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Frishberg, A. ; Kooistra, E.* ; Nuesch-Germano, M.* ; Pecht, T.* ; Milman, N.* ; Reusch, N.* ; Warnat-Herresthal, S.* ; Bruse, N.* ; Händler, K.* ; Theis, H.* ; Kraut, M.* ; van Rijssen, E.* ; van Cranenbroek, B.* ; Koenen, H.J.* ; Heesakkers, H.* ; van den Boogaard, M.J.* ; Zegers, M.* ; Pickkers, P.* ; Becker, M.* ; Aschenbrenner, A.C.* ; Ulas, T.* ; Theis, F.J. ; Shen-Orr, S.S.* ; Schultze, J.L.* ; Kox, M.*

Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19.

Cell Rep. Med. 3:100652 (2022)

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Disease recovery dynamics are often difficult to assess, as patients display heterogeneous recovery courses. To model recovery dynamics, exemplified by severe COVID-19, we apply a computational scheme on longitudinally sampled blood transcriptomes, generating recovery states, which we then link to cellular and molecular mechanisms, presenting a framework for studying the kinetics of recovery compared with non-recovery over time and long-term effects of the disease. Specifically, a decrease in mature neutrophils is the strongest cellular effect during recovery, with direct implications on disease outcome. Furthermore, we present strong indications for global regulatory changes in gene programs, decoupled from cell compositional changes, including an early rise in T cell activation and differentiation, resulting in immune rebalancing between interferon and NF-κB activity and restoration of cell homeostasis. Overall, we present a clinically relevant computational framework for modeling disease recovery, paving the way for future studies of the recovery dynamics in other diseases and tissues.

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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Covid-19 ; Cell Deconvolution ; Disease Modeling ; Disease Recovery ; Gene Regulation ; Immunology ; Medicine ; Systems Biology ; Viral Infection

ISSN (print) / ISBN 2666-3791

e-ISSN 2666-3791

Journal Cell Reports Medicine

Quellenangaben Volume: 3, Issue: 6, Article Number: 100652

Publisher Cell Press

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Institute of Computational Biology (ICB)

Grants Helmholtz-Gemeinschaft
Horizon 2020 Framework Programme
EU H2020
CytoReason
Deutsche Forschungsgemeinschaft
Israel Science Foundation
Horizon 2020