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Duell J, Leipold AM, Appenzeller S, Fuhr V, Rauert-Wunderlich H, Da Via M, Dietrich O, Toussaint C, Imdahl F, Eisele F, Afrin N, Grundheber L, Einsele H, Weinhold N, Rosenwald A, Topp MS, Saliba AE, Rasche L. Sequential antigen loss and branching evolution in lymphoma after CD19- and CD20-targeted T-cell-redirecting therapy. Blood 2024; 143:685-696. [PMID: 37976456 PMCID: PMC10900140 DOI: 10.1182/blood.2023021672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
ABSTRACT CD19 chimeric antigen receptor (CAR) T cells and CD20 targeting T-cell-engaging bispecific antibodies (bispecs) have been approved in B-cell non-Hodgkin lymphoma lately, heralding a new clinical setting in which patients are treated with both approaches, sequentially. The aim of our study was to investigate the selective pressure of CD19- and CD20-directed therapy on the clonal architecture in lymphoma. Using a broad analytical pipeline on 28 longitudinally collected specimen from 7 patients, we identified truncating mutations in the gene encoding CD20 conferring antigen loss in 80% of patients relapsing from CD20 bispecs. Pronounced T-cell exhaustion was identified in cases with progressive disease and retained CD20 expression. We also confirmed CD19 loss after CAR T-cell therapy and reported the case of sequential CD19 and CD20 loss. We observed branching evolution with re-emergence of CD20+ subclones at later time points and spatial heterogeneity for CD20 expression in response to targeted therapy. Our results highlight immunotherapy as not only an evolutionary bottleneck selecting for antigen loss variants but also complex evolutionary pathways underlying disease progression from these novel therapies.
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Affiliation(s)
- Johannes Duell
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Alexander M. Leipold
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Center for Infection Research, Würzburg, Germany
| | - Silke Appenzeller
- Core Unit Bioinformatics, Comprehensive Cancer Center Mainfranken, University Hospital of Würzburg, Würzburg, Germany
| | - Viktoria Fuhr
- Institute of Pathology, University of Würzburg, Würzburg, Germany
| | | | - Matteo Da Via
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Oliver Dietrich
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Center for Infection Research, Würzburg, Germany
| | - Christophe Toussaint
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Center for Infection Research, Würzburg, Germany
| | - Fabian Imdahl
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Center for Infection Research, Würzburg, Germany
| | - Florian Eisele
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Nazia Afrin
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
| | - Lars Grundheber
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Niels Weinhold
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Max S. Topp
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Center for Infection Research, Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology, Würzburg, Germany
| | - Leo Rasche
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
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Wendisch D, Dietrich O, Mari T, von Stillfried S, Ibarra IL, Mittermaier M, Mache C, Chua RL, Knoll R, Timm S, Brumhard S, Krammer T, Zauber H, Hiller AL, Pascual-Reguant A, Mothes R, Bülow RD, Schulze J, Leipold AM, Djudjaj S, Erhard F, Geffers R, Pott F, Kazmierski J, Radke J, Pergantis P, Baßler K, Conrad C, Aschenbrenner AC, Sawitzki B, Landthaler M, Wyler E, Horst D, Hippenstiel S, Hocke A, Heppner FL, Uhrig A, Garcia C, Machleidt F, Herold S, Elezkurtaj S, Thibeault C, Witzenrath M, Cochain C, Suttorp N, Drosten C, Goffinet C, Kurth F, Schultze JL, Radbruch H, Ochs M, Eils R, Müller-Redetzky H, Hauser AE, Luecken MD, Theis FJ, Conrad C, Wolff T, Boor P, Selbach M, Saliba AE, Sander LE. SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis. Cell 2021; 184:6243-6261.e27. [PMID: 34914922 PMCID: PMC8626230 DOI: 10.1016/j.cell.2021.11.033] [Citation(s) in RCA: 227] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/28/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
COVID-19-induced “acute respiratory distress syndrome” (ARDS) is associated with prolonged respiratory failure and high mortality, but the mechanistic basis of lung injury remains incompletely understood. Here, we analyze pulmonary immune responses and lung pathology in two cohorts of patients with COVID-19 ARDS using functional single-cell genomics, immunohistology, and electron microscopy. We describe an accumulation of CD163-expressing monocyte-derived macrophages that acquired a profibrotic transcriptional phenotype during COVID-19 ARDS. Gene set enrichment and computational data integration revealed a significant similarity between COVID-19-associated macrophages and profibrotic macrophage populations identified in idiopathic pulmonary fibrosis. COVID-19 ARDS was associated with clinical, radiographic, histopathological, and ultrastructural hallmarks of pulmonary fibrosis. Exposure of human monocytes to SARS-CoV-2, but not influenza A virus or viral RNA analogs, was sufficient to induce a similar profibrotic phenotype in vitro. In conclusion, we demonstrate that SARS-CoV-2 triggers profibrotic macrophage responses and pronounced fibroproliferative ARDS.
