Single cell transcriptomics reveals heterogeneity and zonation in the adult and infant human liver

Abstract

Background & Aim: The multiple vital functions of the human liver are tightly linked to its complex organization of highly specialized parenchymal and non-parenchymal cells within the liver lobule. Following the recent advances in next generation sequencing at the resolution of isolated cells, whole liver heterogeneity can currently be studied without the need to sort cells, thereby providing a comprehensive atlas of different hepatic populations, for a better understanding of liver functions and potential implications in liver cell transplantation and regenerative medicine. In this study, we aimed at describing a first high-resolution transcriptomic map of the infant and adult human liver by single-cell transcriptomics. Methods, Results & Conclusion: 80,000 liver cells obtained after collagenase digestion of two human livers(Hepatic Biobank; Cliniques Universitaires Saint-Luc) were loaded in a 10X Genomics instrument to generate 8 independent liver cell libraries. The libraries were sequenced using the Illumina technology in order to reach an average of 65,000 reads/cells. The data generated for both donors were analyzed separately and cell clusters were identified and zonated according to previously established functional, transcriptional and histological studies performed in mice and human. A total of ~28,000 single-cell transcriptomes were obtained from the 8 libraries, of which ~78%, 3% and 18% corresponds to hepatocytes, cholangiocytes and non-parenchymal cells, respectively. Taking specific gene expression patterns related to well-known zonated liver metabolic functions as a reference, the single-cell transcriptomes obtained for hepatocytes have been localized along the portocentral axis, revealing the pericentral-, periportal- and midzonal-specific hepatocyte transcriptomes. Within the clusters of cholangiocytes and non-parenchymal cells, our preliminary results identified multiple subpopulations, including 2 distinct populations of hepatic stellate cells, of which the transcriptomic disparities suggests functional specializations. Thus, our study provides a comprehensive transcriptomic map of the native human liver at a high resolution. It contributes to a better understanding of the heterogeneity and complex organization of the liver cell (sub)populations that underlies the physiology of the human liver, i.e. a prerequisite for the development of next generation applications in liver cell therapy