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Zhang X, He B, Lu J, Bao Q, Wang J, Yang Y. The crucial roles and research advances of cGAS‑STING pathway in liver diseases. Ann Med 2024; 56:2394588. [PMID: 39183465 PMCID: PMC11348815 DOI: 10.1080/07853890.2024.2394588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/27/2024] Open
Abstract
Inflammation responses have identified as a key mediator of in various liver diseases with high morbidity and mortality. cGAS-STING signalling is essential in innate immunity since it triggers release of type I interferons and various of proinflammatory cytokines. The potential connection between cGAS-STING pathway and liver inflammatory diseases has recently been reported widely. In our review, the impact of cGAS-STING on liver inflammation and regulatory mechanism are summarized. Furthermore, many inhibitors of cGAS-STING signalling as promising agents to cure liver inflammation are also explored in detail. A comprehensive knowledge of molecular mechanisms of cGAS-STING signalling in liver inflammation is vital for exploring novel treatments and providing recommendations and perspectives for future utilization.
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Affiliation(s)
- Xiaoqian Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Juan Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiongling Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yida Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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2
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Cui X, Dong X, Hu M, Zhou W, Shi W. Large field of view and spatial region of interest transcriptomics in fixed tissue. Commun Biol 2024; 7:1020. [PMID: 39164496 PMCID: PMC11335973 DOI: 10.1038/s42003-024-06694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
Expression profiling in spatially defined regions is crucial for systematically understanding tissue complexity. Here, we report a method of photo-irradiation for in-situ barcoding hybridization and ligation sequencing, named PBHL-seq, which allows targeted expression profiling from the photo-irradiated region of interest in intact fresh frozen and formalin fixation and paraffin embedding (FFPE) tissue samples. PBHL-seq uses photo-caged oligodeoxynucleotides for in situ reverse transcription followed by spatially targeted barcoding of cDNAs to create spatially indexed transcriptomes of photo-illuminated regions. We recover thousands of differentially enriched transcripts from different regions by applying PBHL-seq to OCT-embedded tissue (E14.5 mouse embryo and mouse brain) and FFPE mouse embryo (E15.5). We also apply PBHL-seq to the subcellular microstructures (cytoplasm and nucleus, respectively) and detect thousands of differential expression genes. Thus, PBHL-seq provides an accessible workflow for expression profiles from the region of interest in frozen and FFPE tissue at subcellular resolution with areas expandable to centimeter scale, while preserving the sample intact for downstream analysis to promote the development of transcriptomics.
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Affiliation(s)
- Xiaonan Cui
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Xue Dong
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Mengzhu Hu
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Wenjian Zhou
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Weiyang Shi
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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3
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Huong NTC, Hai NP, Van Khanh C, Kamel MG, Vinh Chau NV, Truong NT, Vinh NT, Elsheikh R, Makram AM, Elsheikh A, Canh HN, Iqtadar S, Hirayama K, Le Hoa PT, Huy NT. New biomarkers for liver involvement by dengue infection in adult Vietnamese patients: a case-control study. BMC Infect Dis 2024; 24:800. [PMID: 39118006 PMCID: PMC11308448 DOI: 10.1186/s12879-024-09527-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/17/2024] [Indexed: 08/10/2024] Open
Abstract
Liver injury with marked elevation of aspartate aminotransferase enzyme (AST) is commonly observed in dengue infection. To understand the pathogenesis of this liver damage, we compared the plasma levels of hepatic specific, centrilobular predominant enzymes (glutamate dehydrogenase, GLDH; glutathione S transferase-α, αGST), periportal enriched 4-hydroxyphenylpyruvate dioxygenase (HPPD), periportal predominant arginase-1 (ARG-1), and other non-specific biomarkers (paraoxonase-1, PON-1) in patients with different outcomes of dengue infection. This hospital-based study enrolled 87 adult dengue patients, stratified into three groups based on plasma AST levels (< 80, 80-400, > 400 U/L) in a 1:1:1 ratio (n = 40, n = 40, n = 40, respectively. The new liver enzymes in the blood samples from the 4th to 6th days of their illness were measured by commercial enzyme-linked immunosorbent assay (ELISA) or colorimetric kits. Based on the diagnosis at discharge days, our patients were classified as 40 (46%) dengue without warning signs (D), 35 (40.2%) dengue with warning signs (DWS), and 11 (12.6%) severe dengue (SD) with either shock (two patients) or AST level over 1000 U/L (nine patients), using the 2009 WHO classification. The group of high AST (> 400 U/L) also had higher ALT, GLDH, ARG-1, and HPPD than the other groups, while the high (> 400 U/L) and moderate (80-400 U/L) AST groups had higher ALT, αGST, ARG-1, and HPPD than the low AST group (< 80 U/L). There was a good correlation between AST, alanine aminotransferase enzyme (ALT), and the new liver biomarkers such as GLDH, αGST, ARG-1, and HPPD. Our findings suggest that dengue-induced liver damage initiates predominantly in the centrilobular area toward the portal area during the dengue progression. Moreover, these new biomarkers should be investigated further to explain the pathogenesis of dengue and to validate their prognostic utility.
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Affiliation(s)
- Nguyen Thi Cam Huong
- Department of Infectious Diseases, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen Phuong Hai
- Department of Infectious Diseases, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Department of Infectious Diseases, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Chau Van Khanh
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki, Japan
- Institute of Malariology, Parasitology, and Entomology Quy Nhon, Quy Nhon, Vietnam
| | - Mohamed Gomaa Kamel
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki, Japan
- Ipswich Hospital, East Suffolk and North Essex NHS Foundation Trust, Colchester, UK
| | | | | | | | - Randa Elsheikh
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki, Japan
- Deanery of Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Abdelrahman M Makram
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki, Japan.
- Department of Anesthesia and Intensive Care Medicine, October 6 University, Giza, Egypt.
| | - Aya Elsheikh
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki, Japan
- Faculty of Medicine, Mansoura Manchester University, Mansoura, Egypt
| | - Hiep Nguyen Canh
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki, Japan
- Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
- Center of Pathology and Cytopathology, Bach Mai Hospital, Hanoi, Vietnam
| | - Somia Iqtadar
- Department of Medicine, King Edward Medical University, Lahore, Pakistan
| | - Kenji Hirayama
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Pham Thi Le Hoa
- Department of Infectious Diseases, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam.
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
| | - Nguyen Tien Huy
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
- Online Research Club (http://www.onlineresearchclub.org), Nagasaki, Japan.
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam.
- School of Medicine and Pharmacy, Duy Tan University, Da Nang, Vietnam.
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4
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Pouyabahar D, Andrews T, Bader GD. Interpretable single-cell factor decomposition using sciRED. RESEARCH SQUARE 2024:rs.3.rs-4819117. [PMID: 39149508 PMCID: PMC11326389 DOI: 10.21203/rs.3.rs-4819117/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) maps gene expression heterogeneity within a tissue. However, identifying biological signals in this data is challenging due to confounding technical factors, sparsity, and high dimensionality. Data factorization methods address this by separating and identifying signals in the data, such as gene expression programs, but the resulting factors must be manually interpreted. We developed Single-Cell Interpretable Residual Decomposition (sciRED) to improve the interpretation of scRNA-seq factor analysis. sciRED removes known confounding effects, uses rotations to improve factor interpretability, maps factors to known covariates, identifies unexplained factors that may capture hidden biological phenomena and determines the genes and biological processes represented by the resulting factors. We apply sciRED to multiple scRNA-seq datasets and identify sex-specific variation in a kidney map, discern strong and weak immune stimulation signals in a PBMC dataset, reduce ambient RNA contamination in a rat liver atlas to help identify strain variation, and reveal rare cell type signatures and anatomical zonation gene programs in a healthy human liver map. These demonstrate that sciRED is useful in characterizing diverse biological signals within scRNA-seq data.
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Affiliation(s)
- Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Tallulah Andrews
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Computer Science, University of Western Ontario, London, Ontario, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, Ontario, Canada
- CIFAR Multiscale Human Program, CIFAR, Toronto, Ontario, Canada
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5
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Pouyabahar D, Andrews T, Bader GD. Interpretable single-cell factor decomposition using sciRED. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.605536. [PMID: 39149356 PMCID: PMC11326131 DOI: 10.1101/2024.08.01.605536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) maps gene expression heterogeneity within a tissue. However, identifying biological signals in this data is challenging due to confounding technical factors, sparsity, and high dimensionality. Data factorization methods address this by separating and identifying signals in the data, such as gene expression programs, but the resulting factors must be manually interpreted. We developed Single-Cell Interpretable Residual Decomposition (sciRED) to improve the interpretation of scRNA-seq factor analysis. sciRED removes known confounding effects, uses rotations to improve factor interpretability, maps factors to known covariates, identifies unexplained factors that may capture hidden biological phenomena and determines the genes and biological processes represented by the resulting factors. We apply sciRED to multiple scRNA-seq datasets and identify sex-specific variation in a kidney map, discern strong and weak immune stimulation signals in a PBMC dataset, reduce ambient RNA contamination in a rat liver atlas to help identify strain variation, and reveal rare cell type signatures and anatomical zonation gene programs in a healthy human liver map. These demonstrate that sciRED is useful in characterizing diverse biological signals within scRNA-seq data.
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Affiliation(s)
- Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Tallulah Andrews
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Computer Science, University of Western Ontario, London, Ontario, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, Ontario, Canada
- CIFAR Multiscale Human Program, CIFAR, Toronto, Ontario, Canada
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6
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Darmasaputra GS, Geerlings CC, Chuva de Sousa Lopes SM, Clevers H, Galli M. Binucleated human hepatocytes arise through late cytokinetic regression during endomitosis M phase. J Cell Biol 2024; 223:e202403020. [PMID: 38727809 PMCID: PMC11090133 DOI: 10.1083/jcb.202403020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/15/2024] Open
Abstract
Binucleated polyploid cells are common in many animal tissues, where they arise by endomitosis, a non-canonical cell cycle in which cells enter M phase but do not undergo cytokinesis. Different steps of cytokinesis have been shown to be inhibited during endomitosis M phase in rodents, but it is currently unknown how human cells undergo endomitosis. In this study, we use fetal-derived human hepatocyte organoids (Hep-Orgs) to investigate how human hepatocytes initiate and execute endomitosis. We find that cells in endomitosis M phase have normal mitotic timings, but lose membrane anchorage to the midbody during cytokinesis, which is associated with the loss of four cortical anchoring proteins, RacGAP1, Anillin, SEPT9, and citron kinase (CIT-K). Moreover, reduction of WNT activity increases the percentage of binucleated cells in Hep-Orgs, an effect that is dependent on the atypical E2F proteins, E2F7 and E2F8. Together, we have elucidated how hepatocytes undergo endomitosis in human Hep-Orgs, providing new insights into the mechanisms of endomitosis in mammals.
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Affiliation(s)
- Gabriella S. Darmasaputra
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Utrecht, Netherlands
| | - Cindy C. Geerlings
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Matilde Galli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Utrecht, Netherlands
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7
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Yin K, Büttner M, Deligiannis IK, Strzelecki M, Zhang L, Talavera-López C, Theis F, Odom DT, Martinez-Jimenez CP. Polyploidisation pleiotropically buffers ageing in hepatocytes. J Hepatol 2024; 81:289-302. [PMID: 38583492 DOI: 10.1016/j.jhep.2024.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND & AIMS Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. METHODS We performed single-nucleus RNA sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent strains that were haploinsufficient for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. RESULTS We observed that ageing in wild-type mice results in nuclei polyploidy and a marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in the CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A-haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbations. CONCLUSIONS Our results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome. IMPACT AND IMPLICATIONS The functional role of hepatocyte polyploidisation during ageing is poorly understood. Using single-nucleus RNA sequencing and BaseScope approaches, we have studied ploidy dynamics during ageing in murine livers with non-deleterious genetic perturbations. We have identified that hepatocytes present different cellular states and the ability to buffer ageing-associated dysfunctions. Tetraploid nuclei exhibit robust transcriptional networks and are better adapted to genomically overcome perturbations. Novel therapeutic interventions aimed at attenuating age-related changes in tissue function could be exploited by manipulation of ploidy dynamics during chronic liver conditions.
