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A molecular single-cell lung atlas of lethal COVID-19

Authors: Melms, Johannes C.; Biermann, Jana; Huang, Huachao; Wang, Yiping; Nair, Ajay; Tagore, Somnath; Katsyv, Igor; Rendeiro, André F.; Amin, Amit Dipak; Schapiro, Denis; Frangieh, Chris J.; Luoma, Adrienne M.; Filliol, Aveline; Fang, Yinshan; Ravichandran, Hiranmayi; Clausi, Mariano G.; Alba, George A.; Rogava, Meri; Chen, Sean W.; Ho, Patricia; Montoro, Daniel T.; Kornberg, Adam E.; Han, Arnold S.; Bakhoum, Mathieu F.; Anandasabapathy, Niroshana; Suárez-Fariñas, Mayte; Bakhoum, Samuel F.; Bram, Yaron; Borczuk, Alain; Guo, Xinzheng V.; Lefkowitch, Jay H.; Marboe, Charles; Lagana, Stephen M.; Del Portillo, Armando; Zorn, Emmanuel; Markowitz, Glen S.; Schwabe, Robert F.; Schwartz, Robert E.; Elemento, Olivier; Saqi, Anjali; Hibshoosh, Hanina; Que, Jianwen; Izar, Benjamin

Online: https://www.nature.com/articles/s41586-021-03569-1

Issue: Nature. 2021 Jul;595(7865):114-119.


Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection1,2, yet the host response at the lung tissue-level is poorly understood. Here, we performed single-nucleus RNA-sequencing of ~116,000 nuclei of lungs from 19 COVID-19 decedents who underwent rapid autopsy and 7 control lungs. Integrated analyses revealed significant alterations in cellular composition, transcriptional cell states, and cell-to-cell interactions, providing insights into the biology of lethal COVID-19. COVID-19 lungs were highly inflamed with dense infiltration of aberrantly activated monocyte-derived macrophages and alveolar macrophages, but demonstrated impaired T cell responses. Monocyte/macrophage-derived IL-1β and epithelial cell-derived IL-6 were unique features of SARS-CoV-2 infection compared to other viral and bacterial causes of pneumonia. Alveolar type 2 cells adopted an inflammation-associated transient progenitor cell state and failed to undergo full transition into alveolar type 1 cells resulting in impaired lung regeneration. Furthermore, we identified expansion of recently described CTHRC1+ pathological fibroblasts3 contributing to rapidly ensuing pulmonary fibrosis in COVID-19. Inference of protein activity and ligand-receptor interactions identified putative drug targets to disrupt deleterious circuits. This atlas enables dissection of lethal COVID-19, may inform our understanding of long-term complications of COVID-19 survivors, and provides an important resource for therapeutic development.