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Dubois V, Lefebvre P, Staels B, Eeckhoute J. Nuclear receptors: pathophysiological mechanisms and drug targets in liver disease. Gut 2024; 73:1562-1569. [PMID: 38862216 DOI: 10.1136/gutjnl-2023-331741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/18/2024] [Indexed: 06/13/2024]
Abstract
Nuclear receptors (NRs) are ligand-dependent transcription factors required for liver development and function. As a consequence, NRs have emerged as attractive drug targets in a wide range of liver diseases. However, liver dysfunction and failure are linked to loss of hepatocyte identity characterised by deficient NR expression and activities. This might at least partly explain why several pharmacological NR modulators have proven insufficiently efficient to improve liver functionality in advanced stages of diseases such as metabolic dysfunction-associated steatotic liver disease (MASLD). In this perspective, we review the most recent advances in the hepatic NR field and discuss the contribution of multiomic approaches to our understanding of their role in the molecular organisation of an intricated transcriptional regulatory network, as well as in liver intercellular dialogues and interorgan cross-talks. We discuss the potential benefit of novel therapeutic approaches simultaneously targeting multiple NRs, which would not only reactivate the hepatic NR network and restore hepatocyte identity but also impact intercellular and interorgan interplays whose importance to control liver functions is further defined. Finally, we highlight the need of considering individual parameters such as sex and disease stage in the development of NR-based clinical strategies.
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Affiliation(s)
- Vanessa Dubois
- Basic and Translational Endocrinology (BaTE), Department of Basic and Applied Medical Sciences, Ghent University, Gent, Belgium
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Jerome Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
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2
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Yin K, Büttner M, Deligiannis IK, Strzelecki M, Zhang L, Talavera-López C, Theis F, Odom DT, Martinez-Jimenez CP. Polyploidisation pleiotropically buffers ageing in hepatocytes. J Hepatol 2024; 81:289-302. [PMID: 38583492 DOI: 10.1016/j.jhep.2024.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND & AIMS Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. METHODS We performed single-nucleus RNA sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent strains that were haploinsufficient for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. RESULTS We observed that ageing in wild-type mice results in nuclei polyploidy and a marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in the CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A-haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbations. CONCLUSIONS Our results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome. IMPACT AND IMPLICATIONS The functional role of hepatocyte polyploidisation during ageing is poorly understood. Using single-nucleus RNA sequencing and BaseScope approaches, we have studied ploidy dynamics during ageing in murine livers with non-deleterious genetic perturbations. We have identified that hepatocytes present different cellular states and the ability to buffer ageing-associated dysfunctions. Tetraploid nuclei exhibit robust transcriptional networks and are better adapted to genomically overcome perturbations. Novel therapeutic interventions aimed at attenuating age-related changes in tissue function could be exploited by manipulation of ploidy dynamics during chronic liver conditions.
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Affiliation(s)
- Kelvin Yin
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Maren Büttner
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany
| | | | | | - Liwei Zhang
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Carlos Talavera-López
- Division of Infectious Diseases and Tropical Medicine, Ludwig-Maximilian-Universität Klinikum, Germany
| | - Fabian Theis
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany; Technical University of Munich, Department of Mathematics, 85748 Garching. Munich, Germany; German Cancer Research Centre, Heidelberg, Germany.
| | - Duncan T Odom
- German Cancer Research Center, Division of Regulatory Genomics and Cancer Evolution (B270), Heidelberg, Germany; Cancer Research UK Cambridge Institute, University of Cambridge, CB20RE, United Kingdom.
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany; Institute of Biotechnology and Biomedicine (BIOTECMED), Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, Spain.
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3
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Bangru S, Chen J, Baker N, Das D, Chembazhi UV, Derham JM, Chorghade S, Arif W, Alencastro F, Duncan AW, Carstens RP, Kalsotra A. ESRP2-microRNA-122 axis directs the postnatal onset of liver polyploidization and maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602336. [PMID: 39026848 PMCID: PMC11257421 DOI: 10.1101/2024.07.06.602336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Hepatocyte polyploidy and maturity are critical to acquiring specialized liver functions. Multiple intra- and extracellular factors influence ploidy, but how they cooperate temporally to steer liver polyploidization and maturation or how post-transcriptional mechanisms integrate into these paradigms is unknown. Here, we identified an important regulatory hierarchy in which postnatal activation of Epithelial-Splicing-Regulatory-Protein-2 (ESRP2) stimulates biogenesis of liver-specific microRNA (miR-122), thereby facilitating polyploidization, maturation, and functional competence of hepatocytes. By determining transcriptome-wide protein-RNA interactions in vivo and integrating them with single-cell and bulk hepatocyte RNA-seq datasets, we delineate an ESRP2-driven RNA processing program that drives sequential replacement of fetal-to-adult transcript isoforms. Specifically, ESRP2 binds the primary miR-122 host gene transcript to promote its processing/biogenesis. Combining constitutive and inducible ESRP2 gain- and loss-of-function mice models with miR-122 rescue experiments, we demonstrate that timed activation of ESRP2 augments miR-122-driven program of cytokinesis failure, ensuring proper onset and extent of hepatocyte polyploidization.
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4
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Xu C, Fang X, Song Y, Xiang Z, Xu X, Wei X. Transcriptional Control: A Directional Sign at the Crossroads of Adult Hepatic Progenitor Cells' Fates. Int J Biol Sci 2024; 20:3544-3556. [PMID: 38993564 PMCID: PMC11234216 DOI: 10.7150/ijbs.93739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
Hepatic progenitor cells (HPCs) have a bidirectional potential to differentiate into hepatocytes and bile duct epithelial cells and constitute a second barrier to liver regeneration in the adult liver. They are usually located in the Hering duct in the portal vein region where various cells, extracellular matrix, cytokines, and communication signals together constitute the niche of HPCs in homeostasis to maintain cellular plasticity. In various types of liver injury, different cellular signaling streams crosstalk with each other and point to the inducible transcription factor set, including FoxA1/2/3, YB-1, Foxl1, Sox9, HNF4α, HNF1α, and HNF1β. These transcription factors exert different functions by binding to specific target genes, and their products often interact with each other, with diverse cascades of regulation in different molecular events that are essential for homeostatic regulation, self-renewal, proliferation, and selective differentiation of HPCs. Furthermore, the tumor predisposition of adult HPCs is found to be significantly increased under transcriptional factor dysregulation in transcriptional analysis, and the altered initial commitment of the differentiation pathway of HPCs may be one of the sources of intrahepatic tumors. Related transcription factors such as HNF4α and HNF1 are expected to be future targets for tumor treatment.
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Affiliation(s)
- Chenhao Xu
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Xixi Fang
- Hangzhou Normal University, Hangzhou 310006, China
| | - Yisu Song
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Ze Xiang
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Xiao Xu
- Zhejiang University School of Medicine, Hangzhou 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
| | - Xuyong Wei
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou 310006, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou 310006, China
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5
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Ehle C, Iyer-Bierhoff A, Wu Y, Xing S, Kiehntopf M, Mosig AS, Godmann M, Heinzel T. Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response. Commun Biol 2024; 7:589. [PMID: 38755249 PMCID: PMC11099168 DOI: 10.1038/s42003-024-06288-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
The hepatic acute-phase response is characterized by a massive upregulation of serum proteins, such as haptoglobin and serum amyloid A, at the expense of liver homeostatic functions. Although the transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has a well-established role in safeguarding liver function and its cistrome spans around 50% of liver-specific genes, its role in the acute-phase response has received little attention so far. We demonstrate that HNF4A binds to and represses acute-phase genes under basal conditions. The reprogramming of hepatic transcription during inflammation necessitates loss of HNF4A function to allow expression of acute-phase genes while liver homeostatic genes are repressed. In a pre-clinical liver organoid model overexpression of HNF4A maintained liver functionality in spite of inflammation-induced cell damage. Conversely, HNF4A overexpression potently impaired the acute-phase response by retaining chromatin at regulatory regions of acute-phase genes inaccessible to transcription. Taken together, our data extend the understanding of dual HNF4A action as transcriptional activator and repressor, establishing HNF4A as gatekeeper for the hepatic acute-phase response.
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Affiliation(s)
- Charlotte Ehle
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University Jena, 07745, Jena, Germany
| | - Aishwarya Iyer-Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University Jena, 07745, Jena, Germany
| | - Yunchen Wu
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University Jena, 07745, Jena, Germany
- Marshall Laboratory of Biomedical Engineering, Department of Pathogen Biology, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Shaojun Xing
- Marshall Laboratory of Biomedical Engineering, Department of Pathogen Biology, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Michael Kiehntopf
- Department of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, 07747, Jena, Germany
| | - Alexander S Mosig
- Institute of Biochemistry II, Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Maren Godmann
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University Jena, 07745, Jena, Germany
| | - Thorsten Heinzel
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University Jena, 07745, Jena, Germany.
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6
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Feng R, Tong C, Lin T, Liu H, Shao C, Li Y, Sticht C, Kan K, Li X, Liu R, Wang S, Wang S, Munker S, Niess H, Meyer C, Liebe R, Ebert MP, Dooley S, Wang H, Ding H, Weng HL. Insulin Determines Transforming Growth Factor β Effects on Hepatocyte Nuclear Factor 4α Transcription in Hepatocytes. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:52-70. [PMID: 37820926 DOI: 10.1016/j.ajpath.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/19/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Loss of hepatocyte nuclear factor 4α (HNF4α) expression is frequently observed in end-stage liver disease and associated with loss of vital liver functions, thus increasing mortality. Loss of HNF4α expression is mediated by inflammatory cytokines, such as transforming growth factor (TGF)-β. However, details of how HNF4α is suppressed are largely unknown to date. Herein, TGF-β did not directly inhibit HNF4α but contributed to its transcriptional regulation by SMAD2/3 recruiting acetyltransferase CREB-binding protein/p300 to the HNF4α promoter. The recruitment of CREB-binding protein/p300 is indispensable for CCAAT/enhancer-binding protein α (C/EBPα) binding, another essential requirement for constitutive HNF4α expression in hepatocytes. Consistent with the in vitro observation, 67 of 98 patients with hepatic HNF4α expressed both phospho-SMAD2 and C/EBPα, whereas 22 patients without HNF4α expression lacked either phospho-SMAD2 or C/EBPα. In contrast to the observed induction of HNF4α, SMAD2/3 inhibited C/EBPα transcription. Long-term TGF-β incubation resulted in C/EBPα depletion, which abrogated HNF4α expression. Intriguingly, SMAD2/3 inhibitory binding to the C/EBPα promoter was abolished by insulin. Two-thirds of patients without C/EBPα lacked membrane glucose transporter type 2 expression in hepatocytes, indicating insulin resistance. Taken together, these data indicate that hepatic insulin sensitivity is essential for hepatic HNF4α expression in the condition of inflammation.
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Affiliation(s)
- Rilu Feng
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Chenhao Tong
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tao Lin
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hui Liu
- Department of Pathology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Chen Shao
- Department of Pathology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Yujia Li
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kejia Kan
- Department of Surgery, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xiaofeng Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Rui Liu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Sai Wang
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shanshan Wang
- Beijing Institute of Hepatology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Stefan Munker
- Department of Medicine II, Liver Centre Munich, University Hospital, Campus Großhadern, Ludwig-Maximilians-University Munich, Munich, Germany; Liver Centre Munich, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Hanno Niess
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany; Biobank of the Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christoph Meyer
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Roman Liebe
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Clinical Cooperation Unit Healthy Metabolism, Center of Preventive Medicine and Digital Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Steven Dooley
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hua Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huiguo Ding
- Department of Gastroenterology and Hepatology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Hong-Lei Weng
- Section Molecular Hepatology, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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7
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Bravo González-Blas C, Matetovici I, Hillen H, Taskiran II, Vandepoel R, Christiaens V, Sansores-García L, Verboven E, Hulselmans G, Poovathingal S, Demeulemeester J, Psatha N, Mauduit D, Halder G, Aerts S. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation. Nat Cell Biol 2024; 26:153-167. [PMID: 38182825 PMCID: PMC10791584 DOI: 10.1038/s41556-023-01316-4] [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: 11/22/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell types. We found that zonation affects gene expression and chromatin accessibility in hepatocytes, among other cell types. These states are driven by the repressors TCF7L1 and TBX3, alongside other core hepatocyte transcription factors, such as HNF4A, CEBPA, FOXA1 and ONECUT1. To examine the architecture of the enhancers driving these cell states, we trained a hierarchical deep learning model called DeepLiver. Our study provides a multimodal understanding of the regulatory code underlying hepatocyte identity and their zonation state that can be used to engineer enhancers with specific activity levels and zonation patterns.
