Fig. 2: Differentially expressed ligands driving upregulated and downregulated intercellular interactions between colonic and ileal infected immature enterocytes and resident immune cells upon infection in the colon and ileum.

a Heatmap showing the number of interactions between immature enterocytes and resident immune cells. Interactions driven by upregulated and downregulated ligands (ligand direction) are shown separately for infected and bystander cells (status), and for ileum and colonic organoids. The intensity of the colour indicates the number of interactions with the immune cell types whose receptor is targeted by the epithelial cells ligands. The numbers on the ligand direction row refer to the number of upregulated or downregulated ligands driving the indicated interactions with immune cells for the different groups/conditions. Abbreviations: Ileum: inf_macrophage infected macrophage, mast mast cell, CD8_Trm_cyto Resident memory cytotoxic T cell, DC2 dendritic cell 2, Trm Tissue-resident memory T cell, gd_Tcell Gamma delta (γδ) T cells, ILC Innate lymphoid cell, mem_Bcell memory B cell, naive_Bcell naive B cell, TFH_like T follicular helper cells, Trm_Th17 Tissue-resident memory Th17 cells, Treg Regulatory T cell, Tcyto Cytotoxic T cell, Tmem Memory T cells. Colon: ILC Innate lymphoid cell, CD8_IL17 IL-17+ CD8+ T cells, DC dendritic cells, GC_Bcell Germinal center B cells, CD4_PD1 mast mast cell, Treg Regulatory T cell, NK Natural Killer cell, CD4_MThi high mitochondrial CD4+ T cell, CD4_memory CD4+ Memory T cell, CD4_activ_fos_high activated CD4+ T cells (high/low c-fos), CD8_LP CD8+ lymphocyte-predominant cells, CD8_IEL CD8+ intraepithelial lymphocytes. b Venn diagrams showing the number of ligands of the infected immature enterocytes–immune cells intercellular network that are unique or shared between the ileum and colon. Upregulated and downregulated ligands are shown separately. The full list of ligands is available as Table 1.