A Rat Liver Cell Atlas Reveals Intrahepatic Myeloid Heterogeneity.

The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) makes it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single cell and single nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains, and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models. Four whole livers were acquired from 8-10 week-old healthy male Dark Agouti and Lewis strains and the resulting total liver homogenates went through 2-step collagenase digestion. To provide a more detailed resource of rat hepatic immune cells, two additional immune-enriched samples were collected. These samples underwent additional washing steps and red blood cell depletion to reduce the hepatocyte-released ambient RNA. The size samples were analyzed using scRNAseq. Liver tissue from an additional two pairs of Lewis and Dark Agouti rats were taken and processed for 10x Genomics single nuclei RNA sequence (snRNA-seq) to further inform parenchymal cell identities.