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Affiliation(s)
- Kelvin Yin
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Maren Büttner
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany
| | | | | | - Liwei Zhang
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Carlos Talavera-López
- Division of Infectious Diseases and Tropical Medicine, Ludwig-Maximilian-Universität Klinikum, Germany
| | - Fabian Theis
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany; Technical University of Munich, Department of Mathematics, 85748 Garching. Munich, Germany; German Cancer Research Centre, Heidelberg, Germany.
| | - Duncan T Odom
- German Cancer Research Center, Division of Regulatory Genomics and Cancer Evolution (B270), Heidelberg, Germany; Cancer Research UK Cambridge Institute, University of Cambridge, CB20RE, United Kingdom.
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany; Institute of Biotechnology and Biomedicine (BIOTECMED), Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, Spain.
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8
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Harnik Y, Yakubovsky O, Hoefflin R, Novoselsky R, Bahar Halpern K, Barkai T, Korem Kohanim Y, Egozi A, Golani O, Addadi Y, Kedmi M, Keidar Haran T, Levin Y, Savidor A, Keren-Shaul H, Mayer C, Pencovich N, Pery R, Shouval DS, Tirosh I, Nachmany I, Itzkovitz S. A spatial expression atlas of the adult human proximal small intestine. Nature 2024; 632:1101-1109. [PMID: 39112711 DOI: 10.1038/s41586-024-07793-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 07/05/2024] [Indexed: 08/17/2024]
Abstract
The mouse small intestine shows profound variability in gene expression along the crypt-villus axis1,2. Whether similar spatial heterogeneity exists in the adult human gut remains unclear. Here we use spatial transcriptomics, spatial proteomics and single-molecule fluorescence in situ hybridization to reconstruct a comprehensive spatial expression atlas of the adult human proximal small intestine. We describe zonated expression and cell type representation for epithelial, mesenchymal and immune cell types. We find that migrating enterocytes switch from lipid droplet assembly and iron uptake at the villus bottom to chylomicron biosynthesis and iron release at the tip. Villus tip cells are pro-immunogenic, recruiting γδ T cells and macrophages to the tip, in contrast to their immunosuppressive roles in mouse. We also show that the human small intestine contains abundant serrated and branched villi that are enriched at the tops of circular folds. Our study presents a detailed resource for understanding the biology of the adult human small intestine.
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Affiliation(s)
- Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oran Yakubovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rouven Hoefflin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Roy Novoselsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Barkai
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Sheba Medical Center, Ramat Gan, Israel
| | - Yael Korem Kohanim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Keidar Haran
- Department of Pathology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Niv Pencovich
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Pery
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror S Shouval
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Nachmany
- Department of General Surgery and Transplantation, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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9
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Chen L, Huang Y, Zhang N, Qu J, Fang Y, Fu J, Yuan Y, Zhang Q, Li H, Wen Z, Yuan L, Chen L, Xu Z, Li Y, Yan H, Izawa H, Li L, Xiang C. Single-cell RNA sequencing reveals reduced intercellular adhesion molecule crosstalk between activated hepatic stellate cells and neutrophils alleviating liver fibrosis in hepatitis B virus transgenic mice post menstrual blood-derived mesenchymal stem cell transplantation. MedComm (Beijing) 2024; 5:e654. [PMID: 39040848 PMCID: PMC11261812 DOI: 10.1002/mco2.654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 07/24/2024] Open
Abstract
Liver fibrosis can cause hepatitis B virus (HBV)-associated hepatocellular carcinoma. Menstrual blood-derived mesenchymal stem cells (MenSCs) can ameliorate liver fibrosis through paracrine. Single-cell RNA sequencing (scRNA-seq) may be used to explore the roadmap of activated hepatic stellate cell (aHSC) inactivation to target liver fibrosis. This study established HBV transgenic (HBV-Tg) mouse model of carbon tetrachloride (CCl4)-induced liver fibrosis and demonstrated that MenSCs migrated to the injured liver to improve serological indices and reduce fibrotic accumulation. RNA-bulk analysis revealed that MenSCs mediated extracellular matrix accumulation and cell adhesion. Liver parenchymal cells and nonparenchymal cells were identified by scRNA-seq in the control, CCl4, and MenSC groups, revealing the heterogeneity of fibroblasts/HSCs. A CellChat analysis revealed that diminished intercellular adhesion molecule (ICAM) signaling is vital for MenSC therapy. Specifically, Icam1 in aHSCs acted on Itgal/Itgb2 and Itgam/Itgb2 in neutrophils, causing decreased adhesion. The expression of Itgal, Itgam, and Itgb2 was higher in CCl4 group than in the control group and decreased after MenSC therapy in neutrophil clusters. The Lcn2, Pglyrp1, Wfdc21, and Mmp8 had high expression and may be potential targets in neutrophils. This study highlights interacting cells, corresponding molecules, and underlying targets for MenSCs in treating HBV-associated liver fibrosis.
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Affiliation(s)
- Lijun Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Research Units of Infectious Disease and MicroecologyChinese Academy of Medical SciencesBeijingChina
| | - Yuqi Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Ning Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jingjing Qu
- Department of Respiratory DiseaseThoracic Disease CentreThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Yangxin Fang
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jiamin Fu
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Yin Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Qi Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Hang Li
- Innovative Precision Medicine (IPM) GroupHangzhouChina
| | - Zuoshi Wen
- Department of CardiologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Li Yuan
- Innovative Precision Medicine (IPM) GroupHangzhouChina
| | - Lu Chen
- Innovative Precision Medicine (IPM) GroupHangzhouChina
| | - Zhenyu Xu
- Innovative Precision Medicine (IPM) GroupHangzhouChina
| | - Yifei Li
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Research Units of Infectious Disease and MicroecologyChinese Academy of Medical SciencesBeijingChina
| | - Huadong Yan
- Infectious Disease DepartmentShulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical CollegeHangzhouChina
| | | | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Research Units of Infectious Disease and MicroecologyChinese Academy of Medical SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
| | - Charlie Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesNational Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Research Units of Infectious Disease and MicroecologyChinese Academy of Medical SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
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10
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Wälchli T, Ghobrial M, Schwab M, Takada S, Zhong H, Suntharalingham S, Vetiska S, Gonzalez DR, Wu R, Rehrauer H, Dinesh A, Yu K, Chen ELY, Bisschop J, Farnhammer F, Mansur A, Kalucka J, Tirosh I, Regli L, Schaller K, Frei K, Ketela T, Bernstein M, Kongkham P, Carmeliet P, Valiante T, Dirks PB, Suva ML, Zadeh G, Tabar V, Schlapbach R, Jackson HW, De Bock K, Fish JE, Monnier PP, Bader GD, Radovanovic I. Single-cell atlas of the human brain vasculature across development, adulthood and disease. Nature 2024; 632:603-613. [PMID: 38987604 PMCID: PMC11324530 DOI: 10.1038/s41586-024-07493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/30/2024] [Indexed: 07/12/2024]
Abstract
A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains incompletely understood1. Here we performed single-cell RNA sequencing analysis of 606,380 freshly isolated endothelial cells, perivascular cells and other tissue-derived cells from 117 samples, from 68 human fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We identify extensive molecular heterogeneity of the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumours and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predict substantial endothelial-to-perivascular cell ligand-receptor cross-talk, including immune-related and angiogenic pathways, thereby revealing a central role for the endothelium within brain neurovascular unit signalling networks. Our single-cell brain atlas provides insights into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.
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Affiliation(s)
- Thomas Wälchli
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland.
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland.
| | - Moheb Ghobrial
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Marc Schwab
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
| | - Shigeki Takada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Hang Zhong
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Samuel Suntharalingham
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sandra Vetiska
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | | | - Ruilin Wu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Anuroopa Dinesh
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
| | - Kai Yu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Edward L Y Chen
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jeroen Bisschop
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Fiona Farnhammer
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ann Mansur
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Luca Regli
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Karl Schaller
- Department of Neurosurgery, University of Geneva Medical Center & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Frei
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Troy Ketela
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Mark Bernstein
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Paul Kongkham
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB & Department of Oncology, KU Leuven, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, P. R. China
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Taufik Valiante
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Krembil Brain Institute, Division of Clinical and Computational Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomaterials and Biomedical Engineering and Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Peter B Dirks
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Departments of Surgery and Molecular Genetics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Hartland W Jackson
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Katrien De Bock
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jason E Fish
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Philippe P Monnier
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Ivan Radovanovic
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
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11
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Qiu ZX, Huang LX, Wang XX, Wang ZL, Li XH, Feng B. Exploring the Pathogenesis of Autoimmune Liver Diseases from the Heterogeneity of Target Cells. J Clin Transl Hepatol 2024; 12:659-666. [PMID: 38993508 PMCID: PMC11233981 DOI: 10.14218/jcth.2023.00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 07/13/2024] Open
Abstract
The incidence of autoimmune liver diseases (ALDs) and research on their pathogenesis are increasing annually. However, except for autoimmune hepatitis, which responds well to immunosuppression, primary biliary cholangitis and primary sclerosing cholangitis are insensitive to immunosuppressive therapy. Besides the known effects of the environment, genetics, and immunity on ALDs, the heterogeneity of target cells provides new insights into their pathogenesis. This review started by exploring the heterogeneity in the development, structures, and functions of hepatocytes and epithelial cells of the small and large bile ducts. For example, cytokeratin (CK) 8 and CK18 are primarily expressed in hepatocytes, while CK7 and CK19 are primarily expressed in intrahepatic cholangiocytes. Additionally, emerging technologies of single-cell RNA sequencing and spatial transcriptomic are being applied to study ALDs. This review offered a new perspective on understanding the pathogenic mechanisms and potential treatment strategies for ALDs.
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Affiliation(s)
| | | | - Xiao-Xiao Wang
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Zi-Long Wang
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Xiao-He Li
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Bo Feng
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
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12
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Savoca M, Takemoto K, Hu J, Li L, Jacob Kendrick B, Zhong Z, Lemasters JJ. MitoTracker Red for isolation of zone-specific hepatocytes and characterization of hepatic sublobular metabolism. Biochem Biophys Res Commun 2024; 735:150457. [PMID: 39146811 DOI: 10.1016/j.bbrc.2024.150457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND The liver lobule is divided into three zones or regions: periportal (PP or Zone 1) that is highly oxidative and active in ureagenesis, pericentral (PC or Zone 3) that is more glycolytic, and midzonal (MZ or Zone 2) with intermediate characteristics. AIM Our goal was to isolate and metabolically characterize hepatocytes from specific sublobular zones. METHODS Mice were administered rhodamine123 (Rh123) or MitoTracker Red (MTR) prior to intravital imaging, liver fixation, or hepatocyte isolation. After in vivo MTR, hepatocytes were isolated and sorted based on MTR fluorescence intensity. Alternatively, E-cadherin (Ecad) and cytochrome P450 2E1 (CYP2E1) immunolabeling was performed in fixed liver slices. Ecad and CYP2E1 gene expression in sorted hepatocytes was assessed by qPCR. Oxygen consumption rates (OCR) of sorted hepatocytes were also assessed. RESULTS Multiphoton microscopy showed Rh123 and MTR fluorescence distributed zonally, decreasing from PP to PC in a flow-dependent fashion. In liver cross-sections, Ecad was expressed periportally and CYP2E1 pericentrally in association with high and low MTR labeling, respectively. Based on MTR fluorescence, hepatocytes were sorted into PP, MZ, and PC populations with PP and PC hepatocytes enriched in Ecad and CYP2E1, respectively. OCR of PP hepatocytes was ∼4 times that of PC hepatocytes. CONCLUSIONS MTR treatment in vivo delineates sublobular hepatic zones and can be used to sort hepatocytes zonally. PP hepatocytes have substantially greater OCR compared to PC and MZ. The results also indicate a sharp midzonal demarcation between hepatocytes with PP characteristics (Ecad) and those with PC features (CYP2E1). This new method to sort hepatocytes in a zone-specific fashion holds the potential to shed light on sublobular hepatocyte metabolism and regulatory pathways in health and disease.
