2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (Rspo3) and pericentral Apc, suggested dysregulation of the Wnt/β-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies.

Table S1. Molecular Cartography probe catalog numbers and target sequences.

Table S2. Number of nuclei sequenced passing QC for each animal.

Table S3. Number of nuclei sequenced passing QC for each animal and cell type.

Table S4. Celltype marker genes of hepatic cell types.

Table S5. Correlation of pseudobulk snRNAseq data and experimental bulk RNAseq data from the same liver samples.

Table S6. Differential expression analysis of hepatic cell types using the scBT method.

Table S7. Functional Enrichment analysis of cell-specific differentially expressed genes.