Periodic Reporting for period 4 - RULLIVER (Rules of self-organization and reengineering of liver tissue)
Reporting period: 2021-04-01 to 2022-12-31
In this project, we worked to better understand how cells and tissues are organized using the liver as model organ. We were trying to figure out what makes some cells different from others and how this affects the way tissues are organized, and thus, how the body works. If we understand these principles, we can find ways to anticipate alterations or change them, for example, in disease.
This project focussed on understanding the mechanisms that control liver tissue formation at the molecular level. The goal was to develop a better understanding of how tissue organization works on a molecular level.
This project investigated how liver tissue self-organizes. Specifically, the goal was to understand how liver cells interact and how cell polarity is uniquely configured to create the unique 3D structure of the liver. We used a combination of experiments in a test tube, in cells, in mice to analyze and manipulate the structure of liver tissue. We studied tissue dynamics, metabolic zonation, and cell-cell interactions to elucidate the rules of tissue organization.
Additionally, we digitally reconstructed mouse liver tissue from microscopy data and combined the data from the manipulation experiments with the 3D tissue model to build a computational 3D model of liver tissue and function. We use this to model metabolic processes but also to improve our understanding of tissue architecture, e.g. structures such as apical bulkheads.
This project focussed on understanding the mechanisms that control liver tissue formation at the molecular level. The goal was to develop a better understanding of how tissue organization works on a molecular level.
This project investigated how liver tissue self-organizes. Specifically, the goal was to understand how liver cells interact and how cell polarity is uniquely configured to create the unique 3D structure of the liver. We used a combination of experiments in a test tube, in cells, in mice to analyze and manipulate the structure of liver tissue. We studied tissue dynamics, metabolic zonation, and cell-cell interactions to elucidate the rules of tissue organization.
Additionally, we digitally reconstructed mouse liver tissue from microscopy data and combined the data from the manipulation experiments with the 3D tissue model to build a computational 3D model of liver tissue and function. We use this to model metabolic processes but also to improve our understanding of tissue architecture, e.g. structures such as apical bulkheads.
From cells to tissues – digital reconstruction of the liver in three dimensions
The liver is crucial for many physiological processes, such as macronutrient metabolism, blood volume regulation, and the breakdown of toxic compounds. It is an organ with a complex 3D tissue structure and comprises several cell types, each with its specific function. Almost 80% of the liver consists of parenchymal cells called hepatocytes that are honeycombed by two 3D microcirculatory systems: the sinusoids that transport blood and the network of bile canaliculi that drain bile into the bile ducts. Hepatocytes are polarized cells, which means that there are functional and spatial differences within the cell. Unlike simple polarized cells, such as epithelia, hepatocytes possess a belt-shaped apical membrane that wraps around the entire cell. The apical surfaces of several hepatocytes pair with neighboring ones to form a small lumen between them. In its entirety, these connected lumina form the bile canalicular network.
Using an image-based computational approach, we recreated the complex tissue architecture of the liver from microscopy data. We use image analysis software to analyse and reconstruct high-resolution light microscopy images and extract quantitative parameters. As a result, we could show that hepatocytes are not orientated randomly in the liver lobule, but are aligned along a common axis. This arrangement reflects a long-range 3D liquid crystal order, a concept borrowed from engineering and used to describe e.g. liquid crystal displays (LCDs) in engineering.
We also use this workflow to describe tissue alterations in human liver disease from patient samples, for example, in non-alcoholic fatty liver disease (NAFLD). We generated a three-dimensional computational model of human liver tissue in different stages of disease and identified a set of structural cellular and tissue parameters that correlate with disease progression. We used these parameters and simulated their effects on the dynamics of biliary fluids in the liver. In our disease model, we predicted an increased pericentral biliary pressure and micro-cholestasis, which is consistent with measured elevated cholestatic biomarkers in patients’ blood. These data can help identify new tissue biomarkers and tissue signatures to describe disease stages in the clinic.
We also used this method to correlate the structural parameters of the bile canalicular network with the measurements of bile transport by intravital microscopy in mice. The data showed inequalities in biliary geometry and hepatocyte transport activity throughout the organ. On the basis of this, our model predicts gradients of bile velocity and pressure in the liver lobule.
Regulation of liver size during development and regeneration
As the saying goes, the liver grows with its tasks. But how do cells collectively sense the overall state of tissue, especially when something goes wrong?
When the liver is injured, it has a unique capacity to repair and regenerate. During this time, it faces the same workload in the body, but with less manpower. The organ becomes overloaded with bile in the bile canaliculi and ducts which leads to a pressure increase. We found that under these circumstances the apical surface of the hepatocytes that make up the network of the bile canaliculi expands and the hepatocytes reinforce their actomyosin cortex, probably to withstand the increase in pressure.
Interestingly, the Hippo transcriptional coactivator YAP senses this reinforcement of the apical actomyosin cortex and travels to the nucleus to act on gene regulation. We interpret this behavior as a mechano-sensory trigger that activates YAP to enable the cell to respond to critical levels of bile acids and make the necessary cellular adjustments through transcriptional regulation.
