The pulmonary vasculature in lethal COVID-19 and idiopathic pulmonary fibrosis at single-cell resolution
Authors: de Rooij Laura P M H , Becker Lisa M , Teuwen Laure-Anne , Boeckx Bram , Jansen Sander , Feys Simon , Verleden Stijn , Liesenborghs Laurens , Stalder Anna K , Libbrecht Sasha , Van Buyten Tina , Philips Gino , Subramanian Abhishek , Dumas Sébastien J , Meta Elda , Borri Mila , Sokol Liliana , Dendooven Amélie , Truong Anh-Co K , Gunst Jan , Van Mol Pierre , Haslbauer Jasmin D , Rohlenova Katerina , Menter Thomas , Boudewijns Robbert , Geldhof Vincent , Vinckier Stefan , Amersfoort Jacob , Wuyts Wim , Van Raemdonck Dirk , Jacobs Werner , Ceulemans Laurens J , Weynand Birgit , Thienpont Bernard , Lammens Martin , Kuehnel Mark , Eelen Guy , Dewerchin Mieke , Schoonjans Luc , Jonigk Danny , van Dorpe Jo , Tzankov Alexandar , Wauters Els , Mazzone Massimiliano , Neyts Johan , Wauters Joost , Lambrechts Diether , Carmeliet Peter 
Published: August 2022

Aims

Severe acute respiratory syndrome coronavirus-2 infection causes COVID-19, which in severe cases evokes life-threatening acute respiratory distress syndrome (ARDS). Transcriptome signatures and the functional relevance of non-vascular cell types (e.g. immune and epithelial cells) in COVID-19 are becoming increasingly evident. However, despite its known contribution to vascular inflammation, recruitment/invasion of immune cells, vascular leakage, and perturbed haemostasis in the lungs of severe COVID-19 patients, an in-depth interrogation of the endothelial cell (EC) compartment in lethal COVID-19 is lacking. Moreover, progressive fibrotic lung disease represents one of the complications of COVID-19 pneumonia and ARDS. Analogous features between idiopathic pulmonary fibrosis (IPF) and COVID-19 suggest partial similarities in their pathophysiology, yet, a head-to-head comparison of pulmonary cell transcriptomes between both conditions has not been implemented to date.

Methods and results

We performed single-nucleus RNA-sequencing on frozen lungs from 7 deceased COVID-19 patients, 6 IPF explant lungs, and 12 controls. The vascular fraction, comprising 38 794 nuclei, could be subclustered into 14 distinct EC subtypes. Non-vascular cell types, comprising 137 746 nuclei, were subclustered and used for EC-interactome analyses. 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. In addition, increased abundance of a population of systemic capillary and venous ECs was identified in COVID-19 and 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. 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.

Conclusions

This study uncovered novel insights into the abundance, expression patterns, and interactomes of EC subtypes in COVID-19 and IPF, relevant for future investigations into the progression and treatment of both lethal conditions.