1
|
Song AH, Williams M, Williamson DFK, Chow SSL, Jaume G, Gao G, Zhang A, Chen B, Baras AS, Serafin R, Colling R, Downes MR, Farré X, Humphrey P, Verrill C, True LD, Parwani AV, Liu JTC, Mahmood F. Analysis of 3D pathology samples using weakly supervised AI. Cell 2024; 187:2502-2520.e17. [PMID: 38729110 DOI: 10.1016/j.cell.2024.03.035] [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: 08/01/2023] [Revised: 01/15/2024] [Accepted: 03/25/2024] [Indexed: 05/12/2024]
Abstract
Human tissue, which is inherently three-dimensional (3D), is traditionally examined through standard-of-care histopathology as limited two-dimensional (2D) cross-sections that can insufficiently represent the tissue due to sampling bias. To holistically characterize histomorphology, 3D imaging modalities have been developed, but clinical translation is hampered by complex manual evaluation and lack of computational platforms to distill clinical insights from large, high-resolution datasets. We present TriPath, a deep-learning platform for processing tissue volumes and efficiently predicting clinical outcomes based on 3D morphological features. Recurrence risk-stratification models were trained on prostate cancer specimens imaged with open-top light-sheet microscopy or microcomputed tomography. By comprehensively capturing 3D morphologies, 3D volume-based prognostication achieves superior performance to traditional 2D slice-based approaches, including clinical/histopathological baselines from six certified genitourinary pathologists. Incorporating greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, further emphasizing the value of capturing larger extents of heterogeneous morphology.
Collapse
Affiliation(s)
- Andrew H Song
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mane Williams
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Drew F K Williamson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah S L Chow
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Guillaume Jaume
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gan Gao
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Andrew Zhang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bowen Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander S Baras
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert Serafin
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, UK; Department of Cellular Pathology, Oxford University Hospitals NHS Foundations Trust, John Radcliffe Hospital, Oxford, UK
| | - Michelle R Downes
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Xavier Farré
- Public Health Agency of Catalonia, Lleida, Spain
| | - Peter Humphrey
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, UK; Department of Cellular Pathology, Oxford University Hospitals NHS Foundations Trust, John Radcliffe Hospital, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lawrence D True
- Department of Laboratory Medicine & Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Anil V Parwani
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, Bioengineering, and Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA.
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
2
|
Cui Y, Guo Y, Kong Y, Zhang G. Association between gut microbiota and autoimmune cholestatic liver disease, a Mendelian randomization study. Front Microbiol 2024; 15:1348027. [PMID: 38601930 PMCID: PMC11004368 DOI: 10.3389/fmicb.2024.1348027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/29/2024] [Indexed: 04/12/2024] Open
Abstract
Background Previous studies have suggested that the gut microbiota (GM) is closely associated with the development of autoimmune cholestatic liver disease (ACLD), but limitations, such as the presence of confounding factors, have resulted in a causal relationship between the gut microbiota and autoimmune cholestatic liver disease that remains uncertain. Thus, we used two-sample Mendelian randomization as a research method to explore the causal relationship between the two. Methods Pooled statistics of gut microbiota from a meta-analysis of genome-wide association studies conducted by the MiBioGen consortium were used as an instrumental variable for exposure factors. The Pooled statistics for primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) were obtained from the R9 version of the FinnGen database (https://r9.finngen.fi/). Inverse-variance Weighted (IVW), cML-MA, MR-Egger regression, Weighted median (WME), Weighted mode (WM), and Simple mode (SM) were used to detect the association between intestinal flora and the causal relationship between intestinal flora and ACLD, in which IVW method was dominant, was assessed based on the effect indicator dominance ratio (odds ratio, OR) and 95% confidence interval (CI). Sensitivity analysis, heterogeneity test, gene pleiotropy test, MR pleiotropy residual sum and outlier test (MR-PRESSO) were combined to verify the stability and reliability of the results. Reverse Mendelian randomization analysis was performed on gut microbiota and found to be causally associated with ACLD. Results The IVW results showed that the relative abundance of the genus Clostridium innocuum group, genus Butyricicoccus, and genus Erysipelatoclostridium was negatively correlated with the risk of PBC, that is, increased abundance reduced the risk of PBC and was a protective, and the relative abundance of the genus Eubacterium hallii was positively correlated with the risk of PSC, which is a risk factor for PSC. Family Clostridiaceae1 and family Lachnospiraceae were negatively correlated with the risk of PSC, which is a protective factor for PSC. Conclusion This study found a causal relationship between gut microbiota and ACLD. This may provide valuable insights into gut microbiota-mediated pathogenesis of ACLD. It is necessary to conduct a large-sample randomized controlled trial (RCT) at a later stage to validate the associated role of the relevant gut microbiota in the risk of ACLD development and to explore the associated mechanisms.
Collapse
Affiliation(s)
- YangLin Cui
- First Clinical College of Medicine, Shandong University of Chinese Medicine, Jinan, China
| | - YuMeng Guo
- First Clinical College of Medicine, Shandong University of Chinese Medicine, Jinan, China
| | - YuChen Kong
- First Clinical College of Medicine, Shandong University of Chinese Medicine, Jinan, China
| | - GuangYe Zhang
- Classical Chinese Medicine Section, Rizhao Hospital of Traditional Chinese Medicine, Rizhao, China
| |
Collapse
|
3
|
Murphy WA, Diehl AM, Loop MS, Fu D, Guy CD, Abdelmalek MF, Karachaliou GS, Sjöstedt N, Neuhoff S, Honkakoski P, Brouwer KLR. Alterations in zonal distribution and plasma membrane localization of hepatocyte bile acid transporters in patients with NAFLD. Hepatol Commun 2024; 8:e0377. [PMID: 38381537 PMCID: PMC10871794 DOI: 10.1097/hc9.0000000000000377] [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: 10/09/2023] [Accepted: 12/16/2023] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND NAFLD is highly prevalent with limited treatment options. Bile acids (BAs) increase in the systemic circulation and liver during NAFLD progression. Changes in plasma membrane localization and zonal distribution of BA transporters can influence transport function and BA homeostasis. However, a thorough characterization of how NAFLD influences these factors is currently lacking. This study aimed to evaluate the impact of NAFLD and the accompanying histologic features on the functional capacity of key hepatocyte BA transporters across zonal regions in human liver biopsies. METHODS A novel machine learning image classification approach was used to quantify relative zonal abundance and plasma membrane localization of BA transporters (bile salt export pump [BSEP], sodium-taurocholate cotransporting polypeptide, organic anion transporting polypeptide [OATP] 1B1 and OATP1B3) in non-diseased (n = 10), NAFL (n = 9), and NASH (n = 11) liver biopsies. Based on these data, membrane-localized zonal abundance (MZA) measures were developed to estimate transporter functional capacity. RESULTS NAFLD diagnosis and histologic scoring were associated with changes in transporter membrane localization and zonation. Increased periportal BSEPMZA (mean proportional difference compared to non-diseased liver of 0.090) and decreased pericentral BSEPMZA (-0.065) were observed with NASH and also in biopsies with higher histologic scores. Compared to Non-diseased Liver, periportal OATP1B3MZA was increased in NAFL (0.041) and NASH (0.047). Grade 2 steatosis (mean proportional difference of 0.043 when compared to grade 0) and grade 1 lobular inflammation (0.043) were associated with increased periportal OATP1B3MZA. CONCLUSIONS These findings provide novel mechanistic insight into specific transporter alterations that impact BA homeostasis in NAFLD. Changes in BSEPMZA likely contribute to altered BA disposition and pericentral microcholestasis previously reported in some patients with NAFLD. BSEPMZA assessment could inform future development and optimization of NASH-related pharmacotherapies.
Collapse
Affiliation(s)
- William A. Murphy
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anna Mae Diehl
- Division of Gastroenterology and Hepatology, Duke University Medical Center, Durham, North Carolina, USA
| | - Matthew Shane Loop
- Department of Health Outcomes Research and Policy, Harrison College of Pharmacy, Auburn University, Auburn, Alabama, USA
| | - Dong Fu
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cynthia D. Guy
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | - Manal F. Abdelmalek
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Georgia Sofia Karachaliou
- Division of Gastroenterology and Hepatology, Duke University Medical Center, Durham, North Carolina, USA
| | - Noora Sjöstedt
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Paavo Honkakoski
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kim L. R. Brouwer
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
4
|
Martínez-Torres D, Maldonado V, Pérez-Gallardo C, Yañez R, Candia V, Kalaidzidis Y, Zerial M, Morales-Navarrete H, Segovia-Miranda F. Phenotypic characterization of liver tissue heterogeneity through a next-generation 3D single-cell atlas. Sci Rep 2024; 14:2823. [PMID: 38307948 PMCID: PMC10837128 DOI: 10.1038/s41598-024-53309-4] [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: 08/26/2023] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Three-dimensional (3D) geometrical models are potent tools for quantifying complex tissue features and exploring structure-function relationships. However, these models are generally incomplete due to experimental limitations in acquiring multiple (> 4) fluorescent channels in thick tissue sections simultaneously. Indeed, predictive geometrical and functional models of the liver have been restricted to few tissue and cellular components, excluding important cellular populations such as hepatic stellate cells (HSCs) and Kupffer cells (KCs). Here, we combined deep-tissue immunostaining, multiphoton microscopy, deep-learning techniques, and 3D image processing to computationally expand the number of simultaneously reconstructed tissue structures. We then generated a spatial single-cell atlas of hepatic architecture (Hep3D), including all main tissue and cellular components at different stages of post-natal development in mice. We used Hep3D to quantitatively study 1) hepatic morphodynamics from early post-natal development to adulthood, and 2) the effect on the liver's overall structure when changing the hepatic environment after removing KCs. In addition to a complete description of bile canaliculi and sinusoidal network remodeling, our analysis uncovered unexpected spatiotemporal patterns of non-parenchymal cells and hepatocytes differing in size, number of nuclei, and DNA content. Surprisingly, we found that the specific depletion of KCs results in morphological changes in hepatocytes and HSCs. These findings reveal novel characteristics of liver heterogeneity and have important implications for both the structural organization of liver tissue and its function. Our next-gen 3D single-cell atlas is a powerful tool to understand liver tissue architecture, opening up avenues for in-depth investigations into tissue structure across both normal and pathological conditions.
Collapse
Affiliation(s)
- Dilan Martínez-Torres
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Valentina Maldonado
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Cristian Pérez-Gallardo
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Rodrigo Yañez
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Valeria Candia
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Hernán Morales-Navarrete
- Department of Systems Biology of Development, University of Konstanz, Konstanz, Germany.
