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Meeusen H, Romagnolo A, Holsink SAC, van den Broek TJM, van Helvoort A, Gorter JA, van Vliet EA, Verkuyl JM, Silva JP, Aronica E. A novel hepatocyte ketone production assay to help the selection of nutrients for the ketogenic diet treatment of epilepsy. Sci Rep 2024; 14:11940. [PMID: 38789658 PMCID: PMC11126716 DOI: 10.1038/s41598-024-62723-7] [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: 08/15/2023] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Abstract
The classic ketogenic diet is an effective treatment option for drug-resistant epilepsy, but its high fat content challenges patient compliance. Optimizing liver ketone production guided by a method comparing substrates for their ketogenic potential may help to reduce the fat content of the diet without loss in ketosis induction. Here, we present a liver cell assay measuring the β-hydroxybutyrate (βHB) yield from fatty acid substrates. Even chain albumin-conjugated fatty acids comprising between 4 and 18 carbon atoms showed a sigmoidal concentration-βHB response curve (CRC) whereas acetate and omega-3 PUFAs produced no CRC. While CRCs were not distinguished by their half-maximal effective concentration (EC50), they differed by maximum response, which related inversely to the carbon chain length and was highest for butyrate. The assay also suitably assessed the βHB yield from fatty acid blends detecting shifts in maximum response from exchanging medium chain fatty acids for long chain fatty acids. The assay further detected a dual role for butyrate and hexanoic acid as ketogenic substrate at high concentration and ketogenic enhancer at low concentration, augmenting the βHB yield from oleic acid and a fatty acid blend. The assay also found propionate to inhibit ketogenesis from oleic acid and a fatty acid blend at low physiological concentration. Although the in vitro assay shows promise as a tool to optimize the ketogenic yield of a fat blend, its predictive value requires human validation.
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Affiliation(s)
- Hester Meeusen
- Department of (Neuro)Pathology, Amsterdam UMC, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
- Department of Nutritional Physiology and Functional Nutrients, Medical & Nutrition Science, Danone Nutricia Research, Uppsalalaan 12, 3584CT, Utrecht, The Netherlands
| | - Alessia Romagnolo
- Department of (Neuro)Pathology, Amsterdam UMC, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
- Department of Nutritional Physiology and Functional Nutrients, Medical & Nutrition Science, Danone Nutricia Research, Uppsalalaan 12, 3584CT, Utrecht, The Netherlands
| | - Sophie A C Holsink
- Department of Nutritional Physiology and Functional Nutrients, Medical & Nutrition Science, Danone Nutricia Research, Uppsalalaan 12, 3584CT, Utrecht, The Netherlands
| | - Thijs J M van den Broek
- Department of Nutritional Physiology and Functional Nutrients, Medical & Nutrition Science, Danone Nutricia Research, Uppsalalaan 12, 3584CT, Utrecht, The Netherlands
| | - Ardy van Helvoort
- Department of Nutritional Physiology and Functional Nutrients, Medical & Nutrition Science, Danone Nutricia Research, Uppsalalaan 12, 3584CT, Utrecht, The Netherlands
- Department of Respiratory Medicine, NUTRIM - Research Institute of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht University, Maastricht, The Netherlands
| | - Jan A Gorter
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Amsterdam UMC, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - J Martin Verkuyl
- Department of Nutritional Physiology and Functional Nutrients, Medical & Nutrition Science, Danone Nutricia Research, Uppsalalaan 12, 3584CT, Utrecht, The Netherlands
| | - Jose P Silva
- Department of Nutritional Physiology and Functional Nutrients, Medical & Nutrition Science, Danone Nutricia Research, Uppsalalaan 12, 3584CT, Utrecht, The Netherlands.
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
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2
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Jiang C, Li P, Ma Y, Yoneda N, Kawai K, Uehara S, Ohnishi Y, Suemizu H, Cao H. Comprehensive gene profiling of the metabolic landscape of humanized livers in mice. J Hepatol 2024; 80:622-633. [PMID: 38049085 PMCID: PMC10947884 DOI: 10.1016/j.jhep.2023.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND & AIMS The human liver transcriptome is complex and highly dynamic, e.g. one gene may produce multiple distinct transcripts, each with distinct posttranscriptional modifications. Direct knowledge of transcriptome dynamics, however, is largely obscured by the inaccessibility of the human liver to treatments and the insufficient annotation of the human liver transcriptome at transcript and RNA modification levels. METHODS We generated mice that carry humanized livers of identical genetic background and subjected them to representative metabolic treatments. We then analyzed the humanized livers with nanopore single-molecule direct RNA sequencing to determine the expression level, m6A modification and poly(A) tail length of all RNA transcript isoforms. Our system allows for the de novo annotation of human liver transcriptomes to reflect metabolic responses and for the study of transcriptome dynamics in parallel. RESULTS Our analysis uncovered a vast number of novel genes and transcripts. Our transcript-level analysis of human liver transcriptomes also identified a multitude of regulated metabolic pathways that were otherwise invisible using conventional short-read RNA sequencing. We revealed for the first time the dynamic changes in m6A and poly(A) tail length of human liver transcripts, many of which are transcribed from key metabolic genes. Furthermore, we performed comparative analyses of gene regulation between humans and mice, and between two individuals using the liver-specific humanized mice, revealing that transcriptome dynamics are highly species- and genetic background-dependent. CONCLUSION Our work revealed a complex metabolic response landscape of the human liver transcriptome and provides a novel resource to understand transcriptome dynamics of the human liver in response to physiologically relevant metabolic stimuli (https://caolab.shinyapps.io/human_hepatocyte_landscape/). IMPACT AND IMPLICATIONS Direct knowledge of the human liver transcriptome is currently very limited, hindering the overall understanding of human liver pathophysiology. We combined a liver-specific humanized mouse model and long-read direct RNA sequencing technology to establish a de novo annotation of the human liver transcriptome and identified a multitude of regulated metabolic pathways that were otherwise invisible using conventional technologies. The extensive regulatory information on human genes we provided could enable basic scientists to infer the pathological relevance of their genes of interest and physician scientists to better pinpoint the changes in metabolic networks underlying a specific pathophysiology.
