Deciphering the state of immune silence in fatal COVID-19 patients

Bost, Pierre; De Sanctis, Francesco; Canè, Stefania; Ugel, Stefano; Donadello, Katia; Castellucci, Monica; Eyal, David; Fiore, Alessandra; Anselmi, Cristina; Barouni, Roza Maria; Trovato, Rosalinda; Caligola, Simone; Lamolinara, Alessia; Iezzi, Manuela; Facciotti, Federica; Mazzariol, Annarita; Gibellini, Davide; De Nardo, Pasquale; Tacconelli, Evelina; Gottin, Leonardo; Polati, Enrico; Schwikowski, Benno; Amit, Ido; Bronte, Vincenzo

Since the beginning of the SARS-CoV-2 pandemic, COVID-19 appeared as a unique disease with unconventional tissue and systemic immune features. Here we show a COVID-19 immune signature associated with severity by integrating single-cell RNA-seq analysis from blood samples and broncho-alveolar lavage fluids with clinical, immunological and functional ex vivo data. This signature is characterized by lung accumulation of naïve lymphoid cells associated with a systemic expansion and activation of myeloid cells. Myeloid-driven immune suppression is a hallmark of COVID-19 evolution, highlighting arginase-1 expression with immune regulatory features of monocytes. Monocyte-dependent and neutrophil-dependent immune suppression loss is associated with fatal clinical outcome in severe patients. Additionally, our analysis shows a lung CXCR6(+) effector memory T cell subset is associated with better prognosis in patients with severe COVID-19. In summary, COVID-19-induced myeloid dysregulation and lymphoid impairment establish a condition of ‘immune silence’ in patients with critical COVID-19.