- Facultad de Ciencias Técnicas, Universidad Internacional Del Ecuador UIDE, Quito, Ecuador.
| | - Fabián Segovia-Miranda
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Liu JTC, Chow SSL, Colling R, Downes MR, Farré X, Humphrey P, Janowczyk A, Mirtti T, Verrill C, Zlobec I, True LD. Engineering the future of 3D pathology. J Pathol Clin Res 2024; 10:e347. [PMID: 37919231 PMCID: PMC10807588 DOI: 10.1002/cjp2.347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/06/2023] [Accepted: 10/15/2023] [Indexed: 11/04/2023]
Abstract
In recent years, technological advances in tissue preparation, high-throughput volumetric microscopy, and computational infrastructure have enabled rapid developments in nondestructive 3D pathology, in which high-resolution histologic datasets are obtained from thick tissue specimens, such as whole biopsies, without the need for physical sectioning onto glass slides. While 3D pathology generates massive datasets that are attractive for automated computational analysis, there is also a desire to use 3D pathology to improve the visual assessment of tissue histology. In this perspective, we discuss and provide examples of potential advantages of 3D pathology for the visual assessment of clinical specimens and the challenges of dealing with large 3D datasets (of individual or multiple specimens) that pathologists have not been trained to interpret. We discuss the need for artificial intelligence triaging algorithms and explainable analysis methods to assist pathologists or other domain experts in the interpretation of these novel, often complex, large datasets.
Collapse
Affiliation(s)
- Jonathan TC Liu
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWAUSA
- Department of Laboratory Medicine & PathologyUniversity of Washington School of MedicineSeattleUSA
- Department of BioengineeringUniversity of WashingtonSeattleUSA
| | - Sarah SL Chow
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWAUSA
| | | | | | | | - Peter Humphrey
- Department of UrologyYale School of MedicineNew HavenCTUSA
| | - Andrew Janowczyk
- Wallace H Coulter Department of Biomedical EngineeringEmory University and Georgia Institute of TechnologyAtlantaGAUSA
- Geneva University HospitalsGenevaSwitzerland
| | - Tuomas Mirtti
- Helsinki University Hospital and University of HelsinkiHelsinkiFinland
- Emory University School of MedicineAtlantaGAUSA
| | - Clare Verrill
- John Radcliffe HospitalUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Inti Zlobec
- Institute for Tissue Medicine and PathologyUniversity of BernBernSwitzerland
| | - Lawrence D True
- Department of Laboratory Medicine & PathologyUniversity of Washington School of MedicineSeattleUSA
| |
Collapse
|
7
|
Ramezani M, Zobeiry M, Abdolahi S, Hatami B, Zali MR, Baghaei K. A crosstalk between epigenetic modulations and non-alcoholic fatty liver disease progression. Pathol Res Pract 2023; 251:154809. [PMID: 37797383 DOI: 10.1016/j.prp.2023.154809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has recently emerged as a major public health concern worldwide due to its rapidly rising prevalence and its potential to progress into end-stage liver disease. While the precise pathophysiology underlying NAFLD remains incompletely understood, it is strongly associated with various environmental triggers and other metabolic disorders. Epigenetics examines changes in gene expression that are not caused by alterations in the DNA sequence itself. There is accumulating evidence that epigenetics plays a key role in linking environmental cues to the onset and progression of NAFLD. Our understanding of how epigenetic mechanisms contribute to NAFLD pathophysiology has expanded considerably in recent years as research on the epigenetics of NAFLD has developed. This review summarizes recent insights into major epigenetic processes that have been implicated in NAFLD pathogenesis including DNA methylation, histone acetylation, and microRNAs that have emerged as promising targets for further investigation. Elucidating epigenetic mechanisms in NAFLD may uncover novel diagnostic biomarkers and therapeutic targets for this disease. However, many questions have remained unanswered regarding how epigenetics promotes NAFLD onset and progression. Additional studies are needed to further characterize the epigenetic landscape of NAFLD and validate the potential of epigenetic markers as clinical tools. Nevertheless, an enhanced understanding of the epigenetic underpinnings of NAFLD promises to provide key insights into disease mechanisms and pave the way for novel prognostic and therapeutic approaches.
Collapse
Affiliation(s)
- Meysam Ramezani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Shahrokh Abdolahi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Behzad Hatami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Gastroenterology and Liver Diseases Research center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
8
|
Rosenberger FA, Thielert M, Strauss MT, Schweizer L, Ammar C, Mädler SC, Metousis A, Skowronek P, Wahle M, Madden K, Gote-Schniering J, Semenova A, Schiller HB, Rodriguez E, Nordmann TM, Mund A, Mann M. Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome. Nat Methods 2023; 20:1530-1536. [PMID: 37783884 PMCID: PMC10555842 DOI: 10.1038/s41592-023-02007-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 08/15/2023] [Indexed: 10/04/2023]
Abstract
Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion of the method to complex tissues would greatly enhance biological insights. Here we describe single-cell Deep Visual Proteomics (scDVP), a technology that integrates high-content imaging, laser microdissection and multiplexed mass spectrometry. scDVP resolves the context-dependent, spatial proteome of murine hepatocytes at a current depth of 1,700 proteins from a cell slice. Half of the proteome was differentially regulated in a spatial manner, with protein levels changing dramatically in proximity to the central vein. We applied machine learning to proteome classes and images, which subsequently inferred the spatial proteome from imaging data alone. scDVP is applicable to healthy and diseased tissues and complements other spatial proteomics and spatial omics technologies.
Collapse
Affiliation(s)
- Florian A Rosenberger
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marvin Thielert
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T Strauss
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lisa Schweizer
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Constantin Ammar
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sophia C Mädler
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Metousis
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Patricia Skowronek
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria Wahle
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Katherine Madden
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Janine Gote-Schniering
- Comprehensive Pneumology Center (CPC) / Institute of Lung Health and Immunity (LHI), Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Anna Semenova
- Comprehensive Pneumology Center (CPC) / Institute of Lung Health and Immunity (LHI), Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC) / Institute of Lung Health and Immunity (LHI), Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Edwin Rodriguez
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thierry M Nordmann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
9
|
Mayer C, Nehring S, Kücken M, Repnik U, Seifert S, Sljukic A, Delpierre J, Morales‐Navarrete H, Hinz S, Brosch M, Chung B, Karlsen T, Huch M, Kalaidzidis Y, Brusch L, Hampe J, Schafmayer C, Zerial M. Apical bulkheads accumulate as adaptive response to impaired bile flow in liver disease. EMBO Rep 2023; 24:e57181. [PMID: 37522754 PMCID: PMC10481669 DOI: 10.15252/embr.202357181] [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: 03/13/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Hepatocytes form bile canaliculi that dynamically respond to the signalling activity of bile acids and bile flow. Little is known about their responses to intraluminal pressure. During embryonic development, hepatocytes assemble apical bulkheads that increase the canalicular resistance to intraluminal pressure. Here, we investigate whether they also protect bile canaliculi against elevated pressure upon impaired bile flow in adult liver. Apical bulkheads accumulate upon bile flow obstruction in mouse models and patients with primary sclerosing cholangitis (PSC). Their loss under these conditions leads to abnormally dilated canaliculi, resembling liver cell rosettes described in other hepatic diseases. 3D reconstruction reveals that these structures are sections of cysts and tubes formed by hepatocytes. Mathematical modelling establishes that they positively correlate with canalicular pressure and occur in early PSC stages. Using primary hepatocytes and 3D organoids, we demonstrate that excessive canalicular pressure causes the loss of apical bulkheads and formation of rosettes. Our results suggest that apical bulkheads are a protective mechanism of hepatocytes against impaired bile flow, highlighting the role of canalicular pressure in liver diseases.
Collapse
Affiliation(s)
- Carlotta Mayer
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Sophie Nehring
- Department of Medicine I, Gastroenterology and HepatologyUniversity Hospital Carl‐Gustav‐Carus, Technische Universität Dresden (TU Dresden)DresdenGermany
| | - Michael Kücken
- Center for Information Services and High‐Performance ComputingTechnische Universität DresdenDresdenGermany
| | - Urska Repnik
- Central Microscopy, Department of BiologyChristian‐Albrechts‐Universtät zu Kiel (CAU)KielGermany
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Aleksandra Sljukic
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Julien Delpierre
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | | | - Sebastian Hinz
- Department of General SurgeryUniversity Hospital RostockRostockGermany
| | - Mario Brosch
- Department of Medicine I, Gastroenterology and HepatologyUniversity Hospital Carl‐Gustav‐Carus, Technische Universität Dresden (TU Dresden)DresdenGermany
- Center for Regenerative Therapies Dresden (CRTD)Technische Universität Dresden (TU Dresden)DresdenGermany
| | - Brian Chung
- Department of Transplantation Medicine, Clinic of Surgery, Inflammatory Medicine and Transplantation, Norwegian PSC Research CenterOslo University Hospital RikshospitaletOsloNorway
- Research Institute of Internal Medicine, Clinic of Surgery, Inflammatory Diseases and TransplantationOslo University Hospital and University of OsloOsloNorway
| | - Tom Karlsen
- Department of Transplantation Medicine, Clinic of Surgery, Inflammatory Medicine and Transplantation, Norwegian PSC Research CenterOslo University Hospital RikshospitaletOsloNorway
- Research Institute of Internal Medicine, Clinic of Surgery, Inflammatory Diseases and TransplantationOslo University Hospital and University of OsloOsloNorway
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Lutz Brusch
- Center for Information Services and High‐Performance ComputingTechnische Universität DresdenDresdenGermany
| | - Jochen Hampe
- Department of Medicine I, Gastroenterology and HepatologyUniversity Hospital Carl‐Gustav‐Carus, Technische Universität Dresden (TU Dresden)DresdenGermany
- Center for Regenerative Therapies Dresden (CRTD)Technische Universität Dresden (TU Dresden)DresdenGermany
| | | | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| |
Collapse
|
10
|
Zhang Y, Feng Y, Chen F, Yu J, Liu X, Liu Y, Ouyang J, Liang M, Zhu Y, Zou L. Insight into the mechanisms of therapeutic hypothermia for asphyxia cardiac arrest using a comprehensive approach of GC-MS/MS and UPLC-Q-TOF-MS/MS based on serum metabolomics. Heliyon 2023; 9:e16247. [PMID: 37274716 PMCID: PMC10238693 DOI: 10.1016/j.heliyon.2023.e16247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
Cardiac arrest (CA) is a severe worldwide health problem. Therapeutic hypothermia is widely used to reduce the cardiac injury and improve the neurological outcomes after CA. However, a few studies have reported the changes of serum metabolic characteristics after CA. The healthy male New Zealand Rabbits successfully resuscitated from 10-min asphyxia-induced CA were divided randomly into the normothermia (NT) group and mild therapeutic hypothermia (HT) group. The sham group underwent sham-operation. Survival was recorded and neurological deficit score (NDS) was assessed. The serum non-targeted metabolomics were detected using ultra-high-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS) and gas chromatography tandem mass spectrometry (GC-MS/MS) at 15 min, 3 h, 6 h and 24 h after return of spontaneous circulation (ROSC). Our study showed that the heart rate (HR) significantly slowed down during 0.5-6 h post ROSC, consistent with the decreasing trend of body temperature in the HT group. Compared with the NT group, the levels of Lac and PCO2 at 24 h post ROSC were lower, while a significant increase in PO2 level at 24 h post ROSC was observed in the HT group. The survival rate of the HT group was significantly higher than that of the NT group, and NDS scores were remarkably increased at 24 h post ROSC in the NT group. Significant differences in metabolic profiles at 15 min, 3 h, 6 h and 24 h post ROSC were observed among the Sham, NT and HT groups. The differential metabolites detected by UPLC-Q-TOF-MS/MS and GC-MS/MS were screened for further study between every two groups (NT vs sham, HT vs sham and HT vs NT) at 15 min, 3 h, 6 h and 24 h post ROSC. Phenylalanine metabolism, alanine, aspartate and glutamate metabolism and tricarboxylic acid (TCA) cycle were enriched in NT vs sham, HT vs sham and HT vs NT respectively. Our study demonstrated that therapeutic hypothermia improves the survival and neurological outcomes in rabbit model of cardiac arrest, and firstly represents the dynamic metabolic changes in the hypothermia therapy for CA by comprehensive UPLC-Q-TOF-MS/MS- and GC-MS/MS-based metabolomics.