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Hanne Hillen
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Roel Vandepoel
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Leticia Sansores-García
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Elisabeth Verboven
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | | | - Jonas Demeulemeester
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikoleta Psatha
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Georg Halder
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium.
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8
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Zhou L, Montalvo AD, Collins JM, Wang D. Quantitative analysis of the UDP-glucuronosyltransferase transcriptome in human tissues. Pharmacol Res Perspect 2023; 11:e01154. [PMID: 37983911 PMCID: PMC10659769 DOI: 10.1002/prp2.1154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/22/2023] Open
Abstract
UDP-glucuronosyltransferases (UGTs) are phase II drug metabolizing enzymes that play important roles in the detoxification of endogenous and exogenous substrates. The 22 human UGTs belong to four families (UGT1, UGT2, UGT3, and UGT8) and differ in their expression, substrate specificity, UDP-sugar preference, and physiological functions. Differential expression/activity of the UGTs contributes to interperson variability in drug responses and toxicity, hormone homeostasis, and disease/cancer risks. However, in normal tissues, the tissue-specific expression profiles and transcriptional regulation of the UGTs are still not fully understood. In this study, we comprehensively analyzed the transcriptome of 22 UGTs in 54 human tissues/regions using RNAseq data from GTEx. We then validated the findings in the liver and small intestine samples using real-time PCR. Our results showed large interindividual variability across tissues in the expression of each UGT and the overall composition of UGT pools, consisting of different UGTs and their splice isoforms. Our results also revealed coexpression of the UGTs, Cytochrome P450s, and many transcription factors in the liver, suggesting potential coregulation or functional coordination. Our results provide the groundwork for future studies to detail further the regulation of the expression and activity of the UGTs.
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Affiliation(s)
- Lucas Zhou
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for PharmacogenomicsUniversity of FloridaGainesvilleFloridaUSA
| | - Abelardo D. Montalvo
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for PharmacogenomicsUniversity of FloridaGainesvilleFloridaUSA
| | - Joseph M. Collins
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for PharmacogenomicsUniversity of FloridaGainesvilleFloridaUSA
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for PharmacogenomicsUniversity of FloridaGainesvilleFloridaUSA
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9
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Shah A, Huck I, Duncan K, Gansemer ER, Liu K, Adajar RC, Apte U, Stamnes MA, Rutkowski DT. Interference with the HNF4-dependent gene regulatory network diminishes endoplasmic reticulum stress in hepatocytes. Hepatol Commun 2023; 7:e0278. [PMID: 37820274 PMCID: PMC10578741 DOI: 10.1097/hc9.0000000000000278] [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: 02/21/2023] [Accepted: 08/08/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND In all eukaryotic cell types, the unfolded protein response (UPR) upregulates factors that promote protein folding and misfolded protein clearance to help alleviate endoplasmic reticulum (ER) stress. Yet, ER stress in the liver is uniquely accompanied by the suppression of metabolic genes, the coordination and purpose of which are largely unknown. METHODS Here, we combined in silico machine learning, in vivo liver-specific deletion of the master regulator of hepatocyte differentiation HNF4α, and in vitro manipulation of hepatocyte differentiation state to determine how the UPR regulates hepatocyte identity and toward what end. RESULTS Machine learning identified a cluster of correlated genes that were profoundly suppressed by persistent ER stress in the liver. These genes, which encode diverse functions including metabolism, coagulation, drug detoxification, and bile synthesis, are likely targets of the master regulator of hepatocyte differentiation HNF4α. The response of these genes to ER stress was phenocopied by liver-specific deletion of HNF4α. Strikingly, while deletion of HNF4α exacerbated liver injury in response to an ER stress challenge, it also diminished UPR activation and partially preserved ER ultrastructure, suggesting attenuated ER stress. Conversely, pharmacological maintenance of hepatocyte identity in vitro enhanced sensitivity to stress. CONCLUSIONS Together, our findings suggest that the UPR regulates hepatocyte identity through HNF4α to protect ER homeostasis even at the expense of liver function.
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Affiliation(s)
- Anit Shah
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Ian Huck
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, Kansas, USA
| | - Kaylia Duncan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Erica R. Gansemer
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Kaihua Liu
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Reed C. Adajar
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Udayan Apte
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, Kansas, USA
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - D. Thomas Rutkowski
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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10
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Sanchez-Quant E, Richter ML, Colomé-Tatché M, Martinez-Jimenez CP. Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge. Genome Biol 2023; 24:234. [PMID: 37848949 PMCID: PMC10583437 DOI: 10.1186/s13059-023-03075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of drug development. Recent advances in single-cell genomics demonstrate liver zonation and ploidy as main drivers of cellular heterogeneity. However, little is known about the impact of hepatocyte specialization on liver function upon metabolic challenge, including hepatic metabolism, detoxification, and protein synthesis. RESULTS Here, we investigate the metabolic capacity of individual human hepatocytes in vitro. We assess how chronic accumulation of lipids enhances cellular heterogeneity and impairs the metabolisms of drugs. Using a phenotyping five-probe cocktail, we identify four functional subgroups of hepatocytes responding differently to drug challenge and fatty acid accumulation. These four subgroups display differential gene expression profiles upon cocktail treatment and xenobiotic metabolism-related specialization. Notably, intracellular fat accumulation leads to increased transcriptional variability and diminishes the drug-related metabolic capacity of hepatocytes. CONCLUSIONS Our results demonstrate that, upon a metabolic challenge such as exposure to drugs or intracellular fat accumulation, hepatocyte subgroups display different and heterogeneous transcriptional responses.
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Affiliation(s)
- Eva Sanchez-Quant
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Lucia Richter
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354, Freising, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany.
| | - Celia Pilar Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
- TUM School of Medicine, Technical University of Munich, Munich (TUM), 80333, Munich, Germany.
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11
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Dubois‐Chevalier J, Gheeraert C, Berthier A, Boulet C, Dubois V, Guille L, Fourcot M, Marot G, Gauthier K, Dubuquoy L, Staels B, Lefebvre P, Eeckhoute J. An extended transcription factor regulatory network controls hepatocyte identity. EMBO Rep 2023; 24:e57020. [PMID: 37424431 PMCID: PMC10481658 DOI: 10.15252/embr.202357020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023] Open
Abstract
Cell identity is specified by a core transcriptional regulatory circuitry (CoRC), typically limited to a small set of interconnected cell-specific transcription factors (TFs). By mining global hepatic TF regulons, we reveal a more complex organization of the transcriptional regulatory network controlling hepatocyte identity. We show that tight functional interconnections controlling hepatocyte identity extend to non-cell-specific TFs beyond the CoRC, which we call hepatocyte identity (Hep-ID)CONNECT TFs. Besides controlling identity effector genes, Hep-IDCONNECT TFs also engage in reciprocal transcriptional regulation with TFs of the CoRC. In homeostatic basal conditions, this translates into Hep-IDCONNECT TFs being involved in fine tuning CoRC TF expression including their rhythmic expression patterns. Moreover, a role for Hep-IDCONNECT TFs in the control of hepatocyte identity is revealed in dedifferentiated hepatocytes where Hep-IDCONNECT TFs are able to reset CoRC TF expression. This is observed upon activation of NR1H3 or THRB in hepatocarcinoma or in hepatocytes subjected to inflammation-induced loss of identity. Our study establishes that hepatocyte identity is controlled by an extended array of TFs beyond the CoRC.
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Affiliation(s)
| | - Céline Gheeraert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Clémence Boulet
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Vanessa Dubois
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
- Basic and Translational Endocrinology (BaTE), Department of Basic and Applied Medical SciencesGhent UniversityGhentBelgium
| | - Loïc Guille
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Marie Fourcot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 – UAR 2014 – PLBSLilleFrance
| | - Guillemette Marot
- Univ. Lille, Inria, CHU Lille, ULR 2694 – METRICS: Évaluation des technologies de santé et des pratiques médicalesLilleFrance
| | - Karine Gauthier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, INRAE USC 1370, École Normale Supérieure de LyonLyonFrance
| | - Laurent Dubuquoy
- Univ. Lille, Inserm, CHU Lille, U1286 – INFINITE – Institute for Translational Research in InflammationLilleFrance
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
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12
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Radi SH, Vemuri K, Martinez-Lomeli J, Sladek FM. HNF4α isoforms: the fraternal twin master regulators of liver function. Front Endocrinol (Lausanne) 2023; 14:1226173. [PMID: 37600688 PMCID: PMC10438950 DOI: 10.3389/fendo.2023.1226173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
In the more than 30 years since the purification and cloning of Hepatocyte Nuclear Factor 4 (HNF4α), considerable insight into its role in liver function has been gleaned from its target genes and mouse experiments. HNF4α plays a key role in lipid and glucose metabolism and intersects with not just diabetes and circadian rhythms but also with liver cancer, although much remains to be elucidated about those interactions. Similarly, while we are beginning to elucidate the role of the isoforms expressed from its two promoters, we know little about the alternatively spliced variants in other portions of the protein and their impact on the 1000-plus HNF4α target genes. This review will address how HNF4α came to be called the master regulator of liver-specific gene expression with a focus on its role in basic metabolism, the contributions of the various isoforms and the intriguing intersection with the circadian clock.
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Affiliation(s)
- Sarah H. Radi
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Jose Martinez-Lomeli
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Frances M. Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
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13
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Wang S, Chen S, Sun J, Han P, Xu B, Li X, Zhong Y, Xu Z, Zhang P, Mi P, Zhang C, Li L, Zhang H, Xia Y, Li S, Heikenwalder M, Yuan D. m 6A modification-tuned sphingolipid metabolism regulates postnatal liver development in male mice. Nat Metab 2023; 5:842-860. [PMID: 37188818 DOI: 10.1038/s42255-023-00808-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Different organs undergo distinct transcriptional, epigenetic and physiological alterations that guarantee their functional maturation after birth. However, the roles of epitranscriptomic machineries in these processes have remained elusive. Here we demonstrate that expression of RNA methyltransferase enzymes Mettl3 and Mettl14 gradually declines during postnatal liver development in male mice. Liver-specific Mettl3 deficiency causes hepatocyte hypertrophy, liver injury and growth retardation. Transcriptomic and N6-methyl-adenosine (m6A) profiling identify the neutral sphingomyelinase, Smpd3, as a target of Mettl3. Decreased decay of Smpd3 transcripts due to Mettl3 deficiency results in sphingolipid metabolism rewiring, characterized by toxic ceramide accumulation and leading to mitochondrial damage and elevated endoplasmic reticulum stress. Pharmacological Smpd3 inhibition, Smpd3 knockdown or Sgms1 overexpression that counteracts Smpd3 can ameliorate the abnormality of Mettl3-deficent liver. Our findings demonstrate that Mettl3-N6-methyl-adenosine fine-tunes sphingolipid metabolism, highlighting the pivotal role of an epitranscriptomic machinery in coordination of organ growth and the timing of functional maturation during postnatal liver development.
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Affiliation(s)
- Shiguan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shanze Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Jianfeng Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pan Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bowen Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xinying Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Youquan Zhong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Peng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ping Mi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for Digestive Disease, Jinan, China
| | - Haiyan Zhang
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Hubei Jiangxia Laboratory, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China.
| | - Shiyang Li
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, China.
- Advanced Medical Research Institute, Shandong University, Jinan, China.
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany.
- The M3 Research Institute, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Shandong Provincial Clinical Research Center for Digestive Disease, Jinan, China.
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14
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Shah A, Huck I, Duncan K, Gansemer ER, Apte U, Stamnes MA, Rutkowski DT. Interference with the HNF4-dependent gene regulatory network diminishes ER stress in hepatocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527889. [PMID: 36798396 PMCID: PMC9934629 DOI: 10.1101/2023.02.09.527889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
In all eukaryotic cell types, the unfolded protein response (UPR) upregulates factors that promote protein folding and misfolded protein clearance to help alleviate endoplasmic reticulum (ER) stress. Yet ER stress in the liver is uniquely accompanied by the suppression of metabolic genes, the coordination and purpose of which is largely unknown. Here, we used unsupervised machine learning to identify a cluster of correlated genes that were profoundly suppressed by persistent ER stress in the liver. These genes, which encode diverse functions including metabolism, coagulation, drug detoxification, and bile synthesis, are likely targets of the master regulator of hepatocyte differentiation HNF4α. The response of these genes to ER stress was phenocopied by liver-specific deletion of HNF4 α. Strikingly, while deletion of HNF4α exacerbated liver injury in response to an ER stress challenge, it also diminished UPR activation and partially preserved ER ultrastructure, suggesting attenuated ER stress. Conversely, pharmacological maintenance of hepatocyte identity in vitro enhanced sensitivity to stress. Several pathways potentially link HNF4α to ER stress sensitivity, including control of expression of the tunicamycin transporter MFSD2A; modulation of IRE1/XBP1 signaling; and regulation of Pyruvate Dehydrogenase. Together, these findings suggest that HNF4α activity is linked to hepatic ER homeostasis through multiple mechanisms.
