, Lyon, France
- Medical Intensive Care Department, Hospices Civils de Lyon, Edouard Herriot Hospital, 69437, Lyon, France
| | - Fabienne Venet
- Immunology Laboratory, Hospices Civils de Lyon, Edouard Herriot Hospital, 5 Place d'Arsonval, 69437, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude, Bernard-Lyon 1, Lyon, France
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7
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Caligola S, Giacobazzi L, Canè S, Vella A, Adamo A, Ugel S, Giugno R, Bronte V. GateMeClass: Gate Mining and Classification of cytometry data. Bioinformatics 2024; 40:btae322. [PMID: 38775676 PMCID: PMC11136448 DOI: 10.1093/bioinformatics/btae322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/28/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
MOTIVATION Cytometry comprises powerful techniques for analyzing the cell heterogeneity of a biological sample by examining the expression of protein markers. These technologies impact especially the field of oncoimmunology, where cell identification is essential to analyze the tumor microenvironment. Several classification tools have been developed for the annotation of cytometry datasets, which include supervised tools that require a training set as a reference (i.e. reference-based) and semisupervised tools based on the manual definition of a marker table. The latter is closer to the traditional annotation of cytometry data based on manual gating. However, they require the manual definition of a marker table that cannot be extracted automatically in a reference-based fashion. Therefore, we are lacking methods that allow both classification approaches while maintaining the high biological interpretability given by the marker table. RESULTS We present a new tool called GateMeClass (Gate Mining and Classification) which overcomes the limitation of the current methods of classification of cytometry data allowing both semisupervised and supervised annotation based on a marker table that can be defined manually or extracted from an external annotated dataset. We measured the accuracy of GateMeClass for annotating three well-established benchmark mass cytometry datasets and one flow cytometry dataset. The performance of GateMeClass is comparable to reference-based methods and marker table-based techniques, offering greater flexibility and rapid execution times. AVAILABILITY AND IMPLEMENTATION GateMeClass is implemented in R language and is publicly available at https://github.com/simo1c/GateMeClass.
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Affiliation(s)
| | - Luca Giacobazzi
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | - Stefania Canè
- Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Antonio Vella
- Section of Immunology, Azienda Ospedaliera Universitaria Integrata (AOUI), Verona, Italy
| | - Annalisa Adamo
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | - Stefano Ugel
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
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8
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Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. J Clin Invest 2024; 134:e176640. [PMID: 38690733 PMCID: PMC11060740 DOI: 10.1172/jci176640] [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: 10/26/2023] [Accepted: 03/12/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUNDPatients hospitalized for COVID-19 exhibit diverse clinical outcomes, with outcomes for some individuals diverging over time even though their initial disease severity appears similar to that of other patients. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity.METHODSWe performed deep immunophenotyping and conducted longitudinal multiomics modeling, integrating 10 assays for 1,152 Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study participants and identifying several immune cascades that were significant drivers of differential clinical outcomes.RESULTSIncreasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, formation of neutrophil extracellular traps, and T cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma Igs and B cells and dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to failure of viral clearance in patients with fatal illness.CONCLUSIONOur longitudinal multiomics profiling study revealed temporal coordination across diverse omics that potentially explain the disease progression, providing insights that can inform the targeted development of therapies for patients hospitalized with COVID-19, especially those who are critically ill.TRIAL REGISTRATIONClinicalTrials.gov NCT04378777.FUNDINGNIH (5R01AI135803-03, 5U19AI118608-04, 5U19AI128910-04, 4U19AI090023-11, 4U19AI118610-06, R01AI145835-01A1S1, 5U19AI062629-17, 5U19AI057229-17, 5U19AI125357-05, 5U19AI128913-03, 3U19AI077439-13, 5U54AI142766-03, 5R01AI104870-07, 3U19AI089992-09, 3U19AI128913-03, and 5T32DA018926-18); NIAID, NIH (3U19AI1289130, U19AI128913-04S1, and R01AI122220); and National Science Foundation (DMS2310836).
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Affiliation(s)
| | - Cole Maguire
- The University of Texas at Austin, Austin, Texas, USA
| | | | - Pramod Shinde
- La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Casey P. Shannon
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Providence Research, Vancouver, British Columbia, Canada
| | - Leqi Xu
- Yale School of Public Health, New Haven, Connecticut, USA
| | - Annmarie Hoch
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Elias K. Haddad
- Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA
| | - IMPACC Network
- The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) Network is detailed in Supplemental Acknowledgments
| | - Elaine F. Reed
- David Geffen School of Medicine at the UCLA, Los Angeles, California, USA
| | - Monica Kraft
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Grace A. McComsey
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Jordan P. Metcalf
- Oklahoma University Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Al Ozonoff
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Charles B. Cairns
- Drexel University, Tower Health Hospital, Philadelphia, Pennsylvania, USA
| | | | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Lindsey B. Rosen
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | | | - Hanno Steen
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Ofer Levy
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Bali Pulendran
- Stanford University School of Medicine, Palo Alto, California, USA
| | - Joann Diray-Arce
- Clinical and Data Coordinating Center (CDCC) and
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kinga K. Smolen
- Precision Vaccines Program, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Rafick P. Sekaly
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | | | - Slim Fourati
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, UCSD, La Jolla, California, USA
| | | | - Leying Guan
- Yale School of Public Health, New Haven, Connecticut, USA
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9
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Goonewardena SN, Chen Q, Tate AM, Grushko OG, Damodaran D, Blakely P, Hayek SS, Pinsky DJ, Rosenson RS. Monocyte-Mediated Thrombosis Linked to Circulating Tissue Factor and Immune Paralysis in COVID-19. Arterioscler Thromb Vasc Biol 2024; 44:1124-1134. [PMID: 38511328 PMCID: PMC11043007 DOI: 10.1161/atvbaha.122.318721] [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: 11/03/2022] [Accepted: 02/29/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND SARS-CoV-2 infections cause COVID-19 and are associated with inflammation, coagulopathy, and high incidence of thrombosis. Myeloid cells help coordinate the initial immune response in COVID-19. Although we appreciate that myeloid cells lie at the nexus of inflammation and thrombosis, the mechanisms that unite the two in COVID-19 remain largely unknown. METHODS In this study, we used systems biology approaches including proteomics, transcriptomics, and mass cytometry to define the circulating proteome and circulating immune cell phenotypes in subjects with COVID-19. RESULTS In a cohort of subjects with COVID-19 (n=35), circulating markers of inflammation (CCL23 [C-C motif chemokine ligand 23] and IL [interleukin]-6) and vascular dysfunction (ACE2 [angiotensin-converting enzyme 2] and TF [tissue factor]) were elevated in subjects with severe compared with mild COVID-19. Additionally, although the total white blood cell counts were similar between COVID-19 groups, CD14+ (cluster of differentiation) monocytes from subjects with severe COVID-19 expressed more TF. At baseline, transcriptomics demonstrated increased IL-6, CCL3, ACOD1 (aconitate decarboxylase 1), C5AR1 (complement component 5a receptor), C5AR2, and TF in subjects with severe COVID-19 compared with controls. Using stress transcriptomics, we found that circulating immune cells from subjects with severe COVID-19 had evidence of profound immune paralysis with greatly reduced transcriptional activation and release of inflammatory markers in response to TLR (Toll-like receptor) activation. Finally, sera from subjects with severe (but not mild) COVID-19 activated human monocytes and induced TF expression. CONCLUSIONS Taken together, these observations further elucidate the pathological mechanisms that underlie immune dysfunction and coagulation abnormalities in COVID-19, contributing to our growing understanding of SARS-CoV-2 infections that could also be leveraged to develop novel diagnostic and therapeutic strategies.
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Affiliation(s)
- Sascha N. Goonewardena
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of MichiganAnn Arbor, Michigan, USA
| | - Qinzhong Chen
- Metabolism and Lipids Unit, Cardiovascular Institute, Marie-Josee and Henry R Kravis Center for Cardiovascular Health, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Ashley M. Tate
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of MichiganAnn Arbor, Michigan, USA
| | - Olga G Grushko
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of MichiganAnn Arbor, Michigan, USA
| | - Dilna Damodaran
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of MichiganAnn Arbor, Michigan, USA
| | - Pennelope Blakely
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of MichiganAnn Arbor, Michigan, USA
| | - Salim S. Hayek
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of MichiganAnn Arbor, Michigan, USA
| | - David J. Pinsky
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of MichiganAnn Arbor, Michigan, USA
| | - Robert S. Rosenson
- Metabolism and Lipids Unit, Cardiovascular Institute, Marie-Josee and Henry R Kravis Center for Cardiovascular Health, Icahn School of Medicine at Mount Sinai, New York, USA
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10
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Baker PJ, Bohrer AC, Castro E, Amaral EP, Snow-Smith M, Torres-Juárez F, Gould ST, Queiroz ATL, Fukutani ER, Jordan CM, Khillan JS, Cho K, Barber DL, Andrade BB, Johnson RF, Hilligan KL, Mayer-Barber KD. The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586885. [PMID: 38585846 PMCID: PMC10996686 DOI: 10.1101/2024.03.27.586885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
SARS-CoV-2 infection leads to vastly divergent clinical outcomes ranging from asymptomatic infection to fatal disease. Co-morbidities, sex, age, host genetics and vaccine status are known to affect disease severity. Yet, how the inflammatory milieu of the lung at the time of SARS-CoV-2 exposure impacts the control of viral replication remains poorly understood. We demonstrate here that immune events in the mouse lung closely preceding SARS-CoV-2 infection significantly impact viral control and we identify key innate immune pathways required to limit viral replication. A diverse set of pulmonary inflammatory stimuli, including resolved antecedent respiratory infections with S. aureus or influenza, ongoing pulmonary M. tuberculosis infection, ovalbumin/alum-induced asthma or airway administration of defined TLR ligands and recombinant cytokines, all establish an antiviral state in the lung that restricts SARS-CoV-2 replication upon infection. In addition to antiviral type I interferons, the broadly inducible inflammatory cytokines TNFα and IL-1 precondition the lung for enhanced viral control. Collectively, our work shows that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and suggests that heterogeneity in pulmonary inflammation that precedes or accompanies SARS-CoV-2 exposure may be a significant factor contributing to the population-wide variability in COVID-19 disease outcomes.
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Affiliation(s)
- Paul J. Baker
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Current Address: Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Andrea C. Bohrer
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Ehydel Castro
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Eduardo P. Amaral
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Maryonne Snow-Smith
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
- Human Eosinophil Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Flor Torres-Juárez
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Sydnee T. Gould
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
- Current Address: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Artur T. L. Queiroz
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Bahia 41810-710, Brazil
- Laboratory of Clinical and Translational Research, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia 40296-710, Brazil
| | - Eduardo R. Fukutani
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Bahia 41810-710, Brazil
- Laboratory of Clinical and Translational Research, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia 40296-710, Brazil
| | - Cassandra M. Jordan
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Jaspal S. Khillan
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, NIAID, NIH, Rockville, Maryland 20852, USA
| | - Kyoungin Cho
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, NIAID, NIH, Rockville, Maryland 20852, USA
| | - Daniel L. Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Bruno B. Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research Initiative, Salvador, Bahia 41810-710, Brazil
- Laboratory of Clinical and Translational Research, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia 40296-710, Brazil
| | - Reed F. Johnson
- SCV2 Virology Core, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Kerry L. Hilligan
- Malaghan Institute of Medical Research, Wellington 6012, New Zealand
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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11
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Liu W, Li W, Zhao Z. Single-Cell Transcriptomics Reveals Pre-existing COVID-19 Vulnerability Factors in Lung Cancer Patients. Mol Cancer Res 2024; 22:240-253. [PMID: 38063850 PMCID: PMC10922768 DOI: 10.1158/1541-7786.mcr-23-0692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/09/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Coronavirus disease 2019 (COVID-19) and cancer are major health threats, and individuals may develop both simultaneously. Recent studies have indicated that patients with cancer are particularly vulnerable to COVID-19, but the molecular mechanisms underlying the associations remain poorly understood. To address this knowledge gap, we collected single-cell RNA-sequencing data from COVID-19, lung adenocarcinoma, small cell lung carcinoma patients, and normal lungs to perform an integrated analysis. We characterized altered cell populations, gene expression, and dysregulated intercellular communication in diseases. Our analysis identified pathologic conditions shared by COVID-19 and lung cancer, including upregulated TMPRSS2 expression in epithelial cells, stronger inflammatory responses mediated by macrophages, increased T-cell response suppression, and elevated fibrosis risk by pathologic fibroblasts. These pre-existing conditions in patients with lung cancer may lead to more severe inflammation, fibrosis, and weakened adaptive immune response upon COVID-19 infection. Our findings revealed potential molecular mechanisms driving an increased COVID-19 risk in patients with lung cancer and suggested preventive and therapeutic targets for COVID-19 in this population. IMPLICATIONS Our work reveals the potential molecular mechanisms contributing to the vulnerability to COVID-19 in patients with lung cancer.
