Fig. 1: Single nuclei multiomics identifies zonated hepatocyte nuclei.
A Nuclei were extracted from samples of frozen mouse liver isolated from control mice (TCF7L2LoxP/LoxP, n = 3) and processed through the 10X Chromium Single Cell Multiome ATAC and Gene Expression pipeline. After QC and filtering, 5,652 nuclei were used for clustering analysis. B The RNA data of all samples was integrated using the reciprocal PCA approach via Seurat. C ATAC data were integrated using the reciprocal LSI approach via Signac, and (D) the Weighted Nearest Neighbor (WNN) approach was used for the integrative analysis of the two modalities. Each modality and the integrative analysis detected the major parenchymal and non-parenchymal cell populations in mouse liver. Hepatocyte nuclei were subdivided into periportal (PP) zone 1, mid-lobular zone 2, and pericentral (PC) zone 3 hepatocytes based on the expression of zonated marker genes, as detailed in the methodology. E Trajectory analysis was performed on hepatocyte nuclei only using Monocle3. The component of WNN hepatocyte-only clustering that was enriched for zone 1 PP marker gene expression was designated as the root node. We considered a gene zonally expressed if it was identified as a differentially expressed gene (DEGs) and was associated with the hepatocyte trajectory. F–H The expression (solid colored line) and accessibility (dashed line) of landmark zonated genes identified by Halpern et al.26. in C57BL/6 mice was examined in our control liver dataset. Shown is the average with the spread (shaded region) representing the SEM. I Pathway analysis revealed enrichment of classically zonated metabolic pathways in TCF7L2LoxP/LoxP livers, including bile secretion, cholesterol metabolism, and xenobiotic metabolism. Source data are provided as a Source Data file. Single nuclei data are available for download at GEO (accession: GSE239480).
