Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Corresponding author: djw{at}bu.edu
Abstract
LncRNAs comprise a heterogeneous class of RNA-encoding genes typified by low expression, nuclear enrichment, high tissue-specificity, and functional diversity, but the vast majority remain uncharacterized. Here, we assembled the mouse liver noncoding transcriptome from >2000 bulk RNA-seq samples and discovered 48,261 liver-expressed lncRNAs, a majority novel. Using these lncRNAs as a single-cell transcriptomic reference set, we elucidated lncRNA dysregulation in mouse models of high fat diet-induced nonalcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis. Trajectory inference analysis revealed lncRNA zonation patterns across the liver lobule in each major liver cell population. Perturbations in lncRNA expression and zonation were common in several disease-associated liver cell types, including nonalcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, a central feature of liver fibrosis. Single-cell-based gene regulatory network analysis using bigSCale2 linked individual lncRNAs to specific biological pathways, and network-essential regulatory lncRNAs with disease-associated functions were identified by their high network centrality metrics. For a subset of these lncRNAs, promoter sequences of the network-defined lncRNA target genes were significantly enriched for lncRNA triplex formation, providing independent mechanistic support for the lncRNA–target gene linkages predicted by the gene regulatory networks. These findings elucidate liver lncRNA cell-type specificities, spatial zonation patterns, associated regulatory networks, and temporal patterns of dysregulation during hepatic disease progression. A subset of the liver disease-associated regulatory lncRNAs identified have human orthologs and are promising candidates for biomarkers and therapeutic targets.
Keywords
- lncRNA
- high fat diet
- carbon tetrachloride
- liver fibrosis
- BigSCale2 networks
- liver disease marker genes
Footnotes
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Abbreviations: CCl4, carbon tetrachloride; GTF, Gene Transfer Format; HFHFD, high fat, high fructose diet; HSC, hepatic stellate cell; lncRNA, long noncoding RNA; lnc, followed by a number: numbering system for set of 48,261 mouse liver expressed lncRNAs, where an asterisk (*) marks mouse liver lncRNAs with a human ortholog; NAFLD, nonalcoholic fatty liver disease; Nam, NASH-associated macrophages; NASH, nonalcoholic steatohepatitis; PC, principal components; PCG, protein-coding gene; scRNA-seq, single-cell RNA sequencing; TGI, transcript-genome identity; TTI, transcript-transcript identity; TTS, triplex target site; UMAP, Uniformed Manifold Approximation and Projection; UMI, unique molecular identifier; VSMC, vascular smooth muscle cell.
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.079580.123.
- Received January 5, 2023.
- Accepted March 9, 2023.
This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
