Demultiplexing Ig repertoires by parallel mRNA/DNA sequencing shows major differential alterations in severe COVID-19
Virginie Pascal,
Marine Dupont,
Paco de Rouault,
David Rizzo,
Delphine Rossille,
Robin Jeannet,
Thomas Daix,
Bruno François,
Steve Genebrier,
Marie Cornic,
Guillaume Monneret,
Fabienne Venet,
Juliette Ferrant,
Mikael Roussel,
Florian Reizine,
Mathieu Le Souhaitier,
Jean-Marc Tadié,
Karin Tarte,
Jean Feuillard,
Michel Cogné
Affiliations
Virginie Pascal
CNRS UMR-7276, INSERM U1262, Team 3 BioPIC of CRIBL, University of Limoges, and Immunology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
Marine Dupont
CNRS UMR-7276, INSERM U1262, Team 1 2MB2C of CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
Paco de Rouault
Department of BioInformatics of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
David Rizzo
CNRS UMR-7276, INSERM U1262, Team 1 2MB2C of CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
Delphine Rossille
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, 35033 Rennes, France
Robin Jeannet
CNRS UMR-7276, INSERM U1262, Team 1 2MB2C of CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France; Inserm CIC 1435, UMR 1092, Faculty of Medicine, University of Limoges, and Réanimation Polyvalente, CHU Dupuytren, 2, 87042 Limoges, France
Thomas Daix
Inserm CIC 1435, UMR 1092, Faculty of Medicine, University of Limoges, and Réanimation Polyvalente, CHU Dupuytren, 2, 87042 Limoges, France
Bruno François
Inserm CIC 1435, UMR 1092, Faculty of Medicine, University of Limoges, and Réanimation Polyvalente, CHU Dupuytren, 2, 87042 Limoges, France
Steve Genebrier
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, 35033 Rennes, France
Marie Cornic
Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, 35033 Rennes, France
Guillaume Monneret
Cellular Immunology Laboratory, Hospices Civils de Lyon, Hôpital Edouard Herriot, Lyon, France
Fabienne Venet
Cellular Immunology Laboratory, Hospices Civils de Lyon, Hôpital Edouard Herriot, Lyon, France
Juliette Ferrant
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France
Mikael Roussel
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, 35033 Rennes, France
Florian Reizine
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, Maladies Infectieuses et Réanimation Médicale, 35033 Rennes, France
Mathieu Le Souhaitier
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, Maladies Infectieuses et Réanimation Médicale, 35033 Rennes, France
Jean-Marc Tadié
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, Maladies Infectieuses et Réanimation Médicale, 35033 Rennes, France
Karin Tarte
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, 35033 Rennes, France
Jean Feuillard
CNRS UMR-7276, INSERM U1262, Team 1 2MB2C of CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
Michel Cogné
Institut national de la santé et de la recherche médicale, Unité Mixte de Recherche U1236, LabEx IGO, Université Rennes 1, Etablissement Français du Sang Bretagne, 35000 Rennes, France; Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, 35033 Rennes, France; Corresponding author
Summary: To understand the fine differential elements that can lead to or prevent acute respiratory distress syndrome (ARDS) in COVID-19 patients, it is crucial to investigate the immune response architecture. We herein dissected the multiple layers of B cell responses by flow cytometry and Ig repertoire analysis from acute phase to recovery. Flow cytometry with FlowSOM analysis showed major changes associated with COVID-19 inflammation such as an increase of double-negative B-cells and ongoing plasma cell differentiation. This paralleled COVID-19-driven expansion of two disconnected B-cell repertoires. Demultiplexing successive DNA and RNA Ig repertoire patterns characterized an early expansion of IgG1 clonotypes with atypically long and uncharged CDR3, the abundance of this inflammatory repertoire being correlated with ARDS and likely pejorative. A superimposed convergent response included convergent anti-SARS-CoV-2 clonotypes. It featured progressively increasing somatic hypermutation together with normal-length or short CDR3 and it persisted until a quiescent memory B-cell stage after recovery.