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Affiliation(s)
- Matthew Savoca
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kenji Takemoto
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jiangting Hu
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Li Li
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - B Jacob Kendrick
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Zhi Zhong
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - John J Lemasters
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
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13
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Seubnooch P, Montani M, Dufour JF, Masoodi M. Spatial lipidomics reveals zone-specific hepatic lipid alteration and remodeling in metabolic dysfunction-associated steatohepatitis. J Lipid Res 2024; 65:100599. [PMID: 39032559 DOI: 10.1016/j.jlr.2024.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
Alteration in lipid metabolism plays a pivotal role in developing metabolic dysfunction-associated steatohepatitis (MASH). However, our understanding of alteration in lipid metabolism across liver zonation in MASH remains limited. Within this study, we investigated MASH-associated zone-specific lipid metabolism in a diet and chemical-induced MASH mouse model. Spatial lipidomics using mass spectrometry imaging in a MASH mouse model revealed 130 lipids from various classes altered across liver zonation and exhibited zone-specific lipid signatures in MASH. Triacylglycerols, diacylglycerols, sphingolipids and ceramides showed distinct zone-specific changes and re-distribution from pericentral to periportal localization in MASH. Saturated and monounsaturated fatty acids (FA) were the primary FA composition of increased lipids in MASH, while polyunsaturated FAs were the major FA composition of decreased lipids. We observed elevated fibrosis in the periportal region, which could be the result of observed metabolic alteration across zonation. Our study provides valuable insights into zone-specific hepatic lipid metabolism and demonstrates the significance of spatial lipidomics in understanding liver lipid metabolism. Identifying unique lipid distribution patterns may offer valuable insights into the pathophysiology of MASH and facilitate the discovery of diagnostic markers associated with liver zonation.
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Affiliation(s)
- Patcharamon Seubnooch
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Matteo Montani
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Jean-Francois Dufour
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Mojgan Masoodi
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland.
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14
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Brazovskaja A, Gomes T, Holtackers R, Wahle P, Körner C, He Z, Schaffer T, Eckel JC, Hänsel R, Santel M, Seimiya M, Denecke T, Dannemann M, Brosch M, Hampe J, Seehofer D, Damm G, Camp JG, Treutlein B. Cell atlas of the regenerating human liver after portal vein embolization. Nat Commun 2024; 15:5827. [PMID: 38992008 PMCID: PMC11239663 DOI: 10.1038/s41467-024-49236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/28/2024] [Indexed: 07/13/2024] Open
Abstract
The liver has the remarkable capacity to regenerate. In the clinic, regeneration is induced by portal vein embolization, which redirects portal blood flow, resulting in liver hypertrophy in locations with increased blood supply, and atrophy of embolized segments. Here, we apply single-cell and single-nucleus transcriptomics on healthy, hypertrophied, and atrophied patient-derived liver samples to explore cell states in the regenerating liver. Our data unveils pervasive upregulation of genes associated with developmental processes, cellular adhesion, and inflammation in post-portal vein embolization liver, disrupted portal-central hepatocyte zonation, and altered cell subtype composition of endothelial and immune cells. Interlineage crosstalk analysis reveals mesenchymal cells as an interaction hub between immune and endothelial cells, and highlights the importance of extracellular matrix proteins in liver regeneration. Moreover, we establish tissue-scale iterative indirect immunofluorescence imaging for high-dimensional spatial analysis of perivascular microenvironments, uncovering changes to tissue architecture in regenerating liver lobules. Altogether, our data is a rich resource revealing cellular and histological changes in human liver regeneration.
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Affiliation(s)
| | - Tomás Gomes
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Rene Holtackers
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Philipp Wahle
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christiane Körner
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Theresa Schaffer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julian Connor Eckel
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - René Hänsel
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), Leipzig University, Leipzig, Germany
| | - Malgorzata Santel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Timm Denecke
- Department of Diagnostic and Interventional Radiology, Leipzig University, Leipzig, Germany
| | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mario Brosch
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technical University Dresden, Dresden, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, Technical University Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technical University Dresden, Dresden, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, University Hospital, Leipzig University, Leipzig, Germany.
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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15
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Queathem ED, Moazzami Z, Stagg DB, Nelson AB, Fulghum K, Hayir A, Seay A, Gillingham JR, d'Avignon DA, Han X, Ruan HB, Crawford PA, Puchalska P. Ketogenesis supports hepatic polyunsaturated fatty acid homeostasis via fatty acid elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602593. [PMID: 39026753 PMCID: PMC11257565 DOI: 10.1101/2024.07.09.602593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Therapeutic interventions targeting hepatic lipid metabolism in metabolic dysfunction-associated steatotic liver disease (MASLD) and steatohepatitis (MASH) remain elusive. Using mass spectrometry-based stable isotope tracing and shotgun lipidomics, we established a novel link between ketogenesis and MASLD pathophysiology. Our findings show that mouse liver and primary hepatocytes consume ketone bodies to support fatty acid (FA) biosynthesis via both de novo lipogenesis (DNL) and FA elongation. Analysis of 13 C-labeled FAs in hepatocytes lacking mitochondrial D-β-hydroxybutyrate dehydrogenase (BDH1) revealed a partial reliance on mitochondrial conversion of D-βOHB to acetoacetate (AcAc) for cytoplasmic DNL contribution, whereas FA elongation from ketone bodies was fully dependent on cytosolic acetoacetyl-CoA synthetase (AACS). Ketone bodies were essential for polyunsaturated FA (PUFA) homeostasis in hepatocytes, as loss of AACS diminished both free and esterified PUFAs. Ketogenic insufficiency depleted liver PUFAs and increased triacylglycerols, mimicking human MASLD, suggesting that ketogenesis supports PUFA homeostasis, and may mitigate MASLD-MASH progression in humans.
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16
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Khanal S, Liu Y, Bamidele AO, Wixom AQ, Washington AM, Jalan-Sakrikar N, Cooper SA, Vuckovic I, Zhang S, Zhong J, Johnson KL, Charlesworth MC, Kim I, Yeon Y, Yoon S, Noh YK, Meroueh C, Timbilla AA, Yaqoob U, Gao J, Kim Y, Lucien F, Huebert RC, Hay N, Simons M, Shah VH, Kostallari E. Glycolysis in hepatic stellate cells coordinates fibrogenic extracellular vesicle release spatially to amplify liver fibrosis. SCIENCE ADVANCES 2024; 10:eadn5228. [PMID: 38941469 PMCID: PMC11212729 DOI: 10.1126/sciadv.adn5228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/24/2024] [Indexed: 06/30/2024]
Abstract
Liver fibrosis is characterized by the activation of perivascular hepatic stellate cells (HSCs), the release of fibrogenic nanosized extracellular vesicles (EVs), and increased HSC glycolysis. Nevertheless, how glycolysis in HSCs coordinates fibrosis amplification through tissue zone-specific pathways remains elusive. Here, we demonstrate that HSC-specific genetic inhibition of glycolysis reduced liver fibrosis. Moreover, spatial transcriptomics revealed a fibrosis-mediated up-regulation of EV-related pathways in the liver pericentral zone, which was abrogated by glycolysis genetic inhibition. Mechanistically, glycolysis in HSCs up-regulated the expression of EV-related genes such as Ras-related protein Rab-31 (RAB31) by enhancing histone 3 lysine 9 acetylation on the promoter region, which increased EV release. Functionally, these glycolysis-dependent EVs increased fibrotic gene expression in recipient HSC. Furthermore, EVs derived from glycolysis-deficient mice abrogated liver fibrosis amplification in contrast to glycolysis-competent mouse EVs. In summary, glycolysis in HSCs amplifies liver fibrosis by promoting fibrogenic EV release in the hepatic pericentral zone, which represents a potential therapeutic target.
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Affiliation(s)
- Shalil Khanal
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuanhang Liu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Alexander Q. Wixom
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexander M. Washington
- Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Nidhi Jalan-Sakrikar
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shawna A. Cooper
- Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Ivan Vuckovic
- Metabolomics Core, Mayo Clinic, Rochester, MN 55905, USA
| | - Song Zhang
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Iljung Kim
- Department of Computer Science, Hanyang University, Seoul 04763, Republic of South Korea
| | - Yubin Yeon
- Department of Computer Science, Hanyang University, Seoul 04763, Republic of South Korea
| | - Sangwoong Yoon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of South Korea
| | - Yung-Kyun Noh
- Department of Computer Science, Hanyang University, Seoul 04763, Republic of South Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of South Korea
| | - Chady Meroueh
- Department of Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Abdul Aziz Timbilla
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Medical Biochemistry, Faculty of Medicine, Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Usman Yaqoob
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinhang Gao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
- Lab of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy; Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Yohan Kim
- Department of Urology, Mayo Clinic, Rochester, MN 55905, USA
| | - Fabrice Lucien
- Department of Urology, Mayo Clinic, Rochester, MN 55905, USA
| | - Robert C. Huebert
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nissim Hay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Michael Simons
- Cardiovascular Research Center, Yale University, New Haven, CI 06510, USA
| | - Vijay H. Shah
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Enis Kostallari
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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17
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Shi J, Li Q, Li J, Zhou J, Zhang X, Wang S, Guo L. Single-Cell RNA Sequencing Reveals the Spatial Heterogeneity and Functional Alteration of Endothelial Cells in Chronic Hepatitis B Infection. Int J Mol Sci 2024; 25:7016. [PMID: 39000126 PMCID: PMC11241719 DOI: 10.3390/ijms25137016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Chronic Hepatitis B virus (CHB) infection is a global health challenge, causing damage ranging from hepatitis to cirrhosis and hepatocellular carcinoma. In our study, single-cell RNA sequencing (scRNA-seq) analysis was performed in livers from mice models with chronic inflammation induced by CHB infection and we found that endothelial cells (ECs) exhibited the largest number of differentially expressed genes (DEGs) among all ten cell types. NF-κB signaling was activated in ECs to induce cell dysfunction and subsequent hepatic inflammation, which might be mediated by the interaction of macrophage-derived and cholangiocyte-derived VISFATIN/Nampt signaling. Moreover, we divided ECs into three subclusters, including periportal ECs (EC_Z1), midzonal ECs (EC_Z2), and pericentral ECs (EC_Z3) according to hepatic zonation. Functional analysis suggested that pericentral ECs and midzonal ECs, instead of periportal ECs, were more vulnerable to HBV infection, as the VISFATIN/Nampt- NF-κB axis was mainly altered in these two subpopulations. Interestingly, pericentral ECs showed increasing communication with macrophages and cholangiocytes via the Nampt-Insr and Nampt-Itga5/Itgb1 axis upon CHB infection, which contribute to angiogenesis and vascular capillarization. Additionally, ECs, especially pericentral ECs, showed a close connection with nature killer (NK) cells and T cells via the Cxcl6-Cxcr6 axis, which is involved in shaping the microenvironment in CHB mice livers. Thus, our study described the heterogeneity and functional alterations of three subclusters in ECs. We revealed the potential role of VISFATIN/Nampt signaling in modulating ECs characteristics and related hepatic inflammation, and EC-derived chemokine Cxcl16 in shaping NK and T cell recruitment, providing key insights into the multifunctionality of ECs in CHB-associated pathologies.