Collapse
Affiliation(s)
- Yiyuan Zhang
- The First Affiliated Hospital of Hunan Normal University, Hunan Provincial Key Laboratory of Molecular Epidemiology, Changsha, Hunan, China
| | - Yang Feng
- The First Affiliated Hospital of Hunan Normal University, Hunan Provincial Key Laboratory of Molecular Epidemiology, Changsha, Hunan, China
- Department of Emergency Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Fang Chen
- Hunan Provincial People's Hospital, Hunan Provincial Key Laboratory of Emergency and Critical Care Metabolomics,Changsha, Hunan, China
| | - Jiang Yu
- Hunan Provincial People's Hospital, Hunan Provincial Key Laboratory of Emergency and Critical Care Metabolomics,Changsha, Hunan, China
| | - Xiehong Liu
- Hunan Provincial People's Hospital, Hunan Provincial Key Laboratory of Emergency and Critical Care Metabolomics,Changsha, Hunan, China
| | - Yanjuan Liu
- Hunan Provincial People's Hospital, Hunan Provincial Key Laboratory of Emergency and Critical Care Metabolomics,Changsha, Hunan, China
| | - Jielin Ouyang
- The First Affiliated Hospital of Hunan Normal University, Hunan Provincial Key Laboratory of Molecular Epidemiology, Changsha, Hunan, China
- Department of Emergency Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Mingyu Liang
- The First Affiliated Hospital of Hunan Normal University, Hunan Provincial Key Laboratory of Molecular Epidemiology, Changsha, Hunan, China
- Department of Emergency Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Yiming Zhu
- Hunan Provincial People's Hospital, Hunan Provincial Key Laboratory of Emergency and Critical Care Metabolomics,Changsha, Hunan, China
| | - Lianhong Zou
- The First Affiliated Hospital of Hunan Normal University, Hunan Provincial Key Laboratory of Molecular Epidemiology, Changsha, Hunan, China
| |
Collapse
|
11
|
Tilg H, Adolph TE, Trauner M. Gut-liver axis: Pathophysiological concepts and clinical implications. Cell Metab 2022; 34:1700-1718. [PMID: 36208625 DOI: 10.1016/j.cmet.2022.09.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/17/2022] [Accepted: 09/16/2022] [Indexed: 02/07/2023]
Abstract
Bidirectional crosstalk along the gut-liver axis controls gastrointestinal health and disease and exploits environmental and host mediators. Nutrients, microbial antigens, metabolites, and bile acids regulate metabolism and immune responses in the gut and liver, which reciprocally shape microbial community structure and function. Perturbation of such host-microbe interactions is observed in a variety of experimental liver diseases and is facilitated by an impaired intestinal barrier, which is fueling hepatic inflammation and disease progression. Clinical evidence describes perturbation of the gut-liver crosstalk in non-alcoholic fatty liver disease, alcoholic liver disease, and primary sclerosing cholangitis. In liver cirrhosis, a common sequela of these diseases, the intestinal microbiota and microbial pathogen-associated molecular patterns constitute liver inflammation and clinical complications, such as hepatic encephalopathy. Understanding the intricate metabolic interplay between the gut and liver in health and disease opens an avenue for targeted therapies in the future, which is probed in controlled clinical trials.
Collapse
Affiliation(s)
- Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University, Innsbruck, Austria.
| | - Timon E Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University, Innsbruck, Austria
| | - Michael Trauner
- Division of Gastroenterology & Hepatology, Department of Internal Medicine III, Medical University, Vienna, Austria
| |
Collapse
|
12
|
Wei X, Murphy MA, Reddy NA, Hao Y, Eggertsen TG, Saucerman JJ, Bochkis IM. Redistribution of lamina-associated domains reshapes binding of pioneer factor FOXA2 in development of nonalcoholic fatty liver disease. Genome Res 2022; 32:1981-1992. [PMID: 36522168 PMCID: PMC9808618 DOI: 10.1101/gr.277149.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is highly prevalent in type 2 diabetes mellitus and the elderly, impacting 40% of individuals over 70. Regulation of heterochromatin at the nuclear lamina has been associated with aging and age-dependent metabolic changes. We previously showed that changes at the lamina in aged hepatocytes and laminopathy models lead to redistribution of lamina-associated domains (LADs), opening of repressed chromatin, and up-regulation of genes regulating lipid synthesis and storage, culminating in fatty liver. Here, we test the hypothesis that change in the expression of lamina-associated proteins and nuclear shape leads to redistribution of LADs, followed by altered binding of pioneer factor FOXA2 and by up-regulation of lipid synthesis and storage, culminating in steatosis in younger NAFLD patients (aged 21-51). Changes in nuclear morphology alter LAD partitioning and reduced lamin B1 signal correlate with increased FOXA2 binding before severe steatosis in young mice placed on a western diet. Nuclear shape is also changed in younger NAFLD patients. LADs are redistrubted and lamin B1 signal decreases similarly in mild and severe steatosis. In contrast, FOXA2 binding is similar in normal and NAFLD patients with moderate steatosis and is repositioned only in NAFLD patients with more severe lipid accumulation. Hence, changes at the nuclear lamina reshape FOXA2 binding with progression of the disease. Our results suggest a role for nuclear lamina in etiology of NAFLD, irrespective of aging, with potential for improved stratification of patients and novel treatments aimed at restoring nuclear lamina function.
Collapse
Affiliation(s)
- Xiaolong Wei
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Megan A Murphy
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Nihal A Reddy
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Yi Hao
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Taylor G Eggertsen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jeffrey J Saucerman
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, USA
| |
Collapse
|
13
|
Younossi ZM, Stepanova M, Nader F, Loomba R, Anstee QM, Ratziu V, Harrison S, Sanyal AJ, Schattenberg JM, Barritt AS, Noureddin M, Bonacci M, Cawkwell G, Wong B, Rinella M. Obeticholic Acid Impact on Quality of Life in Patients With Nonalcoholic Steatohepatitis: REGENERATE 18-Month Interim Analysis. Clin Gastroenterol Hepatol 2022; 20:2050-2058.e12. [PMID: 34274514 DOI: 10.1016/j.cgh.2021.07.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Nonalcoholic steatohepatitis (NASH) affects patients' health-related quality of life (HRQoL). Patient-reported outcomes (PROs) evaluating HRQoL were assessed in the RandomizEd Global Phase 3 Study to Evaluate the Impact on NASH with FibRosis of Obeticholic Acid TreatmEnt (REGENERATE) study, which showed that obeticholic acid (OCA) significantly improved fibrosis in patients with NASH. METHODS Noncirrhotic NASH patients in a phase 3, double-blind, randomized, placebo-controlled, multicenter, international study of OCA were enrolled. The Chronic Liver Disease Questionnaire-NASH and EuroQol EQ-5D-5L were administered at baseline, 6, 12, and 18 months. RESULTS There were 1218 patients (age, 54.1 ± 11.5 y; 57% women; 43% stage F3) in the expanded intent-to-treat population (stages, F1-F3) assigned randomly to 10 mg (N = 407) or 25 mg (N = 404) OCA or placebo (N = 407). Baseline measurements were balanced across treatment groups for EuroQol EQ-5D-5L and Chronic Liver Disease Questionnaire-NASH, including Itch score: 5.75 ± 1.53 (scale 1-7, with 7 representing no itching). Nineteen (1.6%) patients discontinued therapy (protocol mandated) because of grade 3 pruritus. Patients receiving 25 mg OCA experienced mild worsening of itch scores primarily in the first months of treatment: mean ± SE change from baseline -0.66 ± 0.12, -0.44 ± 0.12, and -0.42 ± 0.13 at 6, 12, and 18 months, respectively (all P < .01). No other PRO worsening was associated with 25 mg OCA. Patients experiencing fibrosis improvement, Nonalcoholic Fatty Liver Disease Activity Score decrease (by ≥2 points), or NASH resolution had greater PRO improvements in some domains. CONCLUSIONS NASH patients evaluated in REGENERATE had impaired quality of life and underlying pruritus at baseline. Improvement of NASH corresponded with improvement in several HRQoL domains. Generally mild pruritus occurs early after OCA therapy initiation and does not worsen over time. CLINICALTRIALS gov: NCT02548351.
Collapse
Affiliation(s)
- Zobair M Younossi
- Betty and Guy Beatty Center for Integrated Research, Inova Health System, Falls Church, Virginia; Center for Liver Diseases, Department of Medicine, Inova Fairfax Medical Campus, Falls Church, Virginia.
| | - Maria Stepanova
- Center for Outcomes Research in Liver Disease, Washington, District of Columbia
| | - Fatema Nader
- Center for Outcomes Research in Liver Disease, Washington, District of Columbia
| | - Rohit Loomba
- University of California, San Diego, San Diego, California
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle National Institute for Health Research Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, United Kingdom
| | - Vlad Ratziu
- Sorbonne Université, Institute of Cardiometabolism and Nutrition, Hôpital Pitié-Salpêtrière, INSERM UMRS 1138 CRC, Paris, France
| | | | - Arun J Sanyal
- Virginia Commonwealth University, Richmond, Virginia
| | | | - A Sidney Barritt
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | | | | | - Bruce Wong
- Intercept Pharmaceuticals, New York, New York
| | - Mary Rinella
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | |
Collapse
|
14
|
Chew NWS, Ng CH, Truong E, Noureddin M, Kowdley KV. Nonalcoholic Steatohepatitis Drug Development Pipeline: An Update. Semin Liver Dis 2022; 42:379-400. [PMID: 35709720 DOI: 10.1055/a-1877-9656] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nonalcoholic steatohepatitis (NASH) is a burgeoning global health crisis that mirrors the obesity pandemic. This global health crisis has stimulated active research to develop novel NASH pharmacotherapies targeting dysregulated inflammatory, cellular stress, and fibrogenetic processes that include (1) metabolic pathways to improve insulin sensitivity, de novo lipogenesis, and mitochondrial utilization of fatty acids; (2) cellular injury or inflammatory targets that reduce inflammatory cell recruitment and signaling; (3) liver-gut axis targets that influence bile acid enterohepatic circulation and signaling; and (4) antifibrotic targets. In this review, we summarize several of the therapeutic agents that have been studied in phase 2 and 3 randomized trials. In addition to reviewing novel therapeutic drugs targeting nuclear receptor pathways, liver chemokine receptors, liver lipid metabolism, lipotoxicity or cell death, and glucagon-like peptide-1 receptors, we also discuss the rationale behind the use of combination therapy and the lessons learned from unsuccessful or negative clinical trials.
