Lower respiratory tract single-cell RNA sequencing and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis: a single centre, retrospective, observational study.

Autor:	Feys S; Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium., Vanmassenhove S; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium., Kraisin S; Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium., Yu K; Laboratory of Molecular Immunology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Jacobs C; Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium., Boeckx B; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium., Cambier S; Laboratory of Molecular Immunology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Cunha C; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal., Debaveye Y; Department of Intensive Care Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium., Gonçalves SM; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal., Hermans G; Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium., Humblet-Baron S; Laboratory of Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Jansen S; Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Lagrou K; Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Meersseman P; Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium., Neyts J; Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Peetermans M; Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium., Rocha-Pereira J; Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Schepers R; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium., Spalart V; Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium; Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium., Starick MR; Laboratory of Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Thevissen K; Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium., Van Brussel T; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium., Van Buyten T; Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Van Mol P; Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium., Vandenbriele C; Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium; Cardiology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium., Vanderbeke L; Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium., Wauters E; Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium; Laboratory of Respiratory Diseases and Thoracic Surgery, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium., Wilmer A; Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium., Van Weyenbergh J; Laboratory of Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Van De Veerdonk FL; Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands., Carvalho A; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal., Proost P; Laboratory of Molecular Immunology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium., Martinod K; Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium., Lambrechts D; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium., Wauters J; Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Laboratory of Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven, Belgium. Electronic address: joost.wauters@uzleuven.be.
Jazyk:	angličtina
Zdroj:	The Lancet. Microbe [Lancet Microbe] 2024 Mar; Vol. 5 (3), pp. e247-e260. Date of Electronic Publication: 2024 Jan 24.
DOI:	10.1016/S2666-5247(23)00368-3
Abstrakt:	Background: COVID-19-associated pulmonary aspergillosis (CAPA) is a severe superinfection with the fungus Aspergillus affecting patients who are critically ill with COVID-19. The pathophysiology and the role of neutrophil extracellular traps (NETs) in this infection are largely unknown. We aimed to characterise the immune profile, with a focus on neutrophils and NET concentrations, of critically ill patients with COVID-19, with or without CAPA. Methods: We conducted a single-centre, retrospective, observational study in two patient cohorts, both recruited at University Hospitals Leuven, Belgium. We included adults aged 18 years or older who were admitted to the intensive care unit because of COVID-19 between March 31, 2020, and May 18, 2021, and who were included in the previous Contagious trial (NCT04327570). We investigated the immune cellular landscape of CAPA versus COVID-19 only by performing single-cell RNA sequencing (scRNA-seq) on bronchoalveolar lavage fluid. Bronchoalveolar lavage immune cell fractions were compared between patients with CAPA and patients with COVID-19 only. Additionally, we determined lower respiratory tract NET concentrations using biochemical assays in patients aged 18 years and older who were admitted to the intensive care unit because of severe COVID-19 between March 15, 2020, and Dec 31, 2021, for whom bronchoalveolar lavage was available in the hospital biobank. Bronchoalveolar lavage NET concentrations were compared between patients with CAPA and patients with COVID-19 only and integrated with existing data on immune mediators in bronchoalveolar lavage and 90-day mortality. Findings: We performed scRNA-seq of bronchoalveolar lavage on 43 samples from 39 patients, of whom 36 patients (30 male and six female; 14 with CAPA) were included in downstream analyses. We performed bronchoalveolar lavage NET analyses in 59 patients (46 male and 13 female), of whom 26 had CAPA. By scRNA-seq, patients with CAPA had significantly lower neutrophil fractions than patients with COVID-19 only (16% vs 33%; p=0·0020). The remaining neutrophils in patients with CAPA preferentially followed a hybrid maturation trajectory characterised by expression of genes linked to antigen presentation, with enhanced transcription of antifungal effector pathways. Patients with CAPA also showed depletion of mucosal-associated invariant T cells, reduced T helper 1 and T helper 17 differentiation, and transcriptional defects in specific aspects of antifungal immunity in macrophages and monocytes. We observed increased formation of NETs in patients with CAPA compared with patients with COVID-19 only (DNA complexed with citrullinated histone H3 median 15 898 ng/mL [IQR 4588-86 419] vs 7062 ng/mL [775-14 088]; p=0·042), thereby explaining decreased neutrophil fractions by scRNA-seq. Low bronchoalveolar lavage NET concentrations were associated with increased 90-day mortality in patients with CAPA. Interpretation: Qualitative and quantitative disturbances in monocyte, macrophage, B-cell, and T-cell populations could predispose patients with severe COVID-19 to develop CAPA. Hybrid neutrophils form a specialised response to CAPA, and an adequate neutrophil response to CAPA is a major determinant for survival in these patients. Therefore, measuring bronchoalveolar lavage NETs could have diagnostic and prognostic value in patients with CAPA. Clinicians should be wary of aspergillosis when using immunomodulatory therapy that might inhibit NETosis to treat patients with severe COVID-19. Funding: Research Foundation Flanders, KU Leuven, UZ Leuven, VIB, the Fundação para a Ciência e a Tecnologia, the European Regional Development Fund, la Caixa Foundation, the Flemish Government, and Horizon 2020. Competing Interests: Declaration of interests SF received travel grants from Pfizer and Gilead and a speaker fee from The Healthbook Company. GH received travel fees from Eurosets. YD received travel grants from Pfizer and declares participation in advisory boards of Pfizer and MSD. KL received consultancy fees from MRM Health and Mundipharma, speaker fees and travel support from Pfizer and Gilead, and service fees from Thermo Fisher Scientific and TECOmedical. MP received travel fees from Pfizer. LV received travel fees from Gilead Sciences and Pfizer. KM received royalties to patent numbers US10617742B2, US11400139B2 in relation to the Children’s Hospital Corporation, reports fees for scientific advice to and stock options in Peel Therapeutics, and reports being an inventor on granted US patent numbers US9642822B2 (issued), US11400139B2 (issued), and US11426405B2 (issued). JW received an institutional research fund from Pfizer; received investigator-initiated grants from Pfizer, Gilead, and MSD; received speakers’ and travel fees from Pfizer, Gilead, and MSD; declares participation in advisory boards of Pfizer and Gilead; and declares receipt of study drugs from MSD. All other authors declare no competing interests. (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
Databáze:	MEDLINE
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