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Affiliation(s)
- Jingqi Shi
- Bioinformatics Center of AMMS, Beijing 100039, China
| | - Qingyu Li
- Bioinformatics Center of AMMS, Beijing 100039, China
| | - Jian Li
- Bioinformatics Center of AMMS, Beijing 100039, China
| | - Jianglin Zhou
- Bioinformatics Center of AMMS, Beijing 100039, China
| | | | - Shengqi Wang
- Bioinformatics Center of AMMS, Beijing 100039, China
| | - Liang Guo
- Bioinformatics Center of AMMS, Beijing 100039, China
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18
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Nirgude S, Tichy ED, Liu Z, Pradieu RD, Byrne M, Gil De Gomez L, Mamou B, Bernt KM, Yang W, MacFarland S, Xie M, Kalish JM. Single-nucleus multiomic analysis of Beckwith-Wiedemann syndrome liver reveals PPARA signaling enrichment and metabolic dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599077. [PMID: 38948745 PMCID: PMC11212859 DOI: 10.1101/2024.06.14.599077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Beckwith-Wiedemann Syndrome (BWS) is an epigenetic overgrowth syndrome caused by methylation changes in the human 11p15 chromosomal locus. Patients with BWS exhibit tissue overgrowth, as well as an increased risk of childhood neoplasms in the liver and kidney. To understand the impact of these 11p15 changes, specifically in the liver, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) to generate paired, cell-type-specific transcriptional and chromatin accessibility profiles of both BWS-liver and nonBWS-liver nontumorous tissue. Our integrated RNA+ATACseq multiomic approach uncovered hepatocyte-specific enrichment and activation of the peroxisome proliferator-activated receptor α (PPARA) - a liver metabolic regulator. To confirm our findings, we utilized a BWS-induced pluripotent stem cell (iPSC) model, where cells were differentiated into hepatocytes. Our data demonstrates the dysregulation of lipid metabolism in BWS-liver, which coincided with observed upregulation of PPARA during hepatocyte differentiation. BWS liver cells exhibited decreased neutral lipids and increased fatty acid β-oxidation, relative to controls. We also observed increased reactive oxygen species (ROS) byproducts in the form of peroxidated lipids in BWS hepatocytes, which coincided with increased oxidative DNA damage. This study proposes a putative mechanism for overgrowth and cancer predisposition in BWS liver due to perturbed metabolism.
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19
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D'Alessio AM, Boffa I, De Stefano L, Soria LR, Brunetti-Pierri N. Liver gene transfer for metabolite detoxification in inherited metabolic diseases. FEBS Lett 2024. [PMID: 38884367 DOI: 10.1002/1873-3468.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Inherited metabolic disorders (IMDs) are a growing group of genetic diseases caused by defects in enzymes that mediate cellular metabolism, often resulting in the accumulation of toxic substrates. The liver is a highly metabolically active organ that hosts several thousands of chemical reactions. As such, it is an organ frequently affected in IMDs. In this article, we review current approaches for liver-directed gene-based therapy aimed at metabolite detoxification in a variety of IMDs. Moreover, we discuss current unresolved challenges in gene-based therapies for IMDs.
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Affiliation(s)
- Alfonso M D'Alessio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Iolanda Boffa
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Azienda Ospedaliera Universitaria Federico II, Naples, Italy
| | - Lucia De Stefano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Leandro R Soria
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
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20
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Armingol E, Baghdassarian HM, Lewis NE. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet 2024; 25:381-400. [PMID: 38238518 PMCID: PMC11139546 DOI: 10.1038/s41576-023-00685-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
Abstract
No cell lives in a vacuum, and the molecular interactions between cells define most phenotypes. Transcriptomics provides rich information to infer cell-cell interactions and communication, thus accelerating the discovery of the roles of cells within their communities. Such research relies heavily on algorithms that infer which cells are interacting and the ligands and receptors involved. Specific pressures on different research niches are driving the evolution of next-generation computational tools, enabling new conceptual opportunities and technological advances. More sophisticated algorithms now account for the heterogeneity and spatial organization of cells, multiple ligand types and intracellular signalling events, and enable the use of larger and more complex datasets, including single-cell and spatial transcriptomics. Similarly, new high-throughput experimental methods are increasing the number and resolution of interactions that can be analysed simultaneously. Here, we explore recent progress in cell-cell interaction research and highlight the diversification of the next generation of tools, which have yielded a rich ecosystem of tools for different applications and are enabling invaluable discoveries.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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21
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Munro V, Kelly V, Messner CB, Kustatscher G. Cellular control of protein levels: A systems biology perspective. Proteomics 2024; 24:e2200220. [PMID: 38012370 DOI: 10.1002/pmic.202200220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.
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Affiliation(s)
- Victoria Munro
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Van Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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22
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Gribben C, Galanakis V, Calderwood A, Williams EC, Chazarra-Gil R, Larraz M, Frau C, Puengel T, Guillot A, Rouhani FJ, Mahbubani K, Godfrey E, Davies SE, Athanasiadis E, Saeb-Parsy K, Tacke F, Allison M, Mohorianu I, Vallier L. Acquisition of epithelial plasticity in human chronic liver disease. Nature 2024; 630:166-173. [PMID: 38778114 PMCID: PMC11153150 DOI: 10.1038/s41586-024-07465-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
For many adult human organs, tissue regeneration during chronic disease remains a controversial subject. Regenerative processes are easily observed in animal models, and their underlying mechanisms are becoming well characterized1-4, but technical challenges and ethical aspects are limiting the validation of these results in humans. We decided to address this difficulty with respect to the liver. This organ displays the remarkable ability to regenerate after acute injury, although liver regeneration in the context of recurring injury remains to be fully demonstrated. Here we performed single-nucleus RNA sequencing (snRNA-seq) on 47 liver biopsies from patients with different stages of metabolic dysfunction-associated steatotic liver disease to establish a cellular map of the liver during disease progression. We then combined these single-cell-level data with advanced 3D imaging to reveal profound changes in the liver architecture. Hepatocytes lose their zonation and considerable reorganization of the biliary tree takes place. More importantly, our study uncovers transdifferentiation events that occur between hepatocytes and cholangiocytes without the presence of adult stem cells or developmental progenitor activation. Detailed analyses and functional validations using cholangiocyte organoids confirm the importance of the PI3K-AKT-mTOR pathway in this process, thereby connecting this acquisition of plasticity to insulin signalling. Together, our data indicate that chronic injury creates an environment that induces cellular plasticity in human organs, and understanding the underlying mechanisms of this process could open new therapeutic avenues in the management of chronic diseases.
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Affiliation(s)
- Christopher Gribben
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Vasileios Galanakis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- Liver Unit, Department of Medicine, Cambridge NIHR Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alexander Calderwood
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Eleanor C Williams
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ruben Chazarra-Gil
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Miguel Larraz
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carla Frau
- Berlin Institute of Health Centre for Regenerative Therapies, Berlin, Germany
| | - Tobias Puengel
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Adrien Guillot
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | | | - Edmund Godfrey
- Department of Radiology, Addenbrooke's Hospital, Cambridge, UK
| | - Susan E Davies
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Emmanouil Athanasiadis
- Greek Genome Centre, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | | | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Allison
- Open Targets, Wellcome Genome Campus, Hinxton, UK.
- Liver Unit, Department of Medicine, Cambridge NIHR Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, UK.
- Berlin Institute of Health Centre for Regenerative Therapies, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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23
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Matchett KP, Wilson-Kanamori JR, Portman JR, Kapourani CA, Fercoq F, May S, Zajdel E, Beltran M, Sutherland EF, Mackey JBG, Brice M, Wilson GC, Wallace SJ, Kitto L, Younger NT, Dobie R, Mole DJ, Oniscu GC, Wigmore SJ, Ramachandran P, Vallejos CA, Carragher NO, Saeidinejad MM, Quaglia A, Jalan R, Simpson KJ, Kendall TJ, Rule JA, Lee WM, Hoare M, Weston CJ, Marioni JC, Teichmann SA, Bird TG, Carlin LM, Henderson NC. Multimodal decoding of human liver regeneration. Nature 2024; 630:158-165. [PMID: 38693268 PMCID: PMC11153152 DOI: 10.1038/s41586-024-07376-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The liver has a unique ability to regenerate1,2; however, in the setting of acute liver failure (ALF), this regenerative capacity is often overwhelmed, leaving emergency liver transplantation as the only curative option3-5. Here, to advance understanding of human liver regeneration, we use paired single-nucleus RNA sequencing combined with spatial profiling of healthy and ALF explant human livers to generate a single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation, which emerges during human liver regeneration, and a corollary subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. Four-dimensional intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 reduces hepatocyte growth factor-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation that mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may advance new areas of therapeutic discovery in regenerative medicine.
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Affiliation(s)
- K P Matchett
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Wilson-Kanamori
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Portman
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Kapourani
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - F Fercoq
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - S May
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - E Zajdel
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - M Beltran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - E F Sutherland
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J B G Mackey
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - M Brice
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - G C Wilson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - S J Wallace
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - L Kitto
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - N T Younger
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - R Dobie
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - D J Mole
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - G C Oniscu
- Edinburgh Transplant Centre, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Transplant Surgery, CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - S J Wigmore
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - P Ramachandran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Vallejos
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- The Alan Turing Institute, London, UK
| | - N O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - M M Saeidinejad
- Institute for Liver and Digestive Health, University College London, London, UK
| | - A Quaglia
- Department of Cellular Pathology, Royal Free London NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - R Jalan
- Institute for Liver and Digestive Health, University College London, London, UK
- European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
| | - K J Simpson
- Department of Hepatology, University of Edinburgh and Scottish Liver Transplant Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - T J Kendall
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J A Rule
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - W M Lee
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - M Hoare
- Early Cancer Institute, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C J Weston
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
| | - S A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, Cambridge, UK
| | - T G Bird
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - L M Carlin
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - N C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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24
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Liu Y, Zhou Y, Ahodantin J, Jin Y, Zhu J, Sun Z, Wu X, Su L, Yang Y. Generation and characterization of mature hepatocyte organoids for liver metabolic studies. J Cell Sci 2024; 137:jcs261961. [PMID: 38700490 PMCID: PMC11166457 DOI: 10.1242/jcs.261961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Hepatocyte organoids (HOs) generated in vitro are powerful tools for liver regeneration. However, previously reported HOs have mostly been fetal in nature with low expression levels of metabolic genes characteristic of adult liver functions, hampering their application in studies of metabolic regulation and therapeutic testing for liver disorders. Here, we report development of novel culture conditions that combine optimized levels of triiodothyronine (T3) with the removal of growth factors to enable successful generation of mature hepatocyte organoids (MHOs) of both mouse and human origin with metabolic functions characteristic of adult livers. We show that the MHOs can be used to study various metabolic functions including bile and urea production, zonal metabolic gene expression, and metabolic alterations in both alcoholic liver disease and non-alcoholic fatty liver disease, as well as hepatocyte proliferation, injury and cell fate changes. Notably, MHOs derived from human fetal hepatocytes also show improved hepatitis B virus infection. Therefore, these MHOs provide a powerful in vitro model for studies of human liver physiology and diseases. The human MHOs are potentially also a robust research tool for therapeutic development.