Collapse
Affiliation(s)
- Nicholas W S Chew
- Department of Cardiology, National University Heart Centre, National University Hospital, Singapore, Singapore
| | - Cheng Han Ng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Emily Truong
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Mazen Noureddin
- Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Fatty Liver Program, Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Kris V Kowdley
- Liver Institute Northwest and Elson S. Floyd College of Medicine, Washington State University, Seattle, Washington
| |
Collapse
|
15
|
Abstract
Non-alcoholic fatty liver disease (NAFLD) includes a range of hepatic manifestations, starting with liver steatosis and potentially evolving towards non-alcoholic steatohepatitis (NASH), cirrhosis or even hepatocellular carcinoma. NAFLD is a major health burden, and its incidence is increasing worldwide. Although it is primarily a disease of disturbed metabolism, NAFLD involves several immune cell-mediated inflammatory processes, particularly when reaching the stage of NASH, at which point inflammation becomes integral to the progression of the disease. The hepatic immune cell landscape is diverse at steady state and it further evolves during NASH with direct consequences for disease severity. In this Review, we discuss current concepts related to the role of immune cells in the onset and progression of NASH. A better understanding of the mechanisms by which immune cells contribute to NASH pathogenesis should aid the design of innovative drugs to target NASH, for which current therapeutic options are limited.
Collapse
Affiliation(s)
- Thierry Huby
- Institut National de la Santé et de la Recherche Médicale (Inserm, UMR-S 1166), Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Emmanuel L Gautier
- Institut National de la Santé et de la Recherche Médicale (Inserm, UMR-S 1166), Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Paris, France.
| |
Collapse
|
16
|
Subramanian R, Tang R, Zhang Z, Joshi V, Miner JN, Lo YH. Multimodal NASH prognosis using 3D imaging flow cytometry and artificial intelligence to characterize liver cells. Sci Rep 2022; 12:11180. [PMID: 35778474 PMCID: PMC9249889 DOI: 10.1038/s41598-022-15364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
To improve the understanding of the complex biological process underlying the development of non-alcoholic steatohepatitis (NASH), 3D imaging flow cytometry (3D-IFC) with transmission and side-scattered images were used to characterize hepatic stellate cell (HSC) and liver endothelial cell (LEC) morphology at single-cell resolution. In this study, HSC and LEC were obtained from biopsy-proven NASH subjects with early-stage NASH (F2-F3) and healthy controls. Here, we applied single-cell imaging and 3D digital reconstructions of healthy and diseased cells to analyze a spatially resolved set of morphometric cellular and texture parameters that showed regression with disease progression. By developing a customized autoencoder convolutional neural network (CNN) based on label-free cell transmission and side scattering images obtained from a 3D imaging flow cytometer, we demonstrated key regulated cell types involved in the development of NASH and cell classification performance superior to conventional machine learning methods.
Collapse
Affiliation(s)
- Ramkumar Subramanian
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rui Tang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zunming Zhang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
17
|
Verma A, Manchel A, Melunis J, Hengstler JG, Vadigepalli R. From Seeing to Simulating: A Survey of Imaging Techniques and Spatially-Resolved Data for Developing Multiscale Computational Models of Liver Regeneration. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:917191. [PMID: 37575468 PMCID: PMC10421626 DOI: 10.3389/fsysb.2022.917191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Liver regeneration, which leads to the re-establishment of organ mass, follows a specifically organized set of biological processes acting on various time and length scales. Computational models of liver regeneration largely focused on incorporating molecular and signaling detail have been developed by multiple research groups in the recent years. These modeling efforts have supported a synthesis of disparate experimental results at the molecular scale. Incorporation of tissue and organ scale data using noninvasive imaging methods can extend these computational models towards a comprehensive accounting of multiscale dynamics of liver regeneration. For instance, microscopy-based imaging methods provide detailed histological information at the tissue and cellular scales. Noninvasive imaging methods such as ultrasound, computed tomography and magnetic resonance imaging provide morphological and physiological features including volumetric measures over time. In this review, we discuss multiple imaging modalities capable of informing computational models of liver regeneration at the organ-, tissue- and cellular level. Additionally, we discuss available software and algorithms, which aid in the analysis and integration of imaging data into computational models. Such models can be generated or tuned for an individual patient with liver disease. Progress towards integrated multiscale models of liver regeneration can aid in prognostic tool development for treating liver disease.
Collapse
Affiliation(s)
- Aalap Verma
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Alexandra Manchel
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Justin Melunis
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Jan G. Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States
| |
Collapse
|
18
|
Three-dimensional (3D) liver cell models - a tool for bridging the gap between animal studies and clinical trials when screening liver accumulation and toxicity of nanobiomaterials. Drug Deliv Transl Res 2022; 12:2048-2074. [PMID: 35507131 PMCID: PMC9066991 DOI: 10.1007/s13346-022-01147-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2022] [Indexed: 12/13/2022]
Abstract
Despite the exciting properties and wide-reaching applications of nanobiomaterials (NBMs) in human health and medicine, their translation from bench to bedside is slow, with a predominant issue being liver accumulation and toxicity following systemic administration. In vitro 2D cell-based assays and in vivo testing are the most popular and widely used methods for assessing liver toxicity at pre-clinical stages; however, these fall short in predicting toxicity for NBMs. Focusing on in vitro and in vivo assessment, the accurate prediction of human-specific hepatotoxicity is still a significant challenge to researchers. This review describes the relationship between NBMs and the liver, and the methods for assessing toxicity, focusing on the limitations they bring in the assessment of NBM hepatotoxicity as one of the reasons defining the poor translation for NBMs. We will then present some of the most recent advances towards the development of more biologically relevant in vitro liver methods based on tissue-mimetic 3D cell models and how these could facilitate the translation of NBMs going forward. Finally, we also discuss the low public acceptance and limited uptake of tissue-mimetic 3D models in pre-clinical assessment, despite the demonstrated technical and ethical advantages associated with them.
Collapse
|
19
|
Budelmann D, Laue H, Weiss N, Dahmen U, D'Alessandro LA, Biermayer I, Klingmüller U, Ghallab A, Hassan R, Begher-Tibbe B, Hengstler JG, Schwen LO. Automated Detection of Portal Fields and Central Veins in Whole-Slide Images of Liver Tissue. J Pathol Inform 2022; 13:100001. [PMID: 35242441 PMCID: PMC8860737 DOI: 10.1016/j.jpi.2022.100001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Many physiological processes and pathological phenomena in the liver tissue are spatially heterogeneous. At a local scale, biomarkers can be quantified along the axis of the blood flow, from portal fields (PFs) to central veins (CVs), i.e., in zonated form. This requires detecting PFs and CVs. However, manually annotating these structures in multiple whole-slide images is a tedious task. We describe and evaluate a fully automated method, based on a convolutional neural network, for simultaneously detecting PFs and CVs in a single stained section. Trained on scans of hematoxylin and eosin-stained liver tissue, the detector performed well with an F1 score of 0.81 compared to annotation by a human expert. It does, however, not generalize well to previously unseen scans of steatotic liver tissue with an F1 score of 0.59. Automated PF and CV detection eliminates the bottleneck of manual annotation for subsequent automated analyses, as illustrated by two proof-of-concept applications: We computed lobulus sizes based on the detected PF and CV positions, where results agreed with published lobulus sizes. Moreover, we demonstrate the feasibility of zonated quantification of biomarkers detected in different stainings based on lobuli and zones obtained from the detected PF and CV positions. A negative control (hematoxylin and eosin) showed the expected homogeneity, a positive control (glutamine synthetase) was quantified to be strictly pericentral, and a plausible zonation for a heterogeneous F4/80 staining was obtained. Automated detection of PFs and CVs is one building block for automatically quantifying physiologically relevant heterogeneity of liver tissue biomarkers. Perspectively, a more robust and automated assessment of zonation from whole-slide images will be valuable for parameterizing spatially resolved models of liver metabolism and to provide diagnostic information.
Collapse
Affiliation(s)
| | | | | | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, University Hospital Jena, Jena, Germany
| | - Lorenza A D'Alessandro
- Deutsches Krebsforschungszentrum, Systems Biology of Signal Transduction, Heidelberg, Germany
| | - Ina Biermayer
- Deutsches Krebsforschungszentrum, Systems Biology of Signal Transduction, Heidelberg, Germany
| | - Ursula Klingmüller
- Deutsches Krebsforschungszentrum, Systems Biology of Signal Transduction, Heidelberg, Germany
| | - Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.,Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Reham Hassan
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.,Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Brigitte Begher-Tibbe
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | | |
Collapse
|
20
|
Cadamuro M, Lasagni A, Sarcognato S, Guido M, Fabris R, Strazzabosco M, Strain AJ, Simioni P, Villa E, Fabris L. The Neglected Role of Bile Duct Epithelial Cells in NASH. Semin Liver Dis 2022; 42:34-47. [PMID: 34794182 DOI: 10.1055/s-0041-1739455] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most prevalent liver disease worldwide, and affects 25% of the population in Western countries. NAFLD is the hepatic manifestation of the metabolic syndrome, linked to insulin resistance, which is the common pathogenetic mechanism. In approximately 40% of NAFLD patients, steatosis is associated with necro-inflammation and fibrosis, resulting in nonalcoholic steatohepatitis (NASH), a severe condition that may progress to cirrhosis and liver cancer. Although the hepatocyte represents the main target of the disease, involvement of the bile ducts occurs in a subset of patients with NASH, and is characterized by ductular reaction and activation of the progenitor cell compartment, which incites portal fibrosis and disease progression. We aim to dissect the multiple biological effects that adipokines and metabolic alterations exert on cholangiocytes to derive novel information on the mechanisms driven by insulin resistance, which promote fibro-inflammation and carcinogenesis in NASH.
Collapse
Affiliation(s)
| | - Alberto Lasagni
- Division of General Medicine, Padua University-Hospital, Padua, Italy
| | | | - Maria Guido
- Department of Pathology, Azienda ULSS2 Marca Trevigiana, Treviso, Italy.,Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Roberto Fabris
- Division of Clinica Medica 3, Center for the Study and the Integrated Management of Obesity, Padua University-Hospital, Padua, Italy
| | - Mario Strazzabosco
- Department of Internal Medicine, Digestive Disease Section, Liver Center, Yale University, New Haven, Connecticut
| | - Alastair J Strain
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Paolo Simioni
- Division of General Medicine, Padua University-Hospital, Padua, Italy.,Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Erica Villa
- Gastroenterology Unit, Department of Medical Specialties, University of Modena & Reggio Emilia and Modena University-Hospital, Modena, Italy
| | - Luca Fabris
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy.,Division of General Medicine, Padua University-Hospital, Padua, Italy.,Department of Internal Medicine, Digestive Disease Section, Liver Center, Yale University, New Haven, Connecticut
| |
Collapse
|
21
|
Abstract
Cholestatic and non-alcoholic fatty liver disease (NAFLD) share several key pathophysiological mechanisms which can be targeted by novel therapeutic concepts that are currently developed for both areas. Nuclear receptors (NRs) are ligand-activated transcriptional regulators of key metabolic processes including hepatic lipid and glucose metabolism, energy expenditure and bile acid (BA) homoeostasis, as well as inflammation, fibrosis and cellular proliferation. Dysregulation of these processes contributes to the pathogenesis and progression of cholestatic as well as fatty liver disease, placing NRs at the forefront of novel therapeutic approaches. This includes BA and fatty acid activated NRs such as farnesoid-X receptor (FXR) and peroxisome proliferator-activated receptors, respectively, for which high affinity therapeutic ligands targeting specific or multiple isoforms have been developed. Moreover, novel liver-specific ligands for thyroid hormone receptor beta 1 complete the spectrum of currently available NR-targeted drugs. Apart from FXR ligands, BA signalling can be targeted by mimetics of FXR-activated fibroblast growth factor 19, modulation of their enterohepatic circulation through uptake inhibitors in hepatocytes and enterocytes, as well as novel BA derivatives undergoing cholehepatic shunting (instead of enterohepatic circulation). Other therapeutic approaches more directly target inflammation and/or fibrosis as critical events of disease progression. Combination strategies synergistically targeting metabolic disturbances, inflammation and fibrosis may be ultimately necessary for successful treatment of these complex and multifactorial disorders.