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Affiliation(s)
- Anit Shah
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Ian Huck
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, KS
| | - Kaylia Duncan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Erica R. Gansemer
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Udayan Apte
- Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, KS
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA
| | - D. Thomas Rutkowski
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA
- Department of Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, IA
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15
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Berasain C, Arechederra M, Argemí J, Fernández-Barrena MG, Avila MA. Loss of liver function in chronic liver disease: An identity crisis. J Hepatol 2023; 78:401-414. [PMID: 36115636 DOI: 10.1016/j.jhep.2022.09.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 01/24/2023]
Abstract
Adult hepatocyte identity is constructed throughout embryonic development and fine-tuned after birth. A multinodular network of transcription factors, along with pre-mRNA splicing regulators, define the transcriptome, which encodes the proteins needed to perform the complex metabolic and secretory functions of the mature liver. Transient hepatocellular dedifferentiation can occur as part of the regenerative mechanisms triggered in response to acute liver injury. However, persistent downregulation of key identity genes is now accepted as a strong determinant of organ dysfunction in chronic liver disease, a major global health burden. Therefore, the identification of core transcription factors and splicing regulators that preserve hepatocellular phenotype, and a thorough understanding of how these networks become disrupted in diseased hepatocytes, is of high clinical relevance. In this context, we review the key players in liver differentiation and discuss in detail critical factors, such as HNF4α, whose impairment mediates the breakdown of liver function. Moreover, we present compelling experimental evidence demonstrating that restoration of core transcription factor expression in a chronically injured liver can reset hepatocellular identity, improve function and ameliorate structural abnormalities. The possibility of correcting the phenotype of severely damaged and malfunctional livers may reveal new therapeutic opportunities for individuals with cirrhosis and advanced liver disease.
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Affiliation(s)
- Carmen Berasain
- Program of Hepatology, CIMA, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra, IdiSNA, Pamplona, Spain.
| | - Maria Arechederra
- Program of Hepatology, CIMA, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra, IdiSNA, Pamplona, Spain
| | - Josepmaria Argemí
- Centro de Investigación Biomédica en Red, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra, IdiSNA, Pamplona, Spain; Liver Unit, Clinica Universidad de Navarra, Pamplona, Spain
| | - Maite G Fernández-Barrena
- Program of Hepatology, CIMA, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra, IdiSNA, Pamplona, Spain
| | - Matías A Avila
- Program of Hepatology, CIMA, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red, CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra, IdiSNA, Pamplona, Spain.
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16
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Blackford SJI, Yu TTL, Norman MDA, Syanda AM, Manolakakis M, Lachowski D, Yan Z, Guo Y, Garitta E, Riccio F, Jowett GM, Ng SS, Vernia S, Del Río Hernández AE, Gentleman E, Rashid ST. RGD density along with substrate stiffness regulate hPSC hepatocyte functionality through YAP signalling. Biomaterials 2023; 293:121982. [PMID: 36640555 DOI: 10.1016/j.biomaterials.2022.121982] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
Human pluripotent stem cell-derived hepatocytes (hPSC-Heps) may be suitable for treating liver diseases, but differentiation protocols often fail to yield adult-like cells. We hypothesised that replicating healthy liver niche biochemical and biophysical cues would produce hepatocytes with desired metabolic functionality. Using 2D synthetic hydrogels which independently control mechanical properties and biochemical cues, we found that culturing hPSC-Heps on surfaces matching the stiffness of fibrotic liver tissue upregulated expression of genes for RGD-binding integrins, and increased expression of YAP/TAZ and their transcriptional targets. Alternatively, culture on soft, healthy liver-like substrates drove increases in cytochrome p450 activity and ureagenesis. Knockdown of ITGB1 or reducing RGD-motif-containing peptide concentration in stiff hydrogels reduced YAP activity and improved metabolic functionality; however, on soft substrates, reducing RGD concentration had the opposite effect. Furthermore, targeting YAP activity with verteporfin or forskolin increased cytochrome p450 activity, with forskolin dramatically enhancing urea synthesis. hPSC-Heps could also be successfully encapsulated within RGD peptide-containing hydrogels without negatively impacting hepatic functionality, and compared to 2D cultures, 3D cultured hPSC-Heps secreted significantly less fetal liver-associated alpha-fetoprotein, suggesting furthered differentiation. Our platform overcomes technical hurdles in replicating the liver niche, and allowed us to identify a role for YAP/TAZ-mediated mechanosensing in hPSC-Hep differentiation.
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Affiliation(s)
- Samuel J I Blackford
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Centre for Craniofacial & Regenerative Biology, King's College London, UK; Centre for Gene Therapy & Regenerative Medicine, King's College London, UK; NIHR Imperial BRC iPSC and Organoid Core Facility, Imperial College London, UK.
| | - Tracy T L Yu
- Centre for Craniofacial & Regenerative Biology, King's College London, UK
| | - Michael D A Norman
- Centre for Craniofacial & Regenerative Biology, King's College London, UK
| | - Adam M Syanda
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; NIHR Imperial BRC iPSC and Organoid Core Facility, Imperial College London, UK
| | - Michail Manolakakis
- MRC London Institute of Medical Sciences, UK; Institute of Clinical Sciences, Imperial College London, UK
| | - Dariusz Lachowski
- Cellular and Molecular Biomechanics Laboratory, Department of Bioengineering, Imperial College London, UK
| | - Ziqian Yan
- Centre for Craniofacial & Regenerative Biology, King's College London, UK
| | - Yunzhe Guo
- Centre for Craniofacial & Regenerative Biology, King's College London, UK
| | - Elena Garitta
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; NIHR Imperial BRC iPSC and Organoid Core Facility, Imperial College London, UK
| | - Federica Riccio
- Centre for Gene Therapy & Regenerative Medicine, King's College London, UK
| | - Geraldine M Jowett
- Centre for Craniofacial & Regenerative Biology, King's College London, UK; Centre for Gene Therapy & Regenerative Medicine, King's College London, UK
| | - Soon Seng Ng
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; NIHR Imperial BRC iPSC and Organoid Core Facility, Imperial College London, UK
| | - Santiago Vernia
- MRC London Institute of Medical Sciences, UK; Institute of Clinical Sciences, Imperial College London, UK
| | | | - Eileen Gentleman
- Centre for Craniofacial & Regenerative Biology, King's College London, UK.
| | - S Tamir Rashid
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; NIHR Imperial BRC iPSC and Organoid Core Facility, Imperial College London, UK.
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17
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Zhang J, Guo J, Yang N, Huang Y, Hu T, Rao C. Endoplasmic reticulum stress-mediated cell death in liver injury. Cell Death Dis 2022; 13:1051. [PMID: 36535923 PMCID: PMC9763476 DOI: 10.1038/s41419-022-05444-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022]
Abstract
The endoplasmic reticulum is an important intracellular organelle that plays an important role in maintaining cellular homeostasis. Endoplasmic reticulum stress (ERS) and unfolded protein response (UPR) are induced when the body is exposed to adverse external stimuli. It has been established that ERS can induce different cell death modes, including autophagy, apoptosis, ferroptosis, and pyroptosis, through three major transmembrane receptors on the ER membrane, including inositol requirement enzyme 1α, protein kinase-like endoplasmic reticulum kinase and activating transcription factor 6. These different modes of cell death play an important role in the occurrence and development of various diseases, such as neurodegenerative diseases, inflammation, metabolic diseases, and liver injury. As the largest metabolic organ, the liver is rich in enzymes, carries out different functions such as metabolism and secretion, and is the body's main site of protein synthesis. Accordingly, a well-developed endoplasmic reticulum system is present in hepatocytes to help the liver perform its physiological functions. Current evidence suggests that ERS is closely related to different stages of liver injury, and the death of hepatocytes caused by ERS may be key in liver injury. In addition, an increasing body of evidence suggests that modulating ERS has great potential for treating the liver injury. This article provided a comprehensive overview of the relationship between ERS and four types of cell death. Moreover, we discussed the mechanism of ERS and UPR in different liver injuries and their potential therapeutic strategies.
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Affiliation(s)
- Jian Zhang
- grid.411304.30000 0001 0376 205XSchool of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China ,grid.411304.30000 0001 0376 205XR&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China
| | - Jiafu Guo
- grid.411304.30000 0001 0376 205XSchool of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China ,grid.411304.30000 0001 0376 205XR&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China
| | - Nannan Yang
- grid.411304.30000 0001 0376 205XSchool of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China ,grid.411304.30000 0001 0376 205XR&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China
| | - Yan Huang
- grid.411304.30000 0001 0376 205XSchool of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China ,grid.411304.30000 0001 0376 205XR&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China
| | - Tingting Hu
- grid.411304.30000 0001 0376 205XSchool of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China ,grid.411304.30000 0001 0376 205XR&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China
| | - Chaolong Rao
- grid.411304.30000 0001 0376 205XSchool of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China ,grid.411304.30000 0001 0376 205XR&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China ,grid.411304.30000 0001 0376 205XState Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137 China
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18
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Jiang L, Wang X, Ma F, Wang X, Shi M, Yan Q, Liu M, Chen J, Shi C, Guan XY. PITX2C increases the stemness features of hepatocellular carcinoma cells by up-regulating key developmental factors in liver progenitor. J Exp Clin Cancer Res 2022; 41:211. [PMID: 35765089 PMCID: PMC9238105 DOI: 10.1186/s13046-022-02424-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Tumor cells exhibited phenotypic and molecular characteristics similar to their lineage progenitor cells. Liver developmental signaling pathways are showed to be associated with HCC development and oncogenesis. The similarities of expression profiling between liver progenitors (LPs) and HCC suggest that understanding the molecular mechanism during liver development could provide insights into HCC.
Methods
To profile the dynamic gene expression during liver development, cells from an in vitro liver differentiation model and two paired hepatocellular carcinoma (HCC) samples were analyzed using deep RNA sequencing. The expression levels of selected genes were analyzed by qRT-PCR. Moreover, the role of a key transcription factor, pituitary homeobox 2 (PITX2), was characterized via in vitro and vivo functional assays. Furthermore, molecular mechanism studies were performed to unveil how PITX2C regulate the key developmental factors in LPs, thereby increasing the stemness of HCC.
Results
PITX2 was found to exhibit a similar expression pattern to specific markers of LPs. PITX2 consists of three isoforms (PITX2A/B/C). The expression of PITX2 is associated with tumor size and overall survival rate, whereas only PITX2C expression is associated with AFP and differentiation in clinical patients. PITX2A/B/C has distinct functions in HCC tumorigenicity. PITX2C promotes HCC metastasis, self-renewal and chemoresistance. Molecular mechanism studies showed that PITX2C could up-regulate RALYL which could enhance HCC stemness via the TGF-β pathway. Furthermore, ChIP assays confirmed the role of PITX2C in regulating key developmental factors in LP.
Conclusion
PITX2C is a newly discovered transcription factor involved in hepatic differentiation and could increase HCC stemness by upregulating key transcriptional factors related to liver development.
