Space-time logic of liver gene expression at sub-lobular scale

Abstract

The mammalian liver is a central hub for systemic metabolic homeostasis. Liver tissue is spatially structured, with hepatocytes operating in repeating lobules, and sub-lobule zones performing distinct functions. The liver is also subject to extensive temporal regulation, orchestrated by the interplay of the circadian clock, systemic signals and feeding rhythms. However, liver zonation was previously analyzed as a static phenomenon, and liver chronobiology at tissue level resolution. Here, we use single-cell RNA-seq to investigate the interplay between gene regulation in space and time. Using mixed-effect models of mRNA expression and smFISH validations, we find that many genes in the liver are both zonated and rhythmic, most of them showing multiplicative space-time effects. Such dually regulated genes cover key hepatic functions such as lipid, carbohydrate and amino acid metabolism, but also previously unassociated genes, such as protein chaperones. Our data also suggest that rhythmic and localized expression of Wnt targets could be explained by rhythmically expressed Wnt ligands from non-parenchymal cells near the central vein. Core circadian clock genes are expressed in a non-zonated manner, indicating that the liver clock is robust to zonation. Together, our scRNA-seq analysis reveals how liver function is compartmentalized spatio-temporally at the sub-lobular scale.

Single Cell Gene Expression Analysis in a 3D Microtissue Liver Model Reveals Cell Type-Specific Responses to Pro-Fibrotic TGF-β1 Stimulation

“…Cluster 1 expresses lactoylglutathione lyase ( GLO ), which is involved in the detoxification of a toxic bi-product of glycolysis, methylglyoxal (MG) [ 34 ], suggesting that the glycolysis pathway could be active in these cells. Furthermore, recent a publication also using scRNA-seq has demonstrated that pericentral hepatocytes express a large number of ribosomal related mRNAs [ 35 ], which was also found for cluster 1. In cluster 10, we find increased HILPDA expression, which is involved in regulating lipid droplet formation and triglyceride storage in hypoxic conditions [ 36 , 37 ].…”

The spatio-temporal program of liver zonal regeneration

“…Our experimental data included hepatocytes from two mice sacrificed at 48 hours and two mice at 72 hours after APAP injection, dissociated using Liberase enzyme. In order to include control non-injected hepatocytes, hepatocytes from a previously published study (Droin et al, 2021) were integrated. Notably, the animals were held at the same facility prior to experiment as animals used for our experiments and cells isolation and library construction were performed similarly to the APAP experiments.…”

“…Fatsq files of these two mice were re-aligned and preprocessed as detailed above for our sequencing runs, to eliminate any bioinformatics biases. Individual Seurat objects were created for the two mice, filtering out cells with less than 1,000 total UMI count and with mitochondrial percentage of less than 9% and more than 35%, as was found to capture viable hepatocytes (Droin et al, 2021). These included 923 cells for ZT6A and 1,076 cells for ZT6B.…”

The hepatocyte insulin receptor is required to program rhythmic gene expression and the liver clock

“…It synchronizes peripheral clocks through various neuronal, physiological, and hormonal signals (Bass et Takahashi, 2010; Green et al, 2008; Mohawk et al, 2012). However, tissues outside the suprachiasmatic nucleus contain local clocks and food intake acts as a synchronizing cue for peripheral clocks such as the liver clock (Koronowski et al, 2019) which is particularly sensitive to feeding (Damiola et al, 2000; Droin et al, 2021; Greenwell et al, 2019; Saini et al, 2013; Stokkan et al, 2001; Vollmers et al, 2009; Weger et al, 2021). Insulin production by pancreatic β-cells is under the control of a circadian clock and responsive to feeding (Perelis et al, 2016).…”