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Affiliation(s)
- Yuchen Liu
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA
| | - Yaxing Zhou
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA
| | - James Ahodantin
- Division of Virology, Pathogenesis, and Cancer, Institute of Human Virology, Departments of Pharmacology and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yu Jin
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA
| | - Juanjuan Zhu
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA
| | - Zhonghe Sun
- Cancer Research Technology Program, Frederick National Laboratory for Cancer, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Lishan Su
- Division of Virology, Pathogenesis, and Cancer, Institute of Human Virology, Departments of Pharmacology and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yingzi Yang
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Program in Gastrointestinal Malignancies, Dana-Farber/Harvard Cancer Center, 188 Longwood Ave, Boston, MA 02115, USA
- Program in Gastrointestinal Malignancies, Dana-Farber/Harvard Cancer Center, 188 Longwood Ave, Boston, MA 02115, USA
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25
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Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024; 44:115-132. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Spatial transcriptomics, leveraging sequencing- and imaging-based techniques, has emerged as a groundbreaking technology for mapping gene expression within the complex architectures of tissues. This approach provides an in-depth understanding of cellular and molecular dynamics across various states of healthy and diseased livers. Through the integration of sophisticated bioinformatics strategies, it enables detailed exploration of cellular heterogeneity, transitions in cell states, and intricate cell-cell interactions with remarkable precision. In liver research, spatial transcriptomics has been particularly revelatory, identifying distinct zonated functions of hepatocytes that are crucial for understanding the metabolic and detoxification processes of the liver. Moreover, this technology has unveiled new insights into the pathogenesis of liver diseases, such as the role of lipid-associated macrophages in steatosis and endothelial cell signals in liver regeneration and repair. In the domain of liver cancer, spatial transcriptomics has proven instrumental in delineating intratumor heterogeneity, identifying supportive microenvironmental niches and revealing the complex interplay between tumor cells and the immune system as well as susceptibility to immune checkpoint inhibitors. In conclusion, spatial transcriptomics represents a significant advance in hepatology, promising to enhance our understanding and treatment of liver diseases.
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Affiliation(s)
- Naoto Fujiwara
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Genki Kimura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
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26
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Zhou Y, Zhao Y, Carbonaro M, Chen H, Germino M, Adler C, Ni M, Zhu YO, Kim SY, Altarejos J, Li Z, Burczynski ME, Glass DJ, Sleeman MW, Lee AH, Halasz G, Cheng X. Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis. Metabolism 2024; 154:155830. [PMID: 38428673 DOI: 10.1016/j.metabol.2024.155830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/03/2024]
Abstract
Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal hepatic function. Wnt signaling is a master regulator of spatial liver zonation. A perivenous-periportal Wnt activity gradient orchestrates metabolic zonation by activating gene expression in perivenous hepatocytes, while suppressing gene expression in their periportal counterparts. However, the understanding as to the liver gene zonation and zonation regulators in diseases is limited. Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by fat accumulation, inflammation, and fibrosis. Here, we investigated the perturbation of liver gene zonation in a mouse NASH model by combining spatial transcriptomics, bulk RNAseq and in situ hybridization. Wnt-target genes represented a major subset of genes showing altered spatial expression in the NASH liver. The altered Wnt-target gene expression levels and zonation spatial patterns were in line with the up regulation of Wnt regulators and the augmentation of Wnt signaling. Particularly, we found that the Wnt activator Rspo3 expression was restricted to the perivenous zone in control liver but expanded to the periportal zone in NASH liver. AAV8-mediated RSPO3 overexpression in controls resulted in zonation changes, and further amplified the disturbed zonation of Wnt-target genes in NASH, similarly Rspo3 knockdown in Rspo3+/- mice resulted in zonation changes of Wnt-target genes in both chow and HFD mouse. Interestingly, there were no impacts on steatosis, inflammation, or fibrosis NASH pathology from RSPO3 overexpression nor Rspo3 knockdown. In summary, our study demonstrated the alteration of Wnt signaling in a mouse NASH model, leading to perturbed liver zonation.
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Affiliation(s)
- Ye Zhou
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Yuanqi Zhao
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Marisa Carbonaro
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Helen Chen
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Mary Germino
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Christina Adler
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Min Ni
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Yuan O Zhu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Sun Y Kim
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Judith Altarejos
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Zhe Li
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | | | - David J Glass
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Mark W Sleeman
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Ann-Hwee Lee
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Gabor Halasz
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America
| | - Xiping Cheng
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, United States of America.
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27
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Xu J, Guo P, Hao S, Shangguan S, Shi Q, Volpe G, Huang K, Zuo J, An J, Yuan Y, Cheng M, Deng Q, Zhang X, Lai G, Nan H, Wu B, Shentu X, Wu L, Wei X, Jiang Y, Huang X, Pan F, Song Y, Li R, Wang Z, Liu C, Liu S, Li Y, Yang T, Xu Z, Du W, Li L, Ahmed T, You K, Dai Z, Li L, Qin B, Li Y, Lai L, Qin D, Chen J, Fan R, Li Y, Hou J, Ott M, Sharma AD, Cantz T, Schambach A, Kristiansen K, Hutchins AP, Göttgens B, Maxwell PH, Hui L, Xu X, Liu L, Chen A, Lai Y, Esteban MA. A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nat Genet 2024; 56:953-969. [PMID: 38627598 DOI: 10.1038/s41588-024-01709-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/06/2024] [Indexed: 05/09/2024]
Abstract
The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/β-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.
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Affiliation(s)
- Jiangshan Xu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Pengcheng Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
| | - Shijie Hao
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuncheng Shangguan
- BGI Research, Shenzhen, China
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
| | - Quan Shi
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Keke Huang
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jing Zuo
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Juan An
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Yuan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Mengnan Cheng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Qiuting Deng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Guangyao Lai
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Haitao Nan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Baihua Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyi Shentu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyu Wei
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yujia Jiang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Xin Huang
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fengyu Pan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yumo Song
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Ronghai Li
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Zhifeng Wang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Chuanyu Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Shiping Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | | | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Zhicheng Xu
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Ling Li
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Provincial Genomics Data Center, BGI Research, Shenzhen, China
| | - Tanveer Ahmed
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kai You
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhen Dai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Li Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Baoming Qin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yinxiong Li
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Dajiang Qin
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junling Chen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Rong Fan
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Yongyin Li
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Jinlin Hou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangzhou, China
| | - Michael Ott
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Amar Deep Sharma
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Tobias Cantz
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Berthold Göttgens
- Department of Haematology and Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lijian Hui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xun Xu
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Longqi Liu
- BGI Research, Hangzhou, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Ao Chen
- BGI Research, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- BGI Research, Chongqing, China.
- JFL-BGI STOmics Center, BGI-Shenzhen, Chongqing, China.
| | - Yiwei Lai
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
- BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Miguel A Esteban
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
- 3DC STAR, Spatiotemporal Campus at BGI Shenzhen, Shenzhen, China.
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.
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28
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Miyamoto Y, Kikuta J, Matsui T, Hasegawa T, Fujii K, Okuzaki D, Liu YC, Yoshioka T, Seno S, Motooka D, Uchida Y, Yamashita E, Kobayashi S, Eguchi H, Morii E, Tryggvason K, Shichita T, Kayama H, Atarashi K, Kunisawa J, Honda K, Takeda K, Ishii M. Periportal macrophages protect against commensal-driven liver inflammation. Nature 2024; 629:901-909. [PMID: 38658756 DOI: 10.1038/s41586-024-07372-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The liver is the main gateway from the gut, and the unidirectional sinusoidal flow from portal to central veins constitutes heterogenous zones, including the periportal vein (PV) and the pericentral vein zones1-5. However, functional differences in the immune system in each zone remain poorly understood. Here intravital imaging revealed that inflammatory responses are suppressed in PV zones. Zone-specific single-cell transcriptomics detected a subset of immunosuppressive macrophages enriched in PV zones that express high levels of interleukin-10 and Marco, a scavenger receptor that sequesters pro-inflammatory pathogen-associated molecular patterns and damage-associated molecular patterns, and consequently suppress immune responses. Induction of Marco+ immunosuppressive macrophages depended on gut microbiota. In particular, a specific bacterial family, Odoribacteraceae, was identified to induce this macrophage subset through its postbiotic isoallolithocholic acid. Intestinal barrier leakage resulted in inflammation in PV zones, which was markedly augmented in Marco-deficient conditions. Chronic liver inflammatory diseases such as primary sclerosing cholangitis (PSC) and non-alcoholic steatohepatitis (NASH) showed decreased numbers of Marco+ macrophages. Functional ablation of Marco+ macrophages led to PSC-like inflammatory phenotypes related to colitis and exacerbated steatosis in NASH in animal experimental models. Collectively, commensal bacteria induce Marco+ immunosuppressive macrophages, which consequently limit excessive inflammation at the gateway of the liver. Failure of this self-limiting system promotes hepatic inflammatory disorders such as PSC and NASH.
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Affiliation(s)
- Yu Miyamoto
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
| | - Junichi Kikuta
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Takahiro Matsui
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tetsuo Hasegawa
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
| | - Kentaro Fujii
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yu-Chen Liu
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takuya Yoshioka
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yutaka Uchida
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Erika Yamashita
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan
| | - Shogo Kobayashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Karl Tryggvason
- Cardiovascular and Metabolic Disorders Program, Duke-NUS, Duke-NUS Medical School, Singapore, Singapore
| | - Takashi Shichita
- Laboratory for Neuroinflammation and Repair, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hisako Kayama
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, School of Medicine, Keio University, Tokyo, Japan
| | - Kiyoshi Takeda
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaru Ishii
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan.
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan.
- Life-omics Research Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Osaka, Japan.
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
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29
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Wu B, Shentu X, Nan H, Guo P, Hao S, Xu J, Shangguan S, Cui L, Cen J, Deng Q, Wu Y, Liu C, Song Y, Lin X, Wang Z, Yuan Y, Ma W, Li R, Li Y, Qian Q, Du W, Lai T, Yang T, Liu C, Ma X, Chen A, Xu X, Lai Y, Liu L, Esteban MA, Hui L. A spatiotemporal atlas of cholestatic injury and repair in mice. Nat Genet 2024; 56:938-952. [PMID: 38627596 DOI: 10.1038/s41588-024-01687-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/09/2024] [Indexed: 05/09/2024]
Abstract
Cholestatic liver injuries, characterized by regional damage around the bile ductular region, lack curative therapies and cause considerable mortality. Here we generated a high-definition spatiotemporal atlas of gene expression during cholestatic injury and repair in mice by integrating spatial enhanced resolution omics sequencing and single-cell transcriptomics. Spatiotemporal analyses revealed a key role of cholangiocyte-driven signaling correlating with the periportal damage-repair response. Cholangiocytes express genes related to recruitment and differentiation of lipid-associated macrophages, which generate feedback signals enhancing ductular reaction. Moreover, cholangiocytes express high TGFβ in association with the conversion of liver progenitor-like cells into cholangiocytes during injury and the dampened proliferation of periportal hepatocytes during recovery. Notably, Atoh8 restricts hepatocyte proliferation during 3,5-diethoxycarbonyl-1,4-dihydro-collidin damage and is quickly downregulated after injury withdrawal, allowing hepatocytes to respond to growth signals. Our findings lay a keystone for in-depth studies of cellular dynamics and molecular mechanisms of cholestatic injuries, which may further develop into therapies for cholangiopathies.
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Affiliation(s)
- Baihua Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinyi Shentu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Haitao Nan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Shijie Hao
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiangshan Xu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Shuncheng Shangguan
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- BGI Research, Shenzhen, China
| | - Lei Cui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Cen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiuting Deng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yan Wu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Chang Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yumo Song
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Xiumei Lin
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | | | - Yue Yuan
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Wen Ma
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Ronghai Li
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
| | - Yikang Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qiwei Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Wensi Du
- China National GeneBank, BGI Research, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, BGI Research, Shenzhen, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
| | - Chuanyu Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ao Chen
- BGI Research, Shenzhen, China
| | - Xun Xu
- BGI Research, Shenzhen, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Yiwei Lai
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Longqi Liu
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- China National GeneBank, BGI Research, Shenzhen, China.