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19
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Transcription networks in liver development and acute liver failure. LIVER RESEARCH 2022. [DOI: 10.1016/j.livres.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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20
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Feng R, Kan K, Sticht C, Li Y, Wang S, Liu H, Shao C, Munker S, Niess H, Wang S, Meyer C, Liebe R, Ebert MP, Dooley S, Ding H, Weng H. A hierarchical regulatory network ensures stable albumin transcription under various pathophysiological conditions. Hepatology 2022; 76:1673-1689. [PMID: 35257388 DOI: 10.1002/hep.32414] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/04/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS It remains unknown how patients with liver failure maintain essential albumin levels. Here, we delineate a hierarchical transcription regulatory network that ensures albumin expression under different disease conditions. APPROACH AND RESULTS We examined albumin levels in liver tissues and serum in 157 patients, including 84 with HCC, 38 decompensated cirrhosis, and 35 acute liver failure. Even in patients with liver failure, the average serum albumin concentrations were 30.55 g/L. In healthy subjects and patients with chronic liver diseases, albumin was expressed in hepatocytes. In patients with massive hepatocyte loss, albumin was expressed in liver progenitor cells (LPCs). The albumin gene (ALB) core promoter possesses a TATA box and nucleosome-free area, which allows constitutive RNA polymerase II binding and transcription initiation. Chromatin immunoprecipitation assays revealed that hepatocyte nuclear factor 4 alpha (HNF4α), CCAAT/enhancer-binding protein alpha (C/EBPα), and forkhead box A2 (FOXA2) bound to the ALB enhancer. Knockdown of either of these factors reduced albumin expression in hepatocytes. FOXA2 acts as a pioneer factor to support HNF4α and C/EBPα. In hepatocytes lacking HNF4α and C/EBPα expression, FOXA2 synergized with retinoic acid receptor (RAR) to maintain albumin transcription. RAR nuclear translocation was induced by retinoic acids released by activated HSCs. In patients with massive hepatocyte loss, LPCs expressed HNF4α and FOXA2. RNA sequencing and quantitative PCR analyses revealed that lack of HNF4α and C/EBPα in hepatocytes increased hedgehog ligand biosynthesis. Hedgehog up-regulates FOXA2 expression through glioblastoma family zinc finger 2 binding to the FOXA2 promoter in both hepatocytes and LPCs. CONCLUSIONS A hierarchical regulatory network formed by master and pioneer transcription factors ensures essential albumin expression in various pathophysiological conditions.
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Affiliation(s)
- Rilu Feng
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Kejia Kan
- Department of SurgeryMedical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Carsten Sticht
- NGS Core FacilityMedical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Yujia Li
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Shanshan Wang
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany.,Beijing Institute of HepatologyBeijing You'an HospitalCapital Medical UniversityBeijingChina
| | - Hui Liu
- Department of PathologyBeijing You'an HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Chen Shao
- Department of PathologyBeijing You'an HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Stefan Munker
- Department of Medicine IIUniversity HospitalLudwig-Maximilians-University MunichMunichGermany.,Liver Centre MunichUniversity HospitalLudwig-Maximilians-UniversityMunichGermany
| | - Hanno Niess
- Department of General, Visceral, and Transplant SurgeryLudwig-Maximilians-University MunichMunichGermany.,Biobank of the Department of GeneralVisceral and Transplant SurgeryLudwig-Maximilians-UniversityMunichGermany
| | - Sai Wang
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Christoph Meyer
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Roman Liebe
- Clinic of Gastroenterology, Hepatology and Infectious DiseasesHeinrich Heine UniversityDüsseldorfGermany.,Department of Medicine IISaarland University Medical CenterSaarland UniversityHomburgGermany
| | - Matthias P Ebert
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany.,Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty MannheimHeidelberg UniversityMannheimGermany.,Clinical Cooperation Unit Healthy MetabolismCenter of Preventive Medicine and Digital HealthMedical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Steven Dooley
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
| | - Huiguo Ding
- Department of Gastroenterology and HepatologyBeijing You'an HospitalAffiliated with Capital Medical UniversityBeijingChina
| | - Honglei Weng
- Department of Medicine IIMedical Faculty MannheimUniversity Medical Center MannheimHeidelberg UniversityMannheimGermany
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21
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Gárate-Rascón M, Recalde M, Rojo C, Fernández-Barrena MG, Ávila MA, Arechederra M, Berasain C. SLU7: A New Hub of Gene Expression Regulation—From Epigenetics to Protein Stability in Health and Disease. Int J Mol Sci 2022; 23:ijms232113411. [PMID: 36362191 PMCID: PMC9658179 DOI: 10.3390/ijms232113411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
SLU7 (Splicing factor synergistic lethal with U5 snRNA 7) was first identified as a splicing factor necessary for the correct selection of 3′ splice sites, strongly impacting on the diversity of gene transcripts in a cell. More recent studies have uncovered new and non-redundant roles of SLU7 as an integrative hub of different levels of gene expression regulation, including epigenetic DNA remodeling, modulation of transcription and protein stability. Here we review those findings, the multiple factors and mechanisms implicated as well as the cellular functions affected. For instance, SLU7 is essential to secure liver differentiation, genome integrity acting at different levels and a correct cell cycle progression. Accordingly, the aberrant expression of SLU7 could be associated with human diseases including cancer, although strikingly, it is an essential survival factor for cancer cells. Finally, we discuss the implications of SLU7 in pathophysiology, with particular emphasis on the progression of liver disease and its possible role as a therapeutic target in human cancer.
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Affiliation(s)
- María Gárate-Rascón
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
| | - Miriam Recalde
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
| | - Carla Rojo
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Matías A. Ávila
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - María Arechederra
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
| | - Carmen Berasain
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Avda. Pio XII, n55, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-948-194700; Fax: +34-948-194717
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22
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Loss of FOXA2 induces ER stress and hepatic steatosis and alters developmental gene expression in human iPSC-derived hepatocytes. Cell Death Dis 2022; 13:713. [PMID: 35973994 PMCID: PMC9381545 DOI: 10.1038/s41419-022-05158-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 01/21/2023]
Abstract
FOXA2 has been known to play important roles in liver functions in rodents. However, its role in human hepatocytes is not fully understood. Recently, we generated FOXA2 mutant induced pluripotent stem cell (FOXA2-/-iPSC) lines and illustrated that loss of FOXA2 results in developmental defects in pancreatic islet cells. Here, we used FOXA2-/-iPSC lines to understand the role of FOXA2 on the development and function of human hepatocytes. Lack of FOXA2 resulted in significant alterations in the expression of key developmental and functional genes in hepatic progenitors (HP) and mature hepatocytes (MH) as well as an increase in the expression of ER stress markers. Functional assays demonstrated an increase in lipid accumulation, bile acid synthesis and glycerol production, while a decrease in glucose uptake, glycogen storage, and Albumin secretion. RNA-sequencing analysis further validated the findings by showing a significant increase in genes associated with lipid metabolism, bile acid secretion, and suggested the activation of hepatic stellate cells and hepatic fibrosis in MH lacking FOXA2. Overexpression of FOXA2 reversed the defective phenotypes and improved hepatocyte functionality in iPSC-derived hepatic cells lacking FOXA2. These results highlight a potential role of FOXA2 in regulating human hepatic development and function and provide a human hepatocyte model, which can be used to identify novel therapeutic targets for FOXA2-associated liver disorders.
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23
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Siahpirani AF, Knaack S, Chasman D, Seirup M, Sridharan R, Stewart R, Thomson J, Roy S. Dynamic regulatory module networks for inference of cell type-specific transcriptional networks. Genome Res 2022; 32:1367-1384. [PMID: 35705328 PMCID: PMC9341506 DOI: 10.1101/gr.276542.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
Changes in transcriptional regulatory networks can significantly alter cell fate. To gain insight into transcriptional dynamics, several studies have profiled bulk multi-omic data sets with parallel transcriptomic and epigenomic measurements at different stages of a developmental process. However, integrating these data to infer cell type-specific regulatory networks is a major challenge. We present dynamic regulatory module networks (DRMNs), a novel approach to infer cell type-specific cis-regulatory networks and their dynamics. DRMN integrates expression, chromatin state, and accessibility to predict cis-regulators of context-specific expression, where context can be cell type, developmental stage, or time point, and uses multitask learning to capture network dynamics across linearly and hierarchically related contexts. We applied DRMNs to study regulatory network dynamics in three developmental processes, each showing different temporal relationships and measuring a different combination of regulatory genomic data sets: cellular reprogramming, liver dedifferentiation, and forward differentiation. DRMN identified known and novel regulators driving cell type-specific expression patterns, showing its broad applicability to examine dynamics of gene regulatory networks from linearly and hierarchically related multi-omic data sets.
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Affiliation(s)
- Alireza Fotuhi Siahpirani
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA
- Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Sara Knaack
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Morten Seirup
- Morgridge Institute for Research, Madison, Wisconsin 53715, USA
- Molecular and Environmental Toxicology Program, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin 53715, USA
| | - James Thomson
- Morgridge Institute for Research, Madison, Wisconsin 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin 53715, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93117, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, Wisconsin 53715, USA
- Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53715, USA
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24
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Liu A, Han N, Munoz-Muriedas J, Bender A. Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). PLoS Comput Biol 2022; 18:e1010148. [PMID: 35687583 PMCID: PMC9292124 DOI: 10.1371/journal.pcbi.1010148] [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: 12/08/2021] [Revised: 07/18/2022] [Accepted: 04/26/2022] [Indexed: 01/10/2023] Open
Abstract
Adverse event pathogenesis is often a complex process which compromises multiple events ranging from the molecular to the phenotypic level. In toxicology, Adverse Outcome Pathways (AOPs) aim to formalize this as temporal sequences of events, in which event relationships should be supported by causal evidence according to the tailored Bradford-Hill criteria. One of the criteria is whether events are consistently observed in a certain temporal order and, in this work, we study this time concordance using the concept of “first activation” as data-driven means to generate hypotheses on potentially causal mechanisms. As a case study, we analysed liver data from repeat-dose studies in rats from the TG-GATEs database which comprises measurements across eight timepoints, ranging from 3 hours to 4 weeks post-treatment. We identified time-concordant gene expression-derived events preceding adverse histopathology, which serves as surrogate readout for Drug-Induced Liver Injury (DILI). We find known mechanisms in DILI to be time-concordant, and show further that significance, frequency and log fold change (logFC) of differential expression are metrics which can additionally prioritize events although not necessary to be mechanistically relevant. Moreover, we used the temporal order of transcription factor (TF) expression and regulon activity to identify transcriptionally regulated TFs and subsequently combined this with prior knowledge on functional interactions to derive detailed gene-regulatory mechanisms, such as reduced Hnf4a activity leading to decreased expression and activity of Cebpa. At the same time, also potentially novel events are identified such as Sox13 which is highly significantly time-concordant and shows sustained activation over time. Overall, we demonstrate how time-resolved transcriptomics can derive and support mechanistic hypotheses by quantifying time concordance and how this can be combined with prior causal knowledge, with the aim of both understanding mechanisms of toxicity, as well as potential applications to the AOP framework. We make our results available in the form of a Shiny app (https://anikaliu.shinyapps.io/dili_cascades), which allows users to query events of interest in more detail. Understanding mechanisms from systems-scale biological data is of great relevance in toxicology as well as drug discovery; however how to generate causal hypotheses instead of correlations is by no means clear. In this work, we study the conserved temporal order of events and present an automatable framework to quantify and characterize time concordance across a large set of time-series. We apply this concept to events derived from time-resolved gene expression and histopathology from the TG-GATEs in vivo liver data as a case study. We were able to recover known events involved in the pathogenesis of Drug-Induced Liver Injury (DILI), and identify potentially novel pathway and transcription factors (TFs) which precede adverse histopathology. As complementary sources of evidence for causality, we additionally show how time concordance and prior knowledge on plausible interactions between TFs can be combined to derive causal hypotheses on the TFs’ mode of regulation and interaction partners. Overall, the results derived in our case study can serve as valuable hypothesis-free starting points for the development of Adverse Outcome Pathways for DILI, and demonstrate that our approach provides a novel angle to prioritize mechanistically relevant events.
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Affiliation(s)
- Anika Liu
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
- Systems Modelling and Translational Biology, Data and Computational Sciences, GSK, London, United Kingdom
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AL); (AB)
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Jordi Munoz-Muriedas
- Systems Modelling and Translational Biology, Data and Computational Sciences, GSK, London, United Kingdom
- Computer-Aided Drug Design, UCB, Slough, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AL); (AB)
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25
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Russell JO, Camargo FD. Hippo signalling in the liver: role in development, regeneration and disease. Nat Rev Gastroenterol Hepatol 2022; 19:297-312. [PMID: 35064256 PMCID: PMC9199961 DOI: 10.1038/s41575-021-00571-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 02/07/2023]
Abstract
The Hippo signalling pathway has emerged as a major player in many aspects of liver biology, such as development, cell fate determination, homeostatic function and regeneration from injury. The regulation of Hippo signalling is complex, with activation of the pathway by diverse upstream inputs including signals from cellular adhesion, mechanotransduction and crosstalk with other signalling pathways. Pathological activation of the downstream transcriptional co-activators yes-associated protein 1 (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ, encoded by WWTR1), which are negatively regulated by Hippo signalling, has been implicated in multiple aspects of chronic liver disease, such as the development of liver fibrosis and tumorigenesis. Thus, development of pharmacological inhibitors of YAP-TAZ signalling has been an area of great interest. In this Review, we summarize the diverse roles of Hippo signalling in liver biology and highlight areas where outstanding questions remain to be investigated. Greater understanding of the mechanisms of Hippo signalling in liver function should help facilitate the development of novel therapies for the treatment of liver disease.
