In the increasingly common modern lifestyle characterized by habits such as excessive late nights, smoking, drinking, and high-sugar, high-salt diets, liver diseases are becoming more severe.
As the "chemical factory" of the human body, the liver not only detoxifies but also performs various functions such as metabolism, synthesis, digestion, and immunity. As the organ with the strongest regeneration ability in mammals, understanding the mechanisms controlling liver cell damage and regeneration is of great significance for elucidating malignant transformation and regenerative medicine.
On April 16, led by Hangzhou HaploX Biotechnology and the Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, in collaboration with institutions such as Jilin University, the Fifth Affiliated Hospital of Guangzhou Medical University, Shanxi Medical University, and ShanghaiTech University, two research achievements were simultaneously published in "Nature Genetics".
The joint research team used HaploX's self-developed high-precision large-field spatiotemporal omics technology, Stereo-seq, and single-cell transcriptome sequencing technology, DNBelab C4, to construct a comprehensive high-precision spatiotemporal map of the mouse liver. They respectively revealed the spatial molecular characteristics of the steady state of the mouse liver and the complex molecular mechanisms during liver partial resection, bile stasis injury, and repair processes. The two studies analyzed the complex mechanisms of liver injury and regeneration from different perspectives, offering new insights and strategies for the treatment of liver diseases, as well as liver regeneration and transplantation.
Liver Diagram - Image provided by the research team
The two studies utilizing spatiotemporal omics techniques to analyze liver injury and regeneration processes have left a significant impression. With unprecedented nanoscale resolution and panoramic data at the whole liver lobule level, they captured the spatiotemporal dynamics during liver homeostasis, injury, and regeneration, providing valuable insights for both genomics and hepatology researchers.
High-resolution "life camera" reveals liver regeneration mechanism
The liver lobule is the fundamental unit of mammalian liver structure and function, comprising 500,000 to 1,000,000 lobules in the adult liver. Within each lobule, blood flows from the portal vein zone to the central vein zone, creating gradients of nutrients, hormones, cells, and growth factors, resulting in distinct biological functions of cells at different spatial positions within the lobule.
In previous studies, acquiring in situ morphological information of liver cells often relied on tissue section staining, which made it challenging to resolve gene expression changes at the cellular level. "In recent years, the rapid development of single-cell omics techniques has enabled the acquisition of gene expression information from different cell types within organ tissues. However, isolating cells from tissues in this process loses their spatial information," said Xu Jiangshan, the first author of the paper and associate researcher at Hangzhou Huada Institute of Life Sciences.
As a leading proponent in the field of spatiotemporal omics, Hangzhou Huada Institute of Life Sciences unveiled their independently developed Stereo-seq technology in 2020. This breakthrough technology overcomes resolution and tissue size limitations, akin to an ultra-high-definition "life camera," enabling the mapping of organ and life-wide molecular cellular landscapes.
Based on spatiotemporal omics technology, led by Hangzhou Huada Institute of Life Sciences in collaboration with institutions such as Jilin University, the CAS Center for Excellence in Molecular Cell Science, the Fifth Affiliated Hospital of Guangzhou Medical University, Shanxi Medical University, IRCCS-Istituto Tumori, and Hanover Medical School, the mechanisms of liver homeostasis and partial hepatectomy-induced regeneration were explored.
Initially, the research team studied normal livers and livers after 70% resection, constructing a continuous liver lobule network with nanoscale spatial resolution. This revealed the spatial characteristics of cell types, gene expression, and microenvironmental signals in the steady-state liver of mice, as well as how the spatiotemporal dynamics change accurately during partial liver resection-induced regeneration.
"We resolved the spatial distribution characteristics of gene functions in different locations of liver cells along the portal vein-central vein axis and identified a series of genes with regional distributions," said Xu Jiangshan, noting that this discovery will aid researchers in better understanding the spatial susceptibility differences of liver diseases.
Furthermore, the research team discovered for the first time the existence of immune microstructures in the liver, ranging from 50 to 200 micrometers, locating and analyzing the immune cell composition within them, primarily comprising T cells and monocytes. The team speculated that this might represent a special mechanism of hepatic immune response aiding in the liver's defense against exogenous bacteria or antigens, enriching the understanding of the liver's immune microenvironment.
Through the analysis of liver regeneration after 70% resection, the research team identified and validated a series of key transcription factors involved in maintaining liver zonation, elucidating the spatial coordination mechanisms of metabolic and intercellular regulation networks during liver regeneration.
Co-corresponding author Lai Yiwei, associate researcher at Hangzhou Huada Institute of Life Sciences, stated, "This study fully integrates the previous research achievements of the Center of Excellence in Molecular Cell Science in the field of liver regeneration, along with Huada's strengths in cutting-edge technologies such as spatiotemporal omics, providing rich data resources for a correct understanding of liver homeostasis and regeneration, laying an important foundation for further exploration of mammalian liver physiology and functional disorders."
Exploring different injury regeneration models to comprehensively construct the liver atlas
In another study, the research team led by Hui Lijian, researcher at the CAS Center for Excellence in Molecular Cell Science, in collaboration with Hangzhou Huada Institute of Life Sciences, constructed a spatiotemporal transcriptomic atlas of mouse cholestatic injury and regeneration at the cellular level, revealing the spatiotemporal dynamic characteristics of injury response and microenvironmental signals during this process.
Cholestasis is caused by disturbances in bile secretion and excretion, which may lead to a series of diseases such as cholecystitis, cirrhosis, and liver failure when severe. Previous studies have found that after cholestatic injury, liver cells around the portal vein undergo reprogramming into liver progenitor-like cells, contributing to liver regeneration. As the injury resolves, liver repair initiates, with extensive proliferation of liver cells mainly occurring around the central vein, yet the mechanisms controlling this proliferation remain unclear.
In this study, the research team induced liver injury in mice through drug treatment, mimicking the symptoms of human cholestatic injury, where injuries primarily occurred around the portal vein, with no damage observed near the central vein. Through analysis of spatial interactions in the portal vein region, the research team found that bile duct cells acted as signaling hubs during cholestatic injury, participating in integrating cell interactions within the portal vein region, highly correlated with immune cell remodeling and liver cell reprogramming in this area.
Using spatiotemporal omics technology, the research team revealed two subtypes of liver progenitor-like cells during liver cell reprogramming, with one subtype being closer to the bile duct region along the differentiation trajectory. "Additionally, we discovered important factors that limit liver cell proliferation, providing new perspectives and possible new targets for understanding regional liver injury and treating bile duct-related diseases," said Wu Baihua, co-first author of the paper and doctoral student at the CAS Center for Excellence in Molecular Cell Science. This study constructed a spatiotemporal transcriptomic atlas of cholestatic injury and regeneration, highlighting the central role of ductal-mediated signaling throughout the process. It not only provides valuable data resources for understanding regional liver injury but also offers potential intervention strategies for promoting hepatocyte regeneration under cholestatic conditions.
"Two studies, employing partial hepatectomy and drug-induced liver injury respectively, complement each other and address the questions of liver injury regeneration at different levels, collectively building a comprehensive liver reference atlas," said Hui Li Jian. These findings can be further utilized to uncover potential mechanisms and targets in regional liver injury regeneration and provide a new research paradigm for investigating the complex mechanisms of injury and regeneration in other tissues with heterogeneous distribution.
