The Transcriptome of Hepatic Fibrosis Revealed by Single‐Cell RNA Sequencing

Abstract

Signaling programs of hepatic disease have historically been studied by comparing bulk diseased and healthy liver tissue. As tissues contain heterogeneous cell mixtures, signals from less represented populations can be dampened; however, single-cell RNA sequencing (scRNAseq) circumvents this. In revealing the transcriptomes of individual cells, scRNAseq has exposed the complex division of labor in normal hepatic homeostasis (1) and led to conceptualization of the "fibrotic niche," (2) regions of scarring composed of scar-associated cells, extracellular matrix, and fibrotic programs. In a recent issue of Nature, Ramachandran and colleagues used scRNAseq to resolve the cellular transcriptomes of healthy and cirrhotic human livers, revealing previously unidentified cell types, cell-cell interactions, and fibrotic programs which comprise the human liver fibrotic niche. (3) Additionally, in a parallel Cell Reports paper, the same group verified hepatic stellate cell (HSC) subpopulation zonation within the murine fibrotic niche using scRNAseq. (4) scRNAseq has emerged as a powerful methodology to link genotype with phenotype and reveal transcriptional culprits of diseases. Starting from a range of platforms such as smaller-scale laser capture microdissection to larger-scale flow-activated cell sorting (FACS) and microfluidics, RNAseq applied to individual cells can be used to identify cellular subpopulations, unfold the history of a cell's transcriptome (pseudotime reconstruction), and reconstruct gene regulatory networks. (5) When using full transcripts (as opposed to 5′ or 3′ tails), scRNAseq can demonstrate splice variants, RNA edits, and rare RNA isoforms (e.g., circular RNA) as well as detect transcriptome changes secondary to allelic expression, revealing downstream impacts of single-nucleotide polymorphisms and mutations. (5) Ramachandran and colleagues employ scRNAseq to report a single-cell atlas of nonparenchymal cells (NPC) from five healthy and five cirrhotic human livers. Using FACS, NPCs were separated into cluster of differentiation 45-positive (CD45 + ; resident/ nonresident leukocytes) and CD45 -(nonleukocyte) fractions. Over 100,000 cells (66,135 deemed liverresident) were sequenced with microfluidics-based scRNAseq, clustered using principal component analysis, and identified using known ontogeny markers. This analysis revealed 21 cell populations from 10 lineages, all of which were represented in healthy and cirrhotic livers. Subpopulations expanded within the cirrhotic liver were identified after comparative analysis of cirrhotic and control livers. (3) Using topographical in silico trajectory and in vitro phenotype analyses, Ramachandran and colleagues reveal that three cell subpopulations, two previously unrecognized, interact spatiotemporally to drive fibrosis within the human liver's fibrotic niche. Endothelial cells expressing atypical chemokine receptor 1 (a regulator of chemokine bioavailability which promotes leukocyte recruitment) and plasmalemma vesicleassociated protein (a membrane prote...

Dihydroartemisinin alleviates hepatic fibrosis through inducing ferroptosis in hepatic stellate cells

“…In recent years, many clinical studies have found that patients with liver fibrosis often have severe pathological iron overload symptoms, suggesting that pathological iron overload may play an essential role in the progression of liver fibrosis. [1][2][3] A large amount of basic research has showed that quiescent HSCs do not express transferrin receptor, whereas activated HSCs overexpress transferrin receptor. 26,27 Transferrin receptor has a strong affinity for extracellular free iron, and transports the iron into activated HSCs through the endocytosis pathway.…”

“…Hepatic fibrosis is a common pathological process that all kinds of chronic liver diseases should undergo to develop into hepatocirrhosis and hepatocarcinoma. [1][2][3] During the occurrence of liver fibrosis, the formation of a large number of fibrous nodules and pseudolobules results in the destruction of the liver structure, abnormal liver function, resistance of hepatic sinusoids, and pathological iron overload in the liver tissue, [1][2][3] which could lead to the accumulation of extracellular matrix (ECM), necrosis of hepatocyte, and activation of hepatic stellate cells (HSCs). Importantly, there is no effective treatment for hepatic fibrosis in clinical practice.…”

Multiplexed Digital Spatial Protein Profiling Reveals a Unique Protein Signature for Advanced Liver Fibrosis

“…[12] Moreover, recent studies using scRNA-seq demonstrated that TREM + CD9 + SAMacs were derived from circulating monocytes and demonstrated a pro-brogenic phenotype. [15,23] Collectively, these studies proposed distinct phenotypes of intrahepatic cell populations through scRNA-seq and suggested that the pro-in ammatory phenotype of intrahepatic macrophage switch to anti-in ammatory or pro-brogenic phenotype during the process of liver brosis.…”

A Unique Immune-Related Gene Signature Represents Advanced Liver Fibrosis and Reveals Potential Therapeutic Targets

“…A recent scRNA-seq study demonstrated a previously unidentified macrophage type in the fibrotic niche of the human liver [ 11 ]. TREM2 + CD9 + scar-associated macrophages are monocyte-derived cells in the fibrotic liver and terminally differentiated, showing a pro-fibrogenic phenotype [ 11 , 18 ]. Moreover, LC3-associated phagocytosis was reported in patients with cirrhosis [ 14 , 19 ].…”