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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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2
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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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3
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Meadows V, Yang Z, Basaly V, Guo GL. FXR Friend-ChIPs in the Enterohepatic System. Semin Liver Dis 2023; 43:267-278. [PMID: 37442156 PMCID: PMC10620036 DOI: 10.1055/a-2128-5538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Chronic liver diseases encompass a wide spectrum of hepatic maladies that often result in cholestasis or altered bile acid secretion and regulation. Incidence and cost of care for many chronic liver diseases are rising in the United States with few Food and Drug Administration-approved drugs available for patient treatment. Farnesoid X receptor (FXR) is the master regulator of bile acid homeostasis with an important role in lipid and glucose metabolism and inflammation. FXR has served as an attractive target for management of cholestasis and fibrosis; however, global FXR agonism results in adverse effects in liver disease patients, severely affecting quality of life. In this review, we highlight seminal studies and recent updates on the FXR proteome and identify gaps in knowledge that are essential for tissue-specific FXR modulation. In conclusion, one of the greatest unmet needs in the field is understanding the underlying mechanism of intestinal versus hepatic FXR function.
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Affiliation(s)
- Vik Meadows
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
| | - Zhenning Yang
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
| | - Veronia Basaly
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
- Department of Veterans Affairs, New Jersey Health Care System, East Orange, New Jersey
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4
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Bingham MA, Neijman K, Yang CR, Aponte A, Mak A, Kikuchi H, Jung HJ, Poll BG, Raghuram V, Park E, Chou CL, Chen L, Leipziger J, Knepper MA, Dona M. Circadian gene expression in mouse renal proximal tubule. Am J Physiol Renal Physiol 2023; 324:F301-F314. [PMID: 36727945 PMCID: PMC9988533 DOI: 10.1152/ajprenal.00231.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Circadian variability in kidney function is well recognized but is often ignored as a potential confounding variable in physiological experiments. Here, we have created a data resource consisting of expression levels for mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. Small-sample RNA sequencing was applied to microdissected S1 proximal convoluted tubules and S2 proximal straight tubules. After stringent filtering, the data were analyzed using JTK-Cycle to detect periodicity. The data set is provided as a user-friendly webpage at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox2/. In proximal convoluted tubules, 234 transcripts varied in a circadian manner (4.0% of the total). In proximal straight tubules, 334 transcripts varied in a circadian manner (5.3%). Transcripts previously known to be associated with corticosteroid action and with increased flow were found to be overrepresented among circadian transcripts peaking during the "dark" portion of the day [zeitgeber time (ZT)14-22], corresponding to peak levels of corticosterone and glomerular filtration rate in mice. To ask whether there is a time-of-day dependence of protein abundances in the kidney, we carried out LC-MS/MS-based proteomics in whole mouse kidneys at ZT12 and ZT0. The full data set (n = 6,546 proteins) is available at https://esbl.nhlbi.nih.gov/Databases/Circadian-Proteome/. Overall, 293 proteins were differentially expressed between ZT12 and ZT0 (197 proteins greater at ZT12 and 96 proteins greater at ZT0). Among the regulated proteins, only nine proteins were found to be periodic in the RNA-sequencing analysis, suggesting a high level of posttranscriptional regulation of protein abundances.NEW & NOTEWORTHY Circadian variation in gene expression can be an important determinant in the regulation of kidney function. The authors used RNA-sequencing transcriptomics and LC-MS/MS-based proteomics to identify gene products expressed in a periodic manner. The data were used to construct user-friendly web resources.
