Human NLRP1 Is a Sensor of Pathogenic Coronavirus 3CL Proteases in Lung Epithelial Cells

Inflammation observed in SARS-CoV-2-infected patients suggests that inflammasomes, pro-inflammatory intracellular complexes, regulate various steps of infection. Lung epithelial cells express inflammasome-forming sensors and constitute the primary entry door of SARS-CoV-2. Here, we describe that the NLRP1 inflammasome detects SARS-CoV-2 infection in human lung epithelial cells. Specifically, human NLRP1 is cleaved at the Q333 site by multiple coronavirus 3CL proteases, which triggers inflammasome assembly, cell death and limits the production of infectious viral particles. Analysis of NLRP1-associated pathways unveils that 3CL proteases also cleave and inactivate the pyroptosis executioner Gasdermin (GSDM)-D. Subsequently, Caspase-3 and GSDM-E promote alternative cell pyroptosis, a process exacerbated in cells exhibiting impaired type I interferon production. Finally, analysis of pyroptosis markers in plasma from COVID-19 patients with characterized severe pneumonia due to Interferon alterations highlight GSDM-E/Caspase-3 as potential markers of disease severity. Overall, our findings identify NLRP1 as a sensor of SARS-CoV-2 infection in lung epithelia.Funding: This project was funded by grants to different co-authors as follows: the Fondation pour la Recherche Médicale (F.R.M.) to E.M. , the ERC StG (INFLAME) to E.M., the ERC StG (ANTIViR) to C.G., and by the French Ministry of Health with the participation of the Groupement Interrégional de Recherche Clinique et d’Innovation Sud-Ouest Outre- Mer (PHRCI 2020 IMMUNOMARK-COV) to G-M.B. The ASB3 structure is supported by LABEX, Investissement d’Avenir and foundation Bettencourt grants to O.N. M.P. and R.P. were respectively funded by a CIFRE PhD fellowship and a research grant from InvivoGen. S.B. is supported by a PhD fellowship from Mali Ministry of Education and from the FRM (FDT 12794). S.A.L.C. is supported by a Vaincre La Mucoviscidose (VLM) PhD fellowship.Declaration of Interests: Authors declare no conflict of interest.Ethics Approval Statement: Clinical data and blood samples for plasma isolation and cryopreservation were collected at the Toulouse University Hospital, France, in the frame of the COVID-BioToul biobank. All donors had given written informed consent and the study was approved by the ethical review board “Comité de Protection des Personnes Est-III” (ID-RCB 2020-A01292-37). Trial Registration: ClinicalTrials.gov Identifier: NCT04385108