Transcriptomic profiling of isolated hepatic macrophage subsets (Kupffer cells, Monocyte-derived Macrophages and Monocytes) in common bile duct ligated (CBDL)-mice, mice with acute colitis (DSS), and combinations (CBDL+DSS)

In this study, we aimed to unravel the transcriptional profiles of specific hepatic macrophage subsets during cholestatic liver injury, acute colitis and when colitis is induced as a second hit on advanced cholestatic liver injury. Differentially expressed genes (DEGs) and corresponding pathways were determined via DESeq2 in R and STRING-App comparing groups or cell types as outlined in the 'overall design' section below. Our results highlight the heterogeneity of the liver macrophage (MF) pool and describe functional differences between MF subsets. Longitudinally, the CBDL-associated expression profiles of each macrophage subset remained mostly stable. CBDL-induced cholestatic liver injury was characterized by the emergence of Trem2/Spp1 expressing monocyte-derived macrophages (MoMFs). DSS-colitis as a second hit on cholestatic liver injury enhanced this phenotype of MoMFs. Overall design: This RNA-Seq study investigates 3 cell types (KC, MoMF and Mo) isolated from livers of mice from 5 experimental groups (CBDL2w, CBDL6w, Sham6w, DSS and CBDL+DSS). We aimed to include 4 replicates per group, but for several specific samples, replicates had to be pooled. Differential gene expression was determined for each individual cell type i) comparing each injury group with the control group (Sham6w), ii) comparing cholestatic liver injury at onset with advanced injury (CBDL2w vs CBDL6w), iii) comparing advanced cholestatic liver injury as such with the same injury including acute colitis as a second hit (CBDL6w vs CBDL+DSS). We also determined differential gene expression between cell types within each experimental group.