Apical bulkheads – a novel player in bile canaliculi formation and maintenance
More recently, we found that the formation of bile canaliculi requires specific extensions of the apical membrane that traverses the lumen to ensure its growth as a tubule. We termed these mechanical structures “apical bulkheads” and know that they increase the bile canaliculi resistance to internal pressure.
Exploitation and Dissemination
Overall, this project lead to nine high-impact publications in important scientific journals, such as eLIFE, Cell Systems, Journal of Cell Biology and Nature Medicine. The findings of this project have been extensively presented and discussed at several international conferences, seminars, and workshops. The content was displayed and explained to the general public during the Long Night of Science in Dresden in 2018 and 2022. The host institution acknowledged the significance of the findings from this project with two press releases on the liver bile flow model and the implications of digital tissue reconstruction for research into liver disease.
The liver is crucial for many physiological processes, such as macronutrient metabolism, blood volume regulation, and the breakdown of toxic compounds. It is an organ with a complex 3D tissue structure and comprises several cell types, each with its specific function. Almost 80% of the liver consists of parenchymal cells called hepatocytes that are honeycombed by two 3D microcirculatory systems: the sinusoids that transport blood and the network of bile canaliculi that drain bile into the bile ducts. Hepatocytes are polarized cells, which means that there are functional and spatial differences within the cell. Unlike simple polarized cells, such as epithelia, hepatocytes possess a belt-shaped apical membrane that wraps around the entire cell. The apical surfaces of several hepatocytes pair with neighboring ones to form a small lumen between them. In its entirety, these connected lumina form the bile canalicular network.
Using an image-based computational approach, we recreated the complex tissue architecture of the liver from microscopy data. We use image analysis software to analyse and reconstruct high-resolution light microscopy images and extract quantitative parameters. As a result, we could show that hepatocytes are not orientated randomly in the liver lobule, but are aligned along a common axis. This arrangement reflects a long-range 3D liquid crystal order, a concept borrowed from engineering and used to describe e.g. liquid crystal displays (LCDs) in engineering.
We also use this workflow to describe tissue alterations in human liver disease from patient samples, for example, in non-alcoholic fatty liver disease (NAFLD). We generated a three-dimensional computational model of human liver tissue in different stages of disease and identified a set of structural cellular and tissue parameters that correlate with disease progression. We used these parameters and simulated their effects on the dynamics of biliary fluids in the liver. In our disease model, we predicted an increased pericentral biliary pressure and micro-cholestasis, which is consistent with measured elevated cholestatic biomarkers in patients’ blood. These data can help identify new tissue biomarkers and tissue signatures to describe disease stages in the clinic.
We also used this method to correlate the structural parameters of the bile canalicular network with the measurements of bile transport by intravital microscopy in mice. The data showed inequalities in biliary geometry and hepatocyte transport activity throughout the organ. On the basis of this, our model predicts gradients of bile velocity and pressure in the liver lobule.
Regulation of liver size during development and regeneration
As the saying goes, the liver grows with its tasks. But how do cells collectively sense the overall state of tissue, especially when something goes wrong?
When the liver is injured, it has a unique capacity to repair and regenerate. During this time, it faces the same workload in the body, but with less manpower. The organ becomes overloaded with bile in the bile canaliculi and ducts which leads to a pressure increase. We found that under these circumstances the apical surface of the hepatocytes that make up the network of the bile canaliculi expands and the hepatocytes reinforce their actomyosin cortex, probably to withstand the increase in pressure.
Interestingly, the Hippo transcriptional coactivator YAP senses this reinforcement of the apical actomyosin cortex and travels to the nucleus to act on gene regulation. We interpret this behavior as a mechano-sensory trigger that activates YAP to enable the cell to respond to critical levels of bile acids and make the necessary cellular adjustments through transcriptional regulation.
Apical bulkheads – a novel player in bile canaliculi formation and maintenance
More recently, we found that the formation of bile canaliculi requires specific extensions of the apical membrane that traverses the lumen to ensure its growth as a tubule. We termed these mechanical structures “apical bulkheads” and know that they increase the bile canaliculi resistance to internal pressure.
Exploitation and Dissemination
Overall, this project lead to nine high-impact publications in important scientific journals, such as eLIFE, Cell Systems, Journal of Cell Biology and Nature Medicine. The findings of this project have been extensively presented and discussed at several international conferences, seminars, and workshops. The content was displayed and explained to the general public during the Long Night of Science in Dresden in 2018 and 2022. The host institution acknowledged the significance of the findings from this project with two press releases on the liver bile flow model and the implications of digital tissue reconstruction for research into liver disease.
We recently discovered that liver cells form "apical bulkheads" which act analogous to the bulkheads of a boat or plane and provide mechanical stability to the forming bile canaliculi. These structures contain molecular components which allow them to bear a mechanical load, and they double the pressure that bile canaliculi can hold. Apical bulkheads protect the bile canaliculi network from fluctuations in biliary pressure, and they could possibly be used as structural biomarkers in the diagnosis of liver disease in the future.