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Affiliation(s)
- Wendao Liu
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wenbo Li
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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12
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Takashima Y, Inaba T, Matsuyama T, Yoshii K, Tanaka M, Matsumoto K, Sudo K, Tokuda Y, Omi N, Nakano M, Nakaya T, Fujita N, Sotozono C, Sawa T, Tashiro K, Ohta B. Potential marker subset of blood-circulating cytokines on hematopoietic progenitor-to-Th1 pathway in COVID-19. Front Med (Lausanne) 2024; 11:1319980. [PMID: 38476443 PMCID: PMC10927758 DOI: 10.3389/fmed.2024.1319980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/31/2024] [Indexed: 03/14/2024] Open
Abstract
In this study, we analyzed a relatively large subset of proteins, including 109 kinds of blood-circulating cytokines, and precisely described a cytokine storm in the expression level and the range of fluctuations during hospitalization for COVID-19. Of the proteins analyzed in COVID-19, approximately 70% were detected with Bonferroni-corrected significant differences in comparison with disease severity, clinical outcome, long-term hospitalization, and disease progression and recovery. Specifically, IP-10, sTNF-R1, sTNF-R2, sCD30, sCD163, HGF, SCYB16, IL-16, MIG, SDF-1, and fractalkine were found to be major components of the COVID-19 cytokine storm. Moreover, the 11 cytokines (i.e., SDF-1, SCYB16, sCD30, IL-11, IL-18, IL-8, IFN-γ, TNF-α, sTNF-R2, M-CSF, and I-309) were associated with the infection, mortality, disease progression and recovery, and long-term hospitalization. Increased expression of these cytokines could be explained in sequential pathways from hematopoietic progenitor cell differentiation to Th1-derived hyperinflammation in COVID-19, which might also develop a novel strategy for COVID-19 therapy with recombinant interleukins and anti-chemokine drugs.
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Affiliation(s)
- Yasuo Takashima
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tohru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tasuku Matsuyama
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kengo Yoshii
- Department of Mathematics and Statistics in Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masami Tanaka
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazumichi Matsumoto
- Faculty of Clinical Laboratory, University Hospital Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuki Sudo
- Department of Anesthesiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuichi Tokuda
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Natsue Omi
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naohisa Fujita
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Teiji Sawa
- Department of Anesthesiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- University Hospital Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Bon Ohta
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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13
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Chung KP, Su JY, Wang YF, Budiarto BR, Yeh YC, Cheng JC, Keng LT, Chen YJ, Lu YT, Juan YH, Nakahira K, Ruan SY, Chien JY, Chang HT, Jerng JS, Huang YT, Chen SY, Yu CJ. Immunometabolic features of natural killer cells are associated with infection outcomes in critical illness. Front Immunol 2024; 15:1334882. [PMID: 38426112 PMCID: PMC10902670 DOI: 10.3389/fimmu.2024.1334882] [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: 11/08/2023] [Accepted: 01/10/2024] [Indexed: 03/02/2024] Open
Abstract
Immunosuppression increases the risk of nosocomial infection in patients with chronic critical illness. This exploratory study aimed to determine the immunometabolic signature associated with nosocomial infection during chronic critical illness. We prospectively recruited patients who were admitted to the respiratory care center and who had received mechanical ventilator support for more than 10 days in the intensive care unit. The study subjects were followed for the occurrence of nosocomial infection until 6 weeks after admission, hospital discharge, or death. The cytokine levels in the plasma samples were measured. Single-cell immunometabolic regulome profiling by mass cytometry, which analyzed 16 metabolic regulators in 21 immune subsets, was performed to identify immunometabolic features associated with the risk of nosocomial infection. During the study period, 37 patients were enrolled, and 16 patients (43.2%) developed nosocomial infection. Unsupervised immunologic clustering using multidimensional scaling and logistic regression analyses revealed that expression of nuclear respiratory factor 1 (NRF1) and carnitine palmitoyltransferase 1a (CPT1a), key regulators of mitochondrial biogenesis and fatty acid transport, respectively, in natural killer (NK) cells was significantly associated with nosocomial infection. Downregulated NRF1 and upregulated CPT1a were found in all subsets of NK cells from patients who developed a nosocomial infection. The risk of nosocomial infection is significantly correlated with the predictive score developed by selecting NK cell-specific features using an elastic net algorithm. Findings were further examined in an independent cohort of COVID-19-infected patients, and the results confirm that COVID-19-related mortality is significantly associated with mitochondria biogenesis and fatty acid oxidation pathways in NK cells. In conclusion, this study uncovers that NK cell-specific immunometabolic features are significantly associated with the occurrence and fatal outcomes of infection in critically ill population, and provides mechanistic insights into NK cell-specific immunity against microbial invasion in critical illness.
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Affiliation(s)
- Kuei-Pin Chung
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jia-Ying Su
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yi-Fu Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Bugi Ratno Budiarto
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Yu-Chang Yeh
- Department of Anesthesiology, National Taiwan University Hospital, Taipei, Taiwan
| | - Jui-Chen Cheng
- Department of Integrated Diagnostics & Therapeutics, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Ta Keng
- Department of Internal Medicine, National Taiwan University Hospital, Hsinchu, Taiwan
| | - Yi-Jung Chen
- Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Ting Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsiu Juan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kiichi Nakahira
- Department of Pharmacology, Nara Medical University, Kashihara, Nara, Japan
| | - Sheng-Yuan Ruan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jung-Yien Chien
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hou-Tai Chang
- Department of Critical Care Medicine, Far Eastern Memorial Hospital, New Taipei, Taiwan
- Department of Industrial Engineering and Management, Yuan Ze University, Taoyuan, Taiwan
| | - Jih-Shuin Jerng
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, Hsinchu, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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14
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Farahmandnejad M, Mosaddeghi P, Dorvash M, Sakhteman A, Negahdaripour M, Faridi P. Correlation of Myeloid-Derived Suppressor Cell Expansion with Upregulated Transposable Elements in Severe COVID-19 Unveiled in Single-Cell RNA Sequencing Reanalysis. Biomedicines 2024; 12:315. [PMID: 38397917 PMCID: PMC10887269 DOI: 10.3390/biomedicines12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/14/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Some studies have investigated the potential role of transposable elements (TEs) in COVID-19 pathogenesis and complications. However, to the best of our knowledge, there is no study to examine the possible association of TE expression in cell functions and its potential role in COVID-19 immune response at the single-cell level. In this study, we reanalyzed single-cell RNA seq data of bronchoalveolar lavage (BAL) samples obtained from six severe COVID-19 patients and three healthy donors to assess the probable correlation of TE expression with the immune responses induced by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in COVID-19 patients. Our findings indicate that the expansion of myeloid-derived suppressor cells (MDSCs) may be a characteristic feature of COVID-19. Additionally, a significant increase in TE expression in MDSCs was observed. This upregulation of TEs in COVID-19 may be linked to the adaptability of these cells in response to their microenvironments. Furthermore, it appears that the identification of overexpressed TEs by pattern recognition receptors (PRRs) in MDSCs may enhance the suppressive capacity of these cells. Thus, this study emphasizes the crucial role of TEs in the functionality of MDSCs during COVID-19.
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Affiliation(s)
- Mitra Farahmandnejad
- Quality Control of Drug Products Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran;
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
| | - Pouria Mosaddeghi
- Medicinal Plants Processing Research Center, School of Pharmacy, Shiraz University of Medical Science, Shiraz 71348-14336, Iran;
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
| | - Mohammadreza Dorvash
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia;
| | - Amirhossein Sakhteman
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 80333 Munich, Germany;
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Platform, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3800, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
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15
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Duijvelaar E, Gisby J, Peters JE, Bogaard HJ, Aman J. Longitudinal plasma proteomics reveals biomarkers of alveolar-capillary barrier disruption in critically ill COVID-19 patients. Nat Commun 2024; 15:744. [PMID: 38272877 PMCID: PMC10811341 DOI: 10.1038/s41467-024-44986-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
The pathobiology of respiratory failure in COVID-19 consists of a complex interplay between viral cytopathic effects and a dysregulated host immune response. In critically ill patients, imatinib treatment demonstrated potential for reducing invasive ventilation duration and mortality. Here, we perform longitudinal profiling of 6385 plasma proteins in 318 hospitalised patients to investigate the biological processes involved in critical COVID-19, and assess the effects of imatinib treatment. Nine proteins measured at hospital admission accurately predict critical illness development. Next to dysregulation of inflammation, critical illness is characterised by pathways involving cellular adhesion, extracellular matrix turnover and tissue remodelling. Imatinib treatment attenuates protein perturbations associated with inflammation and extracellular matrix turnover. These proteomic alterations are contextualised using external pulmonary RNA-sequencing data of deceased COVID-19 patients and imatinib-treated Syrian hamsters. Together, we show that alveolar capillary barrier disruption in critical COVID-19 is reflected in the plasma proteome, and is attenuated with imatinib treatment. This study comprises a secondary analysis of both clinical data and plasma samples derived from a clinical trial that was registered with the EU Clinical Trials Register (EudraCT 2020-001236-10, https://www.clinicaltrialsregister.eu/ctr-search/trial/2020-001236-10/NL ) and Netherlands Trial Register (NL8491, https://www.trialregister.nl/trial/8491 ).
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Affiliation(s)
- Erik Duijvelaar
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands.
| | - Jack Gisby
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, UK
| | - James E Peters
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, UK
| | - Harm Jan Bogaard
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Jurjan Aman
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands.
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16
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Wiencke JK, Nissen E, Koestler DC, Tamaki SJ, Tamaki CM, Hansen HM, Warrier G, Hadad S, McCoy L, Rice T, Clarke J, Taylor JW, Salas LA, Christensen BC, Kelsey KT, Butler R, Molinaro AM. Enrichment of a neutrophil-like monocyte transcriptional state in glioblastoma myeloid suppressor cells. RESEARCH SQUARE 2023:rs.3.rs-3793353. [PMID: 38234734 PMCID: PMC10793488 DOI: 10.21203/rs.3.rs-3793353/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glioblastomas (GBM) are lethal central nervous system cancers associated with tumor and systemic immunosuppression. Heterogeneous monocyte myeloid-derived suppressor cells (M-MDSC) are implicated in the altered immune response in GBM, but M-MDSC ontogeny and definitive phenotypic markers are unknown. Using single-cell transcriptomics, we revealed heterogeneity in blood M-MDSC from GBM subjects and an enrichment in a transcriptional state reminiscent of neutrophil-like monocytes (NeuMo), a newly described pathway of monopoiesis in mice. Human NeuMo gene expression and Neu-like deconvolution fraction algorithms were created to quantitate the enrichment of this transcriptional state in GBM subjects. NeuMo populations were also observed in M-MDSCs from lung and head and neck cancer subjects. Dexamethasone (DEX) and prednisone exposures increased the usage of Neu-like states, which were inversely associated with tumor purity and survival in isocitrate dehydrogenase wildtype (IDH WT) gliomas. Anti-inflammatory ZC3HA12/Regnase-1 transcripts were highly correlated with NeuMo expression in tumors and in blood M-MDSC from GBM, lung, and head and neck cancer subjects. Additional novel transcripts of immune-modulating proteins were identified. Collectively, these findings provide a framework for understanding the heterogeneity of M-MDSCs in GBM as cells with different clonal histories and may reshape approaches to study and therapeutically target these cells.
