Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages

Wauters, Els; Van Mol, Pierre; Garg, Abhishek Dinkarnath; Jansen, Sander; Van Herck, Yannick; Vanderbeke, Lore; Bassez, Ayse; Boeckx, Bram; Malengier-Devlies, Bert; Timmerman, Anna; Van Brussel, Thomas; Van Buyten, Tina; Schepers, Rogier; Heylen, Elisabeth; Dauwe, Dieter; Dooms, Christophe; Gunst, Jan; Hermans, Greet; Meersseman, Philippe; Testelmans, Dries; Yserbyt, Jonas; Tejpar, Sabine; De Wever, Walter; Matthys, Patrick; Neyts, Johan; Wauters, Joost; Qian, Junbin; Lambrechts, Diether

How the innate and adaptive host immune system miscommunicate to worsen COVID-19 immunopathology has not been fully elucidated. Here, we perform single-cell deep-immune profiling of bronchoalveolar lavage (BAL) samples from 5 patients with mild and 26 with critical COVID-19 in comparison to BALs from non-COVID-19 pneumonia and normal lung. We use pseudotime inference to build T-cell and monocyte-to-macrophage trajectories and model gene expression changes along them. In mild COVID-19, CD8(+) resident-memory (T(RM)) and CD4(+) T-helper-17 (T(H17)) cells undergo active (presumably antigen-driven) expansion towards the end of the trajectory, and are characterized by good effector functions, while in critical COVID-19 they remain more naïve. Vice versa, CD4(+) T-cells with T-helper-1 characteristics (T(H1)-like) and CD8(+) T-cells expressing exhaustion markers (T(EX)-like) are enriched halfway their trajectories in mild COVID-19, where they also exhibit good effector functions, while in critical COVID-19 they show evidence of inflammation-associated stress at the end of their trajectories. Monocyte-to-macrophage trajectories show that chronic hyperinflammatory monocytes are enriched in critical COVID-19, while alveolar macrophages, otherwise characterized by anti-inflammatory and antigen-presenting characteristics, are depleted. In critical COVID-19, monocytes contribute to an ATP-purinergic signaling-inflammasome footprint that could enable COVID-19 associated fibrosis and worsen disease-severity. Finally, viral RNA-tracking reveals infected lung epithelial cells, and a significant proportion of neutrophils and macrophages that are involved in viral clearance.