Collapse
Affiliation(s)
- Michael Trauner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Claudia Daniela Fuchs
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
22
|
Pelechá M, Villanueva-Bádenas E, Timor-López E, Donato MT, Tolosa L. Cell Models and Omics Techniques for the Study of Nonalcoholic Fatty Liver Disease: Focusing on Stem Cell-Derived Cell Models. Antioxidants (Basel) 2021; 11:86. [PMID: 35052590 PMCID: PMC8772881 DOI: 10.3390/antiox11010086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/24/2021] [Accepted: 12/28/2021] [Indexed: 12/04/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is now the leading cause of chronic liver disease in western countries. The molecular mechanisms leading to NAFLD are only partially understood, and effective therapeutic interventions are clearly needed. Therefore, preclinical research is required to improve knowledge about NAFLD physiopathology and to identify new therapeutic targets. Primary human hepatocytes, human hepatic cell lines, and human stem cell-derived hepatocyte-like cells exhibit different hepatic phenotypes and have been widely used for studying NAFLD pathogenesis. In this paper, apart from employing the different in vitro cell models for the in vitro assessment of NAFLD, we also reviewed other approaches (metabolomics, transcriptomics, and high-content screening). We aimed to summarize the characteristics of different cell types and methods and to discuss their major advantages and disadvantages for NAFLD modeling.
Collapse
Affiliation(s)
- María Pelechá
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (M.P.); (E.V.-B.); (E.T.-L.)
| | - Estela Villanueva-Bádenas
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (M.P.); (E.V.-B.); (E.T.-L.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología, Universidad de Valencia, 46010 Valencia, Spain
| | - Enrique Timor-López
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (M.P.); (E.V.-B.); (E.T.-L.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología, Universidad de Valencia, 46010 Valencia, Spain
| | - María Teresa Donato
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (M.P.); (E.V.-B.); (E.T.-L.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología, Universidad de Valencia, 46010 Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laia Tolosa
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (M.P.); (E.V.-B.); (E.T.-L.)
- Biomedical Research Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| |
Collapse
|
23
|
Vartak N, Drasdo D, Geisler F, Itoh T, P J Oude Elferink R, van de Graaf SFJ, Chiang J, Keitel V, Trauner M, Jansen P, Hengstler JG. On the Mechanisms of Biliary Flux. Hepatology 2021; 74:3497-3512. [PMID: 34164843 DOI: 10.1002/hep.32027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/18/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022]
Abstract
Since the late 1950s, transport of bile in the liver has been described by the "osmotic concept," according to which bile flows into the canaliculi toward the ducts, countercurrent to the blood flow in the sinusoids. However, because of the small size of canaliculi, it was so far impossible to observe, let alone to quantify this process. Still, "osmotic canalicular flow" was a sufficient and plausible explanation for the clearance characteristics of a wide variety of choleretic compounds excreted in bile. Imaging techniques have now been established that allow direct flux analysis in bile canaliculi of the intact liver in living organisms. In contrast to the prevailing osmotic concept these analyses strongly suggest that the transport of small molecules in canalicular bile is diffusion dominated, while canalicular flow is negligibly small. In contrast, with the same experimental approach, it could be shown that in the interlobular ducts, diffusion is augmented by flow. Thus, bile canaliculi can be compared to a standing water zone that is connected to a river. The seemingly subtle difference between diffusion and flow is of relevance for therapy of a wide range of liver diseases including cholestasis and NAFLD. Here, we incorporated the latest findings on canalicular solute transport, and align them with extant knowledge to present an integrated and explanatory framework of bile flux that will undoubtedly be refined further in the future.
Collapse
Affiliation(s)
- Nachiket Vartak
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Dirk Drasdo
- National Institute for Research in Digital Science and Technology, Paris, France
| | - Fabian Geisler
- Clinic and Polyclinic for Internal Medicine II, Kinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Tohru Itoh
- Institute for Quantitative Biosciences, the University of Tokyo, Tokyo, Japan
| | - Ronald P J Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - John Chiang
- North-East Ohio Medical University, Rootstown, OH, USA
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty at Heinrich-Heine-University, Düsseldorf, Germany
| | - Michael Trauner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Peter Jansen
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| |
Collapse
|
24
|
Radun R, Trauner M. Role of FXR in Bile Acid and Metabolic Homeostasis in NASH: Pathogenetic Concepts and Therapeutic Opportunities. Semin Liver Dis 2021; 41:461-475. [PMID: 34289507 PMCID: PMC8492195 DOI: 10.1055/s-0041-1731707] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become the most prevalent cause of liver disease, increasingly contributing to the burden of liver transplantation. In search for effective treatments, novel strategies addressing metabolic dysregulation, inflammation, and fibrosis are continuously emerging. Disturbed bile acid (BA) homeostasis and microcholestasis via hepatocellular retention of potentially toxic BAs may be an underappreciated factor in the pathogenesis of NAFLD and nonalcoholic steatohepatitis (NASH) as its progressive variant. In addition to their detergent properties, BAs act as signaling molecules regulating cellular homeostasis through interaction with BA receptors such as the Farnesoid X receptor (FXR). Apart from being a key regulator of BA metabolism and enterohepatic circulation, FXR regulates metabolic homeostasis and has immune-modulatory effects, making it an attractive therapeutic target in NAFLD/NASH. In this review, the molecular basis and therapeutic potential of targeting FXR with a specific focus on restoring BA and metabolic homeostasis in NASH is summarized.
Collapse
Affiliation(s)
- Richard Radun
- Department of Internal Medicine III, Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Medical University of Vienna, Austria
| | - Michael Trauner
- Department of Internal Medicine III, Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Medical University of Vienna, Austria
| |
Collapse
|
25
|
Shapses M, Tang L, Layne A, Beri A, Rotman Y. Fatty Liver Is an Independent Risk Factor for Delayed Recovery from Anesthesia. Hepatol Commun 2021; 5:1848-1859. [PMID: 34558821 PMCID: PMC8557314 DOI: 10.1002/hep4.1772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022] Open
Abstract
Fatty liver (FL) is associated with altered activity of hepatic drug-metabolizing enzymes, but the clinical significance is unknown. Many anesthetic agents are metabolized in the liver. We aimed to determine whether FL impacts recovery from anesthesia as a surrogate for altered drug metabolism. This was a single-center, retrospective, case-control study of all adults who underwent anesthesia and concurrent abdominal imaging (n = 2,021) in a hospital setting. FL (n = 234) was identified through radiology reports. Anesthesia recovery, the primary endpoint, was defined by Aldrete's recovery score (RS, 0-10), assessed following postanesthesia care unit (PACU) arrival, with RS ≥8 considered discharge eligible. FL and controls were compared using univariate and multivariate analyses, adjusting for confounders. A secondary matched-pairs analysis matched FL and controls 1:1 for confounders. Time from airway removal to discharge eligibility was compared using multivariate Cox regression. On PACU arrival, 54.1% of FL were discharge eligible compared to 61.7% of controls (P = 0.03), with lower activity scores on univariate (P = 0.03) and multivariate analysis (P = 0.03). On matched-pairs analysis, discharge eligibility, activity, consciousness, and total RSs were lower in FL (P ≤ 0.04 for all). Median time from airway removal to discharge eligibility was 43% longer in FL (univariate, P = 0.01; multivariate hazard ratio, 1.32; P = 0.046). To further exclude confounding by obesity, we performed a sensitivity analysis limited to a body mass index <30, where FL was still associated with lower activity (P = 0.03) and total RS (P = 0.03). Conclusion: Patients with FL have delayed recovery from anesthesia, suggesting altered drug metabolism independent of metabolic risk factors.
Collapse
Affiliation(s)
- Mark Shapses
- Liver and Energy Metabolism SectionLiver Diseases BranchNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Lin Tang
- Department of Perioperative MedicineNational Institutes of Health Clinical CenterBethesdaMDUSA
| | - Austin Layne
- Biomedical Translational Research Information SystemNational Institutes of Health Clinical CenterBethesdaMDUSA
| | - Andrea Beri
- Biomedical Translational Research Information SystemNational Institutes of Health Clinical CenterBethesdaMDUSA
| | - Yaron Rotman
- Liver and Energy Metabolism SectionLiver Diseases BranchNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMDUSA
| |
Collapse
|
26
|
Cunningham RP, Porat-Shliom N. Liver Zonation - Revisiting Old Questions With New Technologies. Front Physiol 2021; 12:732929. [PMID: 34566696 PMCID: PMC8458816 DOI: 10.3389/fphys.2021.732929] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the ever-increasing prevalence of non-alcoholic fatty liver disease (NAFLD), the etiology and pathogenesis remain poorly understood. This is due, in part, to the liver's complex physiology and architecture. The liver maintains glucose and lipid homeostasis by coordinating numerous metabolic processes with great efficiency. This is made possible by the spatial compartmentalization of metabolic pathways a phenomenon known as liver zonation. Despite the importance of zonation to normal liver function, it is unresolved if and how perturbations to liver zonation can drive hepatic pathophysiology and NAFLD development. While hepatocyte heterogeneity has been identified over a century ago, its examination had been severely hindered due to technological limitations. Recent advances in single cell analysis and imaging technologies now permit further characterization of cells across the liver lobule. This review summarizes the advances in examining liver zonation and elucidating its regulatory role in liver physiology and pathology. Understanding the spatial organization of metabolism is vital to further our knowledge of liver disease and to provide targeted therapeutic avenues.
