Kupffer cell diversity maintaines liver function in alcohol associated liver disease [scRNA-seq]

Background & Aims: Liver macrophages are heterogeneous and play an important role in alcohol_x0002_associated liver disease (ALD) but there is limited understanding of the functions of specific macrophage subsets in the disease. We used a Western Diet Alcohol (WDA) mouse model of ALD to examine the hepatic myeloid cell compartment by scRNA seq and targeted Kupffer cell (KC) ablation to understand the diversity and function of liver macrophages in ALD. Approach and Results: In the WDA liver, KCs and infiltrating monocytes/macrophages (IMs) each represented about 50% of the myeloid pool. Five major KC clusters all expressed genes associated with receptor mediated endocytosis and lipid metabolism, but most were predicted to be non_x0002_inflammatory and antifibrotic with one minor KC cluster having a pro-inflammatory and extracellular matrix degradation gene signature. IM clusters, in contrast, were predicted to be pro_x0002_inflammatory and pro-fibrotic. In vivo diphtheria toxin based selective KC ablation during alcohol exposure resulted in a liver failure phenotype with increases in PT/INR and bilirubin, loss of differentiated hepatocyte gene expression, and an increase in expression of hepatocyte progenitor markers such as EpCAM, CK-7 and Igf2bp3. Gene set enrichment analysis of whole liver RNAseq from the KC ablated WDA mice showed a similar pattern as seen in human alcoholic hepatitis. Conclusions: In this ALD model, KCs are anti-inflammatory and are critical for maintenance of hepatocyte differentiation. IMs are largely pro-inflammatory and contribute more to liver fibrosis. Future targeting of specific macrophage subsets may provide new approaches to treatment of liver failure and fibrosis in ALD. Overall design: We performed scRNAseq of total liver immune cells of chow fed (n=2), Western Diet only (WD) (n=4), and Western Diet Alcohol (WDA) (n=4) mice after 16 weeks of western diet and alcohol feeding. Total nonparenchymal cells (NPCs) were isolated by liver perfusion, and FACS sorted CD45+ cells were sequenced. Sequencing yield averaged 8,000-9,000 cells per sample and results from all 10 animals were combined for initial clustering.