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Affiliation(s)
- Jacquelyn O Russell
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Fernando D Camargo
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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26
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Abstract
Non-alcoholic fatty liver disease (NAFLD) is emerging as the most common chronic liver disease worldwide. It refers to a range of liver conditions affecting people who drink little or no alcohol. NAFLD comprises non-alcoholic fatty liver and non-alcoholic steatohepatitis (NASH), the more aggressive form of NAFLD. NASH is featured by steatosis, lobular inflammation, hepatocyte injury, and various degrees of fibrosis. Although much progress has been made over the past decades, the pathogenic mechanism of NAFLD remains to be fully elucidated. Hepatocyte nuclear factor 4α (HNF4α) is a nuclear hormone receptor that is highly expressed in hepatocytes. Hepatic HNF4α expression is markedly reduced in NAFLD patients and mouse models of NASH. HNF4α has been shown to regulate bile acid, lipid, glucose, and drug metabolism. In this review, we summarize the recent advances in the understanding of the pathogenesis of NAFLD with a focus on the regulation of HNF4α and the role of hepatic HNF4α in NAFLD. Several lines of evidence have shown that hepatic HNF4α plays a key role in the initiation and progression of NAFLD. Recent data suggest that hepatic HNF4α may be a promising target for treatment of NAFLD.
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27
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White SM, Snyder MP, Yi C. Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes. Nucleic Acids Res 2021; 49:12196-12210. [PMID: 34850122 PMCID: PMC8643643 DOI: 10.1093/nar/gkab1105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/09/2021] [Accepted: 11/15/2021] [Indexed: 12/28/2022] Open
Abstract
The term 'super enhancers' (SE) has been widely used to describe stretches of closely localized enhancers that are occupied collectively by large numbers of transcription factors (TFs) and co-factors, and control the transcription of highly-expressed genes. Through integrated analysis of >600 DNase-seq, ChIP-seq, GRO-seq, STARR-seq, RNA-seq, Hi-C and ChIA-PET data in five human cancer cell lines, we identified a new class of autonomous SEs (aSEs) that are excluded from classic SE calls by the widely used Rank Ordering of Super-Enhancers (ROSE) method. TF footprint analysis revealed that compared to classic SEs and regular enhancers, aSEs are tightly bound by a dense array of master lineage TFs, which serve as anchors to recruit additional TFs and co-factors in trans. In addition, aSEs are preferentially enriched for Cohesins, which likely involve in stabilizing long-distance interactions between aSEs and their distal target genes. Finally, we showed that aSEs can be reliably predicted using a single DNase-seq data or combined with Mediator and/or P300 ChIP-seq. Overall, our study demonstrates that aSEs represent a unique class of functionally important enhancer elements that distally regulate the transcription of highly expressed genes.
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Affiliation(s)
- Shannon M White
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Chunling Yi
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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28
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Gárate-Rascón M, Recalde M, Jimenez M, Elizalde M, Azkona M, Uriarte I, Latasa MU, Urtasun R, Bilbao I, Sangro B, Garcia-Ruiz C, Fernandez-Checa JC, Corrales FJ, Esquivel A, Pineda-Lucena A, Fernández-Barrena MG, Ávila MA, Arechederra M, Berasain C. Splicing Factor SLU7 Prevents Oxidative Stress-Mediated Hepatocyte Nuclear Factor 4α Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage. Hepatology 2021; 74:2791-2807. [PMID: 34170569 DOI: 10.1002/hep.32029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIMS Hepatocellular dedifferentiation is emerging as an important determinant in liver disease progression. Preservation of mature hepatocyte identity relies on a set of key genes, predominantly the transcription factor hepatocyte nuclear factor 4α (HNF4α) but also splicing factors like SLU7. How these factors interact and become dysregulated and the impact of their impairment in driving liver disease are not fully understood. APPROACH AND RESULTS Expression of SLU7 and that of the adult and oncofetal isoforms of HNF4α, driven by its promoter 1 (P1) and P2, respectively, was studied in diseased human and mouse livers. Hepatic function and damage response were analyzed in wild-type and Slu7-haploinsufficient/heterozygous (Slu7+/- ) mice undergoing chronic (CCl4 ) and acute (acetaminophen) injury. SLU7 expression was restored in CCl4 -injured mice using SLU7-expressing adeno-associated viruses (AAV-SLU7). The hepatocellular SLU7 interactome was characterized by mass spectrometry. Reduced SLU7 expression in human and mouse diseased livers correlated with a switch in HNF4α P1 to P2 usage. This response was reproduced in Slu7+/- mice, which displayed increased sensitivity to chronic and acute liver injury, enhanced oxidative stress, and marked impairment of hepatic functions. AAV-SLU7 infection prevented liver injury and hepatocellular dedifferentiation. Mechanistically we demonstrate a unique role for SLU7 in the preservation of HNF4α1 protein stability through its capacity to protect the liver against oxidative stress. SLU7 is herein identified as a key component of the stress granule proteome, an essential part of the cell's antioxidant machinery. CONCLUSIONS Our results place SLU7 at the highest level of hepatocellular identity control, identifying SLU7 as a link between stress-protective mechanisms and liver differentiation. These findings emphasize the importance of the preservation of hepatic functions in the protection from liver injury.
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Affiliation(s)
| | - Miriam Recalde
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | - Maddalen Jimenez
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | - María Elizalde
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | - María Azkona
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | - Iker Uriarte
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - M Uxue Latasa
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | - Raquel Urtasun
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
| | - Idoia Bilbao
- Hepatology Unit, Clínica Universidad de Navarra, Pamplona, Spain
| | - Bruno Sangro
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Hepatology Unit, Clínica Universidad de Navarra, Pamplona, Spain.,Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Carmen Garcia-Ruiz
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Cell Death and Proliferation, IIBB-CSIC, Barcelona, Spain.,Liver Unit, Hospital Clinic, IDIBAPS and CIBEREHD, Barcelona, Spain
| | - José C Fernandez-Checa
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Cell Death and Proliferation, IIBB-CSIC, Barcelona, Spain.,Liver Unit, Hospital Clinic, IDIBAPS and CIBEREHD, Barcelona, Spain
| | - Fernando J Corrales
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Functional Proteomics Laboratory, National Center for Biotechnology, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Argitxu Esquivel
- Molecular Therapeutics Program, CIMA, University of Navarra, Pamplona, Spain
| | | | - Maite G Fernández-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Matías A Ávila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - María Arechederra
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
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Campbell SA, Stephan TL, Lotto J, Cullum R, Drissler S, Hoodless PA. Signalling pathways and transcriptional regulators orchestrating liver development and cancer. Development 2021; 148:272023. [PMID: 34478514 DOI: 10.1242/dev.199814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Liver development is controlled by key signals and transcription factors that drive cell proliferation, migration, differentiation and functional maturation. In the adult liver, cell maturity can be perturbed by genetic and environmental factors that disrupt hepatic identity and function. Developmental signals and fetal genetic programmes are often dysregulated or reactivated, leading to dedifferentiation and disease. Here, we highlight signalling pathways and transcriptional regulators that drive liver cell development and primary liver cancers. We also discuss emerging models derived from pluripotent stem cells, 3D organoids and bioengineering for improved studies of signalling pathways in liver cancer and regenerative medicine.
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Affiliation(s)
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.,Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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30
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Walsh AD, Johnson LJ, Harvey AJ, Kilpatrick TJ, Binder MD. Identification and Characterisation of cis-Regulatory Elements Upstream of the Human Receptor Tyrosine Kinase Gene MERTK. Brain Plast 2021; 7:3-16. [PMID: 34631417 PMCID: PMC8461731 DOI: 10.3233/bpl-200102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND: MERTK encodes a receptor tyrosine kinase that regulates immune homeostasis via phagocytosis of apoptotic cells and cytokine-mediated immunosuppression. MERTK is highly expressed in the central nervous system (CNS), specifically in myeloid derived innate immune cells and its dysregulation is implicated in CNS pathologies including the autoimmune disease multiple sclerosis (MS). OBJECTIVE: While the cell types and tissues that express MERTK have been well described, the genetic elements that define the gene’s promoter and regulate specific transcription domains remain unknown. The primary objective of this study was to define and characterise the human MERTK promoter region. METHODS: We cloned and characterized the 5’ upstream region of MERTK to identify cis-acting DNA elements that promote gene transcription in luciferase reporter assays. In addition, promoter regions were tested for sensitivity to the anti-inflammatory glucocorticoid dexamethasone. RESULTS: This study identified identified both proximal and distal-acting DNA elements that promote transcription. The strongest promoter activity was identified in an ∼850 bp region situated 3 kb upstream of the MERTK transcription start site. Serial deletions of this putative enhancer revealed that the entire region is essential for expression activity. Using in silico analysis, we identified several candidate transcription factor binding sites. Despite a well-established upregulation of MERTK in response to anti-inflammatory glucocorticoids, no DNA region within the 5 kb putative promoter was found to directly respond to dexamethasone treatment. CONCLUSIONS: Elucidating the genetic mechanisms that regulate MERTK expression gives insights into gene regulation during homeostasis and disease, providing potential targets for therapeutic modulation of MERTK transcription.
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Affiliation(s)
- Alexander D. Walsh
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
| | - Laura J. Johnson
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
| | - Alexandra J. Harvey
- School of BioSciences, University of Melbourne, Parkville, Melbourne, Australia
| | - Trevor J. Kilpatrick
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
- The Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, Melbourne, Australia
| | - Michele D. Binder
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne, Australia
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31
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Tachmatzidi EC, Galanopoulou O, Talianidis I. Transcription Control of Liver Development. Cells 2021; 10:cells10082026. [PMID: 34440795 PMCID: PMC8391549 DOI: 10.3390/cells10082026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023] Open
Abstract
During liver organogenesis, cellular transcriptional profiles are constantly reshaped by the action of hepatic transcriptional regulators, including FoxA1-3, GATA4/6, HNF1α/β, HNF4α, HNF6, OC-2, C/EBPα/β, Hex, and Prox1. These factors are crucial for the activation of hepatic genes that, in the context of compact chromatin, cannot access their targets. The initial opening of highly condensed chromatin is executed by a special class of transcription factors known as pioneer factors. They bind and destabilize highly condensed chromatin and facilitate access to other "non-pioneer" factors. The association of target genes with pioneer and non-pioneer transcription factors takes place long before gene activation. In this way, the underlying gene regulatory regions are marked for future activation. The process is called "bookmarking", which confers transcriptional competence on target genes. Developmental bookmarking is accompanied by a dynamic maturation process, which prepares the genomic loci for stable and efficient transcription. Stable hepatic expression profiles are maintained during development and adulthood by the constant availability of the main regulators. This is achieved by a self-sustaining regulatory network that is established by complex cross-regulatory interactions between the major regulators. This network gradually grows during liver development and provides an epigenetic memory mechanism for safeguarding the optimal expression of the regulators.
