Single-cell transcriptome and cell type-specific molecular pathways of human non-alcoholic steatohepatitis

Abstract

The aim of this study is to characterize cell type-specific transcriptional signatures in non-alcoholic steatohepatitis (NASH) to improve our understanding of the disease. We performed single-cell RNA sequencing on liver biopsies from 10 patients with NASH. We applied weighted gene co-expression network analysis and validated our findings using a publicly available RNA sequencing data set derived from 160 patients with non-alcoholic fatty liver disease (NAFLD) and 24 controls with normal liver histology. Our study provides a comprehensive single-cell analysis of NASH pathology in humans, describing 19,627 single-cell transcriptomes from biopsy-proven NASH patients. Our data suggest that the previous notion of ”NASH-associated macrophages” can be explained by an up-regulation of normally existing subpopulations of liver macrophages. Similarly, we describe two distinct populations of activated hepatic stellate cells, associated with the level of fibrosis. Finally, we find that the expression of several circulating markers of NAFLD are co-regulated in hepatocytes together with predicted effector genes from NAFLD genome-wide association studies (GWAS), coupled to abnormalities in the complement system. In sum, our single-cell transcriptomic data set provides insights into novel cell type-specific and general biological processes associated with inflammation and fibrosis, emphasizing the importance of studying cell type-specific biological processes in human NASH.

Integrative network-based analysis on multiple Gene Expression Omnibus datasets identifies novel immune molecular markers implicated in non-alcoholic steatohepatitis

“…Our study also observed that hub gene HLA-DRA was higher expressed in both macrophages and dendritic cells (Figure 8C). Intriguingly, previous reports examining human NASH livers using single-cell RNA sequencing reported that M-Mac-1 included three genes, HLA-DRA, HLA-DQA2 and HLA-DQB2 (63), which was related to NAFLD loci (57,64,65). Further, recent study reported that cDC-related gene expression signatures in human livers were associated with NASH pathology (66).…”

Multidimensional landscape of non‐alcoholic fatty liver disease‐related disease spectrum uncovered by big omics data: Profiling evidence and new perspectives

“…For example, liver-resident KCs have been shown to have complex macrophage polarization, and scRNA-seq analysis has demonstrated differences in macrophage activation in NASH. 29 Non-parenchymal cells from NASH mouse livers have been isolated and marked by Trem2, and single-cell data showed that these cells are monocytederived macrophages. 24,28 Other studies have shown that tumor-associated macrophage-like cells are induced in NASH livers and are linked to hepatic carcinoma.…”

“…26 Additionally, activated hepatic stellate cells have been identified as contributing to fibrosis in NASH through collagen deposition, and the single-cell secretome gene analysis has shown that they secrete stellakines associated with chronic liver injury. 24,29 These studies provide a deeper understanding of NAFLD's cellular and molecular mechanisms and can be used to determine potential therapeutic targets.…”

“…Reproduced under terms of the CC-BY license. 29 Copyright 2022, The Authors, published by Springer Nature. NAFLD, non-alcoholic fatty liver disease; NASH, non-alcoholic steatohepatitis.…”

“…Copyright 2021, The Authors, published by Elsevier Inc. (H) UMAP projection of the four macrophage clusters. Reproduced under terms of the CC‐BY license 29 . Copyright 2022, The Authors, published by Springer Nature.…”