Collapse
Affiliation(s)
- Rory P Cunningham
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Natalie Porat-Shliom
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| |
Collapse
|
27
|
Yoo T, Joo SK, Kim HJ, Kim HY, Sim H, Lee J, Kim HH, Jung S, Lee Y, Jamialahmadi O, Romeo S, Jeong WI, Hwang GS, Kang KW, Kim JW, Kim W, Choi M. Disease-specific eQTL screening reveals an anti-fibrotic effect of AGXT2 in non-alcoholic fatty liver disease. J Hepatol 2021; 75:514-523. [PMID: 33892010 DOI: 10.1016/j.jhep.2021.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Non-alcoholic fatty liver disease (NAFLD) poses an increasing clinical burden. Genome-wide association studies have revealed a limited contribution of genomic variants to the disease, requiring alternative but robust approaches to identify disease-associated variants and genes. We carried out a disease-specific expression quantitative trait loci (eQTL) screen to identify novel genetic factors that specifically act on NAFLD progression on the basis of genotype. METHODS We recruited 125 Korean patients (83 with biopsy-proven NAFLD and 42 without NAFLD) and performed eQTL analyses using 21,272 transcripts and 3,234,941 genotyped and imputed single nucleotide polymorphisms. We then selected eQTLs that were detected only in the NAFLD group, but not in the control group (i.e., NAFLD-eQTLs). An additional cohort of 162 Korean individuals with NAFLD was used for replication. The function of the selected eQTL toward NAFLD development was validated using HepG2, primary hepatocytes and NAFLD mouse models. RESULTS The NAFLD-specific eQTL screening yielded 242 loci. Among them, AGXT2, encoding alanine-glyoxylate aminotransferase 2, displayed decreased expression in patients with NAFLD homozygous for the non-reference allele of rs2291702, compared to no-NAFLD individuals with the same genotype (p = 4.79 × 10-6). This change was replicated in an additional 162 individuals, yielding a combined p value of 8.05 × 10-8 from a total of 245 patients with NAFLD and 42 controls. Knockdown of AGXT2 induced palmitate-overloaded hepatocyte death by increasing endoplasmic reticulum stress, and exacerbated NAFLD diet-induced liver fibrosis in mice, while overexpression of AGXT2 attenuated liver fibrosis and steatosis. CONCLUSIONS We identified a new molecular role for AGXT2 in NAFLD. Our overall approach will serve as an efficient tool for uncovering novel genetic factors that contribute to liver steatosis and fibrosis in patients with NAFLD. LAY SUMMARY Elucidating causal genes for non-alcoholic fatty liver disease (NAFLD) has been challenging due to limited tissue availability and the polygenic nature of the disease. Using liver and blood samples from 125 Korean individuals (83 with NAFLD and 42 without NAFLD), we devised a new analytic method to identify causal genes. Among the candidates, we found that AGXT2-rs2291702 protects against liver fibrosis in a genotype-dependent manner with the potential for therapeutic interventions. Our approach enables the discovery of causal genes that act on the basis of genotype.
Collapse
Affiliation(s)
- Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sae Kyung Joo
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Republic of Korea
| | - Hyo Jung Kim
- Department of Biochemistry and Molecular Biology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Young Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jieun Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Republic of Korea
| | - Hee-Hoon Kim
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Sunhee Jung
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Oveis Jamialahmadi
- Salhgrenska Academy, Institute of Medicine, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden
| | - Stefano Romeo
- Salhgrenska Academy, Institute of Medicine, Department of Molecular and Clinical Medicine, University of Gothenburg, Sweden; Sahlgrenska University Hospital, Cardiology Department, Sweden; Department of Medical and Clinical Science, Clinical Nutrition Unit, University Magna Graecia, Catanzaro, Italy
| | - Won-Il Jeong
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea; Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Keon Wook Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jae Woo Kim
- Department of Biochemistry and Molecular Biology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul, Republic of Korea.
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
28
|
Lam DTUH, Dan YY, Chan YS, Ng HH. Emerging liver organoid platforms and technologies. CELL REGENERATION (LONDON, ENGLAND) 2021; 10:27. [PMID: 34341842 PMCID: PMC8329140 DOI: 10.1186/s13619-021-00089-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Building human organs in a dish has been a long term goal of researchers in pursue of physiologically relevant models of human disease and for replacement of worn out and diseased organs. The liver has been an organ of interest for its central role in regulating body homeostasis as well as drug metabolism. An accurate liver replica should contain the multiple cell types found in the organ and these cells should be spatially organized to resemble tissue structures. More importantly, the in vitro model should recapitulate cellular and tissue level functions. Progress in cell culture techniques and bioengineering approaches have greatly accelerated the development of advance 3-dimensional (3D) cellular models commonly referred to as liver organoids. These 3D models described range from single to multiple cell type containing cultures with diverse applications from establishing patient-specific liver cells to modeling of chronic liver diseases and regenerative therapy. Each organoid platform is advantageous for specific applications and presents its own limitations. This review aims to provide a comprehensive summary of major liver organoid platforms and technologies developed for diverse applications.
Collapse
Affiliation(s)
- Do Thuy Uyen Ha Lam
- Laboratory of precision disease therapeutics, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore, 117597, Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore, 117597, Singapore
- Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Yun-Shen Chan
- Laboratory of precision disease therapeutics, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
| | - Huck-Hui Ng
- Laboratory of precision disease therapeutics, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117559, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117597, Singapore.
| |
Collapse
|
29
|
Yamaguchi M, Yoshihara K, Yachida N, Suda K, Tamura R, Ishiguro T, Enomoto T. The New Era of Three-Dimensional Histoarchitecture of the Human Endometrium. J Pers Med 2021; 11:jpm11080713. [PMID: 34442357 PMCID: PMC8401133 DOI: 10.3390/jpm11080713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022] Open
Abstract
The histology of the endometrium has traditionally been established by observation of two-dimensional (2D) pathological sections. However, because human endometrial glands exhibit coiling and branching morphology, it is extremely difficult to obtain an entire image of the glands by 2D observation. In recent years, the development of three-dimensional (3D) reconstruction of serial pathological sections by computer and whole-mount imaging technology using tissue clearing methods with high-resolution fluorescence microscopy has enabled us to observe the 3D histoarchitecture of tissues. As a result, 3D imaging has revealed that human endometrial glands form a plexus network in the basalis, similar to the rhizome of grass, whereas mouse uterine glands are single branched tubular glands. This review summarizes the relevant literature on the 3D structure of mouse and human endometrium and discusses the significance of the rhizome structure in the human endometrium and the expected role of understanding the 3D tissue structure in future applications to systems biology.
Collapse
|
30
|
Nawroth JC, Petropolis DB, Manatakis DV, Maulana TI, Burchett G, Schlünder K, Witt A, Shukla A, Kodella K, Ronxhi J, Kulkarni G, Hamilton G, Seki E, Lu S, Karalis KC. Modeling alcohol-associated liver disease in a human Liver-Chip. Cell Rep 2021; 36:109393. [PMID: 34289365 PMCID: PMC8342038 DOI: 10.1016/j.celrep.2021.109393] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/03/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022] Open
Abstract
Alcohol-associated liver disease (ALD) is a global health issue and leads to progressive liver injury, comorbidities, and increased mortality. Human-relevant preclinical models of ALD are urgently needed. Here, we leverage a triculture human Liver-Chip with biomimetic hepatic sinusoids and bile canaliculi to model ALD employing human-relevant blood alcohol concentrations (BACs) and multimodal profiling of clinically relevant endpoints. Our Liver-Chip recapitulates established ALD markers in response to 48 h of exposure to ethanol, including lipid accumulation and oxidative stress, in a concentration-dependent manner and supports the study of secondary insults, such as high blood endotoxin levels. We show that remodeling of the bile canalicular network can provide an in vitro quantitative readout of alcoholic liver toxicity. In summary, we report the development of a human ALD Liver-Chip as a powerful platform for modeling alcohol-induced liver injury with the potential for direct translation to clinical research and evaluation of patient-specific responses.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Anke Witt
- Emulate, Inc., 27 Drydock Avenue, Boston, MA 02210, USA
| | | | | | - Janey Ronxhi
- Emulate, Inc., 27 Drydock Avenue, Boston, MA 02210, USA
| | | | | | - Ekihiro Seki
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Shelly Lu
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | |
Collapse
|
31
|
A Scoping Review of Artificial Intelligence and Machine Learning in Bariatric and Metabolic Surgery: Current Status and Future Perspectives. Obes Surg 2021; 31:4555-4563. [PMID: 34264433 DOI: 10.1007/s11695-021-05548-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/12/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023]
Abstract
Artificial intelligence (AI) is a revolution in data analysis with emerging roles in various specialties and with various applications. The objective of this scoping review was to retrieve current literature on the fields of AI that have been applied to metabolic bariatric surgery (MBS) and to investigate potential applications of AI as a decision-making tool of the bariatric surgeon. Initial search yielded 3260 studies published from January 2000 until March 2021. After screening, 49 unique articles were included in the final analysis. Studies were grouped into categories, and the frequency of appearing algorithms, dataset types, and metrics were documented. The heterogeneity of current studies showed that meticulous validation, strict reporting systems, and reliable benchmarking are mandatory for ensuring the clinical validity of future research.
Collapse
|
32
|
Popa SL, Ismaiel A, Cristina P, Cristina M, Chiarioni G, David L, Dumitrascu DL. Non-Alcoholic Fatty Liver Disease: Implementing Complete Automated Diagnosis and Staging. A Systematic Review. Diagnostics (Basel) 2021; 11:diagnostics11061078. [PMID: 34204822 PMCID: PMC8231502 DOI: 10.3390/diagnostics11061078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/05/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Non-alcoholic fatty liver disease (NAFLD) is a fast-growing pathology around the world, being considered the most common chronic liver disease. It is diagnosed based on the presence of steatosis in more than 5% of hepatocytes without significant alcohol consumption. This review aims to provide a comprehensive overview of current studies of artificial intelligence (AI) applications that may help physicians in implementing a complete automated NAFLD diagnosis and staging. Methods: PubMed, EMBASE, Cochrane Library, and WILEY databases were screened for relevant publications in relation to AI applications in NAFLD. The search terms included: (non-alcoholic fatty liver disease OR NAFLD) AND (artificial intelligence OR machine learning OR neural networks OR deep learning OR automated diagnosis OR computer-aided diagnosis OR digital pathology OR automated ultrasound OR automated computer tomography OR automated magnetic imaging OR electronic health records). Results: Our search identified 37 articles about automated NAFLD diagnosis, out of which 15 articles analyzed imagistic techniques, 15 articles analyzed digital pathology, and 7 articles analyzed electronic health records (EHC). All studies included in this review show an accurate capacity of automated diagnosis and staging in NAFLD using AI-based software. Conclusions: We found significant evidence demonstrating that implementing a complete automated system for NAFLD diagnosis, staging, and risk stratification is currently possible, considering the accuracy, sensibility, and specificity of available AI-based tools.
Collapse
Affiliation(s)
- Stefan L. Popa
- 2nd Medical Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (S.L.P.); (L.D.); (D.L.D.)
| | - Abdulrahman Ismaiel
- 2nd Medical Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (S.L.P.); (L.D.); (D.L.D.)
- Correspondence:
| | - Pop Cristina
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (P.C.); (M.C.)
| | - Mogosan Cristina
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (P.C.); (M.C.)
| | - Giuseppe Chiarioni
- Division of Gastroenterology, University of Verona, 1-37126 AOUI Verona, Italy;
| | - Liliana David
- 2nd Medical Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (S.L.P.); (L.D.); (D.L.D.)
| | - Dan L. Dumitrascu
- 2nd Medical Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania; (S.L.P.); (L.D.); (D.L.D.)
| |
Collapse
|
33
|
van Ineveld RL, Kleinnijenhuis M, Alieva M, de Blank S, Barrera Roman M, van Vliet EJ, Martínez Mir C, Johnson HR, Bos FL, Heukers R, Chuva de Sousa Lopes SM, Drost J, Dekkers JF, Wehrens EJ, Rios AC. Revealing the spatio-phenotypic patterning of cells in healthy and tumor tissues with mLSR-3D and STAPL-3D. Nat Biotechnol 2021; 39:1239-1245. [PMID: 34083793 PMCID: PMC7611791 DOI: 10.1038/s41587-021-00926-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 04/16/2021] [Indexed: 12/12/2022]
Abstract
Despite advances in three-dimensional (3D) imaging, it remains challenging to profile all the cells within a large 3D tissue, including the morphology and organization of the many cell types present. Here, we introduce eight-color, multispectral, large-scale single-cell resolution 3D (mLSR-3D) imaging and image analysis software for the parallelized, deep learning-based segmentation of large numbers of single cells in tissues, called segmentation analysis by parallelization of 3D datasets (STAPL-3D). Applying the method to pediatric Wilms tumor, we extract molecular, spatial and morphological features of millions of cells and reconstruct the tumor’s spatio-phenotypic patterning. In situ population profiling and pseudotime ordering reveals a highly disorganized spatial pattern in Wilms tumor compared to healthy fetal kidney, yet cellular profiles closely resembling human fetal kidney cells could be observed. In addition, we identify previously unreported tumor-specific populations, uniquely characterized by their spatial embedding or morphological attributes. Our results demonstrate the use of combining mLSR-3D and STAPL-3D to generate a comprehensive cellular map of human tumors.