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Affiliation(s)
- Evangelia C. Tachmatzidi
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Ourania Galanopoulou
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Iannis Talianidis
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Correspondence:
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32
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Huck I, Morris EM, Thyfault J, Apte U. Hepatocyte-Specific Hepatocyte Nuclear Factor 4 Alpha (HNF4) Deletion Decreases Resting Energy Expenditure by Disrupting Lipid and Carbohydrate Homeostasis. Gene Expr 2021; 20:157-168. [PMID: 33691903 PMCID: PMC8201658 DOI: 10.3727/105221621x16153933463538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hepatocyte nuclear factor 4 alpha (HNF4) is required for hepatocyte differentiation and regulates expression of genes involved in lipid and carbohydrate metabolism including those that control VLDL secretion and gluconeogenesis. Whereas previous studies have focused on specific genes regulated by HNF4 in metabolism, its overall role in whole-body energy utilization has not been studied. In this study, we used indirect calorimetry to determine the effect of hepatocyte-specific HNF4 deletion (HNF4-KO) in mice on whole-body energy expenditure (EE) and substrate utilization in fed, fasted, and high-fat diet (HFD) conditions. HNF4-KO had reduced resting EE during fed conditions and higher rates of carbohydrate oxidation with fasting. HNF4-KO mice exhibited decreased body mass caused by fat mass depletion despite no change in energy intake and evidence of positive energy balance. HNF4-KO mice were able to upregulate lipid oxidation during HFD, suggesting that their metabolic flexibility was intact. However, only hepatocyte-specific HNF4-KO mice exhibited significant reduction in basal metabolic rate and spontaneous activity during HFD. Consistent with previous studies, hepatic gene expression in HNF4-KO supports decreased gluconeogenesis and decreased VLDL export and hepatic -oxidation in HNF4-KO livers across all feeding conditions. Together, our data suggest that deletion of hepatic HNF4 increases dependence on dietary carbohydrates and endogenous lipids for energy during fed and fasted conditions by inhibiting hepatic gluconeogenesis, hepatic lipid export, and intestinal lipid absorption resulting in decreased whole-body energy expenditure. These data clarify the role of hepatic HNF4 on systemic metabolism and energy homeostasis.
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Affiliation(s)
- Ian Huck
- *Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA
| | - E. Matthew Morris
- †Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - John Thyfault
- †Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- ‡Research Service, Kansas City VA Medical Center, Kansas City, KS, USA
| | - Udayan Apte
- *Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA
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33
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Ellero AA, van den Bout I, Vlok M, Cromarty AD, Hurrell T. Continual proteomic divergence of HepG2 cells as a consequence of long-term spheroid culture. Sci Rep 2021; 11:10917. [PMID: 34035320 PMCID: PMC8149451 DOI: 10.1038/s41598-021-89907-9] [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] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/28/2021] [Indexed: 02/04/2023] Open
Abstract
Three-dimensional models are considered a powerful tool for improving the concordance between in vitro and in vivo phenotypes. However, the duration of spheroid culture may influence the degree of correlation between these counterparts. When using immortalised cell lines as model systems, the assumption for consistency and reproducibility is often made without adequate characterization or validation. It is therefore essential to define the biology of each spheroid model by investigating proteomic dynamics, which may be altered relative to culture duration. As an example, we assessed the influence of culture duration on the relative proteome abundance of HepG2 cells cultured as spheroids, which are routinely used to model aspects of the liver. Quantitative proteomic profiling of whole cell lysates labelled with tandem-mass tags was conducted using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In excess of 4800 proteins were confidently identified, which were shared across three consecutive time points over 28 days. The HepG2 spheroid proteome was divergent from the monolayer proteome after 14 days in culture and continued to change over the successive culture time points. Proteins representing the recognised core hepatic proteome, cell junction, extracellular matrix, and cell adhesion proteins were found to be continually modulated.
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Affiliation(s)
- Andrea Antonio Ellero
- Department of Pharmacology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
- Centre for Neuroendocrinology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Iman van den Bout
- Centre for Neuroendocrinology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Physiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Maré Vlok
- Proteomics Unit, Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa
| | - Allan Duncan Cromarty
- Department of Pharmacology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Tracey Hurrell
- Bioengineering and Integrated Genomics Group, Next Generation Health Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa.
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Niborski LL, Paces-Fessy M, Ricci P, Bourgeois A, Magalhães P, Kuzma-Kuzniarska M, Lesaulnier C, Reczko M, Declercq E, Zürbig P, Doucet A, Umbhauer M, Cereghini S. Hnf1b haploinsufficiency differentially affects developmental target genes in a new renal cysts and diabetes mouse model. Dis Model Mech 2021; 14:dmm047498. [PMID: 33737325 PMCID: PMC8126479 DOI: 10.1242/dmm.047498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
Heterozygous mutations in HNF1B cause the complex syndrome renal cysts and diabetes (RCAD), characterized by developmental abnormalities of the kidneys, genital tracts and pancreas, and a variety of renal, pancreas and liver dysfunctions. The pathogenesis underlying this syndrome remains unclear as mice with heterozygous null mutations have no phenotype, while constitutive/conditional Hnf1b ablation leads to more severe phenotypes. We generated a novel mouse model carrying an identified human mutation at the intron-2 splice donor site. Unlike heterozygous mice previously characterized, mice heterozygous for the splicing mutation exhibited decreased HNF1B protein levels and bilateral renal cysts from embryonic day 15, originated from glomeruli, early proximal tubules (PTs) and intermediate nephron segments, concurrently with delayed PT differentiation, hydronephrosis and rare genital tract anomalies. Consistently, mRNA sequencing showed that most downregulated genes in embryonic kidneys were primarily expressed in early PTs and the loop of Henle and involved in ion/drug transport, organic acid and lipid metabolic processes, while the expression of previously identified targets upon Hnf1b ablation, including cystic disease genes, was weakly or not affected. Postnatal analyses revealed renal abnormalities, ranging from glomerular cysts to hydronephrosis and, rarely, multicystic dysplasia. Urinary proteomics uncovered a particular profile predictive of progressive decline in kidney function and fibrosis, and displayed common features with a recently reported urine proteome in an RCAD pediatric cohort. Altogether, our results show that reduced HNF1B levels lead to developmental disease phenotypes associated with the deregulation of a subset of HNF1B targets. They further suggest that this model represents a unique clinical/pathological viable model of the RCAD disease.
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MESH Headings
- Animals
- Animals, Newborn
- Cell Polarity
- Central Nervous System Diseases/genetics
- Central Nervous System Diseases/pathology
- Cilia/pathology
- Dental Enamel/abnormalities
- Dental Enamel/pathology
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/pathology
- Disease Models, Animal
- Embryo, Mammalian/pathology
- Gene Dosage
- Gene Expression Profiling
- Genes, Developmental
- Haploinsufficiency/genetics
- Hepatocyte Nuclear Factor 1-beta/genetics
- Heterozygote
- Humans
- Hydronephrosis/complications
- Kidney Diseases, Cystic/genetics
- Kidney Diseases, Cystic/pathology
- Kidney Glomerulus/pathology
- Kidney Tubules/pathology
- Mice, Inbred C57BL
- Mutation/genetics
- Nephrons/pathology
- RNA Splicing/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Severity of Illness Index
- Mice
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Affiliation(s)
- Leticia L. Niborski
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Mélanie Paces-Fessy
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Pierbruno Ricci
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Adeline Bourgeois
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Pedro Magalhães
- Mosaiques Diagnostics, 30659 Hannover, Germany
- Department of Pediatric Nephrology, Hannover Medical School, 30625 Hannover, Germany
| | - Maria Kuzma-Kuzniarska
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Celine Lesaulnier
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Martin Reczko
- Biomedical Sciences Research Center Alexander Fleming, Institute for Fundamental Biomedical Science, 16672 Athens, Greece
| | - Edwige Declercq
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | | | - Alain Doucet
- Sorbonne Université, Université Paris Descartes, UMRS 1138, CNRS, ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Muriel Umbhauer
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Silvia Cereghini
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
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35
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Chembazhi UV, Bangru S, Hernaez M, Kalsotra A. Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver. Genome Res 2021; 31:576-591. [PMID: 33649154 DOI: 10.1101/2020.05.29.124263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 02/02/2021] [Indexed: 05/24/2023]
Abstract
The adult liver has an exceptional ability to regenerate, but how it maintains its specialized functions during regeneration is unclear. Here, we used partial hepatectomy (PHx) in tandem with single-cell transcriptomics to track cellular transitions and heterogeneities of ∼22,000 liver cells through the initiation, progression, and termination phases of mouse liver regeneration. Our results uncovered that, following PHx, a subset of hepatocytes transiently reactivates an early-postnatal-like gene expression program to proliferate, while a distinct population of metabolically hyperactive cells appears to compensate for any temporary deficits in liver function. Cumulative EdU labeling and immunostaining of metabolic, portal, and central vein-specific markers revealed that hepatocyte proliferation after PHx initiates in the midlobular region before proceeding toward the periportal and pericentral areas. We further demonstrate that portal and central vein proximal hepatocytes retain their metabolically active state to preserve essential liver functions while midlobular cells proliferate nearby. Through combined analysis of gene regulatory networks and cell-cell interaction maps, we found that regenerating hepatocytes redeploy key developmental regulons, which are guided by extensive ligand-receptor-mediated signaling events between hepatocytes and nonparenchymal cells. Altogether, our study offers a detailed blueprint of the intercellular crosstalk and cellular reprogramming that balances the metabolic and proliferative requirements of a regenerating liver.
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Affiliation(s)
- Ullas V Chembazhi
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
- Cancer Center@Illinois, University of Illinois, Urbana, Illinois 61801, USA
| | - Mikel Hernaez
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, 31008 Navarra, Spain
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
- Cancer Center@Illinois, University of Illinois, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
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36
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Wang Z, Zhang Y, Zhang J, Deng Q, Liang H. Controversial roles of hepatocyte nuclear receptor 4 α on tumorigenesis. Oncol Lett 2021; 21:356. [PMID: 33747213 PMCID: PMC7968000 DOI: 10.3892/ol.2021.12617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte nuclear receptor 4 α (HNF4α) is known to be a master transcription regulator of gene expression in multiple biological processes, particularly in liver development and liver function. To date, the function of HNF4α in human cancers has been widely investigated; however, the critical roles of HNF4α in tumorigenesis remain unclear. Numerous controversies exist, even in studies from different research groups but on the same type of cancer. In the present review, the critical roles of HNF4α in tumorigenesis will be summarized and discussed. Furthermore, HNF4α expression profile and alterations will be examined by pan-cancer analysis through bioinformatics, in order to provide a better understanding of the functional roles of this gene in human cancers.
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Affiliation(s)
- Zhu Wang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Ying Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Jianwen Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Qiong Deng
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Hui Liang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
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37
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Relative DNA Methylation and Demethylation Efficiencies during Postnatal Liver Development Regulate Hepatitis B Virus Biosynthesis. J Virol 2021; 95:JVI.02148-20. [PMID: 33361417 DOI: 10.1128/jvi.02148-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) transcription and replication increase progressively throughout postnatal liver development with maximal viral biosynthesis occurring at around 4 weeks of age in the HBV transgenic mouse model of chronic infection. Increasing viral biosynthesis is associated with a corresponding progressive loss of DNA methylation. The loss of DNA methylation is associated with increasing levels of 5-hydroxymethylcytosine (5hmC) residues which correlate with increased liver-enriched pioneer transcription factor Forkhead box protein A (FoxA) RNA levels, a rapid decline in postnatal liver DNA methyltransferase (Dnmt) transcripts, and a very modest reduction in ten-eleven translocation (Tet) methylcytosine dioxygenase expression. These observations are consistent with the suggestion that the balance between active HBV DNA methylation and demethylation is regulated by FoxA recruitment of Tet in the presence of declining Dnmt activity. These changes lead to demethylation of the viral genome during hepatocyte maturation with associated increases in viral biosynthesis. Consequently, manipulation of the relative activities of these two counterbalancing processes might permit the specific silencing of HBV gene expression with the loss of viral biosynthesis and the resolution of chronic HBV infections.IMPORTANCE HBV biosynthesis begins at birth and increases during early postnatal liver development in the HBV transgenic mouse model of chronic infection. The levels of viral RNA and DNA synthesis correlate with pioneer transcription factor FoxA transcript plus Tet methylcytosine dioxygenase-generated 5hmC abundance but inversely with Dnmt transcript levels and HBV DNA methylation. Together, these findings suggest that HBV DNA methylation during neonatal liver development is actively modulated by the relative contributions of FoxA-recruited Tet-mediated DNA demethylation and Dnmt-mediated DNA methylation activities. This mode of gene regulation, mediated by the loss of DNA methylation at hepatocyte-specific viral and cellular promoters, likely contributes to hepatocyte maturation during liver development in addition to the postnatal activation of HBV transcription and replication.
