Periodic Reporting for period 1 - PlasticLiver (Mechanisms of cell plasticity in the liver)
Reporting period: 2022-12-01 to 2024-11-30
The liver is known as a robust organ. Its regenerative capacity has been recognized already in ancient Greek mythology in the story of Prometheus. Unlike other regenerative tissues that contain dedicated stem cells (e.g. skin, intestine), the liver can regenerate cells from mature differentiated cells, which upon stimuli reprogram their fate and even switch into another cell type. However, some disease conditions hamper this remarkable cell plasticity and the liver’s capacity to recover. Deeper fundamental understanding of endogenous regenerative processes is therefore crucial for the development of any promising therapeutic strategy to avoid the most drastic solution, which is a liver transplant.
This project studied mechanisms of cell plasticity in the liver, in the context of cholestatic liver diseases, exemplified by the rare disease Alagille syndrome. Because of gene mutations affecting the Notch signalling pathway, Alagille syndrome presents with a range of phenotypes in many organs, including a severe underdevelopment of intrahepatic bile ducts at birth, resulting in cholestasis, jaundice, pruritus (skin itching), and other complications. The severity of the Alagille syndrome liver phenotype varies broadly and, astonishingly, some individuals recover bile ducts with full function later in life.
Bile ducts are a tree-like structure in the liver, branching from the centre of the organ. They collect bile from the organ periphery and carry it out of the liver, relying on a proper arrangement of cells in the bile duct epithelium. Previous studies in a mouse model of the disease showed that bile duct regeneration is spatially heterogeneous, with the bile ducts recovering differently in the centre and at the periphery of the organ, suggesting distinct mechanisms at play.
This project aimed to determine mechanisms that contribute to the recovery of bile ducts and underlie the regional heterogeneity of this process by using state-of-the-art gene expression profiling methods and advanced microscopy approaches in mouse models. With these data, we aimed to identify molecular pathways for potential intervention in the treatment of cholestatic liver.
This project studied mechanisms of cell plasticity in the liver, in the context of cholestatic liver diseases, exemplified by the rare disease Alagille syndrome. Because of gene mutations affecting the Notch signalling pathway, Alagille syndrome presents with a range of phenotypes in many organs, including a severe underdevelopment of intrahepatic bile ducts at birth, resulting in cholestasis, jaundice, pruritus (skin itching), and other complications. The severity of the Alagille syndrome liver phenotype varies broadly and, astonishingly, some individuals recover bile ducts with full function later in life.
Bile ducts are a tree-like structure in the liver, branching from the centre of the organ. They collect bile from the organ periphery and carry it out of the liver, relying on a proper arrangement of cells in the bile duct epithelium. Previous studies in a mouse model of the disease showed that bile duct regeneration is spatially heterogeneous, with the bile ducts recovering differently in the centre and at the periphery of the organ, suggesting distinct mechanisms at play.
This project aimed to determine mechanisms that contribute to the recovery of bile ducts and underlie the regional heterogeneity of this process by using state-of-the-art gene expression profiling methods and advanced microscopy approaches in mouse models. With these data, we aimed to identify molecular pathways for potential intervention in the treatment of cholestatic liver.
To understand the differences in regional recovery of bile ducts in a mouse model of Alagille syndrome, we analysed gene expression profiles of intrahepatic bile duct organoids, state-of-the-art 3D in vitro models, which were individually derived from central and peripheral parts of the liver. In comparison to control organoids, the analysis showed that the central “Alagille” organoids expressed a unique set of genes which hinted at cell fate commitment issues in this region. We postulated that this is due to the attenuated Notch signalling in the central region, which is compensated at the periphery (Iqbal et al., 2024, Liver International). The regional differences were also evident when we tested a potential therapeutic intervention, Insulin-like growth factor 1 (IGF1). Organoids from the peripheral region of the recovered bile duct trees were more responsive to the treatment than the central organoids. These results demonstrate that IGF1 could be a relevant therapeutic, but only to stimulate proliferation of bile duct cells that are correctly fated (in the periphery).
Intrahepatic bile ducts are embedded in the liver tissue and interact with other cell types, which contributes to their ability to regenerate. Using transcriptomics datasets from our mouse model and individuals with Alagille syndrome and other cholestatic liver diseases, we examined how other liver cell types coped with altered Notch signalling (contribution to Mašek et al., 2024, EMBO Mol. Med). We found that hepatocytes, one of the potential sources of bile duct cells during regeneration, maintain an immature signature, e.g. persistent stemness markers, and reduced expression of pro-inflammatory genes despite liver injury - which could prevent their interaction with the immune system needed for regeneration. Our data thus underscored an important role of the cellular microenvironment in the liver early on that can impact the onset and the progression of the disease.
To further understand the impact of the microenvironment on the organization of the bile ducts (their epithelial polarity) and to corroborate the results from transcriptomic analyses, we used advanced microscopy approaches (high-resolution confocal microscopy and cutting-edge volume electron microscopy) to describe the complex 3D tissue organization in mouse livers. We created a reference dataset of bile ducts including various stages of embryonic and postnatal development, against which we can evaluate the progress of the regenerative processes. Since regenerated bile ducts in Alagille syndrome exhibit defects in epithelial polarity with potential detrimental long-term effects, this approach will help us to propose how to improve the bile duct organization (epithelial polarity) as a part of a treatment strategy.
Intrahepatic bile ducts are embedded in the liver tissue and interact with other cell types, which contributes to their ability to regenerate. Using transcriptomics datasets from our mouse model and individuals with Alagille syndrome and other cholestatic liver diseases, we examined how other liver cell types coped with altered Notch signalling (contribution to Mašek et al., 2024, EMBO Mol. Med). We found that hepatocytes, one of the potential sources of bile duct cells during regeneration, maintain an immature signature, e.g. persistent stemness markers, and reduced expression of pro-inflammatory genes despite liver injury - which could prevent their interaction with the immune system needed for regeneration. Our data thus underscored an important role of the cellular microenvironment in the liver early on that can impact the onset and the progression of the disease.
To further understand the impact of the microenvironment on the organization of the bile ducts (their epithelial polarity) and to corroborate the results from transcriptomic analyses, we used advanced microscopy approaches (high-resolution confocal microscopy and cutting-edge volume electron microscopy) to describe the complex 3D tissue organization in mouse livers. We created a reference dataset of bile ducts including various stages of embryonic and postnatal development, against which we can evaluate the progress of the regenerative processes. Since regenerated bile ducts in Alagille syndrome exhibit defects in epithelial polarity with potential detrimental long-term effects, this approach will help us to propose how to improve the bile duct organization (epithelial polarity) as a part of a treatment strategy.
The project explored region-dependent mechanisms of cell plasticity, an understudied facet of bile duct regeneration in cholestatic liver diseases. It has delivered scientific impact by characterizing regional differences in cell state and identity of recovered bile ducts in Alagille syndrome, delivering testable hypotheses for further research and uncovering major implications for testing of potential therapeutical approaches, such as IGF1 treatment. The novel findings move the state of the art in cell and developmental biology fields and important technical improvements to several methods open the door to multiple future applications and potential scientific collaborations.