Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor

2,3,7,8-Tetrachlorodibenzio-p-dioxin (TCDD) is a persistent environmental contaminant known for aryl hydrocarbon receptor (AHR)-mediated liver effects, including metabolic dysfunction-associated steatotic liver disease (MASLD)-like pathologies such as steatosis, inflammation, and fibrosis. Although previous studies have focused on AHR-mediated regulation of protein-coding genes, recent attention has turned to long non-coding RNAs (lncRNAs) because of their potential roles in the progression of steatotic liver disease (SLD). Using bulk and single-nuclei (sn)RNAseq datasets, we compared the dose-dependent AHR-mediated induction of lncRNA and mRNA expression by TCDD in the mouse and rat liver. This study also investigated cell-specific lncRNA-gene regulation within the murine liver to identify divergent lncRNA expression patterns across different hepatic cell types. Lastly, differentially expressed (DE) lncRNAs associated with human liver diseases were examined to investigate potential mechanistic roles. Comparative analysis of gene expression identified 2,386 mouse and 916 rat DE lncRNAs, with 203 common to both species. In contrast, mice had 6,071 compared to 3,056 rat DE mRNAs, with 1,492 in common. Integration of AHR genomic enrichment and putative dioxin response elements (pDRE) data with DE lncRNAs revealed regulation patterns similar to mRNA-coding genes, with both exhibiting greater frequency proximal to the transcription start site in both mice and rats. snRNAseq analysis also revealed 5,495 DE lncRNAs across all liver cell subtypes. Pericentral and periportal hepatocytes exhibited the most significant changes, with 3,339 and 3,550 DE lncRNAs respectively, followed by macrophages with 2,116. Among all DE genes, 52 previously annotated lncRNAs in hepatocytes were differentially expressed by TCDD, many of which are associated with steatosis, fibrosis, and hepatocellular carcinoma. Collectively, these results suggest AHR-mediated differential expression of lncRNAs may play a significant role in the progression of steatosis to steatohepatitis with fibrosis elicited by TCDD.