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Affiliation(s)
- Molly A Bingham
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Kim Neijman
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Chin-Rang Yang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Angel Aponte
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Angela Mak
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hiroaki Kikuchi
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hyun Jun Jung
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Brian G Poll
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Viswanathan Raghuram
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Euijung Park
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Chung-Lin Chou
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Lihe Chen
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Jens Leipziger
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - Mark A Knepper
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Margo Dona
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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5
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Yang G, Jena PK, Hu Y, Sheng L, Chen SY, Slupsky CM, Davis R, Tepper CG, Wan YJY. The essential roles of FXR in diet and age influenced metabolic changes and liver disease development: a multi-omics study. Biomark Res 2023; 11:20. [PMID: 36803569 PMCID: PMC9938992 DOI: 10.1186/s40364-023-00458-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/24/2023] [Indexed: 02/20/2023] Open
Abstract
BACKGROUND Aging and diet are risks for metabolic diseases. Bile acid receptor farnesoid X receptor (FXR) knockout (KO) mice develop metabolic liver diseases that progress into cancer as they age, which is accelerated by Western diet (WD) intake. The current study uncovers the molecular signatures for diet and age-linked metabolic liver disease development in an FXR-dependent manner. METHODS Wild-type (WT) and FXR KO male mice, either on a healthy control diet (CD) or a WD, were euthanized at the ages of 5, 10, or 15 months. Hepatic transcriptomics, liver, serum, and urine metabolomics as well as microbiota were profiled. RESULTS WD intake facilitated hepatic aging in WT mice. In an FXR-dependent manner, increased inflammation and reduced oxidative phosphorylation were the primary pathways affected by WD and aging. FXR has a role in modulating inflammation and B cell-mediated humoral immunity which was enhanced by aging. Moreover, FXR dictated neuron differentiation, muscle contraction, and cytoskeleton organization in addition to metabolism. There were 654 transcripts commonly altered by diets, ages, and FXR KO, and 76 of them were differentially expressed in human hepatocellular carcinoma (HCC) and healthy livers. Urine metabolites differentiated dietary effects in both genotypes, and serum metabolites clearly separated ages irrespective of diets. Aging and FXR KO commonly affected amino acid metabolism and TCA cycle. Moreover, FXR is essential for colonization of age-related gut microbes. Integrated analyses uncovered metabolites and bacteria linked with hepatic transcripts affected by WD intake, aging, and FXR KO as well as related to HCC patient survival. CONCLUSION FXR is a target to prevent diet or age-associated metabolic disease. The uncovered metabolites and microbes can be diagnostic markers for metabolic disease.
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Affiliation(s)
- Guiyan Yang
- grid.27860.3b0000 0004 1936 9684Department of Pathology and Laboratory Medicine, University of California, Davis Health. Room 3400B, Research Building III, 4645 2nd Ave, Sacramento, CA 95817 USA
| | - Prasant K. Jena
- grid.27860.3b0000 0004 1936 9684Department of Pathology and Laboratory Medicine, University of California, Davis Health. Room 3400B, Research Building III, 4645 2nd Ave, Sacramento, CA 95817 USA
| | - Ying Hu
- grid.27860.3b0000 0004 1936 9684Department of Pathology and Laboratory Medicine, University of California, Davis Health. Room 3400B, Research Building III, 4645 2nd Ave, Sacramento, CA 95817 USA
| | - Lili Sheng
- grid.27860.3b0000 0004 1936 9684Department of Pathology and Laboratory Medicine, University of California, Davis Health. Room 3400B, Research Building III, 4645 2nd Ave, Sacramento, CA 95817 USA
| | - Shin-Yu Chen
- grid.27860.3b0000 0004 1936 9684Department of Nutrition, University of California, Davis, CA USA
| | - Carolyn M. Slupsky
- grid.27860.3b0000 0004 1936 9684Department of Nutrition, University of California, Davis, CA USA
| | - Ryan Davis
- grid.27860.3b0000 0004 1936 9684Department of Pathology and Laboratory Medicine, University of California, Davis Health. Room 3400B, Research Building III, 4645 2nd Ave, Sacramento, CA 95817 USA
| | - Clifford G. Tepper
- grid.27860.3b0000 0004 1936 9684Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA USA
| | - Yu-Jui Yvonne Wan
- Department of Pathology and Laboratory Medicine, University of California, Davis Health. Room 3400B, Research Building III, 4645 2nd Ave, Sacramento, CA, 95817, USA.