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38
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Zhan X, Zhao A. Transcription factor FOXA3 promotes the development of Hepatoblastoma via regulating HNF1A, AFP, and ZFHX3 expression. J Clin Lab Anal 2020; 35:e23686. [PMID: 33368532 PMCID: PMC7957975 DOI: 10.1002/jcla.23686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/19/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
Objective In this research paper, we aimed to study the role of FOXA3 in hepatoblastoma (HB) and the molecular mechanism. Methods Immunohistochemistry was applied to determine the expression situation of FOXA3 and AFP in HB tissues and the adjacent normal tissues. FOXA3, HNF1A, and ZFHX3 expressions in HB tissues and the normal tissues were measured by Western blot. HB cell lines were randomly divided into 4 groups: Model, si‐NC, si‐FOXA3‐1, and si‐FOXA3‐2 group. The HB cell viability and colony formation characteristics in the 4 groups were explored by CCK‐8 and cell cloning formation assay, respectively. The expression of FOXA3, AFP, HNF1A, ZFHX3, and MYC in HB cells after knockdown of FOXA3 was measured. Results FOXA3, AFP, and HNF1A expressions were significantly up‐regulated in HB tissues, while ZFHX3 expression was down‐regulated. Knockdown of FOXA3 markedly inhibited HB cell viability and cloning formation ability. Knockdown of FOXA3 decreased FOXA3, AFP, and HNF1A/MYC expression, while increased ZFHX3 expression. Conclusion FOXA3 promotes the occurrence and development of HB by up‐regulating AFP and HNF1A/MYC expression, and down‐regulating ZFHX3 expression.
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Affiliation(s)
- Xiaoyun Zhan
- Department of Childhood Hematology, Maternal and Child Hospital of Hubei province, Tongji Medical College Huazhong University of Science and Technology, Wuhan, China
| | - Alan Zhao
- Department of Childhood Hematology, Maternal and Child Hospital of Hubei province, Tongji Medical College Huazhong University of Science and Technology, Wuhan, China
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39
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Freeburg SH, Goessling W. Hepatobiliary Differentiation: Principles from Embryonic Liver Development. Semin Liver Dis 2020; 40:365-372. [PMID: 32526786 DOI: 10.1055/s-0040-1709679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Hepatocytes and biliary epithelial cells (BECs), the two endodermal cell types of the liver, originate from progenitor cells called hepatoblasts. Based principally on in vitro data, hepatoblasts are thought to be bipotent stem cells with the potential to produce both hepatocytes and BECs. However, robust in vivo evidence for this model has only recently emerged. We examine the molecular mechanisms that stimulate hepatoblast differentiation into hepatocytes or BECs. In the absence of extrinsic cues, the default fate of hepatoblasts is hepatocyte differentiation. Inductive cues from the hepatic portal vein, however, initiate transcription factor expression in hepatoblasts, driving biliary specification. Defining the mechanisms of hepatobiliary differentiation provides important insights into congenital disorders, such as Alagille syndrome, and may help to better characterize the poorly understood hepatic lineage relationships observed during regeneration from liver injury.
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Affiliation(s)
- Scott H Freeburg
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Wolfram Goessling
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Stem Cell Institute, Cambridge, Massachusetts.,Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard-MIT Division of Health Science and Technology, Cambridge, Massachusetts.,Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts
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40
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Winters SJ, Scoggins CR, Appiah D, Ghooray DT. The hepatic lipidome and HNF4α and SHBG expression in human liver. Endocr Connect 2020; 9:1009-1018. [PMID: 33064664 PMCID: PMC7576643 DOI: 10.1530/ec-20-0401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/16/2020] [Indexed: 01/14/2023]
Abstract
Low plasma levels of sex hormone-binding globulin (SHBG) are a marker for obesity, insulin resistance, non-alcoholic fatty liver disease (NAFLD) and type 2 diabetes. The transcription factor HNF4α is a major determinant of hepatic SHBG expression and thereby serum SHBG levels, and mediates in part the association of low SHBG with hyperinsulinemia and hepatic steatosis. We analyzed the lipidome in human liver specimens from a cohort of patients who underwent hepatic resection as a treatment for cancer, providing insight into hepatic lipids in those without extreme obesity or the clinical diagnosis of NAFLD or non-alcoholic steatohepatitis. Both steatosis and high HOMA-IR were associated with higher levels of saturated and unsaturated FA, other than arachidonic, with the most dramatic rise in 18:1 oleate, consistent with increased stearoyl-CoA desaturase activity. Individuals with low HOMA-IR had low levels of total hepatic fatty acids, while both low and high fatty acid levels characterized the high HOMA-IR group. Both insulin resistance and high levels of hepatic fat were associated with low expression levels of HNF4α and thereby SHBG, but the expression of these genes was also low in the absence of these determinants, implying additional regulatory mechanisms that remain to be determined. The relationship of all FA studied to HNFα and SHBG mRNAs was inverse, and similar to that for total triglyceride concentrations, irrespective of chain length and saturation vs unsaturation.
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Affiliation(s)
- Stephen J Winters
- Division of Endocrinology, Metabolism and Diabetes, University of Louisville, Louisville, Kentucky, USA
- Correspondence should be addressed to S J Winters:
| | - Charles R Scoggins
- Division of Surgical Oncology, University of Louisville, Louisville, Kentucky, USA
| | - Duke Appiah
- Department of Public Health, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Dushan T Ghooray
- Division of Endocrinology, Metabolism and Diabetes, University of Louisville, Louisville, Kentucky, USA
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41
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Control of Cell Identity by the Nuclear Receptor HNF4 in Organ Pathophysiology. Cells 2020; 9:cells9102185. [PMID: 32998360 PMCID: PMC7600215 DOI: 10.3390/cells9102185] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatocyte Nuclear Factor 4 (HNF4) is a transcription factor (TF) belonging to the nuclear receptor family whose expression and activities are restricted to a limited number of organs including the liver and gastrointestinal tract. In this review, we present robust evidence pointing to HNF4 as a master regulator of cellular differentiation during development and a safekeeper of acquired cell identity in adult organs. Importantly, we discuss that transient loss of HNF4 may represent a protective mechanism upon acute organ injury, while prolonged impairment of HNF4 activities could contribute to organ dysfunction. In this context, we describe in detail mechanisms involved in the pathophysiological control of cell identity by HNF4, including how HNF4 works as part of cell-specific TF networks and how its expression/activities are disrupted in injured organs.
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42
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Reizel Y, Morgan A, Gao L, Lan Y, Manduchi E, Waite EL, Wang AW, Wells A, Kaestner KH. Collapse of the hepatic gene regulatory network in the absence of FoxA factors. Genes Dev 2020; 34:1039-1050. [PMID: 32561546 PMCID: PMC7397852 DOI: 10.1101/gad.337691.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022]
Abstract
Here, Reizel et al. investigated the FoxA factor's role in maintaining the regulatory network needed for liver development, and ablated all FoxA genes in the adult mouse liver. They found that loss of FoxA caused rapid and massive reduction in the expression of critical liver genes, and that FoxA proteins are be required for maintaining enhancer activity, chromatin accessibility, nucleosome positioning, and binding of HNF4α. The FoxA transcription factors are critical for liver development through their pioneering activity, which initiates a highly complex regulatory network thought to become progressively resistant to the loss of any individual hepatic transcription factor via mutual redundancy. To investigate the dispensability of FoxA factors for maintaining this regulatory network, we ablated all FoxA genes in the adult mouse liver. Remarkably, loss of FoxA caused rapid and massive reduction in the expression of critical liver genes. Activity of these genes was reduced back to the low levels of the fetal prehepatic endoderm stage, leading to necrosis and lethality within days. Mechanistically, we found FoxA proteins to be required for maintaining enhancer activity, chromatin accessibility, nucleosome positioning, and binding of HNF4α. Thus, the FoxA factors act continuously, guarding hepatic enhancer activity throughout adult life.
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Affiliation(s)
- Yitzhak Reizel
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ashleigh Morgan
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Long Gao
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yemin Lan
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Elisabetta Manduchi
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eric L Waite
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Amber W Wang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew Wells
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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43
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Pastore N, Huynh T, Herz NJ, Calcagni' A, Klisch TJ, Brunetti L, Kim KH, De Giorgi M, Hurley A, Carissimo A, Mutarelli M, Aleksieva N, D'Orsi L, Lagor WR, Moore DD, Settembre C, Finegold MJ, Forbes SJ, Ballabio A. TFEB regulates murine liver cell fate during development and regeneration. Nat Commun 2020; 11:2461. [PMID: 32424153 PMCID: PMC7235048 DOI: 10.1038/s41467-020-16300-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/20/2020] [Indexed: 12/29/2022] Open
Abstract
It is well established that pluripotent stem cells in fetal and postnatal liver (LPCs) can differentiate into both hepatocytes and cholangiocytes. However, the signaling pathways implicated in the differentiation of LPCs are still incompletely understood. Transcription Factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy, is known to be involved in osteoblast and myeloid differentiation, but its role in lineage commitment in the liver has not been investigated. Here we show that during development and upon regeneration TFEB drives the differentiation status of murine LPCs into the progenitor/cholangiocyte lineage while inhibiting hepatocyte differentiation. Genetic interaction studies show that Sox9, a marker of precursor and biliary cells, is a direct transcriptional target of TFEB and a primary mediator of its effects on liver cell fate. In summary, our findings identify an unexplored pathway that controls liver cell lineage commitment and whose dysregulation may play a role in biliary cancer.
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Affiliation(s)
- Nunzia Pastore
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Tuong Huynh
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Niculin J Herz
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alessia Calcagni'
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tiemo J Klisch
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kangho Ho Kim
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marco De Giorgi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ayrea Hurley
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, 80078, Italy
| | | | - Niya Aleksieva
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Luca D'Orsi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, 80078, Italy
| | - William R Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David D Moore
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, 80078, Italy
- Department of Translational Medicine, Medical Genetics, Federico II University, Naples, 80131, Italy
| | - Milton J Finegold
- Department of Pathology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Stuart J Forbes
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Andrea Ballabio
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, 80078, Italy.
- Department of Translational Medicine, Medical Genetics, Federico II University, Naples, 80131, Italy.
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44
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Dubois V, Gheeraert C, Vankrunkelsven W, Dubois‐Chevalier J, Dehondt H, Bobowski‐Gerard M, Vinod M, Zummo FP, Güiza F, Ploton M, Dorchies E, Pineau L, Boulinguiez A, Vallez E, Woitrain E, Baugé E, Lalloyer F, Duhem C, Rabhi N, van Kesteren RE, Chiang C, Lancel S, Duez H, Annicotte J, Paumelle R, Vanhorebeek I, Van den Berghe G, Staels B, Lefebvre P, Eeckhoute J. Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver. Mol Syst Biol 2020; 16:e9156. [PMID: 32407006 PMCID: PMC7224309 DOI: 10.15252/msb.20199156] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023] Open
Abstract
Liver injury triggers adaptive remodeling of the hepatic transcriptome for repair/regeneration. We demonstrate that this involves particularly profound transcriptomic alterations where acute induction of genes involved in handling of endoplasmic reticulum stress (ERS) is accompanied by partial hepatic dedifferentiation. Importantly, widespread hepatic gene downregulation could not simply be ascribed to cofactor squelching secondary to ERS gene induction, but rather involves a combination of active repressive mechanisms. ERS acts through inhibition of the liver-identity (LIVER-ID) transcription factor (TF) network, initiated by rapid LIVER-ID TF protein loss. In addition, induction of the transcriptional repressor NFIL3 further contributes to LIVER-ID gene repression. Alteration to the liver TF repertoire translates into compromised activity of regulatory regions characterized by the densest co-recruitment of LIVER-ID TFs and decommissioning of BRD4 super-enhancers driving hepatic identity. While transient repression of the hepatic molecular identity is an intrinsic part of liver repair, sustained disequilibrium between the ERS and LIVER-ID transcriptional programs is linked to liver dysfunction as shown using mouse models of acute liver injury and livers from deceased human septic patients.