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
| | - Miguel A Esteban
- BGI Research, Hangzhou, China.
- BGI Research, Shenzhen, China.
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University-BGI Research Center for Integrative Biology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Lijian Hui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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30
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Belicova L, Van Hul N, Andersson ER. Understanding liver repair through space and time. Nat Genet 2024; 56:740-742. [PMID: 38730127 DOI: 10.1038/s41588-024-01741-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Affiliation(s)
- Lenka Belicova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Van Hul
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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31
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Xiong E, Liu P, Deng R, Zhang K, Yang R, Li J. Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro. Natl Sci Rev 2024; 11:nwae118. [PMID: 38742234 PMCID: PMC11089818 DOI: 10.1093/nsr/nwae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/16/2024] Open
Abstract
Single-nucleotide variants (SNVs) are the most common type variation of sequence alterations at a specific location in the genome, thus involving significant clinical and biological information. The assay of SNVs has engaged great awareness, because many genome-wide association studies demonstrated that SNVs are highly associated with serious human diseases. Moreover, the investigation of SNV expression levels in single cells are capable of visualizing genetic information and revealing the complexity and heterogeneity of single-nucleotide mutation-related diseases. Thus, developing SNV assay approaches in vitro, particularly in single cells, is becoming increasingly in demand. In this review, we summarized recent progress in the enzyme-free and enzyme-mediated strategies enabling SNV assay transition from sensing interface to the test tube and single cells, which will potentially delve deeper into the knowledge of SNV functions and disease associations, as well as discovering new pathways to diagnose and treat diseases based on individual genetic profiles. The leap of SNV assay achievements will motivate observation and measurement genetic variations in single cells, even within living organisms, delve into the knowledge of SNV functions and disease associations, as well as open up entirely new avenues in the diagnosis and treatment of diseases based on individual genetic profiles.
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Affiliation(s)
- Erhu Xiong
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Pengfei Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Ronghua Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Jinghong Li
- Department of Chemistry, Center for Bioanalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Institute of Life Science and Technology, Beijing 102206, China
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32
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Santos AA, Delgado TC, Marques V, Ramirez-Moncayo C, Alonso C, Vidal-Puig A, Hall Z, Martínez-Chantar ML, Rodrigues CM. Spatial metabolomics and its application in the liver. Hepatology 2024; 79:1158-1179. [PMID: 36811413 PMCID: PMC11020039 DOI: 10.1097/hep.0000000000000341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023]
Abstract
Hepatocytes work in highly structured, repetitive hepatic lobules. Blood flow across the radial axis of the lobule generates oxygen, nutrient, and hormone gradients, which result in zoned spatial variability and functional diversity. This large heterogeneity suggests that hepatocytes in different lobule zones may have distinct gene expression profiles, metabolic features, regenerative capacity, and susceptibility to damage. Here, we describe the principles of liver zonation, introduce metabolomic approaches to study the spatial heterogeneity of the liver, and highlight the possibility of exploring the spatial metabolic profile, leading to a deeper understanding of the tissue metabolic organization. Spatial metabolomics can also reveal intercellular heterogeneity and its contribution to liver disease. These approaches facilitate the global characterization of liver metabolic function with high spatial resolution along physiological and pathological time scales. This review summarizes the state of the art for spatially resolved metabolomic analysis and the challenges that hinder the achievement of metabolome coverage at the single-cell level. We also discuss several major contributions to the understanding of liver spatial metabolism and conclude with our opinion on the future developments and applications of these exciting new technologies.
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Affiliation(s)
- André A. Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa C. Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Congenital Metabolic Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Vanda Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Carmen Ramirez-Moncayo
- Institute of Clinical Sciences, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | | | - Antonio Vidal-Puig
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Centro Investigation Principe Felipe, Valencia, Spain
| | - Zoe Hall
- Division of Systems Medicine, Imperial College London, London, UK
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Cecilia M.P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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33
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Raya Tonetti F, Eguileor A, Mrdjen M, Pathak V, Travers J, Nagy LE, Llorente C. Gut-liver axis: Recent concepts in pathophysiology in alcohol-associated liver disease. Hepatology 2024:01515467-990000000-00873. [PMID: 38691396 DOI: 10.1097/hep.0000000000000924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/20/2024] [Indexed: 05/03/2024]
Abstract
The growing recognition of the role of the gut microbiome's impact on alcohol-associated diseases, especially in alcohol-associated liver disease, emphasizes the need to understand molecular mechanisms involved in governing organ-organ communication to identify novel avenues to combat alcohol-associated diseases. The gut-liver axis refers to the bidirectional communication and interaction between the gut and the liver. Intestinal microbiota plays a pivotal role in maintaining homeostasis within the gut-liver axis, and this axis plays a significant role in alcohol-associated liver disease. The intricate communication between intestine and liver involves communication between multiple cellular components in each organ that enable them to carry out their physiological functions. In this review, we focus on novel approaches to understanding how chronic alcohol exposure impacts the microbiome and individual cells within the liver and intestine, as well as the impact of ethanol on the molecular machinery required for intraorgan and interorgan communication.
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Affiliation(s)
- Fernanda Raya Tonetti
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Alvaro Eguileor
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Marko Mrdjen
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
| | - Vai Pathak
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jared Travers
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Gastroenterology and Hepatology, University Hospital, Cleveland, Ohio, USA
| | - Laura E Nagy
- Department of Molecular Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Cristina Llorente
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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34
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Okada J, Landgraf A, Xiaoli AM, Liu L, Horton M, Schuster VL, Yang F, Sidoli S, Qiu Y, Kurland IJ, Eliscovich C, Shinoda K, Pessin JE. Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591168. [PMID: 38746329 PMCID: PMC11092462 DOI: 10.1101/2024.04.29.591168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The liver acts as a master regulator of metabolic homeostasis in part by performing gluconeogenesis. This process is dysregulated in type 2 diabetes, leading to elevated hepatic glucose output. The parenchymal cells of the liver (hepatocytes) are heterogeneous, existing on an axis between the portal triad and the central vein, and perform distinct functions depending on location in the lobule. Here, using single cell analysis of hepatocytes across the liver lobule, we demonstrate that gluconeogenic gene expression ( Pck1 and G6pc ) is relatively low in the fed state and gradually increases first in the periportal hepatocytes during the initial fasting period. As the time of fasting progresses, pericentral hepatocyte gluconeogenic gene expression increases, and following entry into the starvation state, the pericentral hepatocytes show similar gluconeogenic gene expression to the periportal hepatocytes. Similarly, pyruvate-dependent gluconeogenic activity is approximately 10-fold higher in the periportal hepatocytes during the initial fasting state but only 1.5-fold higher in the starvation state. In parallel, starvation suppresses canonical beta-catenin signaling and modulates expression of pericentral and periportal glutamine synthetase and glutaminase, resulting in an enhanced pericentral glutamine-dependent gluconeogenesis. These findings demonstrate that hepatocyte gluconeogenic gene expression and gluconeogenic activity are highly spatially and temporally plastic across the liver lobule, underscoring the critical importance of using well-defined feeding and fasting conditions to define the basis of hepatic insulin resistance and glucose production.
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35
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Bagga AD, Johnson BP, Zhang Q. Spatially Dependent Tissue Distribution of Thyroid Hormones by Plasma Thyroid Hormone Binding Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.572629. [PMID: 38187691 PMCID: PMC10769377 DOI: 10.1101/2023.12.20.572629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Plasma thyroid hormone (TH) binding proteins (THBPs), including thyroxine-binding globulin (TBG), transthyretin (TTR), and albumin (ALB), carry THs to extrathyroidal sites, where THs are unloaded locally and then taken up via membrane transporters into the tissue proper. The respective roles of THBPs in supplying THs for tissue uptake are not completely understood. To investigate this, we developed a spatial human physiologically based kinetic (PBK) model of THs, which produces several novel findings. (1) Contrary to postulations that TTR and/or ALB are the major local T4 contributors, the three THBPs may unload comparable amounts of T4 in Liver, a rapidly perfused organ; however, their contributions in slowly perfused tissues follow the order of abundances of T4TBG, T4TTR, and T4ALB. The T3 amounts unloaded from or loaded onto THBPs in a tissue acting as a T3 sink or source respectively follow the order of abundance of T3TBG, T3ALB, and T3TTR regardless of perfusion rate. (2) Any THBP alone is sufficient to maintain spatially uniform TH tissue distributions. (3) The TH amounts unloaded by each THBP species are spatially dependent and nonlinear in a tissue, with ALB being the dominant contributor near the arterial end but conceding to TBG near the venous end. (4) Spatial gradients of TH transporters and metabolic enzymes may modulate these contributions, producing spatially invariant or heterogeneous TH tissue concentrations depending on whether the blood-tissue TH exchange operates in near-equilibrium mode. In summary, our modeling provides novel insights into the differential roles of THBPs in local TH tissue distribution.
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Affiliation(s)
- Anish D. Bagga
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Brian P. Johnson
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, GA 30322, USA
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36
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Tian H, Rajbhandari P, Tarolli J, Decker AM, Neelakantan TV, Angerer T, Zandkarimi F, Remotti H, Frache G, Winograd N, Stockwell BR. Multimodal mass spectrometry imaging identifies cell-type-specific metabolic and lipidomic variation in the mammalian liver. Dev Cell 2024; 59:869-881.e6. [PMID: 38359832 DOI: 10.1016/j.devcel.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 05/11/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Spatial single-cell omics provides a readout of biochemical processes. It is challenging to capture the transient lipidome/metabolome from cells in a native tissue environment. We employed water gas cluster ion beam secondary ion mass spectrometry imaging ([H2O]n>28K-GCIB-SIMS) at ≤3 μm resolution using a cryogenic imaging workflow. This allowed multiple biomolecular imaging modes on the near-native-state liver at single-cell resolution. Our workflow utilizes desorption electrospray ionization (DESI) to build a reference map of metabolic heterogeneity and zonation across liver functional units at tissue level. Cryogenic dual-SIMS integrated metabolomics, lipidomics, and proteomics in the same liver lobules at single-cell level, characterizing the cellular landscape and metabolic states in different cell types. Lipids and metabolites classified liver metabolic zones, cell types and subtypes, highlighting the power of spatial multi-omics at high spatial resolution for understanding celluar and biomolecular organizations in the mammalian liver.
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Affiliation(s)
- Hua Tian
- Environmental and Occupational Health, Pitt Public Health, Pittsburgh, PA 15261, USA; Children's Neuroscience Institute, School of Medicine, Pittsburgh, PA 15224, USA.
| | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - Aubrianna M Decker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - Tina Angerer
- The Luxembourg Institute of Science and Technology, 4362 Esch-sur-Alzette, Luxembourg; Department of Pharmaceutical Biosciences, Uppsala University, 751 05 Uppsala, Sweden
| | | | - Helen Remotti
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gilles Frache
- The Luxembourg Institute of Science and Technology, 4362 Esch-sur-Alzette, Luxembourg
| | - Nicholas Winograd
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.