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6
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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: 23] [Impact Index Per Article: 23.0] [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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7
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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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8
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Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis. Nat Commun 2022; 13:5324. [PMID: 36088459 PMCID: PMC9464213 DOI: 10.1038/s41467-022-33063-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
Tissue injury triggers activation of mesenchymal lineage cells into wound-repairing myofibroblasts, whose unrestrained activity leads to fibrosis. Although this process is largely controlled at the transcriptional level, whether the main transcription factors involved have all been identified has remained elusive. Here, we report multi-omics analyses unraveling Basonuclin 2 (BNC2) as a myofibroblast identity transcription factor. Using liver fibrosis as a model for in-depth investigations, we first show that BNC2 expression is induced in both mouse and human fibrotic livers from different etiologies and decreases upon human liver fibrosis regression. Importantly, we found that BNC2 transcriptional induction is a specific feature of myofibroblastic activation in fibrotic tissues. Mechanistically, BNC2 expression and activities allow to integrate pro-fibrotic stimuli, including TGFβ and Hippo/YAP1 signaling, towards induction of matrisome genes such as those encoding type I collagen. As a consequence, Bnc2 deficiency blunts collagen deposition in livers of mice fed a fibrogenic diet. Additionally, our work establishes BNC2 as potentially druggable since we identified the thalidomide derivative CC-885 as a BNC2 inhibitor. Altogether, we propose that BNC2 is a transcription factor involved in canonical pathways driving myofibroblastic activation in fibrosis. Myofibroblasts contribute to the development of liver fibrosis. Here, the authors report that the transcription factor Basonuclin 2 (BNC2) integrates fibrogenic signals and drives myofibroblastic transcriptional activation in liver fibrosis.
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9
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Salbert G, Sérandour AA, Staels B, Lefebvre P, Eeckhoute J. The conundrum of the functional relationship between transcription factors and chromatin. Epigenomics 2022; 14:223-225. [PMID: 35034474 DOI: 10.2217/epi-2021-0509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Gilles Salbert
- Université de Rennes 1, UMR6290 CNRS, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042, Rennes Cedex, France
| | | | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000, Lille, France
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000, Lille, France
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000, Lille, France
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10
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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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11
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Dubois-Chevalier J, Dubois V, Staels B, Lefebvre P, Eeckhoute J. Perspectives on the use of super-enhancers as a defining feature of cell/tissue-identity genes. Epigenomics 2020; 12:715-723. [PMID: 32396464 DOI: 10.2217/epi-2019-0290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Super-enhancers (SE) have become a popular concept and are widely used as a feature defining key identity genes. Here, we provide perspectives on the use of SE to define and identify cell/tissue-identity genes. By mining SE and their associated genes using murine functional genomics data, we highlight and discuss current limitations and open questions regarding both the sensitivity and specificity of identity genes/transcription factors predicted by SE. In this context, we point to cell/tissue-specific promoters as an important additional level of information, which we propose to combine with SE when aiming to define potential identity genes.
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Affiliation(s)
- Julie Dubois-Chevalier
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Vanessa Dubois
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Bart Staels
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Philippe Lefebvre
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Jérôme Eeckhoute
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
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12
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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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13
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Mazrooei P, Kron KJ, Zhu Y, Zhou S, Grillo G, Mehdi T, Ahmed M, Severson TM, Guilhamon P, Armstrong NS, Huang V, Yamaguchi TN, Fraser M, van der Kwast T, Boutros PC, He HH, Bergman AM, Bristow RG, Zwart W, Lupien M. Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors. Cancer Cell 2019; 36:674-689.e6. [PMID: 31735626 DOI: 10.1016/j.ccell.2019.10.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 08/02/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022]
Abstract
Thousands of noncoding somatic single-nucleotide variants (SNVs) of unknown function are reported in tumors. Partitioning the genome according to cistromes reveals the enrichment of somatic SNVs in prostate tumors as opposed to adjacent normal tissue cistromes of master transcription regulators, including AR, FOXA1, and HOXB13. This parallels enrichment of prostate cancer genetic predispositions over these transcription regulators' tumor cistromes, exemplified at the 8q24 locus harboring both risk variants and somatic SNVs in cis-regulatory elements upregulating MYC expression. However, Massively Parallel Reporter Assays reveal that few SNVs can alter the transactivation potential of individual cis-regulatory elements. Instead, similar to inherited risk variants, SNVs accumulate in cistromes of master transcription regulators required for prostate cancer development.
