Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity

• Published in: JHEP reports 2021-06, Vol.3 (3), p.100278-100278, Article 100278
• Main Authors: Payen, Valéry L., Lavergne, Arnaud, Alevra Sarika, Niki, Colonval, Megan, Karim, Latifa, Deckers, Manon, Najimi, Mustapha, Coppieters, Wouter, Charloteaux, Benoît, Sokal, Etienne M., El Taghdouini, Adil
• Format: Article
• Language: English
• Subjects: BSA, bovine serum albumin; CC, cholangiocyte; CV, central vein; DEG, differentially expressed gene; EC, endothelial cell; ECM, extracellular matrix; Extracellular matrix; FFPE, formaldehyde-fixed paraffin embedded; GAG, glycosaminoglycan; Gastroenterology; Gastroenterology & hepatology; Gastroentérologie & hépatologie; GEO, Gene Expression Omnibus; GO, gene ontology; HEP, hepatocyte; Hepatocyte; Hepatology; HLA, human leukocyte antigen; HRP, horseradish peroxidase; HSC, hepatic stellate cell; Human health sciences; Immunology and Allergy; Internal Medicine; ISH, in situ hybridisation; KLR, killer lectin-like receptor; Liver cell atlas; LP, lymphoid cell; MP, macrophage; MZ, midzonal; PC, pericentral; PP, periportal; PV, portal vein; Sciences de la santé humaine; scRNA-seq, single-cell RNA-sequencing; TBS, Tris buffered saline; TSA, tyramide signal amplification; UMAP, uniform manifold approximation and projection; UMI, unique molecular identifier; VIM, vimentin; Zonation
• ISSN: 2589-5559; 2589-5559
• DOI: 10.1016/j.jhepr.2021.100278

The multiple vital functions of the human liver are performed by highly specialised parenchymal and non-parenchymal cells organised in complex collaborative sinusoidal units. Although crucial for homeostasis, the cellular make-up of the human liver remains to be fully elucidated. Here, single-cell RNA-sequencing was used to unravel the heterogeneity of human liver cells, in particular of hepatocytes (HEPs) and hepatic stellate cells (HSCs). The transcriptome of ~25,000 freshly isolated human liver cells was profiled using droplet-based RNA-sequencing. Recently published data sets and RNA in situ hybridisation were integrated to validate and locate newly identified cell populations. In total, 22 cell populations were annotated that reflected the heterogeneity of human parenchymal and non-parenchymal liver cells. More than 20,000 HEPs were ordered along the portocentral axis to confirm known, and reveal previously undescribed, zonated liver functions. The existence of 2 subpopulations of human HSCs with unique gene expression signatures and distinct intralobular localisation was revealed (i.e. portal and central vein-concentrated GPC3+ HSCs and perisinusoidally located DBH+ HSCs). In particular, these data suggest that, although both subpopulations collaborate in the production and organisation of extracellular matrix, GPC3+ HSCs specifically express genes involved in the metabolism of glycosaminoglycans, whereas DBH+ HSCs display a gene signature that is reminiscent of antigen-presenting cells. This study highlights metabolic zonation as a key determinant of HEP transcriptomic heterogeneity and, for the first time, outlines the existence of heterogeneous HSC subpopulations in the human liver. These findings call for further research on the functional implications of liver cell heterogeneity in health and disease. This study resolves the cellular landscape of the human liver in an unbiased manner and at high resolution to provide new insights into human liver cell biology. The results highlight the physiological heterogeneity of human hepatic stellate cells. [Display omitted] •A cell atlas from the near-native transcriptome of >25,000 human liver cells is presented.•Hepatocytes were ordered along the portocentral axis to reveal previously undescribed gene expression patterns and zonated liver functions.•Two subpopulations of human hepatic stellate cells (HSCs) are reported, characterised by different spatial distribution in the native tissue.•Characteristic