Figure 4.

Transcriptional changes in intestinal biopsy samples from patients with COVID-19 compared with control individuals. (A) Hierarchical clustering of average expression changes for 1063 genes (rows) with induced (red) or depleted (blue) expression (FDR, ≤0.05) in the EC and LP of intestinal biopsy samples from patients with COVID-19. The panel on the left indicates significant genes for each tissue fraction in yellow. The color bar indicates the average log₂ fold change (FC). (B) The top enriched pathways (KEGG) that are induced (red) or depleted (blue) in the LP of patients with COVID-19 are displayed. The dashed line indicates the P ≤ .05 cutoff. Gene names are indicated for main pathways. (C) Deconvolution of main gastrointestinal cell types enriched or depleted in the LP of patients with COVID-19 compared with control individuals. Reference single cell RNA–seq cell-type signatures were taken from Smillie et al¹⁸ (P ≤ .05, Fisher exact test). (D) Average expression changes for DC markers in the EC and LP. Reference small conditional RNA–seq cell-type signatures were taken from Martin et al. The color bar indicates the average log₂(FC). (E) Hierarchical clustering of average expression changes (columns) in the EC and LP for genes related to antiviral response to SARS-CoV-2 in post mortem lung tissue of patients with COVID-19, as described by Blanco-Mello et al (top) and for cytokines and chemokines (bottom). The color bar indicates the average log₂ FC. (F) The gene expression levels for the top 10 significant chemokines and cytokines in the LP of patients with COVID-19 and control individuals. ∗P < .05, ∗∗P < .01. moDC, monocyte-derived dendritic cell.