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Author(s): Simon F. Brunner [sup.1] , Nicola D. Roberts [sup.1] , Luke A. Wylie [sup.1] , Luiza Moore [sup.1] , Sarah J. Aitken [sup.2] [sup.3] , Susan E. Davies [sup.3] [...], The most common causes of chronic liver disease are excess alcohol intake, viral hepatitis and non-alcoholic fatty liver disease, with the clinical spectrum ranging in severity from hepatic inflammation to cirrhosis, liver failure or hepatocellular carcinoma (HCC). The genome of HCC exhibits diverse mutational signatures, resulting in recurrent mutations across more than 30 cancer genes.sup.1-7. Stem cells from normal livers have a low mutational burden and limited diversity of signatures.sup.8, which suggests that the complexity of HCC arises during the progression to chronic liver disease and subsequent malignant transformation. Here, by sequencing whole genomes of 482 microdissections of 100-500 hepatocytes from 5 normal and 9 cirrhotic livers, we show that cirrhotic liver has a higher mutational burden than normal liver. Although rare in normal hepatocytes, structural variants, including chromothripsis, were prominent in cirrhosis. Driver mutations, such as point mutations and structural variants, affected 1-5% of clones. Clonal expansions of millimetres in diameter occurred in cirrhosis, with clones sequestered by the bands of fibrosis that surround regenerative nodules. Some mutational signatures were universal and equally active in both non-malignant hepatocytes and HCCs; some were substantially more active in HCCs than chronic liver disease; and others--arising from exogenous exposures--were present in a subset of patients. The activity of exogenous signatures between adjacent cirrhotic nodules varied by up to tenfold within each patient, as a result of clone-specific and microenvironmental forces. Synchronous HCCs exhibited the same mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease. Whole-genome sequencing of liver microdissections from five healthy individuals and nine with cirrhosis demonstrates the effects of liver disease on the genome, including increased rates of mutation, complex structural variation and different mutational signatures.

Author(s): J. Gray Camp [sup.1] , Keisuke Sekine [sup.2] , Tobias Gerber [sup.1] , Henry Loeffler-Wirth [sup.3] , Hans Binder [sup.3] , Malgorzata Gac [sup.1] , Sabina Kanton [sup.1] , [...], Single-cell RNA sequencing analysis of two- and three-dimensional hepatic differentiation reveals that both systems recapitulate certain transcriptomic features of human hepatogenesis. Growing livers in a dish The mechanisms by which interactions between different cell types influence lineage identity and cell maturation during human development are unknown. Barbara Treutlein and colleagues use single-cell RNA-sequencing to analyse the emergence of hepatocytes lineages in a three-dimensional organoid system that is based on the reconstitution of hepatic, stromal and endothelial interactions. They compare their findings in vitro with data they obtain from fetal and adult human livers, and show that hepatocytes from the organoids closely resemble fetal liver cells. Through a chemical screen, they show that the three-dimensional system can be used to explore how signalling pathways influence endothelial network and hepatoblast formation. Conventional two-dimensional differentiation from pluripotency fails to recapitulate cell interactions occurring during organogenesis. Three-dimensional organoids generate complex organ-like tissues.sup.1; however, it is unclear how heterotypic interactions affect lineage identity. Here we use single-cell RNA sequencing.sup.2,3 to reconstruct hepatocyte-like lineage progression from pluripotency in two-dimensional culture. We then derive three-dimensional liver bud organoids.sup.4 by reconstituting hepatic, stromal, and endothelial interactions, and deconstruct heterogeneity during liver bud development. We find that liver bud hepatoblasts diverge from the two-dimensional lineage, and express epithelial migration signatures characteristic of organ budding. We benchmark three-dimensional liver buds against fetal and adult human liver single-cell RNA sequencing data, and find a striking correspondence between the three-dimensional liver bud and fetal liver cells. We use a receptor-ligand pairing analysis and a high-throughput inhibitor assay to interrogate signalling in liver buds, and show that vascular endothelial growth factor (VEGF) crosstalk potentiates endothelial network formation and hepatoblast differentiation. Our molecular dissection reveals interlineage communication regulating organoid development, and illuminates previously inaccessible aspects of human liver development.

Spot14 is a putative transcriptional regulator for genes involved in fatty acid synthesis. The Spot14 gene is activated in response to lipogenic stimuli such as dietary carbohydrate and is also [...]