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37
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Scheidecker B, Poulain S, Sugimoto M, Arakawa H, Kim SH, Kawanishi T, Kato Y, Danoy M, Nishikawa M, Sakai Y. Mechanobiological stimulation in organ-on-a-chip systems reduces hepatic drug metabolic capacity in favor of regenerative specialization. Biotechnol Bioeng 2024; 121:1435-1452. [PMID: 38184801 DOI: 10.1002/bit.28653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
Hepatic physiology depends on the liver's complex structural composition which among others, provides high oxygen supply rates, locally differential oxygen tension, endothelial paracrine signaling, as well as residual hemodynamic shear stress to resident hepatocytes. While functional improvements were shown by implementing these factors into hepatic culture systems, direct cause-effect relationships are often not well characterized-obfuscating their individual contribution in more complex microphysiological systems. By comparing increasingly complex hepatic in vitro culture systems that gradually implement these parameters, we investigate the influence of the cellular microenvironment to overall hepatic functionality in pharmacological applications. Here, hepatocytes were modulated in terms of oxygen tension and supplementation, endothelial coculture, and exposure to fluid shear stress delineated from oxygen influx. Results from transcriptomic and metabolomic evaluation indicate that particularly oxygen supply rates are critical to enhance cellular functionality-with cellular drug metabolism remaining comparable to physiological conditions after prolonged static culture. Endothelial signaling was found to be a major contributor to differential phenotype formation known as metabolic zonation, indicated by WNT pathway activity. Lastly, oxygen-delineated shear stress was identified to direct cellular fate towards increased hepatic plasticity and regenerative phenotypes at the cost of drug metabolic functionality - in line with regenerative effects observed in vivo. With these results, we provide a systematic evaluation of critical parameters and their impact in hepatic systems. Given their adherence to physiological effects in vivo, this highlights the importance of their implementation in biomimetic devices, such as organ-on-a-chip systems. Considering recent advances in basic liver biology, direct translation of physiological structures into in vitro models is a promising strategy to expand the capabilities of pharmacological models.
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Affiliation(s)
| | - Stéphane Poulain
- Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Hiroshi Arakawa
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Soo H Kim
- Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Takumi Kawanishi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Yukio Kato
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Mathieu Danoy
- Department of Chemical System Engineering, University of Tokyo, Tokyo, Japan
| | - Masaki Nishikawa
- Department of Chemical System Engineering, University of Tokyo, Tokyo, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, University of Tokyo, Tokyo, Japan
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38
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Mladenić K, Lenartić M, Marinović S, Polić B, Wensveen FM. The "Domino effect" in MASLD: The inflammatory cascade of steatohepatitis. Eur J Immunol 2024; 54:e2149641. [PMID: 38314819 DOI: 10.1002/eji.202149641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is an increasingly common complication of obesity, affecting over a quarter of the global adult population. A key event in the pathophysiology of MASLD is the development of metabolic-associated steatohepatitis (MASH), which greatly increases the chances of developing cirrhosis and hepatocellular carcinoma. The underlying cause of MASH is multifactorial, but accumulating evidence indicates that the inflammatory process in the hepatic microenvironment typically follows a pattern that can be roughly divided into three stages: (1) Detection of hepatocyte stress by tissue-resident immune cells including γδ T cells and CD4-CD8- double-negative T cells, followed by their secretion of pro-inflammatory mediators, most notably IL-17A. (2) Recruitment of pro-inflammatory cells, mostly of the myeloid lineage, and initiation of inflammation through secretion of effector-type cytokines such as TNF, TGF-β, and IL-1β. (3) Escalation of the inflammatory response by recruitment of lymphocytes including Th17, CD8 T, and B cells leading to chronic inflammation, hepatic stellate cell activation, and fibrosis. Here we will discuss these three stages and how they are consecutively linked like falling domino tiles to the pathophysiology of MASH. Moreover, we will highlight the clinical potential of inflammation as a biomarker and therapeutic target for the treatment of MASLD.
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Affiliation(s)
- Karlo Mladenić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Maja Lenartić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Sonja Marinović
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Division of Molecular Medicine, Laboratory for Personalized Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Bojan Polić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Felix M Wensveen
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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39
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Sun J, Esplugues E, Bort A, Cardelo MP, Ruz-Maldonado I, Fernández-Tussy P, Wong C, Wang H, Ojima I, Kaczocha M, Perry R, Suárez Y, Fernández-Hernando C. Fatty acid binding protein 5 suppression attenuates obesity-induced hepatocellular carcinoma by promoting ferroptosis and intratumoral immune rewiring. Nat Metab 2024; 6:741-763. [PMID: 38664583 DOI: 10.1038/s42255-024-01019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/26/2024] [Indexed: 04/28/2024]
Abstract
Due to the rise in overnutrition, the incidence of obesity-induced hepatocellular carcinoma (HCC) will continue to escalate; however, our understanding of the obesity to HCC developmental axis is limited. We constructed a single-cell atlas to interrogate the dynamic transcriptomic changes during hepatocarcinogenesis in mice. Here we identify fatty acid binding protein 5 (FABP5) as a driver of obesity-induced HCC. Analysis of transformed cells reveals that FABP5 inhibition and silencing predispose cancer cells to lipid peroxidation and ferroptosis-induced cell death. Pharmacological inhibition and genetic ablation of FABP5 ameliorates the HCC burden in male mice, corresponding to enhanced ferroptosis in the tumour. Moreover, FABP5 inhibition induces a pro-inflammatory tumour microenvironment characterized by tumour-associated macrophages with increased expression of the co-stimulatory molecules CD80 and CD86 and increased CD8+ T cell activation. Our work unravels the dual functional role of FABP5 in diet-induced HCC, inducing the transformation of hepatocytes and an immunosuppressive phenotype of tumour-associated macrophages and illustrates FABP5 inhibition as a potential therapeutic approach.
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Affiliation(s)
- Jonathan Sun
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Enric Esplugues
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Alicia Bort
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Magdalena P Cardelo
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Inmaculada Ruz-Maldonado
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Pablo Fernández-Tussy
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Clara Wong
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Hehe Wang
- Department of Chemistry, Stony Brook University, New York, NY, USA
| | - Iwao Ojima
- Department of Chemistry, Stony Brook University, New York, NY, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, New York, NY, USA
| | - Martin Kaczocha
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, New York, NY, USA
- Department of Anesthesiology, Renaissance School of Medicine. Stony Brook University, New York, NY, USA
| | - Rachel Perry
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine (Endocrinology), Yale University School of Medicine, New Haven, CT, USA
| | - Yajaira Suárez
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA.
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, CT, USA.
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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Berggren KA, Schwartz RE, Kleiner RE, Ploss A. The impact of epitranscriptomic modifications on liver disease. Trends Endocrinol Metab 2024; 35:331-346. [PMID: 38212234 DOI: 10.1016/j.tem.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
RNA modifications have emerged as important mechanisms of gene regulation. Developmental, metabolic, and cell cycle regulatory processes are all affected by epitranscriptomic modifications, which control gene expression in a dynamic manner. The hepatic tissue is highly metabolically active and has an impressive ability to regenerate after injury. Cell proliferation, differentiation, and metabolism, which are all essential to the liver response to injury and regeneration, are regulated via RNA modification. Two such modifications, N6-methyladenosine (m6A)and 5-methylcytosine (m5C), have been identified as prognostic disease markers and potential therapeutic targets for liver diseases. Here, we describe progress in understanding the role of RNA modifications in liver biology and disease and discuss specific areas where unexpected results could lead to improved future understanding.
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Affiliation(s)
- Keith A Berggren
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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Plata-Gómez AB, de Prado-Rivas L, Sanz A, Deleyto-Seldas N, García F, de la Calle Arregui C, Silva C, Caleiras E, Graña-Castro O, Piñeiro-Yáñez E, Krebs J, Leiva-Vega L, Muñoz J, Jain A, Sabio G, Efeyan A. Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver. Nat Commun 2024; 15:1878. [PMID: 38499523 PMCID: PMC10948770 DOI: 10.1038/s41467-024-46032-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 02/09/2024] [Indexed: 03/20/2024] Open
Abstract
The metabolic functions of the liver are spatially organized in a phenomenon called zonation, linked to the differential exposure of portal and central hepatocytes to nutrient-rich blood. The mTORC1 signaling pathway controls cellular metabolism in response to nutrients and insulin fluctuations. Here we show that simultaneous genetic activation of nutrient and hormone signaling to mTORC1 in hepatocytes results in impaired establishment of postnatal metabolic and zonal identity of hepatocytes. Mutant hepatocytes fail to upregulate postnatally the expression of Frizzled receptors 1 and 8, and show reduced Wnt/β-catenin activation. This defect, alongside diminished paracrine Wnt2 ligand expression by endothelial cells, underlies impaired postnatal maturation. Impaired zonation is recapitulated in a model of constant supply of nutrients by parenteral nutrition to piglets. Our work shows the role of hepatocyte sensing of fluctuations in nutrients and hormones for triggering a latent metabolic zonation program.
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Affiliation(s)
- Ana Belén Plata-Gómez
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain
| | - Lucía de Prado-Rivas
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain
| | - Alba Sanz
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain
| | - Nerea Deleyto-Seldas
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain
| | - Fernando García
- Proteomics Unit. Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Celia de la Calle Arregui
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain
| | - Camila Silva
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain
| | - Eduardo Caleiras
- Histopathology Unit. Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit. Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Department of Basic Medical Sciences, Institute of Applied Molecular Medicine (IMMA-Nemesio Díez), School of Medicine, San Pablo-CEU University, CEU Universities, Boadilla del Monte, Madrid, Spain
| | - Elena Piñeiro-Yáñez
- Bioinformatics Unit. Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Joseph Krebs
- Department of Pediatrics, Saint Louis University, Saint Louis, MO, USA
| | - Luis Leiva-Vega
- Myocardial Pathophysiology, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit. Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Cell Signalling and Clinical Proteomics Group, Biocruces Bizkaia Health Research Institute & Ikerbasque Basque Foundation for Science, Bilbao, Spain
| | - Ajay Jain
- Department of Pediatrics, Saint Louis University, Saint Louis, MO, USA
| | - Guadalupe Sabio
- Myocardial Pathophysiology, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Alejo Efeyan
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain.
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42
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Wang S, Wang X, Shan Y, Tan Z, Su Y, Cao Y, Wang S, Dong J, Gu J, Wang Y. Region-specific cellular and molecular basis of liver regeneration after acute pericentral injury. Cell Stem Cell 2024; 31:341-358.e7. [PMID: 38402618 DOI: 10.1016/j.stem.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Liver injuries often occur in a zonated manner. However, detailed regenerative responses to such zonal injuries at cellular and molecular levels remain largely elusive. By using a fate-mapping strain, Cyp2e1-DreER, to elucidate liver regeneration after acute pericentral injury, we found that pericentral regeneration is primarily compensated by the expansion of remaining pericentral hepatocytes, and secondarily by expansion of periportal hepatocytes. Employing single-cell RNA sequencing, spatial transcriptomics, immunostaining, and in vivo functional assays, we demonstrated that the upregulated expression of the mTOR/4E-BP1 axis and lactate dehydrogenase A in hepatocytes contributes to pericentral regeneration, while activation of transforming growth factor β (TGF-β1) signaling in the damaged area mediates fibrotic responses and inhibits hepatocyte proliferation. Inhibiting the pericentral accumulation of monocytes and monocyte-derived macrophages through an Arg-Gly-Asp (RGD) peptide-based strategy attenuates these cell-derived TGF-β1 signalings, thus improving pericentral regeneration. Our study provides integrated and high-resolution spatiotemporal insights into the cellular and molecular basis of pericentral regeneration.
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Affiliation(s)
- Shuyong Wang
- Hepatopancreatobiliary Center, Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Beijing 102218, China; Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, the Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xuan Wang
- Hepatopancreatobiliary Center, Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Yiran Shan
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Zuolong Tan
- Department of Stem Cell and Regenerative Medicine, Beijing Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yuxin Su
- Hepatopancreatobiliary Center, Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Yannan Cao
- Hepatopancreatobiliary Center, Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Shuang Wang
- Hepatopancreatobiliary Center, Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Jiahong Dong
- Hepatopancreatobiliary Center, Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Beijing 102218, China; School of Clinical Medicine, Tsinghua University, Beijing 100084, China
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China.
| | - Yunfang Wang
- Hepatopancreatobiliary Center, Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Beijing 102218, China; School of Clinical Medicine, Tsinghua University, Beijing 100084, China.
