Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2

Anvita Bhargava; Ugo Szachnowski; Maxime Chazal; Dominika Foretek; Vincent Caval; Sophie-Marie Aicher; Juliana Pipoli da Fonseca; Patricia Jeannin; Guillaume Beauclair; Marc Monot; Antonin Morillon; Nolwenn Jouvenet

doi:10.1016/j.isci.2023.108449

Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2

iScience. 2023 Nov 13;26(12):108449. doi: 10.1016/j.isci.2023.108449. eCollection 2023 Dec 15.

Affiliations

¹ Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France.
² CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France.
³ Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France.
⁴ Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France.
⁵ Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France.

Abstract

Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S⁺ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S⁺ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.

Keywords: Cell; Transcriptomics; Virology.