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Affiliation(s)
- Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ken J Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yanyun Zhu
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Tahmid Mehdi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Guilhamon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | | | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robert G Bristow
- CRUK Manchester Institute and Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
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14
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Lee YY, Mok MT, Kang W, Yang W, Tang W, Wu F, Xu L, Yan M, Yu Z, Lee SD, Tong JHM, Cheung YS, Lai PBS, Yu DY, Wang Q, Wong GLH, Chan AM, Yip KY, To KF, Cheng ASL. Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. Nucleic Acids Res 2019; 46:8832-8847. [PMID: 29992318 PMCID: PMC6158508 DOI: 10.1093/nar/gky589] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 06/19/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic sequencing of hepatocellular carcinoma (HCC) uncovers a paucity of actionable mutations, underscoring the necessity to exploit epigenetic vulnerabilities for therapeutics. In HCC, EZH2-mediated H3K27me3 represents a major oncogenic chromatin modification, but how it modulates the therapeutic vulnerability of signaling pathways remains unknown. Here, we show EZH2 acts antagonistically to AKT signaling in maintaining H3K27 methylome through epigenetic silencing of IGFBP4. ChIP-seq revealed enrichment of Ezh2/H3K27me3 at silenced loci in HBx-transgenic mouse-derived HCCs, including Igfbp4 whose down-regulation significantly correlated with EZH2 overexpression and poor survivals of HCC patients. Functional characterizations demonstrated potent growth- and invasion-suppressive functions of IGFBP4, which was associated with transcriptomic alterations leading to deregulation of multiple signaling pathways. Mechanistically, IGFBP4 stimulated AKT/EZH2 phosphorylation to abrogate H3K27me3-mediated silencing, forming a reciprocal feedback loop that suppressed core transcription factor networks (FOXA1/HNF1A/HNF4A/KLF9/NR1H4) for normal liver homeostasis. Consequently, the in vivo tumorigenicity of IGFBP4-silenced HCC cells was vulnerable to pharmacological inhibition of EZH2, but not AKT. Our study unveils chromatin regulation of a novel liver tumor suppressor IGFBP4, which constitutes an AKT-EZH2 reciprocal loop in driving H3K27me3-mediated epigenetic reprogramming. Defining the aberrant chromatin landscape of HCC sheds light into the mechanistic basis of effective EZH2-targeted inhibition.
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Affiliation(s)
- Ying-Ying Lee
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Myth Ts Mok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Weiqin Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenshu Tang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Liangliang Xu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingfei Yan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhuo Yu
- Department of Liver Disease, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sau-Dan Lee
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Joanna H M Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yue-Sun Cheung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Dae-Yeul Yu
- Disease Model Research Laboratory, Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Qianben Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Grace L H Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrew M Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
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15
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The nuclear bile acid receptor FXR is a PKA- and FOXA2-sensitive activator of fasting hepatic gluconeogenesis. J Hepatol 2018; 69:1099-1109. [PMID: 29981427 DOI: 10.1016/j.jhep.2018.06.