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Affiliation(s)
- Daniel Wendisch
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Oliver Dietrich
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Tommaso Mari
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Proteome Dynamics, Berlin, Germany
| | | | - Ignacio L Ibarra
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mirja Mittermaier
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany
| | - Christin Mache
- Unit 17 Influenza and other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Robert Lorenz Chua
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Rainer Knoll
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Sara Timm
- Core Facility Electron Microscopy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sophia Brumhard
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Tobias Krammer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Henrik Zauber
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Proteome Dynamics, Berlin, Germany
| | - Anna Luisa Hiller
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Pascual-Reguant
- Charité - Universitätsmedizin Berlin, Department of Rheumatology and Clinical Immunology, Charité; Deutsches Rheumaforschungszentrum, Immunodynamics, a Leibniz Institute, Berlin, Germany
| | - Ronja Mothes
- Deutsches Rheumaforschungszentrum, Immunodynamics, a Leibniz Institute, Berlin, Germany; Charité - Universitätsmedizin Berlin, Department of Neuropathology, Berlin, Germany
| | - Roman David Bülow
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Jessica Schulze
- Unit 17 Influenza and other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Alexander M Leipold
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sonja Djudjaj
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz-Center for Infection Research (HZI), Braunschweig, Germany
| | - Fabian Pott
- Berlin Institute of Health (BIH), Berlin, Germany; Charité - Universitätsmedizin Berlin, Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Kazmierski
- Berlin Institute of Health (BIH), Berlin, Germany; Charité - Universitätsmedizin Berlin, Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Josefine Radke
- Berlin Institute of Health (BIH), Berlin, Germany; Charité - Universitätsmedizin Berlin, Department of Neuropathology, Berlin, Germany
| | - Panagiotis Pergantis
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Kevin Baßler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Claudia Conrad
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany; PRECISE Platform for Genomics and Epigenomics at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), and University of Bonn, Bonn, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Birgit Sawitzki
- Charité, Universitätsmedizin Berlin, Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - David Horst
- Charité - Universitätsmedizin Berlin, Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Stefan Hippenstiel
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany
| | - Andreas Hocke
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany
| | - Frank L Heppner
- Charité - Universitätsmedizin Berlin, Department of Neuropathology, Berlin, Germany; Cluster of Excellence, NeuroCure, Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
| | - Alexander Uhrig
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Carmen Garcia
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Machleidt
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Herold
- German Center for Lung Research (DZL), Germany; Division of Infectious Diseases, Pulmonary and Critical Care Medicine, Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center, Giessen, Germany; Institute of Lung Health (ILH), Giessen, Germany
| | - Sefer Elezkurtaj
- Charité - Universitätsmedizin Berlin, Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Charlotte Thibeault
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany
| | - Clément Cochain
- Comprehensive Heart Failure Center Wuerzburg, University Hospital Würzburg, Germany; Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Norbert Suttorp
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Christine Goffinet
- Berlin Institute of Health (BIH), Berlin, Germany; Charité - Universitätsmedizin Berlin, Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Florian Kurth
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany; PRECISE Platform for Genomics and Epigenomics at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), and University of Bonn, Bonn, Germany
| | - Helena Radbruch
- Charité - Universitätsmedizin Berlin, Department of Neuropathology, Berlin, Germany
| | - Matthias Ochs
- Core Facility Electron Microscopy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany; Institute of Functional Anatomy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Holger Müller-Redetzky
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Anja E Hauser
- Charité - Universitätsmedizin Berlin, Department of Rheumatology and Clinical Immunology, Charité; Deutsches Rheumaforschungszentrum, Immunodynamics, a Leibniz Institute, Berlin, Germany
| | - Malte D Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Mathematics, Technische Universität München, Garching bei München, Germany
| | - Christian Conrad
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thorsten Wolff
- Unit 17 Influenza and other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Proteome Dynamics, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany.
| | - Leif Erik Sander
- Charité - Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), Germany.
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