SARS-CoV-2, COVID-19, IPF, Transcriptomics, Single-nucleus RNA-seq, Lung, Endothelial cells Receptor–ligand interaction analysis of ECs with non-vascular cell types in the pulmonary micro-environment revealed numerous previously unknown interactions specifically enriched/depleted in COVID-19 and/or IPF. COVID-19 systemic ECs closely resembled their IPF counterparts, and a set of 30 genes was found congruently enriched in systemic ECs across studies. In addition, increased abundance of a population of systemic capillary and venous ECs was identified in COVID-19 and IPF. Pulmonary ECs of deceased COVID-19 patients showed an enrichment of genes involved in cellular stress, as well as signatures suggestive of dampened immunomodulation and impaired vessel wall integrity. Non-vascular cell types, comprising 137 746 nuclei, were subclustered and used for EC-interactome analyses. The vascular fraction, comprising 38 794 nuclei, could be subclustered into 14 distinct EC subtypes. We performed single-nucleus RNA-sequencing on frozen lungs from 7 deceased COVID-19 patients, 6 IPF explant lungs, and 12 controls. Laura P M H de Rooij, Lisa M Becker, Laure-Anne Teuwen, Bram Boeckx, Sander Jansen, Simon Feys, Stijn Verleden, Laurens Liesenborghs, Anna K Stalder, Sasha Libbrecht, Tina Van Buyten, Gino Philips, Abhishek Subramanian, Sébastien J Dumas, Elda Meta, Mila Borri, Liliana Sokol, Amélie Dendooven, Anh-Co K Truong, Jan Gunst, Pierre Van Mol, Jasmin D Haslbauer, Katerina Rohlenova, Thomas Menter, Robbert Boudewijns, Vincent Geldhof, Stefan Vinckier, Jacob Amersfoort, Wim Wuyts, Dirk Van Raemdonck, Werner Jacobs, Laurens J Ceulemans, Birgit Weynand, Bernard Thienpont, Martin Lammens, Mark Kuehnel, Guy Eelen, Mieke Dewerchin, Luc Schoonjans, Danny Jonigk, Jo van Dorpe, Alexandar Tzankov, Els Wauters, Massimiliano Mazzone, Johan Neyts, Joost Wauters, Diether Lambrechts, Peter Carmeliet, The pulmonary vasculature in lethal COVID-19 and idiopathic pulmonary fibrosis at single-cell resolution, Cardiovascular Research, Volume 119, Issue 2, February 2023, Pages 520–535,
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