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Affiliation(s)
- J K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Emily Nissen
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS
| | - Stan J Tamaki
- Parnassus Flow Cytometry CoLab, University of California San Francisco, San Francisco, CA 94143-0511, USA
| | - Courtney M Tamaki
- Parnassus Flow Cytometry CoLab, University of California San Francisco, San Francisco, CA 94143-0511, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Sara Hadad
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Jennifer Clarke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Rondi Butler
- Department of Epidemiology, Brown University, Providence, RI
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
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17
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Wang Y, Shen M, Li Y, Shao J, Zhang F, Guo M, Zhang Z, Zheng S. COVID-19-associated liver injury: Adding fuel to the flame. Cell Biochem Funct 2023; 41:1076-1092. [PMID: 37947373 DOI: 10.1002/cbf.3883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/12/2023]
Abstract
COVID-19 is mainly characterized by respiratory disorders and progresses to multiple organ involvement in severe cases. With expansion of COVID-19 and SARS-CoV-2 research, correlative liver injury has been revealed. It is speculated that COVID-19 patients exhibited abnormal liver function, as previously observed in the SARS and MERS pandemics. Furthermore, patients with underlying diseases such as chronic liver disease are more susceptible to SARS-CoV-2 and indicate a poor prognosis accompanied by respiratory symptoms, systemic inflammation, or metabolic diseases. Therefore, COVID-19 has the potential to impair liver function, while individuals with preexisting liver disease suffer from much worse infected conditions. COVID-19 related liver injury may be owing to direct cytopathic effect, immune dysfunction, gut-liver axis interaction, and inappropriate medication use. However, discussions on these issues are infancy. Expanding research have revealed that angiotensin converting enzyme 2 (ACE2) expression mediated the combination of virus and target cells, iron metabolism participated in the virus life cycle and the fate of target cells, and amino acid metabolism regulated immune response in the host cells, which are all closely related to liver health. Further exploration holds great significance in elucidating the pathogenesis, facilitating drug development, and advancing clinical treatment of COVID-19-related liver injury. This article provides a review of the clinical and laboratory hepatic characteristics in COVID-19 patients, describes the etiology and impact of liver injury, and discusses potential pathophysiological mechanisms.
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Affiliation(s)
- Yingqian Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Therapeutic Material of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Min Shen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Yujia Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Therapeutic Material of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiangjuan Shao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Therapeutic Material of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Feng Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Therapeutic Material of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mei Guo
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Therapeutic Material of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zili Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Therapeutic Material of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shizhong Zheng
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Key Laboratory of Therapeutic Material of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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18
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Angioni R, Bonfanti M, Caporale N, Sánchez-Rodríguez R, Munari F, Savino A, Pasqualato S, Buratto D, Pagani I, Bertoldi N, Zanon C, Ferrari P, Ricciardelli E, Putaggio C, Ghezzi S, Elli F, Rotta L, Scardua A, Weber J, Cecatiello V, Iorio F, Zonta F, Cattelan AM, Vicenzi E, Vannini A, Molon B, Villa CE, Viola A, Testa G. RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity. Cell Rep Med 2023; 4:101266. [PMID: 37944530 PMCID: PMC10694673 DOI: 10.1016/j.xcrm.2023.101266] [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: 07/08/2022] [Revised: 03/16/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges because of subsequent waves and long-term consequences of great concern. Here, we chart the molecular basis of COVID-19 pathogenesis by analyzing patients' immune responses at single-cell resolution across disease course and severity. This approach confirms cell subpopulation-specific dysregulation in COVID-19 across disease course and severity and identifies a severity-associated activation of the receptor for advanced glycation endproducts (RAGE) pathway in monocytes. In vitro THP1-based experiments indicate that monocytes bind the SARS-CoV-2 S1-receptor binding domain (RBD) via RAGE, pointing to RAGE-Spike interaction enabling monocyte infection. Thus, our results demonstrate that RAGE is a functional receptor of SARS-CoV-2 contributing to COVID-19 severity.
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Affiliation(s)
- Roberta Angioni
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Matteo Bonfanti
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Nicolò Caporale
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Ricardo Sánchez-Rodríguez
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Fabio Munari
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Aurora Savino
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | | | - Damiano Buratto
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Nicole Bertoldi
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Carlo Zanon
- Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Paolo Ferrari
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | | | - Cristina Putaggio
- Infectious Disease Unit, Padova University Hospital, 35128 Padova, Italy
| | - Silvia Ghezzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Francesco Elli
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
| | - Luca Rotta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | | | - Janine Weber
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | | | - Francesco Iorio
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | | | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Barbara Molon
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy
| | - Carlo Emanuele Villa
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Antonella Viola
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Fondazione Istituto di Ricerca Pediatrica - Città Della Speranza, 35127 Padova, Italy.
| | - Giuseppe Testa
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy.
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19
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Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L. Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565292. [PMID: 37986828 PMCID: PMC10659275 DOI: 10.1101/2023.11.03.565292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.
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20
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Hackney JA, Shivram H, Vander Heiden J, Overall C, Orozco L, Gao X, Kim E, West N, Qamra A, Chang D, Chakrabarti A, Choy DF, Combes AJ, Courau T, Fragiadakis GK, Rao AA, Ray A, Tsui J, Hu K, Kuhn NF, Krummel MF, Erle DJ, Kangelaris K, Sarma A, Lyon Z, Calfee CS, Woodruff PG, Ghale R, Mick E, Byrne A, Zha BS, Langelier C, Hendrickson CM, van der Wijst MG, Hartoularos GC, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Ye CJ, Ramalingam T, McBride JM, Cai F, Teterina A, Bao M, Tsai L, Rosas IO, Regev A, Kapadia SB, Bauer RN, Rosenberger CM. A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling. iScience 2023; 26:107813. [PMID: 37810211 PMCID: PMC10551843 DOI: 10.1016/j.isci.2023.107813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/12/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Altered myeloid inflammation and lymphopenia are hallmarks of severe infections. We identified the upregulated EN-RAGE gene program in airway and blood myeloid cells from patients with acute lung injury from SARS-CoV-2 or other causes across 7 cohorts. This program was associated with greater clinical severity and predicted future mechanical ventilation and death. EN-RAGEhi myeloid cells express features consistent with suppressor cell functionality, including low HLA-DR and high PD-L1. Sustained EN-RAGE program expression in airway and blood myeloid cells correlated with clinical severity and increasing expression of T cell dysfunction markers. IL-6 upregulated many EN-RAGE program genes in monocytes in vitro. IL-6 signaling blockade by tocilizumab in a placebo-controlled clinical trial led to rapid normalization of EN-RAGE and T cell gene expression. This identifies IL-6 as a key driver of myeloid dysregulation associated with worse clinical outcomes in COVID-19 patients and provides insights into shared pathophysiological mechanisms in non-COVID-19 ARDS.
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Affiliation(s)
| | - Haridha Shivram
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Chris Overall
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Luz Orozco
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xia Gao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Kim
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nathan West
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Aditi Qamra
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Diana Chang
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - David F. Choy
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Tristan Courau
- University of California San Francisco, San Francisco, CA, USA
| | | | - Arjun Arkal Rao
- University of California San Francisco, San Francisco, CA, USA
| | - Arja Ray
- University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- University of California San Francisco, San Francisco, CA, USA
| | - Kenneth Hu
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - David J. Erle
- University of California San Francisco, San Francisco, CA, USA
| | | | - Aartik Sarma
- University of California San Francisco, San Francisco, CA, USA
| | - Zoe Lyon
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Rajani Ghale
- University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- University of California San Francisco, San Francisco, CA, USA
| | - Ashley Byrne
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Monique G.P. van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tianna Grant
- University of California San Francisco, San Francisco, CA, USA
| | - Raymund Bueno
- University of California San Francisco, San Francisco, CA, USA
| | - David S. Lee
- University of California San Francisco, San Francisco, CA, USA
| | | | - Yang Sun
- University of California San Francisco, San Francisco, CA, USA
| | - Richard Perez
- University of California San Francisco, San Francisco, CA, USA
| | | | - Alyssa Ward
- University of California San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Fang Cai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anastasia Teterina
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Min Bao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Larry Tsai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivan O. Rosas
- Baylor College of Medicine, 7200 Cambridge St, Houston, TX 77030, USA
| | - Aviv Regev
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
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21
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Chilosi M, Doglioni C, Ravaglia C, Piciucchi S, Dubini A, Stefanizzi L, Poletti V. COVID-19. Biology, pathophysiology, and immunology: a pathologist view. Pathologica 2023; 115:248-256. [PMID: 38054899 DOI: 10.32074/1591-951x-954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 12/07/2023] Open
Abstract
Even if the SARS-CoV-2 pandemic has been declared over, several risks and clinical problems remain to be faced, including long-COVID sequelae and possible outbreaks of pathogenic variants. Intense research on COVID-19 has provided in these few years a striking amount of data covering different fields and disciplines, which can help to provide a knowledge shield against new potential infective spreads, and may also potentially be applied to other fields of medicine, including oncology and neurology. Nevertheless, areas of uncertainty still remain regarding the pathogenic mechanisms that subtend the multifaceted manifestations of the disease. To better clarify the pathogenesis of the disease, a systematic multidisciplinary evaluation of the many mechanisms involved in COVID-19 is mandatory, including clinical, physiological, radiological, immunological and pathological studies. In COVID-19 syndrome the pathological studies have been mainly performed on autopsy cases, and only a few studies are available on biopsies. Nevertheless, these studies have provided relevant information that can substantially contribute to decipher the complex scenario characterizing the different forms of COVID-19 and long-COVID-19. In this review the data provided by pathological investigations are recapitulated and discussed, in the light of different hypothesis and data provided by clinical, physiological and immunological data.
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Affiliation(s)
- Marco Chilosi
- Department of Pathology, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Claudio Doglioni
- Department of Pathology, San Raffaele Scientific Institute. Milan, Italy
| | - Claudia Ravaglia
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Sara Piciucchi
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | | | | | - Venerino Poletti
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
- Department of Pathology, Ospedale GB Morgagni, Forlì, Italy
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22
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Tang SW, Helmeste DM, Leonard BE. COVID-19 as a polymorphic inflammatory spectrum of diseases: a review with focus on the brain. Acta Neuropsychiatr 2023; 35:248-269. [PMID: 36861428 DOI: 10.1017/neu.2023.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
There appear to be huge variations and aberrations in the reported data in COVID-19 2 years now into the pandemic. Conflicting data exist at almost every level and also in the reported epidemiological statistics across different regions. It is becoming clear that COVID-19 is a polymorphic inflammatory spectrum of diseases, and there is a wide range of inflammation-related pathology and symptoms in those infected with the virus. The host's inflammatory response to COVID-19 appears to be determined by genetics, age, immune status, health status and stage of disease. The interplay of these factors may decide the magnitude, duration, types of pathology, symptoms and prognosis in the spectrum of COVID-19 disorders, and whether neuropsychiatric disorders continue to be significant. Early and successful management of inflammation reduces morbidity and mortality in all stages of COVID-19.