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Affiliation(s)
- Vanessa Dubois
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
- Present address:
Clinical and Experimental EndocrinologyDepartment of Chronic Diseases, Metabolism and Ageing (CHROMETA)KU LeuvenLeuvenBelgium
| | - Céline Gheeraert
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Wouter Vankrunkelsven
- Clinical Division and Laboratory of Intensive Care MedicineDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | | | - Hélène Dehondt
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | | | - Manjula Vinod
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | | | - Fabian Güiza
- Clinical Division and Laboratory of Intensive Care MedicineDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Maheul Ploton
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Emilie Dorchies
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Laurent Pineau
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Alexis Boulinguiez
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Emmanuelle Vallez
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Eloise Woitrain
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Eric Baugé
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Fanny Lalloyer
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Christian Duhem
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Nabil Rabhi
- UMR 8199 ‐ EGIDCNRSInstitut Pasteur de LilleUniversity of LilleLilleFrance
| | - Ronald E van Kesteren
- Center for Neurogenomics and Cognitive ResearchNeuroscience Campus AmsterdamVU UniversityAmsterdamThe Netherlands
| | - Cheng‐Ming Chiang
- Simmons Comprehensive Cancer CenterDepartments of Biochemistry and PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Steve Lancel
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Hélène Duez
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | | | - Réjane Paumelle
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Ilse Vanhorebeek
- Clinical Division and Laboratory of Intensive Care MedicineDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Greet Van den Berghe
- Clinical Division and Laboratory of Intensive Care MedicineDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Bart Staels
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Philippe Lefebvre
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
| | - Jérôme Eeckhoute
- Inserm, CHU LilleInstitut Pasteur de LilleU1011‐EGIDUniversity of LilleLilleFrance
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45
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Karagianni P, Moulos P, Schmidt D, Odom DT, Talianidis I. Bookmarking by Non-pioneer Transcription Factors during Liver Development Establishes Competence for Future Gene Activation. Cell Rep 2020; 30:1319-1328.e6. [PMID: 32023452 PMCID: PMC7003066 DOI: 10.1016/j.celrep.2020.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/02/2019] [Accepted: 12/31/2019] [Indexed: 01/01/2023] Open
Abstract
Transcription factor binding to enhancer and promoter regions critical for homeostatic adult gene activation is established during development. To understand how cell-specific gene expression patterns are generated, we study the developmental timing of association of two prominent hepatic transcription factors with gene regulatory regions. Most individual binding events display extraordinarily high temporal variations during liver development. Early and persistent binding is necessary, but not sufficient, for gene activation. Stable gene expression patterns are the result of combinatorial activity of multiple transcription factors, which mark regulatory regions long before activation and promote progressive broadening of active chromatin domains. Both temporally stable and dynamic, short-lived binding events contribute to the developmental maturation of active promoter configurations. The results reveal a developmental bookmarking function of master regulators and illuminate remarkable parallels between the principles employed for gene activation during development, during evolution, and upon mitotic exit.
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Affiliation(s)
- Panagiota Karagianni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Herakleion, Crete, Greece; Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece
| | - Panagiotis Moulos
- Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece
| | - Dominic Schmidt
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Duncan T Odom
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Iannis Talianidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Herakleion, Crete, Greece.
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46
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Cebola I. Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1480. [PMID: 32020788 DOI: 10.1002/wsbm.1480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
Metabolic diseases such as nonalcoholic fatty liver disease (NAFLD) result from complex interactions between intrinsic and extrinsic factors, including genetics and exposure to obesogenic environments. These risk factors converge in aberrant gene expression patterns in the liver, which are underlined by altered cis-regulatory networks. In homeostasis and in disease states, liver cis-regulatory networks are established by coordinated action of liver-enriched transcription factors (TFs), which define enhancer landscapes, activating broad gene programs with spatiotemporal resolution. Recent advances in DNA sequencing have dramatically expanded our ability to map active transcripts, enhancers and TF cistromes, and to define the 3D chromatin topology that contains these elements. Deployment of these technologies has allowed investigation of the molecular processes that regulate liver development and metabolic homeostasis. Moreover, genomic studies of NAFLD patients and NAFLD models have demonstrated that the liver undergoes pervasive regulatory rewiring in NAFLD, which is reflected by aberrant gene expression profiles. We have therefore achieved an unprecedented level of detail in the understanding of liver cis-regulatory networks, particularly in physiological conditions. Future studies should aim to map active regulatory elements with added levels of resolution, addressing how the chromatin landscapes of different cell lineages contribute to and are altered in NAFLD and NAFLD-associated metabolic states. Such efforts would provide additional clues into the molecular factors that trigger this disease. This article is categorized under: Biological Mechanisms > Metabolism Biological Mechanisms > Regulatory Biology Laboratory Methods and Technologies > Genetic/Genomic Methods.
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Affiliation(s)
- Inês Cebola
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, UK
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47
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Yu Y, Li M, Song Y, Xu J, Qi F. Overexpression of long noncoding RNA CUDR promotes hepatic differentiation of human umbilical cord mesenchymal stem cells. Mol Med Rep 2019; 21:1051-1058. [PMID: 31894319 PMCID: PMC7003026 DOI: 10.3892/mmr.2019.10897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 10/23/2019] [Indexed: 11/10/2022] Open
Abstract
Previous studies have shown that long noncoding RNAs (lncRNAs) are capable of regulating cell differentiation and pluripotency. The objective of the present study was to explore the effect of lncRNA cancer upregulated drug resistant (CUDR) on the hepatic differentiation of human umbilical cord mesenchymal stem cells (HuMSCs). HuMSCs were subjected to a hepatogenic differentiation protocol. The level of CUDR was monitored by reverse transcription-quantitative PCR (RT-qPCR) following certain stages of hepatic differentiation. Lentivirus transfection was used to achieve CUDR overexpression. The hepatocyte-related proteins and mRNAs were then examined by immunofluorescence, ELISA and RT-qPCR analyses. The results showed that CUDR was upregulated during the hepatic differentiation of HuMSCs. Upregulation of CUDR can improve hepatic differentiation of HuMSCs, including hepatocyte-related genes and proteins. In addition, it was also found that liver-enriched transcription factors were upregulated after CUDR overexpression. Moreover, there was an association between the Wnt/β-catenin pathway and CUDR. In summary, these results demonstrated that the overexpression of CUDR could improve the hepatic differentiation of HuMSCs, therefore it could be an ideal source for regenerative therapy.
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Affiliation(s)
- Yabin Yu
- Department of Hepatobiliary Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu 223300, P.R. China
| | - Meng Li
- Department of Pathology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Yan Song
- Department of Hepatobiliary Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu 223300, P.R. China
| | - Jianbo Xu
- Department of Hepatobiliary Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu 223300, P.R. China
| | - Fuzhen Qi
- Department of Hepatobiliary Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu 223300, P.R. China
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48
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Chemically-Defined, Xeno-Free, Scalable Production of hPSC-Derived Definitive Endoderm Aggregates with Multi-Lineage Differentiation Potential. Cells 2019; 8:cells8121571. [PMID: 31817235 PMCID: PMC6953099 DOI: 10.3390/cells8121571] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/30/2022] Open
Abstract
For the production and bio-banking of differentiated derivatives from human pluripotent stem cells (hPSCs) in large quantities for drug screening and cellular therapies, well-defined and robust procedures for differentiation and cryopreservation are required. Definitive endoderm (DE) gives rise to respiratory and digestive epithelium, as well as thyroid, thymus, liver, and pancreas. Here, we present a scalable, universal process for the generation of DE from human-induced pluripotent stem cells (hiPSCs) and embryonic stem cells (hESCs). Optimal control during the differentiation process was attained in chemically-defined and xeno-free suspension culture, and high flexibility of the workflow was achieved by the introduction of an efficient cryopreservation step at the end of DE differentiation. DE aggregates were capable of differentiating into hepatic-like, pancreatic, intestinal, and lung progenitor cells. Scale-up of the differentiation process using stirred-tank bioreactors enabled production of large quantities of DE aggregates. This process provides a useful advance for versatile applications of DE lineages, in particular for cell therapies and drug screening.
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49
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Oropeza CE, Tarnow G, Sridhar A, Taha TY, Shalaby RE, McLachlan A. The Regulation of HBV Transcription and Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1179:39-69. [PMID: 31741333 DOI: 10.1007/978-981-13-9151-4_3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hepatitis B virus (HBV) is a major human pathogen lacking a reliable curative therapy. Current therapeutics target the viral reverse transcriptase/DNA polymerase to inhibit viral replication but generally fail to resolve chronic HBV infections. Due to the limited coding potential of the HBV genome, alternative approaches for the treatment of chronic infections are desperately needed. An alternative approach to the development of antiviral therapeutics is to target cellular gene products that are critical to the viral life cycle. As transcription of the viral genome is an essential step in the viral life cycle, the selective inhibition of viral RNA synthesis is a possible approach for the development of additional therapeutic modalities that might be used in combination with currently available therapies. To address this possibility, a molecular understanding of the relationship between viral transcription and replication is required. The first step is to identify the transcription factors that are the most critical in controlling the levels of HBV RNA synthesis and to determine their in vivo role in viral biosynthesis. Mapping studies in cell culture utilizing reporter gene constructs permitted the identification of both ubiquitous and liver-enriched transcription factors capable of modulating transcription from the four HBV promoters. However, it was challenging to determine their relative importance for viral biosynthesis in the available human hepatoma replication systems. This technical limitation was addressed, in part, by the development of non-hepatoma HBV replication systems where viral biosynthesis was dependent on complementation with exogenously expressed transcription factors. These systems revealed the importance of specific nuclear receptors and hepatocyte nuclear factor 3 (HNF3)/forkhead box A (FoxA) transcription factors for HBV biosynthesis. Furthermore, using the HBV transgenic mouse model of chronic viral infection, the importance of various nuclear receptors and FoxA isoforms could be established in vivo. The availability of this combination of systems now permits a rational approach toward the development of selective host transcription factor inhibitors. This might permit the development of a new class of therapeutics to aid in the treatment and resolution of chronic HBV infections, which currently affects approximately 1 in 30 individuals worldwide and kills up to a million people annually.
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Affiliation(s)
- Claudia E Oropeza
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Grant Tarnow
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Abhayavarshini Sridhar
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Taha Y Taha
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Rasha E Shalaby
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.,Department of Microbiology and Immunology, Faculty of Medicine, Tanta University, Egypt, Egypt
| | - Alan McLachlan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
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50
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Wolke C, Gürtler S, Peter D, Weingärtner J, Domanska G, Lendeckel U, Schild L. Vitamin B6 deficiency in new born rats affects hepatic cardiolipin composition and oxidative phosphorylation. Exp Biol Med (Maywood) 2019; 244:1619-1628. [PMID: 31752529 DOI: 10.1177/1535370219889880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Vitamin B6 deficiency during pregnancy translates into a severe vitamin B6 deficiency (plasma levels decreased by 97%) in new-born rats. Further, hallmarks are increased (+89%) concentrations of homocysteine, gross changes in gene methylation and expression, and metabolic alterations including lipid metabolism. This study focuses on determining the effects of vitamin B6-deficiency on cardiolipin composition and oxidative phosphorylation in liver. For this purpose, hepatic cardiolipin composition was analyzed by means of LC/MS/MS, and mitochondrial oxygen consumption was determined by using a Clark-type electrode in a rat model of vitamin B6 deficiency. Liver mitochondria from new-born rats with pre-term vitamin B6 deficiency responded with substantial alterations in cardiolipin composition that include the following changes in the amounts of cardiolipin incorporated fatty acids: increase in C16, decrease in C18, decrease in saturated fatty acid, as well as increase in amount of oxidized cardiolipin species. These changes were accompanied by significantly decreased capacity of oxidative phosphorylation. In conclusion, vitamin B6 deficiency in new born rats induces massive alterations of cardiolipin composition and function of liver mitochondria. These findings support the importance of sufficient periconceptional supply of vitamin B6 to prevent vitamin B6 deficiency.Impact statementVitamin B6 (VitB6) is an active co-enzyme for more than 150 enzymes and is required for a great diversity of biosynthesis and metabolic reactions. There is an increased need for VitB6 during pregnancy and sufficient supply of VitB6 is crucial for the prevention of cleft palate and neural tube defects. We show that liver mitochondria from new-born rats with pre-term VitB6 deficiency respond with substantial alterations in cardiolipin (CL) composition and in the amount of oxidized CL species. These changes are associated with a decrease in the efficiency of oxidative phosphorylation. The results of this study support the significance of sufficient supply of VitB6 during pregnancy (and periconceptional) for diminishing the number of early abortions and minimizing malformation. The established link between VitB6 deficiency, CL composition, and mitochondrial respiration/energy production provides mechanistic insight as to how the VitB6 deficiency translates into the known pathophysiological and clinically relevant conditions.
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Affiliation(s)
- Carmen Wolke
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald D-17475, Germany
| | - Sarah Gürtler
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald D-17475, Germany
| | - Daniela Peter
- Department of Pathological Biochemistry, Otto-von-Guericke University Magdeburg, Magdeburg D-39120, Germany
| | - Jens Weingärtner
- Institute of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald D-17489, Germany
| | - Grazyna Domanska
- Institute of Immunology, University Medicine Greifswald, Greifswald D-17475, Germany
| | - Uwe Lendeckel
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald D-17475, Germany
| | - Lorenz Schild
- Department of Pathological Biochemistry, Otto-von-Guericke University Magdeburg, Magdeburg D-39120, Germany
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