The spatio-temporal program of liver zonal regeneration

Abstract

The liver carries a remarkable ability to regenerate rapidly after acute zonal damage. Single-cell approaches are necessary to study this process, given the spatial heterogeneity of multiple liver cell types. Here, we use spatially-resolved single cell RNA sequencing (scRNAseq) to study the dynamics of mouse liver regeneration after acute acetaminophen (APAP) intoxication. We find that hepatocytes proliferate throughout the liver lobule, creating the mitotic pressure required to repopulate the necrotic pericentral zone rapidly. A subset of hepatocytes located at the regenerating front transiently up-regulate fetal-specific genes, including Afp and Cdh17, as they reprogram to a pericentral state. Zonated endothelial, hepatic-stellate cell (HSC) and macrophage populations are differentially involved in immune recruitment, proliferation and matrix remodeling. We observe massive transient infiltration of myeloid cells, yet stability of lymphoid cell abundance, in accordance with global decline in antigen presentation. Our study provides a resource for understanding the coordinated programs of zonal liver regeneration. doi: https://doi.org/10.1101/2021.08.11.455924

Interactively exploring the data

This online tool enables to interact and explore the datasets prodiced in the study. Data are also available to download.

Single cell RNA sequencing

Our scRNAseq dataset is comprised of ~24k cells sequenced at different time points after APAP administration - 0h, 24h, 48h, 72h, 96h and 1w. In addition, the spatial localisation of hepatocytes, endothelial cells (LVEC and LSEC) and HSCs was computationally inferred, to establish the spatio-temporal maps for those cell types.

In the Single cell RNA tab, data are presented in both UMAP plot and and gene plot modes. Cells in the UMAP can be colored by their cell type clustering (default), by their timepoint, or by their expression level of any gene of interest. The selected gene’s temporal dynamics over time are plotted as well, stratified by cell types and classified into different zones for hepatocytes, endothelial cells and HSCs. Expression level can be scaled for each cell type separately, or for all cell types together (default).

Spatial Transcriptomics

We also performed spatial transcriptiomics, using 10x Visium. Six slides of livers from 24h, 48h and 27h after APAP injection (two mice per time point) were sequenced. spots were first classified to either fibrotic (1) or non-fibrotic (0) based on their expression levels of Collagens and/or on their histology. Fibrotic areas were then skeletonized, to estimate the localization of central-most coordinates in the tissue (marked in black in the plots). Spots were then assigned into one of three lobule layers - 1 (pericentral/perinecrotic), 2 (mid lobule) and 3 (periportal), based on their distance from the skeletonized central coordinates. Spot with shorthest distance to a central coordinate exceeding 350um (the typical porto-central axis size in mouse) were not assigned a layer (denoted as NaN in the plots).

In the Spatial transcriptomics tab, the Visium spots are plotted by their position in each slide, with black dots marking the central position of the lobules. Spots can be colored by their classification into lobule layer, by their fibrotic classification, or by their expression level of any gene of interest.

This tool was created based on MCView by Amos Tanay lab at the Weizmann Institute of Science and with the invaluable help of Aviezer Lifshitz.

In memory of Elad Chomsky