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Affiliation(s)
- Siu Wa Tang
- Department of Psychiatry, University of California, Irvine, Irvine, CA, USA
- Institute of Brain Medicine, Hong Kong, China
| | - Daiga Maret Helmeste
- Department of Psychiatry, University of California, Irvine, Irvine, CA, USA
- Institute of Brain Medicine, Hong Kong, China
| | - Brian E Leonard
- Institute of Brain Medicine, Hong Kong, China
- Department of Pharmacology, National University of Ireland, Galway, Ireland
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23
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Brinjikji W, Kallmes DF, Virmani R, de Meyer SF, Yoo AJ, Humphries W, Zaidat OO, Teleb MS, Jones JG, Siddiqui AH, Andersson T, Nogueira RG, Gil SM, Douglas A, Rossi R, Rentzos A, Ceder E, Carlqvist J, Dunker D, Jood K, Tatlisumak T, Doyle KM. Endotheliitis and cytokine storm as a mechanism of clot formation in COVID-19 ischemic stroke patients: A histopathologic study of retrieved clots. Interv Neuroradiol 2023:15910199231185804. [PMID: 37769315 DOI: 10.1177/15910199231185804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Studies during the COVID-19 pandemic have demonstrated an association between COVID-19 virus infection and the development of acute ischemic stroke, particularly large vessel occlusion (LVO). Studying the characteristics and immunohistochemistry of retrieved stroke emboli during mechanical thrombectomy for LVO may offer insights into the pathogenesis of LVO in COVID-19 patients. We examined retrieved COVID-19 emboli from the STRIP, EXCELLENT, and RESTORE registries and compared their characteristics to a control group. METHODS We identified COVID-positive LVO patients from the STRIP, RESTORE, and EXCELLENT studies who underwent mechanical thrombectomy. These patients were matched to a control group controlling for stroke etiology based on Trial of Org 10172 in Acute Stroke Treatment criteria. All clots were stained with Martius Scarlet Blue (MSB) along with immunohistochemistry for interleukin-6 (IL-6), C-reactive protein (CRP), von Willebrand factor (vWF), CD66b, fibrinogen, and citrullinated Histone H3. Clot composition was compared between groups. RESULTS Nineteen COVID-19-positive patients and 38 controls were included. COVID-19-positive patients had a significantly higher percentage of CRP and vWF. There was no difference in IL-6, fibrin, CD66b, or citrullinated Histone H3 between groups. Based on MSB staining, there was no statistically significant difference regarding the percentage of red blood cells, white blood cells, fibrin, and platelets. CONCLUSIONS Our study found higher concentrations of CRP and vWF in retrieved clots of COVID-19-positive stroke patients compared to COVID-19-negative controls. These findings support the potential role of systemic inflammation as indicated by elevated CRP and endothelial injury as indicated by elevated vWF as precipitating factors in thrombus development in these patients.
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Affiliation(s)
| | | | - Renu Virmani
- Department of Pathology, CVPath Institute, Gaithersburg, MD, USA
| | - Simon F de Meyer
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - Albert J Yoo
- Neurointervention, Texas Stroke Institute, Plano, TX, USA
| | | | - Osama O Zaidat
- Department of Neuroscience, Mercy Health St Vincent Medical Center, Toledo, OH, USA
| | - Mohamed S Teleb
- Neurointerventional Surgery, Stroke, and Neurocritical Care, Banner Health, Mesa, AZ, USA
| | - Jesse G Jones
- Department of Neurosurgery, University of Alabama, Birmingham, AL, USA
| | - Adnan H Siddiqui
- Departments of Neurosurgery and Radiology, State University of New York at Buffalo, New York, NY, USA
| | - Tommy Andersson
- Department of Neuroradiology, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Raul G Nogueira
- Department of Neurology and Neurosurgery, University of Pittsburgh Medical Center, UPMC Stroke Institute, Pittsburgh, PA, USA
| | - Sara Molina Gil
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM-SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Andrew Douglas
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM-SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Rosanna Rossi
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM-SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Alexander Rentzos
- Department of Interventional and Diagnostic Neuroradiology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Erik Ceder
- Department of Interventional and Diagnostic Neuroradiology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Jeanette Carlqvist
- Department of Interventional and Diagnostic Neuroradiology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Dennis Dunker
- Department of Interventional and Diagnostic Neuroradiology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Katarina Jood
- Department of Clinical Neurosciences, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Turgut Tatlisumak
- Department of Clinical Neurosciences, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Karen M Doyle
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM-SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
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24
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Billi AC, Wasikowski R, Ma F, Yalavarthi S, Hoy CK, Zuo Y, Patrick MT, Shah N, Parker C, Aaronson C, Harbaugh A, Lucido MF, Shedden K, Rao K, IglayReger HB, Burant CF, Kahlenberg JM, Tsoi LC, Gudjonsson JE, Knight JS, Kanthi Y. Key patient demographics shape innate immune topography in noncritical hypoxic COVID-19 pneumonia. JCI Insight 2023; 8:e166110. [PMID: 37606044 PMCID: PMC10543737 DOI: 10.1172/jci.insight.166110] [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: 10/10/2022] [Accepted: 07/11/2023] [Indexed: 08/23/2023] Open
Abstract
Risk of severe disease and death due to COVID-19 is increased in certain patient demographic groups, including those of advanced age, male sex, and obese body mass index. Investigations of the biological variations that contribute to this risk have been hampered by heterogeneous severity, with immunologic features of critical disease potentially obscuring differences between risk groups. To examine immune heterogeneity related to demographic risk factors, we enrolled 38 patients hospitalized with clinically homogeneous COVID-19 pneumonia - defined as oxygen saturation less than 94% on room air without respiratory failure, septic shock, or multiple organ dysfunction - and performed single-cell RNA-Seq of leukocytes collected at admission. Examination of individual risk factors identified strong shifts within neutrophil and monocyte/dendritic cell (Mo/DC) compartments, revealing altered immune cell type-specific responses in higher risk COVID-19 patient subgroups. Specifically, we found transcriptional evidence of altered neutrophil maturation in aged versus young patients and enhanced cytokine responses in Mo/DCs of male versus female patients. Such innate immune cell alterations may contribute to outcome differences linked to these risk factors. They also highlight the importance of diverse patient cohorts in studies of therapies targeting the immune response in COVID-19.
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Affiliation(s)
| | | | - Feiyang Ma
- Division of Rheumatology, Department of Internal Medicine
| | | | - Claire K. Hoy
- Division of Rheumatology, Department of Internal Medicine
| | - Yu Zuo
- Division of Rheumatology, Department of Internal Medicine
| | | | - Neha Shah
- Division of Cardiovascular Medicine, Department of Internal Medicine
| | | | - Chad Aaronson
- Division of Rheumatology, Department of Internal Medicine
| | | | | | - Kerby Shedden
- Division of Rheumatology, Department of Internal Medicine
| | - Krishna Rao
- Division of Infectious Disease, Department of Internal Medicine
| | | | - Charles F. Burant
- A. Alfred Taubman Medical Research Institute
- Department of Internal Medicine
- Department of Nutritional Sciences
| | | | - Lam C. Tsoi
- Department of Dermatology
- Department of Computational Medicine and Bioinformatics, and
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Yogendra Kanthi
- Division of Cardiovascular Medicine, Department of Internal Medicine
- Laboratory of Vascular Thrombosis and Inflammation, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
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25
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Hurst JH, Mohan AA, Dalapati T, George IA, Aquino JN, Lugo DJ, Pfeiffer TS, Rodriguez J, Rotta AT, Turner NA, Burke TW, McClain MT, Henao R, DeMarco CT, Louzao R, Denny TN, Walsh KM, Xu Z, Mejias A, Ramilo O, Woods CW, Kelly MS. Differential host responses within the upper respiratory tract and peripheral blood of children and adults with SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.31.23293337. [PMID: 37577568 PMCID: PMC10418569 DOI: 10.1101/2023.07.31.23293337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Age is among the strongest risk factors for severe outcomes from SARS-CoV-2 infection. We sought to evaluate associations between age and both mucosal and systemic host responses to SARS-CoV-2 infection. We profiled the upper respiratory tract (URT) and peripheral blood transcriptomes of 201 participants (age range of 1 week to 83 years), including 137 non-hospitalized individuals with mild SARS-CoV-2 infection and 64 uninfected individuals. Among uninfected children and adolescents, young age was associated with upregulation of innate and adaptive immune pathways within the URT, suggesting that young children are primed to mount robust mucosal immune responses to exogeneous respiratory pathogens. SARS-CoV-2 infection was associated with broad induction of innate and adaptive immune responses within the URT of children and adolescents. Peripheral blood responses among SARS-CoV-2-infected children and adolescents were dominated by interferon pathways, while upregulation of myeloid activation, inflammatory, and coagulation pathways was observed only in adults. Systemic symptoms among SARS-CoV-2-infected subjects were associated with blunted innate and adaptive immune responses in the URT and upregulation of many of these same pathways within peripheral blood. Finally, within individuals, robust URT immune responses were correlated with decreased peripheral immune activation, suggesting that effective immune responses in the URT may promote local viral control and limit systemic immune activation and symptoms. These findings demonstrate that there are differences in immune responses to SARS-CoV-2 across the lifespan, including between young children and adolescents, and suggest that these varied host responses contribute to observed differences in the clinical presentation of SARS-CoV-2 infection by age. One Sentence Summary Age is associated with distinct upper respiratory and peripheral blood transcriptional responses among children and adults with SARS-CoV-2 infection.
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26
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Resende ADS, de Oliveira YLM, de Franca MNF, Magalhães LS, Correa CB, Fukutani KF, Lipscomb MW, de Moura TR. Obesity in Severe COVID-19 Patients Has a Distinct Innate Immune Phenotype. Biomedicines 2023; 11:2116. [PMID: 37626613 PMCID: PMC10452870 DOI: 10.3390/biomedicines11082116] [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: 06/23/2023] [Revised: 07/13/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023] Open
Abstract
Obesity alters the capacity of effective immune responses in infections. To further address this phenomenon in the context of COVID-19, this study investigated how the immunophenotype of leukocytes was altered in individuals with obesity in severe COVID-19. This cross-sectional study enrolled 27 ICU COVID-19 patients (67% women, 56.33 ± 19.55 years) that were assigned to obese (BMI ≥ 30 kg/m2, n = 9) or non-obese (BMI < 30kg/m2, n = 18) groups. Monocytes, NK, and both Low-Density (LD) and High-Density (HD) neutrophils were isolated from peripheral blood samples, and surface receptors' frequency and expression patterns were analyzed by flow cytometry. Clinical status and biochemical data were additionally evaluated. The frequency of monocytes was negatively correlated with BMI, while NK cells and HD neutrophils were positively associated (p < 0.05). Patients with obesity showed a significant reduction of monocytes, and these cells expressed high levels of PD-L1 (p < 0.05). A higher frequency of NK cells and increased expression of TREM-1+ on HD neutrophils were detected in obese patients (p < 0.05). The expression of receptors related to antigen-presentation, phagocytosis, chemotaxis, inflammation and suppression were strongly correlated with clinical markers only in obese patients (p < 0.05). Collectively, these outcomes revealed that obesity differentially affected, and largely depressed, innate immune response in severe COVID-19.
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Affiliation(s)
- Ayane de Sá Resende
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju 49060-100, Sergipe, Brazil; (Y.L.M.d.O.); (M.N.F.d.F.); (L.S.M.); (C.B.C.); (K.F.F.)
| | - Yrna Lorena Matos de Oliveira
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju 49060-100, Sergipe, Brazil; (Y.L.M.d.O.); (M.N.F.d.F.); (L.S.M.); (C.B.C.); (K.F.F.)
| | - Mariana Nobre Farias de Franca
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju 49060-100, Sergipe, Brazil; (Y.L.M.d.O.); (M.N.F.d.F.); (L.S.M.); (C.B.C.); (K.F.F.)
| | - Lucas Sousa Magalhães
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju 49060-100, Sergipe, Brazil; (Y.L.M.d.O.); (M.N.F.d.F.); (L.S.M.); (C.B.C.); (K.F.F.)
- Department of Parasitology and Pathology, ICBS, Federal University of Alagoas, Maceio 57072-900, Alagoas, Brazil
| | - Cristiane Bani Correa
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju 49060-100, Sergipe, Brazil; (Y.L.M.d.O.); (M.N.F.d.F.); (L.S.M.); (C.B.C.); (K.F.F.)
- Physiological Sciences Graduate Program, Federal University of Sergipe, São Cristovao 49100-000, Sergipe, Brazil
| | - Kiyoshi Ferreira Fukutani
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju 49060-100, Sergipe, Brazil; (Y.L.M.d.O.); (M.N.F.d.F.); (L.S.M.); (C.B.C.); (K.F.F.)
| | | | - Tatiana Rodrigues de Moura
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju 49060-100, Sergipe, Brazil; (Y.L.M.d.O.); (M.N.F.d.F.); (L.S.M.); (C.B.C.); (K.F.F.)
