A multi-organ post-mortem cellular analysis

The clinical indications of COVID-19 can range from asymptomatic infection to death, the latter often caused by acute respiratory distress syndrome, hyper-inflammation or multiple organ failure. However, numerous questions remain on the physiopathology of this illness, particularly since genetic studies are compromised by the deterioration of post-mortem material. American researchers at Harvard University and the Massachusetts Institute of Technology have created an organ bank from 17 deceased COVID-19 patients. The bank comprises 11 organs in total. Using this material, they carried out a single-cell transcriptome (sc/snRNA-seq), in other words a complete analysis of genes over- or under-expressed in COVID-19 subjects.

In the lungs, 28 cell subtypes were identified, amongst the parenchymal, endothelial and immune system cells. Many changes were observed within the transcriptional programmes of several cell types. AT2 pneumocytes showed a marked antiviral and inflammatory response, as well as programmed cell death (STAT1). The genes associated with the production of surfactant, a lubricant necessary for respiratory functions, were under-expressed. To complete the destruction of the respiratory epithelium (AT1 pneumocytes) by the virus, several regeneration strategies were implemented by AT2 progenitor cells, but proved to be ineffective in reconstituting the alveoli.

At the same time, an expansion of fibroblasts was observed. Levels of viral RNA were highest in the macrophages, mastocytes and endothelial cells, and low in pneumocytes, due to their dying massively.  Viral RNA was also found in some specific blood cells, including B cells. Those cells carrying the viral genome initiated specific immune programmes, mobilized by the emission of TNF and API proteins, and certain cytokines (CXCL10, CXCL11). Analyses show that the more the virus multiplies, the faster death occurs after symptoms appear.

To assess the impact of tissue context in vivo, the researchers used a supplementary cohort of 14 donors (of whom 3 were healthy) in conjunction with a specific profiling algorithm (DSP). This spatial analysis took into consideration non-infected pulmonary areas and showed that in COVID-19 patients, the alveoli experience a marked increase in genes activated by interferon as well as by oxidative stress (aggressions caused by oxygen-derived molecules such as free radicals). However, the genes linked to TNF⍺, IL2-STAT5 and TGFβ are much less expressed. A decrease in the expression of genes related to the integrity of the epithelium (claudins and tight junctions) was noted, which illustrates the destruction of the alveolar barrier. Unlike in other studies, very few viral genomes were found outside of the lungs (liver, heart, kidneys). In the heart, the PLCG2 gene, whose function is unknown, is very overexpressed.

By integrating research by the GWAS (Genome Wide Association Study) into their data, they identified certain genes associated with the risks of COVID-19: 14 genes were overexpressed in the lungs of sick patients and 21 were specifically overexpressed in at least one cell type. AT2 pneumocytes are the cells that show the most genetic predisposition to severe cases (FOXP4, OAS3, FYCO1, NFKBIZ, DPP9). The others are hair cells, TCD8 lymphocytes and macrophages (CCRL2). Predisposition genes are derived from multiple genomic regions.

This analysis, which involved a large number of organs and which was carried out using a bio-bank of post-mortem severe COVID-19 cases, is complementary to another study which did not analyse only the lungs (see previous article). This research provides essential data for the scientific community involved in the study of the physiopathology of COVID-19, and future meta-analyses will give it even greater significance.