Collapse
Affiliation(s)
- Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Michiel Kleinnijenhuis
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Sam de Blank
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Mario Barrera Roman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Esmée J van Vliet
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Clara Martínez Mir
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Hannah R Johnson
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Frank L Bos
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | | | | | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Johanna F Dekkers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. .,Cancer Genomics Netherlands, Oncode Institute, Utrecht, the Netherlands.
| |
Collapse
|
34
|
Ma Q, Liao X, Shao C, Lin Y, Wu T, Sun Y, Feng ST, Ye J, Zhong B. Normalization of γ-glutamyl transferase levels is associated with better metabolic control in individuals with nonalcoholic fatty liver disease. BMC Gastroenterol 2021; 21:215. [PMID: 33971815 PMCID: PMC8112063 DOI: 10.1186/s12876-021-01790-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The normalization of liver biochemical parameters usually reflects the histological response to treatment for nonalcoholic fatty liver disease (NAFLD). Researchers have not clearly determined whether different liver enzymes exhibit various metabolic changes during the follow-up period in patients with NAFLD. METHODS We performed a retrospective analysis of patients with NAFLD who were receiving therapy from January 2011 to December 2019. Metabolism indexes, including glucose levels, lipid profiles, uric acid levels and liver biochemical parameters, were measured. Magnetic resonance imaging-based proton density fat fraction (MRI-PDFF) and liver ultrasound were used to evaluate steatosis. All patients received recommendations for lifestyle modifications and guideline-recommended pharmacological treatments with indications for drug therapy for metabolic abnormalities. RESULTS Overall, 1048 patients with NAFLD were included and received lifestyle modification recommendations and pharmaceutical interventions, including 637 (60.7%) patients with abnormal GGT levels and 767 (73.2%) patients with abnormal ALT levels. Patients with concurrent ALT and GGT abnormalities presented higher levels of metabolism indexes and higher liver fat content than those in patients with single or no abnormalities. After 12 months of follow-up, the cumulative normalization rate of GGT was considerably lower than that of ALT (38% vs. 62%, P < 0.001). Greater weight loss resulted in higher cumulative normalization rates of GGT and ALT. Weight loss (OR = 1.21, 95% CI 1.11-1.32, P < 0.001), ALT normalization (OR = 2.75, 95% CI 1.41-5.36, P = 0.01) and lower TG and HOMA-IR values (OR = 2.03, 95% CI 1.11-3.71, P = 0.02; OR = 2.04, 95% CI 1.07-3.89, P = 0.03) were independent protective factors for GGT normalization. Elevated baseline GGT (OR = 0.99, 95% CI 0.98-0.99, P = 0.01) was a risk factor. CONCLUSIONS For NAFLD patients with concurrently increased ALT and GGT levels, a lower normalization rate of GGT was observed, rather than ALT. Good control of weight and insulin resistance was a reliable predictor of GGT normalization.
Collapse
Affiliation(s)
- Qianqian Ma
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan II Road, Yuexiu District, Guangzhou, 510080, China
| | - Xianhua Liao
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan II Road, Yuexiu District, Guangzhou, 510080, China
| | - Congxiang Shao
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan II Road, Yuexiu District, Guangzhou, 510080, China
| | - Yansong Lin
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan II Road, Yuexiu District, Guangzhou, 510080, China
| | - Tingfeng Wu
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan II Road, Yuexiu District, Guangzhou, 510080, China
| | - Yanhong Sun
- Department of Clinical Laboratories, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shi-Ting Feng
- Department of Radiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Junzhao Ye
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan II Road, Yuexiu District, Guangzhou, 510080, China.
| | - Bihui Zhong
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan II Road, Yuexiu District, Guangzhou, 510080, China.
| |
Collapse
|
35
|
Schmitz R, Madesta F, Nielsen M, Krause J, Steurer S, Werner R, Rösch T. Multi-scale fully convolutional neural networks for histopathology image segmentation: From nuclear aberrations to the global tissue architecture. Med Image Anal 2021; 70:101996. [DOI: 10.1016/j.media.2021.101996] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 11/23/2020] [Accepted: 02/08/2021] [Indexed: 12/28/2022]
|
36
|
Vartak N, Guenther G, Joly F, Damle-Vartak A, Wibbelt G, Fickel J, Jörs S, Begher-Tibbe B, Friebel A, Wansing K, Ghallab A, Rosselin M, Boissier N, Vignon-Clementel I, Hedberg C, Geisler F, Hofer H, Jansen P, Hoehme S, Drasdo D, Hengstler JG. Intravital Dynamic and Correlative Imaging of Mouse Livers Reveals Diffusion-Dominated Canalicular and Flow-Augmented Ductular Bile Flux. Hepatology 2021; 73:1531-1550. [PMID: 32558958 DOI: 10.1002/hep.31422] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Small-molecule flux in tissue microdomains is essential for organ function, but knowledge of this process is scant due to the lack of suitable methods. We developed two independent techniques that allow the quantification of advection (flow) and diffusion in individual bile canaliculi and in interlobular bile ducts of intact livers in living mice, namely fluorescence loss after photoactivation and intravital arbitrary region image correlation spectroscopy. APPROACH AND RESULTS The results challenge the prevailing "mechano-osmotic" theory of canalicular bile flow. After active transport across hepatocyte membranes, bile acids are transported in the canaliculi primarily by diffusion. Only in the interlobular ducts is diffusion augmented by regulatable advection. Photoactivation of fluorescein bis-(5-carboxymethoxy-2-nitrobenzyl)-ether in entire lobules demonstrated the establishment of diffusive gradients in the bile canalicular network and the sink function of interlobular ducts. In contrast to the bile canalicular network, vectorial transport was detected and quantified in the mesh of interlobular bile ducts. CONCLUSIONS The liver consists of a diffusion-dominated canalicular domain, where hepatocytes secrete small molecules and generate a concentration gradient and a flow-augmented ductular domain, where regulated water influx creates unidirectional advection that augments the diffusive flux.
Collapse
Affiliation(s)
- Nachiket Vartak
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Georgia Guenther
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | | | - Amruta Damle-Vartak
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Gudrun Wibbelt
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,University of Potsdam, Potsdam-Golm, Germany
| | - Simone Jörs
- Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Brigitte Begher-Tibbe
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | | | | | - Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany.,Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | | | | | | | | | - Fabian Geisler
- Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
| | - Peter Jansen
- Universiteit van Amsterdam, Amsterdam, the Netherlands
| | | | - Dirk Drasdo
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany.,Inria, Paris, France
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| |
Collapse
|
37
|
Gao B, Sakaguchi K, Ogawa T, Kagawa Y, Kubo H, Shimizu T. Functional Analysis of Induced Human Ballooned Hepatocytes in a Cell Sheet-Based Three Dimensional Model. Tissue Eng Regen Med 2021; 18:217-224. [PMID: 33517537 DOI: 10.1007/s13770-020-00297-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/22/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Ballooned hepatocytes (BH) are a key histological hallmark of nonalcoholic steatohepatitis (NASH), yet their consequences for liver-specific functions are unknown. METHODS In our previous study, an experimental model of human induced-BHs (iBH) has been successfully developed based on cell sheet technology. This study aimed to determine the functions of iBHs in the primary human hepatocyte/normal human dermal fibroblast (PHH/NHDF) co-culture cell sheets. Normal hepatocytes in the PHH/3T3-J2 co-culture cell sheets were set as a control, since 3T3-J2 murine embryonic fibroblasts have exhibited previously long term maintenance of PHH functions. RESULTS It was found that, albumin secretion was not affected in iBHs, but urea synthesis as well as cytochrome P450 enzyme (CYP) activities including CYP1A2 and CYP3A4, were significantly reduced in iBHs. Besides, loss of bile canaliculi was observed in iBHs. These findings are consistent with clinical studies of human NASH. In addition, PHH/NHDF cell sheets demonstrated two fold higher TGF-β1 secretion compared with PHH/3T3-J2 cell sheets. Furthermore, treatment with a TGF-β inhibitor and a semi-synthetic bile acid analogue (obeticholic acid, phase 3 trial of NASH therapy) ameliorated the histological appearance of established iBHs. CONCLUSION In summary, this study demonstrates the priority of iBHs in recapitulating not only histology but also clinically relevant hepatic dysfunctions in human NASH and suggests TGF-β and bile acid related signal pathway may play important roles in the formation of iBHs.
Collapse
Affiliation(s)
- Botao Gao
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Materials Products, National Engineering Research Center for Healthcare Devices, Guangdong Institute of Medical Instruments, Guangdong Academy of Sciences, Guangzhou, 510550, China.,Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Katsuhisa Sakaguchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Advanced Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Tetsuya Ogawa
- Ogino Memorial Laboratory, Nihon Kohden Corporation, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Yuki Kagawa
- Ogino Memorial Laboratory, Nihon Kohden Corporation, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Hirotsugu Kubo
- Ogino Memorial Laboratory, Nihon Kohden Corporation, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Tatsuya Shimizu
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan.
| |
Collapse
|
38
|
Liu H, Wang F, Liu B, Zheng Z, Zhao J, Zhang J. Application of three-dimensional reconstruction with a Hisense computer-assisted system in upper pancreatic lymph node dissection during laparoscopic-assisted radical gastrectomy. Asian J Surg 2021; 44:730-737. [PMID: 33500172 DOI: 10.1016/j.asjsur.2020.12.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/27/2020] [Accepted: 12/16/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/OBJECTIVE To investigate the feasibility of three-dimensional (3D) reconstruction with an interactive Hisense computer-assisted system (CAS) for preoperative planning and intraoperative guidance during laparoscopic-assisted upper pancreatic lymph node dissection in distal gastrectomy for gastric cancer. METHODS This study included 28 patients who underwent preoperative 3D reconstruction of the upper border of the pancreas using Hisense CAS (3D reconstruction group) for preoperative planning and intraoperative navigation. To determine its efficacy, the clinical data of these patients were compared with those of 28 patients who did not undergo 3D reconstruction (control group). RESULTS Fifty-six cases of laparoscopic-assisted distal gastrectomy were performed. Three-dimensional reconstruction was successful in all the patients in the 3D reconstruction group, and real-time navigation was performed during the operation. The rate of correspondence between the 3D reconstruction images and intraoperative findings was 100%. The time taken for upper pancreatic lymph node dissection, number of upper pancreatic lymph node dissections, and number of unnecessary injuries during surgery were superior in the 3D reconstruction group than in the control group. The results of the remaining parameters were not statistically significant. CONCLUSION Preoperative planning with interactive Hisense CAS 3D reconstruction technology can improve surgeons' understanding of each patient's individual anatomy and can reveal anatomical variations, which is helpful for accurate preoperative planning and intraoperative navigation. This technique is helpful for the implementation of the precise dissection of lymph nodes at the upper edge of the pancreas and improves the quality and safety of the surgery.