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27
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Shaw JA, Malherbe ST, Walzl G, du Plessis N. Suppressive myeloid cells in SARS-CoV-2 and Mycobacterium tuberculosis co-infection. Front Immunol 2023; 14:1222911. [PMID: 37545508 PMCID: PMC10399583 DOI: 10.3389/fimmu.2023.1222911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
Epidemiologic data show that both current and previous tuberculosis (TB) increase the risk of in-hospital mortality from coronavirus disease-2019 (COVID-19), and there is a similar trend for poor outcomes from Mycobacterium tuberculosis (Mtb) infection after recent SARS-CoV-2. A shared dysregulation of immunity explains the dual risk posed by co-infection, but the specific mechanisms are being explored. While initial attention focused on T cell immunity, more comprehensive analyses revealed a dysfunctional innate immune response in COVID-19, characterized by reduced numbers of dendritic cells, NK cells and a redistribution of mononuclear phagocytes towards intermediate myeloid subsets. During hyper- or chronic inflammatory processes, activation signals from molecules such as growth factors and alarmins lead to the expansion of an immature population of myeloid cells called myeloid-deprived suppressor cells (MDSC). These cells enter a state of pathological activation, lose their ability to rapidly clear pathogens, and instead become broadly immunosuppressive. MDSC are enriched in the peripheral blood of patients with severe COVID-19; associated with mortality; and with higher levels of inflammatory cytokines. In TB, MDSC have been implicated in loss of control of Mtb in the granuloma and ineffective innate and T cell immunity to the pathogen. Considering that innate immune sensing serves as first line of both anti-bacterial and anti-viral defence mechanisms, we propose MDSC as a crucial mechanism for the adverse clinical trajectories of TB-COVID-19 coinfection.
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28
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Liu C, Zhang Y, Gao X, Wang G. Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI. BMC Biol 2023; 21:159. [PMID: 37468850 PMCID: PMC10354926 DOI: 10.1186/s12915-023-01658-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) has revolutionized the transcriptomics field by advancing analyses from tissue-level to cell-level resolution. Despite the great advances in the development of computational methods for various steps of scRNA-seq analyses, one major bottleneck of the existing technologies remains in identifying the molecular relationship between disease phenotype and cell subpopulations, where "disease phenotype" refers to the clinical characteristics of each patient sample, and subpopulation refer to groups of single cells, which often do not correspond to clusters identified by standard single-cell clustering analysis. Here, we present PACSI, a method aimed at distinguishing cell subpopulations associated with disease phenotypes at the single-cell level. RESULTS PACSI takes advantage of the topological properties of biological networks to introduce a proximity-based measure that quantifies the correlation between each cell and the disease phenotype of interest. Applied to simulated data and four case studies, PACSI accurately identified cells associated with disease phenotypes such as diagnosis, prognosis, and response to immunotherapy. In addition, we demonstrated that PACSI can also be applied to spatial transcriptomics data and successfully label spots that are associated with poor survival of breast carcinoma. CONCLUSIONS PACSI is an efficient method to identify cell subpopulations associated with disease phenotypes. Our research shows that it has a broad range of applications in revealing mechanistic and clinical insights of diseases.
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Affiliation(s)
- Chonghui Liu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yan Zhang
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China.
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
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29
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Margaroli C, Fram T, Sharma NS, Patel SB, Tipper J, Robison SW, Russell DW, Fortmann SD, Banday MM, Soto-Vazquez Y, Abdalla T, Saitornuang S, Madison MC, Leal SM, Harrod KS, Erdmann NB, Gaggar A. Interferon-dependent signaling is critical for viral clearance in airway neutrophils. JCI Insight 2023; 8:e167042. [PMID: 37071484 PMCID: PMC10322684 DOI: 10.1172/jci.insight.167042] [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: 11/08/2022] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
Neutrophilic inflammation characterizes several respiratory viral infections, including COVID-19-related acute respiratory distress syndrome, although its contribution to disease pathogenesis remains poorly understood. Blood and airway immune cells from 52 patients with severe COVID-19 were phenotyped by flow cytometry. Samples and clinical data were collected at 2 separate time points to assess changes during ICU stay. Blockade of type I interferon and interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) signaling was performed in vitro to determine their contribution to viral clearance in A2 neutrophils. We identified 2 neutrophil subpopulations (A1 and A2) in the airway compartment, where loss of the A2 subset correlated with increased viral burden and reduced 30-day survival. A2 neutrophils exhibited a discrete antiviral response with an increased interferon signature. Blockade of type I interferon attenuated viral clearance in A2 neutrophils and downregulated IFIT3 and key catabolic genes, demonstrating direct antiviral neutrophil function. Knockdown of IFIT3 in A2 neutrophils led to loss of IRF3 phosphorylation, with consequent reduced viral catabolism, providing the first discrete mechanism to our knowledge of type I interferon signaling in neutrophils. The identification of this neutrophil phenotype and its association with severe COVID-19 outcomes emphasizes its likely importance in other respiratory viral infections and potential for new therapeutic approaches in viral illness.
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Affiliation(s)
- Camilla Margaroli
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Program in Protease and Matrix Biology
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Timothy Fram
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nirmal S. Sharma
- Program in Protease and Matrix Biology
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Siddharth B. Patel
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
| | | | - Sarah W. Robison
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Program in Protease and Matrix Biology
| | - Derek W. Russell
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Program in Protease and Matrix Biology
| | | | - Mudassir M. Banday
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Yixel Soto-Vazquez
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Program in Protease and Matrix Biology
| | - Tarek Abdalla
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Program in Protease and Matrix Biology
| | | | - Matthew C. Madison
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Program in Protease and Matrix Biology
| | - Sixto M. Leal
- Department of Pathology, Division of Laboratory Medicine, and
| | | | - Nathaniel B. Erdmann
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Amit Gaggar
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Program in Protease and Matrix Biology
- Lung Health Center and Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Birmingham VA Medical Center, Birmingham, Alabama, USA
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30
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Rombauts A, Bódalo Torruella M, Abelenda-Alonso G, Perera-Bel J, Ferrer-Salvador A, Acedo-Terrades A, Gabarrós-Subirà M, Oriol I, Gudiol C, Nonell L, Carratalà J. Dynamics of Gene Expression Profiling and Identification of High-Risk Patients for Severe COVID-19. Biomedicines 2023; 11:biomedicines11051348. [PMID: 37239019 DOI: 10.3390/biomedicines11051348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of hospitalized adult COVID-19 patients and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with RT-PCR-confirmed SARS-CoV-2 infection, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 h of admission and on day 7. There were 2572 differently expressed genes in patients with ARDS at baseline and 1149 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to an immune regulation loss. This led, in turn, to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in the latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.
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Affiliation(s)
- Alexander Rombauts
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | | | - Gabriela Abelenda-Alonso
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Júlia Perera-Bel
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Anna Ferrer-Salvador
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | - Maria Gabarrós-Subirà
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Isabel Oriol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Carlota Gudiol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Jordi Carratalà
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Koh JY, Ko JH, Lim SY, Bae S, Huh K, Cho SY, Kang CI, Chung DR, Chung CR, Kim SH, Peck KR, Lee JS. Triple immune modulator therapy for aberrant hyperinflammatory responses in severe COVID-19. Clin Immunol 2023; 251:109628. [PMID: 37119951 PMCID: PMC10139747 DOI: 10.1016/j.clim.2023.109628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
A dysregulated hyperinflammatory response is a key pathogenesis of severe COVID-19, but optimal immune modulator treatment has not been established. To evaluate the clinical effectiveness of double (glucocorticoids and tocilizumab) and triple (plus baricitinib) immune modulator therapy for severe COVID-19, a retrospective cohort study was conducted. For the immunologic investigation, a single-cell RNA sequencing analysis was performed in serially collected PBMCs and neutrophil specimens. Triple immune modulator therapy was a significant factor in a multivariable analysis for 30-day recovery. In the scRNA-seq analysis, type I and II IFN response-related pathways were suppressed by GC, and the IL-6-associated signature was additionally downregulated by TOC. Adding BAR to GC and TOC distinctly downregulated the ISGF3 cluster. Adding BAR also regulated the pathologically activated monocyte and neutrophil subpopulation induced by aberrant IFN signals. Triple immune modulator therapy in severe COVID-19 improved 30-day recovery through additional regulation of the aberrant hyperinflammatory immune response.
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Affiliation(s)
| | - Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - So Yun Lim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seongman Bae
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chi Ryang Chung
- Department of Critical Care Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Jeong Seok Lee
- Genome Insight, Inc., San Diego, La Jolla, CA, USA; Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
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Fernández-Moreno R, Valle-Arroyo J, Páez-Vega A, Salinas A, Cano A, Pérez AB, Torre-Cisneros J, Cantisán S. Memory SARS-CoV-2 T-cell response in convalescent COVID-19 patients with undetectable specific IgG antibodies: a comparative study. Front Immunol 2023; 14:1142918. [PMID: 37180143 PMCID: PMC10169638 DOI: 10.3389/fimmu.2023.1142918] [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: 01/12/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023] Open
Abstract
Background During the COVID-19 pandemic, a variable percentage of patients with SARS-CoV-2 infection failed to elicit humoral response. This study investigates whether patients with undetectable SARS-CoV-2 IgG are able to generate SARS-CoV-2 memory T cells with proliferative capacity upon stimulation. Methods This cross-sectional study was conducted with convalescent COVID-19 patients, diagnosed with a positive real-time PCR (RT-PCR) from nasal and pharyngeal swab specimens. COVID-19 patients were enrolled ≥3 months after the last PCR positive. Proliferative T-cell response after whole blood stimulation was assessed using the FASCIA assay. Results A total of 119 participants (86 PCR-confirmed COVID-19 patients and 33 healthy controls) were randomly filtered from an initial cohort. Of these 86 patients, 59 had detectable (seropositive) and 27 had undetectable (seronegative) SARS-CoV-2 IgG. Seropositive patients were subclassified as asymptomatic/mild or severe according to the oxygen supplementation requirement. SARS-CoV-2 CD3+ and CD4+ T cells showed significantly lower proliferative response in seronegative than in seropositive patients. The ROC curve analysis indicated that ≥ 5 CD4+ blasts/μL of blood defined a "positive SARS-CoV-2 T cell response". According to this cut-off, 93.2% of seropositive patients had a positive T-cell response compared to 50% of seronegative patients and 20% of negative controls (chi-square; p < 0.001). Conclusions This proliferative assay is useful not only to discriminate convalescent patients from negative controls, but also to distinguish seropositive patients from those with undetectable SARS-CoV-2 IgG antibodies. Memory T cells in seronegative patients are able to respond to SARSCoV-2 peptides, although at a lower magnitude than seropositive patients.
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Affiliation(s)
- Raquel Fernández-Moreno
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
| | - Jorge Valle-Arroyo
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
| | - Aurora Páez-Vega
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
| | - Ana Salinas
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
| | - Angela Cano
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
- Infectious Diseases Unit, Reina Sofía University Hospital, Cordoba, Spain
| | - Ana B Pérez
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
- Microbiology Unit, Reina Sofía University Hospital, Cordoba, Spain
| | - Julián Torre-Cisneros
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
- Infectious Diseases Unit, Reina Sofía University Hospital, Cordoba, Spain
| | - Sara Cantisán
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofía University Hospital, University of Cordoba, Cordoba, Spain
- Infectious Diseases Unit, Reina Sofía University Hospital, Cordoba, Spain
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Transcriptional reprogramming of infiltrating neutrophils drives lung pathology in severe COVID-19 despite low viral load. Blood Adv 2023; 7:778-799. [PMID: 36399523 PMCID: PMC9906672 DOI: 10.1182/bloodadvances.2022008834] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/28/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022] Open
Abstract
Troubling disparities in COVID-19-associated mortality emerged early, with nearly 70% of deaths confined to Black/African American (AA) patients in some areas. However, targeted studies on this vulnerable population are scarce. Here, we applied multiomics single-cell analyses of immune profiles from matching airways and blood samples of Black/AA patients during acute SARS-CoV-2 infection. Transcriptional reprogramming of infiltrating IFITM2+/S100A12+ mature neutrophils, likely recruited via the IL-8/CXCR2 axis, leads to persistent and self-sustaining pulmonary neutrophilia with advanced features of acute respiratory distress syndrome (ARDS) despite low viral load in the airways. In addition, exacerbated neutrophil production of IL-8, IL-1β, IL-6, and CCL3/4, along with elevated levels of neutrophil elastase and myeloperoxidase, were the hallmarks of transcriptionally active and pathogenic airway neutrophilia. Although our analysis was limited to Black/AA patients and was not designed as a comparative study across different ethnicities, we present an unprecedented in-depth analysis of the immunopathology that leads to acute respiratory distress syndrome in a well-defined patient population disproportionally affected by severe COVID-19.
