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Labeau A, Fery-Simonian L, Lefevre-Utile A, Pourcelot M, Bonnet-Madin L, Soumelis V, Lotteau V, Vidalain PO, Amara A, Meertens L. Characterization and functional interrogation of the SARS-CoV-2 RNA interactome. Cell Rep 2022; 39:110744. [PMID: 35477000 PMCID: PMC9040432 DOI: 10.1016/j.celrep.2022.110744] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 03/19/2021] [Revised: 07/28/2021] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic, which has led to a devastating global health crisis. The emergence of variants that escape neutralizing responses emphasizes the urgent need to deepen our understanding of SARS-CoV-2 biology. Using a comprehensive identification of RNA-binding proteins (RBPs) by mass spectrometry (ChIRP-MS) approach, we identify 107 high-confidence cellular factors that interact with the SARS-CoV-2 genome during infection. By systematically knocking down their expression in human lung epithelial cells, we find that the majority of the identified RBPs are SARS-CoV-2 proviral factors. In particular, we show that HNRNPA2B1, ILF3, QKI, and SFPQ interact with the SARS-CoV-2 genome and promote viral RNA amplification. Our study provides valuable resources for future investigations into the mechanisms of SARS-CoV-2 replication and the identification of host-centered antiviral therapies.
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Affiliation(s)
- Athéna Labeau
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Luc Fery-Simonian
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Alain Lefevre-Utile
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Marie Pourcelot
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Lucie Bonnet-Madin
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Vassili Soumelis
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Pierre-Olivier Vidalain
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Ali Amara
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France.
| | - Laurent Meertens
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France.
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