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43
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Baghdassarian HM, Lewis NE. Resource allocation in mammalian systems. Biotechnol Adv 2024; 71:108305. [PMID: 38215956 PMCID: PMC11182366 DOI: 10.1016/j.biotechadv.2023.108305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
Cells execute biological functions to support phenotypes such as growth, migration, and secretion. Complementarily, each function of a cell has resource costs that constrain phenotype. Resource allocation by a cell allows it to manage these costs and optimize their phenotypes. In fact, the management of resource constraints (e.g., nutrient availability, bioenergetic capacity, and macromolecular machinery production) shape activity and ultimately impact phenotype. In mammalian systems, quantification of resource allocation provides important insights into higher-order multicellular functions; it shapes intercellular interactions and relays environmental cues for tissues to coordinate individual cells to overcome resource constraints and achieve population-level behavior. Furthermore, these constraints, objectives, and phenotypes are context-dependent, with cells adapting their behavior according to their microenvironment, resulting in distinct steady-states. This review will highlight the biological insights gained from probing resource allocation in mammalian cells and tissues.
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Affiliation(s)
- Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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Chen J, Wu J, Bai Y, Yang C, Wang J. Recent advances of single-cell RNA sequencing in toxicology research: Insight into hepatotoxicity and nephrotoxicity. CURRENT OPINION IN TOXICOLOGY 2024; 37:100462. [DOI: 10.1016/j.cotox.2024.100462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
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45
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Heida A, van Dijk T, Smit M, Koehorst M, Koster M, Kloosterhuis N, Havinga R, Bloks VW, Wolters JC, de Bruin A, Kuivenhoven JA, de Boer JF, Kuipers F, van de Sluis B. Changes in bile acid composition are correlated with reduced intestinal cholesterol uptake in intestine-specific WASH-deficient mice. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159445. [PMID: 38086439 DOI: 10.1016/j.bbalip.2023.159445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The Wiskott-Aldrich syndrome protein and SCAR homolog (WASH) complex is a pentameric protein complex localized at endosomes, where it facilitates the transport of numerous receptors from endosomes toward the plasma membrane. Recent studies have shown that the WASH complex plays an essential role in cholesterol and glucose homeostasis in humans and mice. To investigate the physiological importance of intestinal WASH, we ablated the WASH component WASHC1 specifically in murine enterocytes. Male and female intestine-specific WASHC1-deficient mice (Washc1IKO) were challenged with either a standard chow diet or a high-cholesterol (1.25 %) diet (HCD). Washc1IKO mice fed a standard diet did not present any apparent phenotype, but when fed an HCD, their hepatic cholesterol levels were ~ 50 % lower compared to those observed in control mice. The intestinal cholesterol absorption was almost 2-fold decreased in Washc1IKO mice, which translated into increased fecal neutral sterol loss. The intestinal expression of cholesterogenic genes, such as Hmgcs1, Hmgcr, and Ldlr, was significantly higher in Washc1IKO mice than in control mice and correlated with increased whole-body de novo cholesterol synthesis, likely to compensate for impaired intestinal cholesterol absorption. Unexpectedly, the ratio of biliary 12α-/non-12α-hydroxylated bile acids (BAs) was decreased in Washc1IKO mice and reversing this reduced ratio by feeding the mice with the HCD supplemented with 0.5 % (w/w) sodium cholate normalized the improvement of hepatic cholesterol levels in Washc1IKO mice. Our data indicate that the intestinal WASH complex plays an important role in intestinal cholesterol absorption, likely by modulating biliary BA composition.
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Affiliation(s)
- Andries Heida
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Theo van Dijk
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marieke Smit
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martijn Koehorst
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mirjam Koster
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Niels Kloosterhuis
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rick Havinga
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Justina C Wolters
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alain de Bruin
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | - Jan Albert Kuivenhoven
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan Freark de Boer
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bart van de Sluis
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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46
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Harris JM, Magri A, Faria AR, Tsukuda S, Balfe P, Wing PAC, McKeating JA. Oxygen-dependent histone lysine demethylase 4 restricts hepatitis B virus replication. J Biol Chem 2024; 300:105724. [PMID: 38325742 PMCID: PMC10914488 DOI: 10.1016/j.jbc.2024.105724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Mammalian cells have evolved strategies to regulate gene expression when oxygen is limited. Hypoxia-inducible factors (HIF) are the major transcriptional regulators of host gene expression. We previously reported that HIFs bind and activate hepatitis B virus (HBV) DNA transcription under low oxygen conditions; however, the global cellular response to low oxygen is mediated by a family of oxygenases that work in concert with HIFs. Recent studies have identified a role for chromatin modifiers in sensing cellular oxygen and orchestrating transcriptional responses, but their role in the HBV life cycle is as yet undefined. We demonstrated that histone lysine demethylase 4 (KDM4) can restrict HBV, and pharmacological or oxygen-mediated inhibition of the demethylase increases viral RNAs derived from both episomal and integrated copies of the viral genome. Sequencing studies demonstrated that KDM4 is a major regulator of the hepatic transcriptome, which defines hepatocellular permissivity to HBV infection. We propose a model where HBV exploits cellular oxygen sensors to replicate and persist in the liver. Understanding oxygen-dependent pathways that regulate HBV infection will facilitate the development of physiologically relevant cell-based models that support efficient HBV replication.
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Affiliation(s)
- James M Harris
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrea Magri
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ana Rita Faria
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Senko Tsukuda
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Balfe
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter A C Wing
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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47
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Kang SWS, Cunningham RP, Miller CB, Brown LA, Cultraro CM, Harned A, Narayan K, Hernandez J, Jenkins LM, Lobanov A, Cam M, Porat-Shliom N. A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling. Nat Commun 2024; 15:1799. [PMID: 38418824 PMCID: PMC10902380 DOI: 10.1038/s41467-024-45751-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal and pericentral axis. How the mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combine intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We find that periportal and pericentral mitochondria are morphologically and functionally distinct; beta-oxidation is elevated in periportal regions, while lipid synthesis is predominant in the pericentral mitochondria. In addition, comparative phosphoproteomics reveals spatially distinct patterns of mitochondrial composition and potential regulation via phosphorylation. Acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifts mitochondrial phenotypes in the periportal and pericentral regions, linking nutrient gradients across the lobule and mitochondrial heterogeneity. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. These findings have important implications for liver physiology and disease.
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Affiliation(s)
- Sun Woo Sophie Kang
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rory P Cunningham
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Colin B Miller
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lauryn A Brown
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Constance M Cultraro
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Programs, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Programs, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jonathan Hernandez
- Surgical Oncology Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Natalie Porat-Shliom
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA.
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48
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Sun J, Xie F, Wang J, Luo J, Chen T, Jiang Q, Xi Q, Liu GE, Zhang Y. Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds. MICROBIOME 2024; 12:33. [PMID: 38374121 PMCID: PMC10877772 DOI: 10.1186/s40168-023-01743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND Domesticated pigs serve as an ideal animal model for biomedical research and also provide the majority of meat for human consumption in China. Porcine intramuscular fat content associates with human health and diseases and is essential in pork quality. The molecular mechanisms controlling lipid metabolism and intramuscular fat accretion across tissues in pigs, and how these changes in response to pig breeds, remain largely unknown. RESULTS We surveyed the tissue-resident cell types of the porcine jejunum, colon, liver, and longissimus dorsi muscle between Lantang and Landrace breeds by single-cell RNA sequencing. Combining lipidomics and metagenomics approaches, we also characterized gene signatures and determined key discriminating markers of lipid digestibility, absorption, conversion, and deposition across tissues in two pig breeds. In Landrace, lean-meat swine mainly exhibited breed-specific advantages in lipid absorption and oxidation for energy supply in small and large intestinal epitheliums, nascent high-density lipoprotein synthesis for reverse cholesterol transport in enterocytes and hepatocytes, bile acid formation, and secretion for fat emulsification in hepatocytes, as well as intestinal-microbiota gene expression involved in lipid accumulation product. In Lantang, obese-meat swine showed a higher synthesis capacity of chylomicrons responsible for high serum triacylglycerol levels in small intestinal epitheliums, the predominant characteristics of lipid absorption in muscle tissue, and greater intramuscular adipcytogenesis potentials from muscular fibro-adipogenic progenitor subpopulation. CONCLUSIONS The findings enhanced our understanding of the cellular biology of lipid metabolism and opened new avenues to improve animal production and human diseases. Video Abstract.
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Affiliation(s)
- Jiajie Sun
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Fang Xie
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jing Wang
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Junyi Luo
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qingyan Jiang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qianyun Xi
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, BARC-East, Beltsville, MD, 20705, USA.
| | - Yongliang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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49
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Ruz-Maldonado I, Gonzalez JT, Zhang H, Sun J, Bort A, Kabir I, Kibbey RG, Suárez Y, Greif DM, Fernández-Hernando C. Heterogeneity of hepatocyte dynamics restores liver architecture after chemical, physical or viral damage. Nat Commun 2024; 15:1247. [PMID: 38341404 PMCID: PMC10858916 DOI: 10.1038/s41467-024-45439-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Midlobular hepatocytes are proposed to be the most plastic hepatic cell, providing a reservoir for hepatocyte proliferation during homeostasis and regeneration. However, other mechanisms beyond hyperplasia have been little explored and the contribution of other hepatocyte subpopulations to regeneration has been controversial. Thus, re-examining hepatocyte dynamics during regeneration is critical for cell therapy and treatment of liver diseases. Using a mouse model of hepatocyte- and non-hepatocyte- multicolor lineage tracing, we demonstrate that midlobular hepatocytes also undergo hypertrophy in response to chemical, physical, and viral insults. Our study shows that this subpopulation also combats liver impairment after infection with coronavirus. Furthermore, we demonstrate that pericentral hepatocytes also expand in number and size during the repair process and Galectin-9-CD44 pathway may be critical for driving these processes. Notably, we also identified that transdifferentiation and cell fusion during regeneration after severe injury contribute to recover hepatic function.
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Affiliation(s)
- Inmaculada Ruz-Maldonado
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
- Departments of Internal Medicine (Endocrinology) and Cellular & Molecular Physiology, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - John T Gonzalez
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Hanming Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan Sun
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alicia Bort
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Inamul Kabir
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Richard G Kibbey
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
- Departments of Internal Medicine (Endocrinology) and Cellular & Molecular Physiology, Yale University, New Haven, CT, USA
| | - Yajaira Suárez
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Daniel M Greif
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Center of Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA.
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Porat-Shliom N. Compartmentalization, cooperation, and communication: The 3Cs of Hepatocyte zonation. Curr Opin Cell Biol 2024; 86:102292. [PMID: 38064779 PMCID: PMC10922296 DOI: 10.1016/j.ceb.2023.102292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 02/15/2024]
Abstract
The unique architecture of the liver allows for spatial compartmentalization of its functions, also known as liver zonation. In contrast to organelles and cells, this compartment is devoid of a surrounding membrane, rendering traditional biochemical tools ineffective for studying liver zonation. Recent advancements in tissue imaging and single-cell technologies have provided new insights into the complexity of tissue organization, rich cellular composition, and the gradients that shape zonation. Hepatocyte gene expression profiles and metabolic programs differ based on their location. Non-parenchymal cells further support hepatocytes from different zones through local secretion of factors that instruct hepatocyte activities. Collectively, these elements form a cohesive and dynamic network of cell-cell interactions that vary across space, time, and disease states. This review will examine the cell biology of hepatocytes in vivo, presenting the latest discoveries and emerging principles that govern tissue-level and sub-cellular compartmentalization.
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Affiliation(s)
- Natalie Porat-Shliom
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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