Single-cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice

Abstract

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.

TCDD dysregulation of lncRNA expression, liver zonation and intercellular communication across the liver lobule

“…We identified more than 4,000 lncRNAs whose expression is dysregulated by TCDD in one or more liver cell types, including 684 lncRNAs specifically deregulated in NPCs. We also discovered 121 lncRNAs, and 689 protein-coding genes, whose zonated expression in hepatocytes across the liver lobule is disrupted by TCDD, the latter finding being consistent with the major zonal toxicity recently described for TCDD 28 . Gene regulatory networks constructed from the snRNA-seq expression data identified liver network-essential lncRNA regulators specifically linked to functional gene ontology terms, such as cell adhesion, cell migration and extracellular matrix in control (healthy) liver, and fatty acid metabolic process, peroxisome, and xenobiotic metabolic process in TCDD-exposed liver.…”

“…Individual lncRNAs have been linked to hepatotoxicity induced by foreign chemical exposures 26, 27 , however, a global investigation of the roles of lncRNAs in foreign chemical-induced hepatotoxicity, and in particular TCDD-induced hepatoxicity, is lacking. Recently, Nault et al used snRNA-seq to characterize liver cell type-specific transcriptional changes in a chronic (28 day) TCDD exposure model and reported widespread dysregulation of gene expression in multiple liver cell types, as well as marked expansion of the liver macrophage population and extensive TCDD-induced changes in hepatic zonation 18, 28 . However, the effects of TCDD on the thousands of liver-expressed lncRNAs recently identified and shown to be amenable to analysis using snRNA-seq 22 were not considered.…”

Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension

“… 3 GEO: GSE136103 Mouse single-nuclei RNA-seq validation dataset 51 Nault et al. 51 GEO: GSE148339 Experimental Models: Organisms/Strains Mouse: C57BL/6JRj: WT Janvier Labs SC-C57J-M Software and Algorithms Scripts for data analysis Original scripts https://doi.org/10.5281/zenodo.10230613 AnnotationDbi 52 Pagès et al. 52 1.60 PCAtools 53 Blighe and Lun 53 2.10 DESeq2 54 Love et al.…”

Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery

“…Correlation of regional tissue damage assessments with spatial expression aids in elucidating the toxic mechanisms of drugs and the pathophysiology of hepatic injury. A study integrating single-nucleus RNA sequencing and ST revealed a spatially dependent dose-response relationship between liver lipid accumulation and inflammatory responses induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), elucidating the specificity of cellular phenotypes and transcriptional alterations in various hepatic regions induced by TCDD and the molecular mechanisms underlying TCDD-induced nonalcoholic fatty liver disease progression 113 .…”