Fig. 1: Expression of NRF2-driven genes is suppressed in COVID-19 patient biopsies.

a, b, c Reanalysis of data published by Blanco-Melo et al.¹⁴ (a) Bar-chart of the number of transcripts showing significant differential expression (adjusted p value < 0.05 and log2(FC) > 1.0). Data from COVID19 lung biopsies was normalized against healthy lung biopsies, and in cell lines Calu3, NHBE, and A549 infected with either SARS-CoV2, Influenza A virus (IAV), Respiratory Syncytial virus (RSV), or human parainfluenza virus type 3 (HPIV3) against mock treated cells. Expression and p values were calculated with DESeq2 using Wald test statistic and Benjamini-Hochberg correction for multiple testing. b Heat map of the subset of genes significantly differentially expressed in COVID19 biopsies and simultaneously differentially expressed in at least 3 of the other conditions tested. The genes in each cluster were used for pathway enrichment analysis. Genes in cluster 1 are dominantly down-regulated in COVID19 biopsies while a sub-cluster of genes in cluster 1 are up-regulated in the cell lines. Conversely, genes in cluster 2 are predominantly up-regulated in biopsies and in most other test-samples. A subcluster of the genes in cluster 2 are down regulated in the cell lines. For each cluster, the significantly enriched pathways are listed (EnrichR). c Cloud analysis of NRF2-driven differentially expressed genes. Subsets annotated as inflammation/NFκB signaling and Type I IFN signaling exhibit different expression patterns. The experiment is a reanalysis of data from Blanco-Melo et al. [https://doi.org/10.1101/2020.03.24.004655]. d Reanalysis of the data from Desai et al.¹⁵ GEO accession code GSE150316. Heat map of NRF2 target genes of the lung autopsies from the five COVID19 patients. Healthy lung samples were used as negative control.