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/14/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Embedded into a complex signaling network that coordinates glucose uptake, usage and production, the nuclear bile acid receptor FXR is expressed in several glucose-processing organs including the liver. Hepatic gluconeogenesis is controlled through allosteric regulation of gluconeogenic enzymes and by glucagon/cAMP-dependent transcriptional regulatory pathways. We aimed to elucidate the role of FXR in the regulation of fasting hepatic gluconeogenesis. METHODS The role of FXR in hepatic gluconeogenesis was assessed in vivo and in mouse primary hepatocytes. Gene expression patterns in response to glucagon and FXR agonists were characterized by quantitative reverse transcription PCR and microarray analysis. FXR phosphorylation by protein kinase A was determined by mass spectrometry. The interaction of FOXA2 with FXR was identified by cistromic approaches and in vitro protein-protein interaction assays. The functional impact of the crosstalk between FXR, the PKA and FOXA2 signaling pathways was assessed by site-directed mutagenesis, transactivation assays and restoration of FXR expression in FXR-deficient hepatocytes in which gene expression and glucose production were assessed. RESULTS FXR positively regulates hepatic glucose production through two regulatory arms, the first one involving protein kinase A-mediated phosphorylation of FXR, which allowed for the synergistic activation of gluconeogenic genes by glucagon, agonist-activated FXR and CREB. The second arm involves the inhibition of FXR's ability to induce the anti-gluconeogenic nuclear receptor SHP by the glucagon-activated FOXA2 transcription factor, which physically interacts with FXR. Additionally, knockdown of Foxa2 did not alter glucagon-induced and FXR agonist enhanced expression of gluconeogenic genes, suggesting that the PKA and FOXA2 pathways regulate distinct subsets of FXR responsive genes. CONCLUSIONS Thus, hepatic glucose production is regulated during physiological fasting by FXR, which integrates the glucagon/cAMP signal and the FOXA2 signal, by being post-translationally modified, and by engaging in protein-protein interactions, respectively. LAY SUMMARY Activation of the nuclear bile acid receptor FXR regulates gene expression networks, controlling lipid, cholesterol and glucose metabolism, which are mostly effective after eating. Whether FXR exerts critical functions during fasting is unknown. The results of this study show that FXR transcriptional activity is regulated by the glucagon/protein kinase A and the FOXA2 signaling pathways, which act on FXR through phosphorylation and protein-protein interactions, respectively, to increase hepatic glucose synthesis.
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16
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Bobowski-Gerard M, Zummo FP, Staels B, Lefebvre P, Eeckhoute J. Retinoids Issued from Hepatic Stellate Cell Lipid Droplet Loss as Potential Signaling Molecules Orchestrating a Multicellular Liver Injury Response. Cells 2018; 7:cells7090137. [PMID: 30217095 PMCID: PMC6162435 DOI: 10.3390/cells7090137] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Hepatic stellate cells (HSCs) serve as the main body storage compartment for vitamin A through retinyl ester (RE)-filled lipid droplets (LDs). Upon liver injury, HSCs adopt a myofibroblastic phenotype characterized by an elevated expression of extracellular matrix proteins and a concomitant loss of LDs. On the one hand, LD breakdown has been suggested to provide the energy required for HSC activation into myofibroblast-like cells. On the other hand, this process could mitigate HSC activation following the transformation of released REs into retinoic acids (RAs), ligands for nuclear receptors exerting antifibrotic transcriptional regulatory activities in HSCs. Importantly, RAs may also constitute a means for HSCs to orchestrate the liver response to injury by triggering transcriptional effects in multiple additional surrounding liver cell populations. We envision that new approaches, such as single-cell technologies, will allow to better define how RAs are issued from LD loss in HSCs exert a multicellular control of the liver (patho)physiology.
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Affiliation(s)
- Marie Bobowski-Gerard
- Institut Pasteur de Lille, The University of Lille, Inserm, CHU Lille, U1011-EGID, F-59000 Lille, France.
| | - Francesco Paolo Zummo
- Institut Pasteur de Lille, The University of Lille, Inserm, CHU Lille, U1011-EGID, F-59000 Lille, France.
| | - Bart Staels
- Institut Pasteur de Lille, The University of Lille, Inserm, CHU Lille, U1011-EGID, F-59000 Lille, France.
| | - Philippe Lefebvre
- Institut Pasteur de Lille, The University of Lille, Inserm, CHU Lille, U1011-EGID, F-59000 Lille, France.
| | - Jérôme Eeckhoute
- Institut Pasteur de Lille, The University of Lille, Inserm, CHU Lille, U1011-EGID, F-59000 Lille, France.