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34
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Barnett KC, Xie Y, Asakura T, Song D, Liang K, Taft-Benz SA, Guo H, Yang S, Okuda K, Gilmore RC, Loome JF, Oguin Iii TH, Sempowski GD, Randell SH, Heise MT, Lei YL, Boucher RC, Ting JPY. An epithelial-immune circuit amplifies inflammasome and IL-6 responses to SARS-CoV-2. Cell Host Microbe 2023; 31:243-259.e6. [PMID: 36563691 PMCID: PMC9731922 DOI: 10.1016/j.chom.2022.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/12/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Elevated levels of cytokines IL-1β and IL-6 are associated with severe COVID-19. Investigating the underlying mechanisms, we find that while primary human airway epithelia (HAE) have functional inflammasomes and support SARS-CoV-2 replication, they are not the source of IL-1β released upon infection. In leukocytes, the SARS-CoV-2 E protein upregulates inflammasome gene transcription via TLR2 to prime, but not activate, inflammasomes. SARS-CoV-2-infected HAE supply a second signal, which includes genomic and mitochondrial DNA, to stimulate leukocyte IL-1β release. Nuclease treatment, STING, and caspase-1 inhibition but not NLRP3 inhibition blocked leukocyte IL-1β release. After release, IL-1β stimulates IL-6 secretion from HAE. Therefore, infection alone does not increase IL-1β secretion by either cell type. Rather, bi-directional interactions between the SARS-CoV-2-infected epithelium and immune bystanders stimulates both IL-1β and IL-6, creating a pro-inflammatory cytokine circuit. Consistent with these observations, patient autopsy lungs show elevated myeloid inflammasome gene signatures in severe COVID-19.
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Affiliation(s)
- Katherine C Barnett
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yuying Xie
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Takanori Asakura
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dingka Song
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaixin Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Oral and Craniofacial Biomedicine Program, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sharon A Taft-Benz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haitao Guo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shuangshuang Yang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rodney C Gilmore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer F Loome
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Scott H Randell
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yu Leo Lei
- Department of Periodontics and Oral Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48104, USA; Department of Otolaryngology-Head and Neck Surgery, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jenny P-Y Ting
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Wang T, Hu Y, Dusi S, Qi F, Sartoris S, Ugel S, De Sanctis F. "Open Sesame" to the complexity of pattern recognition receptors of myeloid-derived suppressor cells in cancer. Front Immunol 2023; 14:1130060. [PMID: 36911674 PMCID: PMC9992799 DOI: 10.3389/fimmu.2023.1130060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Pattern recognition receptors are primitive sensors that arouse a preconfigured immune response to broad stimuli, including nonself pathogen-associated and autologous damage-associated molecular pattern molecules. These receptors are mainly expressed by innate myeloid cells, including granulocytes, monocytes, macrophages, and dendritic cells. Recent investigations have revealed new insights into these receptors as key players not only in triggering inflammation processes against pathogen invasion but also in mediating immune suppression in specific pathological states, including cancer. Myeloid-derived suppressor cells are preferentially expanded in many pathological conditions. This heterogeneous cell population includes immunosuppressive myeloid cells that are thought to be associated with poor prognosis and impaired response to immune therapies in various cancers. Identification of pattern recognition receptors and their ligands increases the understanding of immune-activating and immune-suppressive myeloid cell functions and sheds light on myeloid-derived suppressor cell differences from cognate granulocytes and monocytes in healthy conditions. This review summarizes the different expression, ligand recognition, signaling pathways, and cancer relations and identifies Toll-like receptors as potential new targets on myeloid-derived suppressor cells in cancer, which might help us to decipher the instruction codes for reverting suppressive myeloid cells toward an antitumor phenotype.
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Affiliation(s)
- Tian Wang
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Yushu Hu
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Silvia Dusi
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Fang Qi
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Silvia Sartoris
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Stefano Ugel
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
| | - Francesco De Sanctis
- Department of Medicine, Section of Immunology, University of Verona, Verona, Italy
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Jiang C, Jiang K, Li X, Zhang N, Zhu W, Meng L, Zhang Y, Lu S. Evaluation of immunoprotection against coronavirus disease 2019: Novel variants, vaccine inoculation, and complications. J Pharm Anal 2023; 13:1-10. [PMID: 36317070 PMCID: PMC9605787 DOI: 10.1016/j.jpha.2022.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022] Open
Abstract
The strikingly rapidly mutating nature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome has been a constant challenge during the coronavirus disease 2019 (COVID-19) pandemic. In this study, various techniques, including reverse transcription-quantitative polymerase chain reaction, antigen-detection rapid diagnostic tests, and high-throughput sequencing were analyzed under different scenarios and spectra for the etiological diagnosis of COVID-19 at the population scale. This study aimed to summarize the latest research progress and provide up-to-date understanding of the methodology used for the evaluation of the immunoprotection conditions against future variants of SARS-CoV-2. Our novel work reviewed the current methods for the evaluation of the immunoprotection status of a specific population (endogenous antibodies) before and after vaccine inoculation (administered with biopharmaceutical antibody products). The present knowledge of the immunoprotection status regarding the COVID-19 complications was also discussed. Knowledge on the immunoprotection status of specific populations can help guide the design of pharmaceutical antibody products, inform practice guidelines, and develop national regulations with respect to the timing of and need for extra rounds of vaccine boosters.
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Affiliation(s)
- Congshan Jiang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Kaichong Jiang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Xiaowei Li
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Ning Zhang
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Wenhua Zhu
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, 710061, China,Institute of Molecular and Translational Medicine (IMTM), and Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Liesu Meng
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, 710061, China,Institute of Molecular and Translational Medicine (IMTM), and Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Yanmin Zhang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China,Corresponding author.
| | - Shemin Lu
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, 710061, China,Corresponding author. National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China.
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López-Martínez C, Martín-Vicente P, Gómez de Oña J, López-Alonso I, Gil-Peña H, Cuesta-Llavona E, Fernández-Rodríguez M, Crespo I, Salgado Del Riego E, Rodríguez-García R, Parra D, Fernández J, Rodríguez-Carrio J, Jimeno-Demuth FJ, Dávalos A, Chapado LA, Coto E, Albaiceta GM, Amado-Rodríguez L. Transcriptomic clustering of critically ill COVID-19 patients. Eur Respir J 2023; 61:13993003.00592-2022. [PMID: 36104291 PMCID: PMC9478362 DOI: 10.1183/13993003.00592-2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/19/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may cause a severe disease, termed coronavirus disease 2019 (COVID-19), with significant mortality. Host responses to this infection, mainly in terms of systemic inflammation, have emerged as key pathogenetic mechanisms and their modulation has shown a mortality benefit. METHODS In a cohort of 56 critically ill COVID-19 patients, peripheral blood transcriptomes were obtained at admission to an intensive care unit (ICU) and clustered using an unsupervised algorithm. Differences in gene expression, circulating microRNAs (c-miRNAs) and clinical data between clusters were assessed, and circulating cell populations estimated from sequencing data. A transcriptomic signature was defined and applied to an external cohort to validate the findings. RESULTS We identified two transcriptomic clusters characterised by expression of either interferon-related or immune checkpoint genes, respectively. Steroids have cluster-specific effects, decreasing lymphocyte activation in the former but promoting B-cell activation in the latter. These profiles have different ICU outcomes, despite no major clinical differences at ICU admission. A transcriptomic signature was used to identify these clusters in two external validation cohorts (with 50 and 60 patients), yielding similar results. CONCLUSIONS These results reveal different underlying pathogenetic mechanisms and illustrate the potential of transcriptomics to identify patient endotypes in severe COVID-19 with the aim to ultimately personalise their therapies.
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Affiliation(s)
- Cecilia López-Martínez
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Paula Martín-Vicente
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Juan Gómez de Oña
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Servicio de Genética Molecular, Hospital Universitario Central de Asturias, Oviedo, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Inés López-Alonso
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
- Departamento de Morfología y Biología Celular, Universidad de Oviedo, Oviedo, Spain
| | - Helena Gil-Peña
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Servicio de Pediatría, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Elías Cuesta-Llavona
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Servicio de Genética Molecular, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Margarita Fernández-Rodríguez
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Irene Crespo
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Madrid, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - Estefanía Salgado Del Riego
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Unidad de Cuidados Intensivos Polivalente, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Raquel Rodríguez-García
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Madrid, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Diego Parra
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Javier Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Javier Rodríguez-Carrio
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | | | - Alberto Dávalos
- Instituto Madrileño de Estudios Avanzados (IMDEA) Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Luis A Chapado
- Instituto Madrileño de Estudios Avanzados (IMDEA) Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Eliecer Coto
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Servicio de Genética Molecular, Hospital Universitario Central de Asturias, Oviedo, Spain
- Red de Investigación Renal (REDINREN), Madrid, Spain
- Departamento de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Guillermo M Albaiceta
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Spain
- G.M. Albaiceta and L. Amado-Rodríguez share last authorship
| | - Laura Amado-Rodríguez
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Spain
- Departamento de Medicina, Universidad de Oviedo, Oviedo, Spain
- G.M. Albaiceta and L. Amado-Rodríguez share last authorship
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Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. Single-cell RNA-seq methods to interrogate virus-host interactions. Semin Immunopathol 2023; 45:71-89. [PMID: 36414692 PMCID: PMC9684776 DOI: 10.1007/s00281-022-00972-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aaron J Wilk
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Madeline J Lee
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Purvesh Khatri
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Medicine, Center for Biomedical Informatics Research, Stanford, CA, USA.
- Inflammatix, Inc., Sunnyvale, CA, 94085, USA.
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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Arish M, Qian W, Narasimhan H, Sun J. COVID-19 immunopathology: From acute diseases to chronic sequelae. J Med Virol 2023; 95:e28122. [PMID: 36056655 PMCID: PMC9537925 DOI: 10.1002/jmv.28122] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 01/17/2023]
Abstract
The clinical manifestation of coronavirus disease 2019 (COVID-19) mainly targets the lung as a primary affected organ, which is also a critical site of immune cell activation by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, recent reports also suggest the involvement of extrapulmonary tissues in COVID-19 pathology. The interplay of both innate and adaptive immune responses is key to COVID-19 management. As a result, a robust innate immune response provides the first line of defense, concomitantly, adaptive immunity neutralizes the infection and builds memory for long-term protection. However, dysregulated immunity, both innate and adaptive, can skew towards immunopathology both in acute and chronic cases. Here we have summarized some of the recent findings that provide critical insight into the immunopathology caused by SARS-CoV-2, in acute and post-acute cases. Finally, we further discuss some of the immunomodulatory drugs in preclinical and clinical trials for dampening the immunopathology caused by COVID-19.
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Affiliation(s)
- Mohd Arish
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Wei Qian
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Harish Narasimhan
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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40
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Immunophenotype and function of circulating myeloid derived suppressor cells in COVID-19 patients. Sci Rep 2022; 12:22570. [PMID: 36581679 PMCID: PMC9799710 DOI: 10.1038/s41598-022-26943-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
The pathogenesis of coronavirus disease 2019 (COVID-19) is not fully elucidated. COVID-19 is due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which causes severe illness and death in some people by causing immune dysregulation and blood T cell depletion. Increased numbers of myeloid-derived suppressor cells (MDSCs) play a diverse role in the pathogenesis of many infections and cancers but their function in COVID-19 remains unclear. To evaluate the function of MDSCs in relation with the severity of COVID-19. 26 PCR-confirmed COVID-19 patients including 12 moderate and 14 severe patients along with 11 healthy age- and sex-matched controls were enrolled. 10 ml whole blood was harvested for cell isolation, immunophenotyping and stimulation. The immunophenotype of MDSCs by flow cytometry and T cells proliferation in the presence of MDSCs was evaluated. Serum TGF-β was assessed by ELISA. High percentages of M-MDSCs in males and of P-MDSCs in female patients were found in severe and moderate affected patients. Isolated MDSCs of COVID-19 patients suppressed the proliferation and intracellular levels of IFN-γ in T cells despite significant suppression of T regulatory cells but up-regulation of precursor regulatory T cells. Serum analysis shows increased levels of TGF-β in severe patients compared to moderate and control subjects (HC) (P = 0.003, P < 0.0001, respectively). The frequency of MDSCs in blood shows higher frequency among both moderate and severe patients and may be considered as a predictive factor for disease severity. MDSCs may suppress T cell proliferation by releasing TGF-β.
