A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding. ### Competing Interest Statement A.K.S. reports compensation for consulting and/or SAB membership from Merck, Honeycomb Biotechnologies, Cellarity, Repertoire Immune Medicines, Ochre Bio, Third Rock Ventures, Hovione, Relation Therapeutics, FL82, Senda Biosciences, Empress Therapeutics, IntrECate Biotherapeutics, and Dahlia Biosciences unrelated to this work. A.R. is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and until August 31, 2020 was an SAB member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov and ThermoFisher Scientific. From August 1, 2020, A.R. is an employee of Genentech, a member of the Roche Group, with equity in Roche. I.S.V. consults for Guidepoint Global, Mosaic, and NextRNA. G.S. consults in Alnylam Pharmaceuticals, Merck, Generon, Glympse Bio, Inc., Mayday Foundation, Novartis Pharmaceuticals, Quest Diagnostics, Surrozen, Terra Firma, Zomagen Bioscience, Pandion Therapeutics, Inc., Durect Corporation; royalty from UpToDate Inc. and Editor service for Hepatology Communications. Y.P. receives grant support from Enanta Pharmaceuticals, CymaBay Therapeutics, Morphic Therapeutic; consulting and/or SAB in Ambys Medicines, Morphic Therapeutics, Enveda Therapeutics, BridgeBio Pharma, as well as being an Editor of American Journal of Physiology-Gastrointestinal and Liver Physiology. Z.G.J. receives grant support from Gilead Science, Pfizer and compensation for consulting from Olix Pharmaceuticals. L.P, T.H., S.W, J.B, E.M, and J.R. are employees and/or stockholders of NanoString Technologies. B.I. has received honoraria from consulting with Merck, Janssen Pharmaceuticals, AstraZeneca, and Volastra Therapeutics. A.R. and O.R.R. are inventors on multiple patents from the Broad Institute related to single cell and spatial genomics.