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17
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Swinstead EE, Paakinaho V, Hager GL. Chromatin reprogramming in breast cancer. Endocr Relat Cancer 2018; 25:R385-R404. [PMID: 29692347 PMCID: PMC6029727 DOI: 10.1530/erc-18-0033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
Abstract
Reprogramming of the chromatin landscape is a critical component to the transcriptional response in breast cancer. Effects of sex hormones such as estrogens and progesterone have been well described to have a critical impact on breast cancer proliferation. However, the complex network of the chromatin landscape, enhancer regions and mode of function of steroid receptors (SRs) and other transcription factors (TFs), is an intricate web of signaling and functional processes that is still largely misunderstood at the mechanistic level. In this review, we describe what is currently known about the dynamic interplay between TFs with chromatin and the reprogramming of enhancer elements. Emphasis has been placed on characterizing the different modes of action of TFs in regulating enhancer activity, specifically, how different SRs target enhancer regions to reprogram chromatin in breast cancer cells. In addition, we discuss current techniques employed to study enhancer function at a genome-wide level. Further, we have noted recent advances in live cell imaging technology. These single-cell approaches enable the coupling of population-based assays with real-time studies to address many unsolved questions about SRs and chromatin dynamics in breast cancer.
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Affiliation(s)
- Erin E Swinstead
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
- Institute of BiomedicineUniversity of Eastern Finland, Kuopio, Finland
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
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18
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Diehl AG, Boyle AP. Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. Nucleic Acids Res 2018; 46:1878-1894. [PMID: 29361190 PMCID: PMC5829737 DOI: 10.1093/nar/gky018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/15/2017] [Accepted: 01/08/2018] [Indexed: 12/24/2022] Open
Abstract
The mouse is widely used as system to study human genetic mechanisms. However, extensive rewiring of transcriptional regulatory networks often confounds translation of findings between human and mouse. Site-specific gain and loss of individual transcription factor binding sites (TFBS) has caused functional divergence of orthologous regulatory loci, and so we must look beyond this positional conservation to understand common themes of regulatory control. Fortunately, transcription factor co-binding patterns shared across species often perform conserved regulatory functions. These can be compared to 'regulatory sentences' that retain the same meanings regardless of sequence and species context. By analyzing TFBS co-occupancy patterns observed in four human and mouse cell types, we learned a regulatory grammar: the rules by which TFBS are combined into meaningful regulatory sentences. Different parts of this grammar associate with specific sets of functional annotations regardless of sequence conservation and predict functional signatures more accurately than positional conservation. We further show that both species-specific and conserved portions of this grammar are involved in gene expression divergence and human disease risk. These findings expand our understanding of transcriptional regulatory mechanisms, suggesting that phenotypic divergence and disease risk are driven by a complex interplay between deeply conserved and species-specific transcriptional regulatory pathways.
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Affiliation(s)
- Adam G Diehl
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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19
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Dubois-Chevalier J, Mazrooei P, Lupien M, Staels B, Lefebvre P, Eeckhoute J. Organizing combinatorial transcription factor recruitment at cis-regulatory modules. Transcription 2017; 9:233-239. [PMID: 29105538 DOI: 10.1080/21541264.2017.1394424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Gene transcriptional regulation relies on cis-regulatory DNA modules (CRMs), which serve as nexus sites for integration of multiple transcription factor (TF) activities. Here, we provide evidence and discuss recent literature indicating that TF recruitment to CRMs is organized into combinations of trans-regulatory protein modules (TRMs). We propose that TRMs are functional entities composed of TFs displaying the most highly interdependent chromatin binding which are, in addition, able to modulate their recruitment to CRMs through inter-TRM effects. These findings shed light on the architectural organization of TF recruitment encoded by their recognition motifs within CRMs.