Collapse
Affiliation(s)
- Hao Liu
- General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Feifei Wang
- Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, 266000, Shandong, China
| | - Bo Liu
- General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Ziwen Zheng
- General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Junjiang Zhao
- General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Jian Zhang
- General Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
| |
Collapse
|
39
|
Abstract
In 2020, there have been substantial advances in nonalcoholic fatty liver disease mechanisms, diagnostics and treatment. Key developments include the identification of a cellular and tissue signature to provide new insights into pathophysiology, advancements in non-invasive diagnostics and publication of interim results of the first phase III trial to demonstrate improvement in hepatic fibrosis.
Collapse
|
40
|
Li L, Xie P, Lin W, Liu J, Chen J, Guo Z, Bin C, An W, Zhang C, Zhan Y. CKIP-1 augments autophagy in steatotic hepatocytes by inhibiting Akt/mTOR signal pathway. Exp Cell Res 2020; 397:112341. [PMID: 33191205 DOI: 10.1016/j.yexcr.2020.112341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 09/26/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD), which is characterized by aberrant accumulation of intrahepatic triglycerides and lipid droplets (LDs) in the liver cells, is becoming increasingly prevalent at an alarming rate worldwide. LDs can be consumed by either hydrolysis or autophagy, which is shown to be of importance in the regulation of hepatic lipid metabolism. We have shown that deficiency of pleckstrin homology domain-containing casein kinase 2 interacting protein-1 (CKIP-1), a scaffold protein that interacts with various proteins in multiple signal pathways, in mice aggravates high-fat diet induced fatty liver. However, its underlying mechanisms remain largely unknown. In this study, we found that the mRNA and protein levels of CKIP-1 decreased dramatically in steatotic HepG2 cells induced by oleic acid (OA) treatment. Coincidently, hepatic autophagy was also dynamically regulated in steatotic HepG2 cells. In addition, overexpression of CKIP-1 activated autophagy by suppression of Akt/mTOR signaling, which in turn reduced lipid accumulation. Moreover, these phenomena were reversed in CKIP-1-shRNA transfected steatotic hepatocytes. To further evaluate the potential role of CKIP-1 in autophagy, we determined the level of autophagy related proteins in CKIP-1 knockout mice. These results supported our findings in vitro. In summary, we found CKIP-1 to be a positive regulator of hepatic autophagy and a promising therapeutic target for treatment of NAFLD.
Collapse
Affiliation(s)
- Li Li
- Department of Gastroenterology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Ping Xie
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, 100069, China
| | - Wenjun Lin
- Department of Gastroenterology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Jinsheng Liu
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Jing Chen
- Department of Gastroenterology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Zihao Guo
- Department of Gastroenterology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Chuxuan Bin
- Department of Gastroenterology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Wei An
- Department of Cell Biology, Municipal Laboratory for Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, 100069, China.
| | - Chuan Zhang
- Department of Gastroenterology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
| | - Yutao Zhan
- Department of Gastroenterology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
| |
Collapse
|
41
|
Ramli MNB, Lim YS, Koe CT, Demircioglu D, Tng W, Gonzales KAU, Tan CP, Szczerbinska I, Liang H, Soe EL, Lu Z, Ariyachet C, Yu KM, Koh SH, Yaw LP, Jumat NHB, Lim JSY, Wright G, Shabbir A, Dan YY, Ng HH, Chan YS. Human Pluripotent Stem Cell-Derived Organoids as Models of Liver Disease. Gastroenterology 2020; 159:1471-1486.e12. [PMID: 32553762 DOI: 10.1053/j.gastro.2020.06.010] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 06/02/2020] [Accepted: 06/06/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS There are few in vitro models for studying the 3-dimensional interactions among different liver cell types during organogenesis or disease development. We aimed to generate hepatic organoids that comprise different parenchymal liver cell types and have structural features of the liver, using human pluripotent stem cells. METHODS We cultured H1 human embryonic stem cells (WA-01, passage 27-40) and induced pluripotent stem cells (GM23338) with a series of chemically defined and serum-free media to induce formation of posterior foregut cells, which were differentiated in 3 dimensions into hepatic endoderm spheroids and stepwise into hepatoblast spheroids. Hepatoblast spheroids were reseeded in a high-throughput format and induced to form hepatic organoids; development of functional bile canaliculi was imaged live. Levels of albumin and apolipoprotein B were measured in cell culture supernatants using an enzyme-linked immunosorbent assay. Levels of gamma glutamyl transferase and alkaline phosphatase were measured in cholangiocytes. Organoids were incubated with troglitazone for varying periods and bile transport and accumulation were visualized by live-imaging microscopy. Organoids were incubated with oleic and palmitic acid, and formation of lipid droplets was visualized by staining. We compared gene expression profiles of organoids incubated with free fatty acids or without. We also compared gene expression profiles between liver tissue samples from patients with nonalcoholic steatohepatitis (NASH) versus without. We quantified hepatocyte and cholangiocyte populations in organoids using immunostaining and flow cytometry; cholangiocyte proliferation of cholangiocytes was measured. We compared the bile canaliculi network in the organoids incubated with versus without free fatty acids by live imaging. RESULTS Cells in organoids differentiated into hepatocytes and cholangiocytes, based on the expression of albumin and cytokeratin 7. Hepatocytes were functional, based on secretion of albumin and apolipoprotein B and cytochrome P450 activity; cholangiocytes were functional, based on gamma glutamyl transferase and alkaline phosphatase activity and proliferative responses to secretin. The organoids organized a functional bile canaliculi system, which was disrupted by cholestasis-inducing drugs such as troglitazone. Organoids incubated with free fatty acids had gene expression signatures similar to those of liver tissues from patients with NASH. Incubation of organoids with free fatty acid-enriched media resulted in structural changes associated with nonalcoholic fatty liver disease, such as decay of bile canaliculi network and ductular reactions. CONCLUSIONS We developed a hepatic organoid platform with human cells that can be used to model complex liver diseases, including NASH.
Collapse
Affiliation(s)
| | - Yee Siang Lim
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Chwee Tat Koe
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Deniz Demircioglu
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Weiquan Tng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Kevin Andrew Uy Gonzales
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore; Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York City, New York
| | - Cheng Peow Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Iwona Szczerbinska
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Hongqing Liang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Einsi Lynn Soe
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Zhiping Lu
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | | | - Ka Man Yu
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Shu Hui Koh
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Lai Ping Yaw
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Nur Halisah Binte Jumat
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - John Soon Yew Lim
- Institute of Medical Biology, A∗STAR, Singapore; Skin Research Institute of Singapore, A∗STAR, Singapore
| | - Graham Wright
- Institute of Medical Biology, A∗STAR, Singapore; Skin Research Institute of Singapore, A∗STAR, Singapore
| | - Asim Shabbir
- Department of Surgery, University Surgical Cluster, National University Hospital, Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Hospital, Singapore
| | - Huck-Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yun-Shen Chan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore.
| |
Collapse
|
42
|
Yu C, Wan Y, Piao L, Wu Cheng X. Can cysteinyl cathepsin activity control diet-induced NAFLD? IJC HEART & VASCULATURE 2020; 28:100516. [PMID: 32373709 PMCID: PMC7195526 DOI: 10.1016/j.ijcha.2020.100516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 11/25/2022]
Key Words
- CSTB, cathepsin B
- CTSB+/+, wild-type
- CTSB−/−, cathepsin B deficiency
- CTSs, cathepsins
- FABP4, fatty acid binding protein 4
- FPC, fructose-palmitate-cholesterol
- LDL, low density lipoprotein
- MMP, metalloproteinase
- NAFLD, Non-alcoholic fatty liver disease
- NASH, non-alcoholic steatohepatitis
- Scad, short-chain acyl dehydrogenase-1
Collapse
Affiliation(s)
| | | | - Limei Piao
- Department of Cardiology and Hypertension, Yanbian University Hospital, Yanji, China
| | - Xian Wu Cheng
- Department of Cardiology and Hypertension, Yanbian University Hospital, Yanji, China
| |
Collapse
|
43
|
Karschau J, Scholich A, Wise J, Morales-Navarrete H, Kalaidzidis Y, Zerial M, Friedrich BM. Resilience of three-dimensional sinusoidal networks in liver tissue. PLoS Comput Biol 2020; 16:e1007965. [PMID: 32598356 PMCID: PMC7351228 DOI: 10.1371/journal.pcbi.1007965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/10/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Can three-dimensional, microvasculature networks still ensure blood supply if individual links fail? We address this question in the sinusoidal network, a plexus-like microvasculature network, which transports nutrient-rich blood to every hepatocyte in liver tissue, by building on recent advances in high-resolution imaging and digital reconstruction of adult mice liver tissue. We find that the topology of the three-dimensional sinusoidal network reflects its two design requirements of a space-filling network that connects all hepatocytes, while using shortest transport routes: sinusoidal networks are sub-graphs of the Delaunay graph of their set of branching points, and also contain the corresponding minimum spanning tree, both to good approximation. To overcome the spatial limitations of experimental samples and generate arbitrarily-sized networks, we developed a network generation algorithm that reproduces the statistical features of 0.3-mm-sized samples of sinusoidal networks, using multi-objective optimization for node degree and edge length distribution. Nematic order in these simulated networks implies anisotropic transport properties, characterized by an empirical linear relation between a nematic order parameter and the anisotropy of the permeability tensor. Under the assumption that all sinusoid tubes have a constant and equal flow resistance, we predict that the distribution of currents in the network is very inhomogeneous, with a small number of edges carrying a substantial part of the flow-a feature known for hierarchical networks, but unexpected for plexus-like networks. We quantify network resilience in terms of a permeability-at-risk, i.e., permeability as function of the fraction of removed edges. We find that sinusoidal networks are resilient to random removal of edges, but vulnerable to the removal of high-current edges. Our findings suggest the existence of a mechanism counteracting flow inhomogeneity to balance metabolic load on the liver.
Collapse
Affiliation(s)
| | - André Scholich
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Jonathan Wise
- cfaed, TU Dresden, Dresden, Germany
- Univ. Grenoble Alpes, CNRS, LPMMC, Grenoble, France
| | | | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence ‘Physics of Life’, TU Dresden, Dresden, Germany
| | - Benjamin M. Friedrich
- cfaed, TU Dresden, Dresden, Germany
- Cluster of Excellence ‘Physics of Life’, TU Dresden, Dresden, Germany
| |
Collapse
|
44
|
High-definition medicine: modelling NAFLD in 3D. Nat Rev Gastroenterol Hepatol 2020; 17:66-67. [PMID: 31857709 DOI: 10.1038/s41575-019-0256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
|