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Bosteels C, Van Damme KFA, De Leeuw E, Declercq J, Maes B, Bosteels V, Hoste L, Naesens L, Debeuf N, Deckers J, Cole B, Pardons M, Weiskopf D, Sette A, Weygaerde YV, Malfait T, Vandecasteele SJ, Demedts IK, Slabbynck H, Allard S, Depuydt P, Van Braeckel E, De Clercq J, Martens L, Dupont S, Seurinck R, Vandamme N, Haerynck F, Roychowdhury DF, Vandekerckhove L, Guilliams M, Tavernier SJ, Lambrecht BN. Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Rep Med 2022; 3:100833. [PMID: 36459994 PMCID: PMC9663750 DOI: 10.1016/j.xcrm.2022.100833] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/12/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
GM-CSF promotes myelopoiesis and inflammation, and GM-CSF blockade is being evaluated as a treatment for COVID-19-associated hyperinflammation. Alveolar GM-CSF is, however, required for monocytes to differentiate into alveolar macrophages (AMs) that control alveolar homeostasis. By mapping cross-species AM development to clinical lung samples, we discovered that COVID-19 is marked by defective GM-CSF-dependent AM instruction and accumulation of pro-inflammatory macrophages. In a multi-center, open-label RCT in 81 non-ventilated COVID-19 patients with respiratory failure, we found that inhalation of rhu-GM-CSF did not improve mean oxygenation parameters compared with standard treatment. However, more patients on GM-CSF had a clinical response, and GM-CSF inhalation induced higher numbers of virus-specific CD8 effector lymphocytes and class-switched B cells, without exacerbating systemic hyperinflammation. This translational proof-of-concept study provides a rationale for further testing of inhaled GM-CSF as a non-invasive treatment to improve alveolar gas exchange and simultaneously boost antiviral immunity in COVID-19. This study is registered at ClinicalTrials.gov (NCT04326920) and EudraCT (2020-001254-22).
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Affiliation(s)
- Cedric Bosteels
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Karel F A Van Damme
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Elisabeth De Leeuw
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Jozefien Declercq
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bastiaan Maes
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Victor Bosteels
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Laboratory of ER Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium
| | - Levi Hoste
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Primary Immunodeficiency Research Lab, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
| | - Leslie Naesens
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Primary Immunodeficiency Research Lab, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
| | - Nincy Debeuf
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Julie Deckers
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Basiel Cole
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Marion Pardons
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Daniela Weiskopf
- Center for Autoimmunity and Inflammation and Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Autoimmunity and Inflammation and Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | | | - Thomas Malfait
- Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | | | - Ingel K Demedts
- Department of Pulmonary Medicine, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Hans Slabbynck
- Department of Pulmonary Medicine, ZNA General Hospital, 2000 Antwerp, Belgium
| | - Sabine Allard
- Department of Internal Medicine, Universitair Ziekenhuis Brussel, 1000 Brussels, Belgium
| | - Pieter Depuydt
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Intensive Care Unit, Ghent University Hospital, 9000 Ghent, Belgium
| | - Eva Van Braeckel
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Jozefien De Clercq
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Infectious Diseases, Ghent University Hospital, 9000 Ghent, Belgium
| | - Liesbet Martens
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Dupont
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, 9000 Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, 9000 Ghent, Belgium; VIB Single Cell Core, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Primary Immunodeficiency Research Lab, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
| | | | - Linos Vandekerckhove
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Infectious Diseases, Ghent University Hospital, 9000 Ghent, Belgium
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Simon J Tavernier
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Primary Immunodeficiency Research Lab, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium; Department of Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium; Laboratory of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, 9000 Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, 9000 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium.
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The Association of Low CD4 Expression on Monocytes and Low CD8+ T-Cell Count at Hospital Admission Predicts the Need for Mechanical Ventilation in Patients With COVID-19 Pneumonia: A Prospective Monocentric Cohort Study. Crit Care Explor 2022; 4:e0810. [PMID: 36518218 PMCID: PMC9742091 DOI: 10.1097/cce.0000000000000810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To identify COVID-19-associated immunophenotyping patterns at hospital admission and to determine if some patterns could predict the need for mechanical ventilation (MV). DESIGN Prospective observational monocentric cohort study. SETTING A university-affiliated hospital in Marseille, France. PATIENTS Thirty patients presenting with laboratory-confirmed COVID-19 pneumonia were enrolled within the first 48 hours of hospital admission and compared with 18 healthy controls. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Whole-blood leukocytes were immunophenotyped with a rapid and simplified one-step flow cytometry method. Thirty-eight immune and five laboratory parameters were compared first between COVID-19 patients and controls and then between the COVID-19 patients who received or not MV during their stays. The variables that significantly discriminated MV from non-MV patients in univariate analysis were entered into a multiple stepwise logistic regression analysis. The COVID-19 patients were predominantly male (87%), aged 61 years (50-71 yr), and 93% received early corticosteroid therapy. Sixteen patients (53%) were managed with noninvasive respiratory support, and 14 (47%) required MV. Compared with controls, COVID-19 patients were characterized by an immune signature featuring: 1) decreased HLA-DR expression on monocytes; 2) reduced basophils, eosinophils, T-cells, NK cells, and nonclassical monocyte count; and 3) up regulation of CD169 on monocytes, CD64 on neutrophils, the adhesion/migration markers (CD62L and CD11b), and the checkpoint inhibitor CD274 on myeloid cells. Among the COVID-19 patients, those who received MV had lower level of CD4 and HLA-DR on monocytes, lower CD8+ T-cell count, and higher lactate dehydrogenase at hospital admission. In multivariate analysis, only CD4 on monocytes (p = 0.032) and CD8+ T-cell count (p = 0.026) were associated with MV requirement. The model combining these two variables provided an area under curve of 0.97 (95% CI, 0.83-0.99). CONCLUSIONS The association of low CD4 on monocytes and low CD8+ T-cell count at hospital admission was highly predictive of the need for MV in hospitalized patients with COVID-19 pneumonia.
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Gupta GS. The Lactate and the Lactate Dehydrogenase in Inflammatory Diseases and Major Risk Factors in COVID-19 Patients. Inflammation 2022; 45:2091-2123. [PMID: 35588340 PMCID: PMC9117991 DOI: 10.1007/s10753-022-01680-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/04/2022] [Accepted: 05/03/2022] [Indexed: 12/15/2022]
Abstract
Lactate dehydrogenase (LDH) is a terminating enzyme in the metabolic pathway of anaerobic glycolysis with end product of lactate from glucose. The lactate formation is crucial in the metabolism of glucose when oxygen is in inadequate supply. Lactate can also be formed and utilised by different cell types under fully aerobic conditions. Blood LDH is the marker enzyme, which predicts mortality in many conditions such as ARDS, serious COVID-19 and cancer patients. Lactate plays a critical role in normal physiology of humans including an energy source, a signaling molecule and a pH regulator. Depending on the pH, lactate exists as the protonated acidic form (lactic acid) at low pH or as sodium salt (sodium lactate) at basic pH. Lactate can affect the immune system and act as a signaling molecule, which can provide a "danger" signal for life. Several reports provide evidence that the serum lactate represents a chemical marker of severity of disease similar to LDH under inflammatory conditions. Since the mortality rate is much higher among COVID-19 patients, associated with high serum LDH, this article is aimed to review the LDH as a therapeutic target and lactate as potential marker for monitoring treatment response of inflammatory diseases. Finally, the review summarises various LDH inhibitors, which offer potential applications as therapeutic agents for inflammatory diseases, associated with high blood LDH. Both blood LDH and blood lactate are suggested as risk factors for the mortality of patients in serious inflammatory diseases.
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Affiliation(s)
- G S Gupta
- Department of Biophysics, Panjab University, Chandigarh, 160014, India.
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44
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Gardiman E, Bianchetto-Aguilera F, Gasperini S, Tiberio L, Scandola M, Lotti V, Gibellini D, Salvi V, Bosisio D, Cassatella MA, Tamassia N. SARS-CoV-2-Associated ssRNAs Activate Human Neutrophils in a TLR8-Dependent Fashion. Cells 2022; 11:3785. [PMID: 36497044 PMCID: PMC9738506 DOI: 10.3390/cells11233785] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
COVID-19 disease is characterized by a dysregulation of the innate arm of the immune system. However, the mechanisms whereby innate immune cells, including neutrophils, become activated in patients are not completely understood. Recently, we showed that GU-rich RNA sequences from the SARS-CoV-2 genome (i.e., SCV2-RNA1 and SCV2-RNA2) activate dendritic cells. To clarify whether human neutrophils may also represent targets of SCV2-RNAs, neutrophils were treated with either SCV2-RNAs or, as a control, R848 (a TLR7/8 ligand), and were then analyzed for several functional assays and also subjected to RNA-seq experiments. Results highlight a remarkable response of neutrophils to SCV2-RNAs in terms of TNFα, IL-1ra, CXCL8 production, apoptosis delay, modulation of CD11b and CD62L expression, and release of neutrophil extracellular traps. By RNA-seq experiments, we observed that SCV2-RNA2 promotes a transcriptional reprogramming of neutrophils, characterized by the induction of thousands of proinflammatory genes, similar to that promoted by R848. Furthermore, by using CU-CPT9a, a TLR8-specific inhibitor, we found that SCV2-RNA2 stimulates neutrophils exclusively via TLR8-dependent pathways. In sum, our study proves that single-strand RNAs from the SARS-CoV-2 genome potently activate human neutrophils via TLR8, thus uncovering a potential mechanism whereby neutrophils may contribute to the pathogenesis of severe COVID-19 disease.
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Affiliation(s)
- Elisa Gardiman
- General Pathology Section, Department of Medicine, University of Verona, 37134 Verona, Italy
| | | | - Sara Gasperini
- General Pathology Section, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Laura Tiberio
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Matteo Scandola
- General Pathology Section, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Virginia Lotti
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy
| | - Davide Gibellini
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy
| | - Valentina Salvi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Daniela Bosisio
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marco A. Cassatella
- General Pathology Section, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Nicola Tamassia
- General Pathology Section, Department of Medicine, University of Verona, 37134 Verona, Italy
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45
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Wang C, Yu R, Zhang S, Zhao Y, Qi C, Zhu Z, Chen X, Bi J, Xu P, Cheng L, Zhang X. Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines. Brief Funct Genomics 2022; 21:423-432. [PMID: 36281737 DOI: 10.1093/bfgp/elac033] [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: 08/14/2022] [Revised: 09/08/2022] [Accepted: 09/21/2022] [Indexed: 12/15/2022] Open
Abstract
The elevated levels of inflammatory cytokines have attracted much attention during the treatment of COVID-19 patients. The conclusions of current observational studies are often controversial in terms of the causal effects of COVID-19 on various cytokines because of the confounding factors involving underlying diseases. To resolve this problem, we conducted a Mendelian randomization analysis by integrating the GWAS data of COVID-19 and 41 cytokines. As a result, the levels of 2 cytokines were identified to be promoted by COVID-19 and had unsignificant pleiotropy. In comparison, the levels of 10 cytokines were found to be inhibited and had unsignificant pleiotropy. Among down-regulated cytokines, CCL2, CCL3 and CCL7 were members of CC chemokine family. We then explored the potential molecular mechanism for a significant causal association at a single cell resolution based on single-cell RNA data, and discovered the suppression of CCL3 and the inhibition of CCL3-CCR1 interaction in classical monocytes (CMs) of COVID-19 patients. Our findings may indicate that the capability of COVID-19 in decreasing the chemotaxis of lymphocytes by inhibiting the CCL3-CCR1 interaction in CMs.