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Affiliation(s)
- Julie Dubois-Chevalier
- a Université de Lille - Inserm - Chru de Lille, Institut Pasteur de Lille , U1011- EGID, F-59000 Lille , France
| | - Parisa Mazrooei
- b The Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics , University of Toronto , Toronto , ON M5G 1L7 , Canada
| | - Mathieu Lupien
- b The Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics , University of Toronto , Toronto , ON M5G 1L7 , Canada
| | - Bart Staels
- a Université de Lille - Inserm - Chru de Lille, Institut Pasteur de Lille , U1011- EGID, F-59000 Lille , France
| | - Philippe Lefebvre
- a Université de Lille - Inserm - Chru de Lille, Institut Pasteur de Lille , U1011- EGID, F-59000 Lille , France
| | - Jérôme Eeckhoute
- a Université de Lille - Inserm - Chru de Lille, Institut Pasteur de Lille , U1011- EGID, F-59000 Lille , France
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20
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Legry V, Francque S, Haas JT, Verrijken A, Caron S, Chávez-Talavera O, Vallez E, Vonghia L, Dirinck E, Verhaegen A, Kouach M, Lestavel S, Lefebvre P, Van Gaal L, Tailleux A, Paumelle R, Staels B. Bile Acid Alterations Are Associated With Insulin Resistance, but Not With NASH, in Obese Subjects. J Clin Endocrinol Metab 2017; 102:3783-3794. [PMID: 28938455 DOI: 10.1210/jc.2017-01397] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/31/2017] [Indexed: 12/15/2022]
Abstract
CONTEXT Bile acids (BAs) are signaling molecules controlling energy homeostasis that can be both toxic and protective for the liver. BA alterations have been reported in obesity, insulin resistance (IR), and nonalcoholic steatohepatitis (NASH). However, whether BA alterations contribute to NASH independently of the metabolic status is unclear. OBJECTIVE To assess BA alterations associated with NASH independently of body mass index and IR. DESIGN AND SETTING Patients visiting the obesity clinic of the Antwerp University Hospital (a tertiary referral facility) were recruited from 2006 to 2014. PATIENTS Obese patients with biopsy-proven NASH (n = 32) and healthy livers (n = 26) were matched on body mass index and homeostasis model assessment of IR. MAIN OUTCOME MEASURES Transcriptomic analyses were performed on liver biopsies. Plasma concentrations of 21 BA species and 7α-hydroxy-4-cholesten-3-one, a marker of BA synthesis, were determined by liquid chromatography-tandem mass spectrometry. Plasma fibroblast growth factor 19 was measured by enzyme-linked immunosorbent assay. RESULTS Plasma BA concentrations did not correlate with any hepatic lesions, whereas, as previously reported, primary BA strongly correlated with IR. Transcriptomic analyses showed unaltered hepatic BA metabolism in NASH patients. In line, plasma 7α-hydroxy-4-cholesten-3-one was unchanged in NASH. Moreover, no sign of hepatic BA accumulation or activation of BA receptors-farnesoid X, pregnane X, and vitamin D receptors-was found. Finally, plasma fibroblast growth factor 19, secondary-to-primary BA, and free-to-conjugated BA ratios were similar, suggesting unaltered intestinal BA metabolism and signaling. CONCLUSIONS In obese patients, BA alterations are related to the metabolic phenotype associated with NASH, especially IR, but not liver necroinflammation.
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Affiliation(s)
- Vanessa Legry
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Sven Francque
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, 2650 Edegem/Antwerp, Belgium
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk/Antwerp, Belgium
| | - Joel T Haas
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - An Verrijken
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk/Antwerp, Belgium
- Department of Endocrinology, Diabetes and Metabolism, Antwerp University Hospital, 2650 Egedem/Antwerp, Belgium
| | - Sandrine Caron
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Oscar Chávez-Talavera
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Emmanuelle Vallez
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Luisa Vonghia
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, 2650 Edegem/Antwerp, Belgium
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk/Antwerp, Belgium
| | - Eveline Dirinck
- Department of Endocrinology, Diabetes and Metabolism, Antwerp University Hospital, 2650 Egedem/Antwerp, Belgium
| | - Ann Verhaegen
- Department of Endocrinology, Diabetes and Metabolism, Antwerp University Hospital, 2650 Egedem/Antwerp, Belgium
| | - Mostafa Kouach
- Plateau de Spectrométrie de Masse-Groupe de Recherche sur les formes Injectables et les Technologies Associées, (PSM-GRITA), Faculté de Pharmacie, F-59000 Lille, France
| | - Sophie Lestavel
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Philippe Lefebvre
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Luc Van Gaal
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk/Antwerp, Belgium
- Department of Endocrinology, Diabetes and Metabolism, Antwerp University Hospital, 2650 Egedem/Antwerp, Belgium
| | - Anne Tailleux
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Réjane Paumelle
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
| | - Bart Staels
- Université Lille, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1011-European Genomic Institute for Diabetes, F-59000 Lille, France
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