Dose-dependent disruption of hepatic zonation by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice: integration of single-nuclei RNA sequencing and spatial transcriptomics

Abstract

ABSTRACT2,3,7,8-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.SYNOPSISSingle-nuclei RNA sequencing (snRNAseq) and spatial transcriptomics were integrated to investigate cell-specific and spatially resolved dose-dependent changes elicited by TCDD. We show that TCDD causes a loss of zonal characteristics that disrupts spatially defined metabolic functions.- Dose-dependent analyses show higher responsiveness of central hepatocytes despite hepatotoxicity occurring initially in the portal region.- Integration of snRNAseq and spatial transcriptomics demonstrates a loss of hepatocytes with portal characteristics.- TCDD disrupted spatially resolved expression of β-catenin signaling members that are critical in maintaining liver zonation.- Spatial transcriptomics and snRNAseq shows induction of R-spondin3 from nonparenchymal cells which serve as cue for the β-catenin pathway.

Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension

“…We utilized MuSiC 70 and NNLS 71 algorithms to estimate the cell type proportions in the study dataset for cell type deconvolution. The reference objects were constructed from single-cell RNA-seq (scRNAseq) of CD45-positive cells in healthy and 4-week CCl4 mice models 3 (n = 2) and whole liver single-nuclei RNA-seq (snRNA-seq) of models induced with 2,3,7,8-Tetrachlorodibenzo-p-dioxin 72 (TCDD, n = 24). Only significant DE markers of each cell cluster, identified with Seurat's FindAllMarkers (parameters: absolute logFC threshold = 1.5, test = Wilcoxon, min.pct = 0.25), were used during deconvolution.…”