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Affiliation(s)
- Chao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Yue Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Changlu Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Xinyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Jianxing Bi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Peigang Xu
- Chongqing Research Institute of Harbin Institute of Technology
| | - Liang Cheng
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang, China, 150028.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Xue Zhang
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang, China, 150028.,McKusick-Zhang Center for Genetic Medicine, Peking Union Medical College, Beijing, China, 100005
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LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Revach OY, Mehta A, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M. Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients. Cell Rep Med 2022; 3:100779. [PMID: 36208629 PMCID: PMC9510054 DOI: 10.1016/j.xcrm.2022.100779] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 08/02/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2023]
Abstract
Mechanisms of neutrophil involvement in severe coronavirus disease 2019 (COVID-19) remain incompletely understood. Here, we collect longitudinal blood samples from 306 hospitalized COVID-19+ patients and 86 controls and perform bulk RNA sequencing of enriched neutrophils, plasma proteomics, and high-throughput antibody profiling to investigate relationships between neutrophil states and disease severity. We identify dynamic switches between six distinct neutrophil subtypes. At days 3 and 7 post-hospitalization, patients with severe disease display a granulocytic myeloid-derived suppressor cell-like gene expression signature, while patients with resolving disease show a neutrophil progenitor-like signature. Humoral responses are identified as potential drivers of neutrophil effector functions, with elevated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunoglobulin G1 (IgG1)-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirm that while patient-derived IgG antibodies induce phagocytosis in healthy donor neutrophils, IgA antibodies predominantly induce neutrophil cell death. Overall, our study demonstrates a dysregulated myelopoietic response in severe COVID-19 and a potential role for IgA-dominant responses contributing to mortality.
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Affiliation(s)
- Thomas J LaSalle
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA.
| | - Anna L K Gonye
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Irena Gushterova
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyle R Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Brian C Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Nihaarika Sharma
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F Thomas
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M Lilly
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N Mckaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole C Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily M Blaum
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola B Lirofonis
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Or-Yam Revach
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arnav Mehta
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abraham Sonny
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Roby P Bhattacharyya
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Blair Alden Parry
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marcia B Goldberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael R Filbin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Moshe Sade-Feldman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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Rondovic G, Djordjevic D, Udovicic I, Stanojevic I, Zeba S, Abazovic T, Vojvodic D, Abazovic D, Khan W, Surbatovic M. From Cytokine Storm to Cytokine Breeze: Did Lessons Learned from Immunopathogenesis Improve Immunomodulatory Treatment of Moderate-to-Severe COVID-19? Biomedicines 2022; 10:2620. [PMID: 36289881 PMCID: PMC9599155 DOI: 10.3390/biomedicines10102620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Complex immune response to infection has been highlighted, more than ever, during the COVID-19 pandemic. This review explores the immunomodulatory treatment of moderate-to-severe forms of this viral sepsis in the context of specific immunopathogenesis. Our objective is to analyze in detail the existing strategies for the use of immunomodulators in COVID-19. Immunomodulating therapy is very challenging; there are still underpowered or, in other ways, insufficient studies with inconclusive or conflicting results regarding a rationale for adding a second immunomodulatory drug to dexamethasone. Bearing in mind that a "cytokine storm" is not present in the majority of COVID-19 patients, it is to be expected that the path to the adequate choice of a second immunomodulatory drug is paved with uncertainty. Anakinra, a recombinant human IL-1 receptor antagonist, is a good choice in this setting. Yet, the latest update of the COVID-19 Treatment Guidelines Panel (31 May 2022) claims that there is insufficient evidence to recommend either for or against the use of anakinra for the treatment of COVID-19. EMA's human medicines committee recommended extending the indication of anakinra to include treatment of COVID-19 in adult patients only recently (17 December 2021). It is obvious that this is still a work in progress, with few ongoing clinical trials. With over 6 million deaths from COVID-19, this is the right time to speed up this process. Our conclusion is that, during the course of COVID-19, the immune response is changing from the early phase to the late phase in individual patients, so immunomodulating therapy should be guided by individual responses at different time points.
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Affiliation(s)
- Goran Rondovic
- Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defence, Crnotravska 17, 11000 Belgrade, Serbia
| | - Dragan Djordjevic
- Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defence, Crnotravska 17, 11000 Belgrade, Serbia
| | - Ivo Udovicic
- Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defence, Crnotravska 17, 11000 Belgrade, Serbia
| | - Ivan Stanojevic
- Faculty of Medicine of the Military Medical Academy, University of Defence, Crnotravska 17, 11000 Belgrade, Serbia
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
| | - Snjezana Zeba
- Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defence, Crnotravska 17, 11000 Belgrade, Serbia
| | - Tanja Abazovic
- Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
| | - Danilo Vojvodic
- Faculty of Medicine of the Military Medical Academy, University of Defence, Crnotravska 17, 11000 Belgrade, Serbia
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
| | - Dzihan Abazovic
- Biocell Hospital, Omladinskih Brigada 86a, 11000 Belgrade, Serbia
| | - Wasim Khan
- Division of Trauma & Orthopaedic Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 2QQ, UK
| | - Maja Surbatovic
- Clinic of Anesthesiology and Intensive Therapy, Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defence, Crnotravska 17, 11000 Belgrade, Serbia
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48
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Montaldo E, Lusito E, Bianchessi V, Caronni N, Scala S, Basso-Ricci L, Cantaffa C, Masserdotti A, Barilaro M, Barresi S, Genua M, Vittoria FM, Barbiera G, Lazarevic D, Messina C, Xue E, Marktel S, Tresoldi C, Milani R, Ronchi P, Gattillo S, Santoleri L, Di Micco R, Ditadi A, Belfiori G, Aleotti F, Naldini MM, Gentner B, Gardiman E, Tamassia N, Cassatella MA, Hidalgo A, Kwok I, Ng LG, Crippa S, Falconi M, Pettinella F, Scapini P, Naldini L, Ciceri F, Aiuti A, Ostuni R. Cellular and transcriptional dynamics of human neutrophils at steady state and upon stress. Nat Immunol 2022; 23:1470-1483. [PMID: 36138183 PMCID: PMC7615267 DOI: 10.1038/s41590-022-01311-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/10/2022] [Indexed: 02/04/2023]
Abstract
Traditionally viewed as poorly plastic, neutrophils are now recognized as functionally diverse; however, the extent and determinants of neutrophil heterogeneity in humans remain unclear. We performed a comprehensive immunophenotypic and transcriptome analysis, at a bulk and single-cell level, of neutrophils from healthy donors and patients undergoing stress myelopoiesis upon exposure to growth factors, transplantation of hematopoietic stem cells (HSC-T), development of pancreatic cancer and viral infection. We uncover an extreme diversity of human neutrophils in vivo, reflecting the rates of cell mobilization, differentiation and exposure to environmental signals. Integrated control of developmental and inducible transcriptional programs linked flexible granulopoietic outputs with elicitation of stimulus-specific functional responses. In this context, we detected an acute interferon (IFN) response in the blood of patients receiving HSC-T that was mirrored by marked upregulation of IFN-stimulated genes in neutrophils but not in monocytes. Systematic characterization of human neutrophil plasticity may uncover clinically relevant biomarkers and support the development of diagnostic and therapeutic tools.
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Affiliation(s)
- Elisa Montaldo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Eleonora Lusito
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valentina Bianchessi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicoletta Caronni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Basso-Ricci
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Carla Cantaffa
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alice Masserdotti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mattia Barilaro
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simona Barresi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Genua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Maria Vittoria
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Barbiera
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences (COSR), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Carlo Messina
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisabetta Xue
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sarah Marktel
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Tresoldi
- Molecular Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Milani
- Immunohematology and Transfusion Medicine Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Ronchi
- Immunohematology and Transfusion Medicine Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Salvatore Gattillo
- Immunohematology and Transfusion Medicine Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Santoleri
- Immunohematology and Transfusion Medicine Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Ditadi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulio Belfiori
- Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Aleotti
- Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Gardiman
- Section of General Pathology, Department of Medicine, University of Verona, Verona, Italy
| | - Nicola Tamassia
- Section of General Pathology, Department of Medicine, University of Verona, Verona, Italy
| | | | - Andrés Hidalgo
- Area of Cell and Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), A*STAR, Biopolis, Singapore, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR, Biopolis, Singapore, Singapore
| | - Stefano Crippa
- Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Falconi
- Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesca Pettinella
- Section of General Pathology, Department of Medicine, University of Verona, Verona, Italy
| | - Patrizia Scapini
- Section of General Pathology, Department of Medicine, University of Verona, Verona, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Fabio Ciceri
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Renato Ostuni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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49
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Targeting tumour-reprogrammed myeloid cells: the new battleground in cancer immunotherapy. Semin Immunopathol 2022; 45:163-186. [PMID: 36161514 PMCID: PMC9513014 DOI: 10.1007/s00281-022-00965-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/13/2022] [Indexed: 11/08/2022]
Abstract
Tumour microenvironment is a complex ecosystem in which myeloid cells are the most abundant immune elements. This cell compartment is composed by different cell types, including neutrophils, macrophages, dendritic cells, and monocytes but also unexpected cell populations with immunosuppressive and pro-tumour roles. Indeed, the release of tumour-derived factors influences physiological haematopoiesis producing unconventional cells with immunosuppressive and tolerogenic functions such as myeloid-derived suppressor cells. These pro-tumour myeloid cell populations not only support immune escape directly but also assist tumour invasion trough non-immunological activities. It is therefore not surprising that these cell subsets considerably impact in tumour progression and cancer therapy resistance, including immunotherapy, and are being investigated as potential targets for developing a new era of cancer therapy. In this review, we discuss emerging strategies able to modulate the functional activity of these tumour-supporting myeloid cells subverting their accumulation, recruitment, survival, and functions. These innovative approaches will help develop innovative, or improve existing, cancer treatments.
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50
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Fredericks AM, Jentzsch MS, Cioffi WG, Cohen M, Fairbrother WG, Gandhi SJ, Harrington EO, Nau GJ, Reichner JS, Ventetuolo CE, Levy MM, Ayala A, Monaghan SF. Deep RNA sequencing of intensive care unit patients with COVID-19. Sci Rep 2022; 12:15755. [PMID: 36130991 PMCID: PMC9491252 DOI: 10.1038/s41598-022-20139-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/09/2022] [Indexed: 02/04/2023] Open
Abstract
COVID-19 has impacted millions of patients across the world. Molecular testing occurring now identifies the presence of the virus at the sampling site: nasopharynx, nares, or oral cavity. RNA sequencing has the potential to establish both the presence of the virus and define the host's response in COVID-19. Single center, prospective study of patients with COVID-19 admitted to the intensive care unit where deep RNA sequencing (> 100 million reads) of peripheral blood with computational biology analysis was done. All patients had positive SARS-CoV-2 PCR. Clinical data was prospectively collected. We enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. Entropy calculated from alternative RNA splicing and transcription start/end predicted mortality in these patients. Current upper respiratory tract testing for COVID-19 only determines if the virus is present. Deep RNA sequencing with appropriate computational biology may provide important prognostic information and point to therapeutic foci to be precisely targeted in future studies.
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Affiliation(s)
- Alger M Fredericks
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, 593 Eddy Street, Middle House 211, Providence, RI, 02903, USA
| | - Maximilian S Jentzsch
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, 593 Eddy Street, Middle House 211, Providence, RI, 02903, USA
| | - William G Cioffi
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, 593 Eddy Street, Middle House 211, Providence, RI, 02903, USA
| | - Maya Cohen
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Alpert Medical School of Brown University/Rhode Island Hospital, Providence, USA
| | | | | | | | - Gerard J Nau
- Division of Infectious Disease, Department of Medicine, Alpert Medical School of Brown University /Rhode Island Hospital, Providence, USA
| | - Jonathan S Reichner
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, 593 Eddy Street, Middle House 211, Providence, RI, 02903, USA
| | - Corey E Ventetuolo
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Alpert Medical School of Brown University/Rhode Island Hospital, Providence, USA
| | - Mitchell M Levy
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Alpert Medical School of Brown University/Rhode Island Hospital, Providence, USA
| | - Alfred Ayala
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, 593 Eddy Street, Middle House 211, Providence, RI, 02903, USA
| | - Sean F Monaghan
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, 593 Eddy Street, Middle House 211, Providence, RI, 02903, USA.
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