A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery

AbstractChronic liver disease and hepatocellular carcinoma (HCC) are life-threatening diseases with limited treatment options. The lack of clinically relevant/tractable experimental models hampers therapeutic discovery. Here, we develop a simple and robust human liver cell-based system modeling a clinical prognostic liver signature (PLS) predicting long-term liver disease progression toward HCC. Using the PLS as a readout, followed by validation in nonalcoholic steatohepatitis/fibrosis/HCC animal models and patient-derived liver spheroids, we identify nizatidine, a histamine receptor H2 (HRH2) blocker, for treatment of advanced liver disease and HCC chemoprevention. Moreover, perturbation studies combined with single cell RNA-Seq analyses of patient liver tissues uncover hepatocytes and HRH2+, CLEC5Ahigh, MARCOlow liver macrophages as potential nizatidine targets. The PLS model combined with single cell RNA-Seq of patient tissues enables discovery of urgently needed targets and therapeutics for treatment of advanced liver disease and cancer prevention.

Download Full-text

A human liver cell-based system modeling a clinical prognostic liver signature combined with single cell RNA-seq for discovery of novel liver disease therapeutics

Journal of Hepatology ◽

10.1016/s0168-8278(20)30611-5 ◽

2020 ◽

Vol 73 ◽

pp. S28-S29

Author(s):

Emilie Crouchet ◽

Simonetta Bandiera ◽

Naoto Fujiwara ◽

Shen Li ◽

Hussein El Saghire ◽

...

Keyword(s):

Liver Disease ◽

Single Cell ◽

Liver Cell ◽

Human Liver ◽

System Modeling ◽

Rna Seq ◽

Human Liver Cell

Download Full-text

A Human Liver Cell Atlas: Revealing Cell Type Heterogeneity and Adult Liver Progenitors by Single-Cell RNA-sequencing

10.1101/649194 ◽

2019 ◽

Cited By ~ 1

Author(s):

Nadim Aizarani ◽

Antonio Saviano ◽

Sagar ◽

Laurent Mailly ◽

Sarah Durand ◽

...

Keyword(s):

Endothelial Cells ◽

Single Cell ◽

Rna Sequencing ◽

Liver Cell ◽

Human Liver ◽

Treatment Options ◽

Normal Liver ◽

Stem Cell Population ◽

Human Liver Cell ◽

Single Cell Rna Sequencing

ABSTRACTThe human liver is an essential multifunctional organ, and liver diseases are rising with limited treatment options. However, the cellular complexity and heterogeneity of the liver remain poorly understood. Here, we performed single-cell RNA-sequencing of ~5,000 cells from normal liver tissue of 6 human donors to construct the first human liver cell atlas. Our analysis revealed previously unknown sub-types among endothelial cells, Kupffer cells, and hepatocytes with transcriptome-wide zonation of these populations. We show that the EPCAM+ population is highly heterogeneous and consists of hepatocyte progenitors, cholangiocytes and a MUC6+ stem cell population with a specific potential to form liver organoids. As proof-of-principle, we applied our atlas to unravel phenotypic changes in cells from hepatocellular carcinoma tissue and to investigate cellular phenotypes of human hepatocytes and liver endothelial cells engrafted into a humanized FAH-/- mouse liver. Our human liver cell atlas provides a powerful and innovative resource enabling the discovery of previously unknown cell types in the normal and diseased liver.

Download Full-text

Comparing in vitro human liver models to in vivo human liver using RNA-Seq

Archives of Toxicology ◽

10.1007/s00204-020-02937-6 ◽

2020 ◽

Author(s):

Rajinder Gupta ◽

Yannick Schrooders ◽

Duncan Hauser ◽

Marcel van Herwijnen ◽

Wiebke Albrecht ◽

...

Keyword(s):

Liver Cell ◽

Liver Tissue ◽

Hepg2 Cells ◽

Human Liver ◽

Rna Seq ◽

Cell Models ◽

Human Liver Tissue ◽

Human Liver Cell

Abstract The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue.

Download Full-text

Liver Abnormalities after Elimination of HCV Infection: Persistent Epigenetic and Immunological Perturbations Post-Cure

Pathogens ◽

10.3390/pathogens10010044 ◽

2021 ◽

Vol 10 (1) ◽

pp. 44

Author(s):

Stephen J. Polyak ◽

I. Nicholas Crispe ◽

Thomas F. Baumert

Keyword(s):

Liver Disease ◽

Hepatitis C ◽

Human Liver ◽

Large Scale ◽

Liver Slice ◽

Hcv Infection ◽

Advanced Liver Disease ◽

Experimental Systems ◽

Human Liver Cell ◽

Hepatic Innate Immunity

Chronic hepatitis C (CHC) is a major cause of hepatocellular carcinoma (HCC) worldwide. While directly acting antiviral (DAA) drugs are now able to cure virtually all hepatitis C virus (HCV) infections, even in subjects with advanced liver disease, what happens to the liver and progression of the disease after DAA-induced cure of viremia is only beginning to emerge. Several large-scale clinical studies in different patient populations have shown that patients with advanced liver disease maintain a risk for developing HCC even when the original instigator, the virus, is eliminated by DAAs. Here we review emerging studies derived from multiple, complementary experimental systems involving patient liver tissues, human liver cell cultures, human liver slice cultures, and animal models, showing that HCV infection induces epigenetic, signaling, and gene expression changes in the liver associated with altered hepatic innate immunity and liver cancer risk. Of critical importance is the fact that these virus-induced abnormalities persist after DAA cure of HCV. These nascent findings portend the discovery of pathways involved in post-HCV immunopathogenesis, which may be clinically actionable targets for more comprehensive care of DAA-cured individuals.

Download Full-text

Protocol for Single-Cell RNA-Sequencing of Cryopreserved Human Liver Cells

10.21203/rs.2.9620/v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Nadim Aizarani ◽

Antonio Saviano ◽

Sagar ◽

Laurent Mailly ◽

Sarah Durand ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Liver Cell ◽

Human Liver ◽

Liver Cells ◽

Human Liver Cells ◽

Human Liver Cell ◽

Single Cell Rna Sequencing

Abstract This is a protocol describing how to perform scRNA-seq of cryopreserved human liver cells using the mCEL-Seq2 protocol as described in the following paper.Title: A Human Liver Cell Atlas reveals Heterogeneity and Epithelial ProgenitorsAuthors: Nadim Aizarani, Antonio Saviano, Sagar, Laurent Mailly, Sarah Durand, Patrick Pessaux, Thomas F. Baumert, Dominic GrünJournal: Nature

Download Full-text