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Affiliation(s)
- Chengfei Jiang
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ping Li
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yonghe Ma
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nao Yoneda
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Kenji Kawai
- Pathology Center, Translational Research and Contract Research Service Division, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Shotaro Uehara
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Yasuyuki Ohnishi
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Hiroshi Suemizu
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Haiming Cao
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Fuster-Martínez I, Català-Senent JF, Hidalgo MR, Roig FJ, Esplugues JV, Apostolova N, García-García F, Blas-García A. Integrated transcriptomic landscape of the effect of anti-steatotic treatments in high-fat diet mouse models of non-alcoholic fatty liver disease. J Pathol 2024; 262:377-389. [PMID: 38180387 DOI: 10.1002/path.6242] [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: 06/18/2023] [Revised: 10/20/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
High-fat diet (HFD) mouse models are widely used in research to develop medications to treat non-alcoholic fatty liver disease (NAFLD), as they mimic the steatosis, inflammation, and hepatic fibrosis typically found in this complex human disease. The aims of this study were to identify a complete transcriptomic signature of these mouse models and to characterize the transcriptional impact exerted by different experimental anti-steatotic treatments. For this reason, we conducted a systematic review and meta-analysis of liver transcriptomic studies performed in HFD-fed C57BL/6J mice, comparing them with control mice and HFD-fed mice receiving potential anti-steatotic treatments. Analyzing 21 studies broaching 24 different treatments, we obtained a robust HFD transcriptomic signature that included 2,670 differentially expressed genes and 2,567 modified gene ontology biological processes. Treated HFD mice generally showed a reversion of this HFD signature, although the extent varied depending on the treatment. The biological processes most frequently reversed were those related to lipid metabolism, response to stress, and immune system, whereas processes related to nitrogen compound metabolism were generally not reversed. When comparing this HFD signature with a signature of human NAFLD progression, we identified 62 genes that were common to both; 10 belonged to the group that were reversed by treatments. Altered expression of most of these 10 genes was confirmed in vitro in hepatocytes and hepatic stellate cells exposed to a lipotoxic or a profibrogenic stimulus, respectively. In conclusion, this study provides a vast amount of information about transcriptomic changes induced during the progression and regression of NAFLD and identifies some relevant targets. Our results may help in the assessment of treatment efficacy, the discovery of unmet therapeutic targets, and the search for novel biomarkers. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Isabel Fuster-Martínez
- Departamento de Farmacología, Universitat de València, Valencia, Spain
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
| | - José F Català-Senent
- Computational Biomedicine Laboratory, Principe Felipe Research Center, Valencia, Spain
| | - Marta R Hidalgo
- Computational Biomedicine Laboratory, Principe Felipe Research Center, Valencia, Spain
| | - Francisco J Roig
- Computational Biomedicine Laboratory, Principe Felipe Research Center, Valencia, Spain
- Facultad de Ciencias de la Salud, Universidad San Jorge, Campus Universitario Villanueva de Gállego, Zaragoza, Spain
| | - Juan V Esplugues
- Departamento de Farmacología, Universitat de València, Valencia, Spain
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Madrid, Spain
| | - Nadezda Apostolova
- Departamento de Farmacología, Universitat de València, Valencia, Spain
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Madrid, Spain
| | | | - Ana Blas-García
- FISABIO (Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana), Valencia, Spain
- CIBEREHD (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Madrid, Spain
- Departamento de Fisiología, Universitat de València, Valencia, Spain
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Ruppert PMM, Kersten S. Mechanisms of hepatic fatty acid oxidation and ketogenesis during fasting. Trends Endocrinol Metab 2024; 35:107-124. [PMID: 37940485 DOI: 10.1016/j.tem.2023.10.002] [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: 08/31/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/10/2023]
Abstract
Fasting is part of many weight management and health-boosting regimens. Fasting causes substantial metabolic adaptations in the liver that include the stimulation of fatty acid oxidation and ketogenesis. The induction of fatty acid oxidation and ketogenesis during fasting is mainly driven by interrelated changes in plasma levels of various hormones and an increase in plasma nonesterified fatty acid (NEFA) levels and is mediated transcriptionally by the peroxisome proliferator-activated receptor (PPAR)α, supported by CREB3L3 (cyclic AMP-responsive element-binding protein 3 like 3). Compared with men, women exhibit higher ketone levels during fasting, likely due to higher NEFA availability, suggesting that the metabolic response to fasting shows sexual dimorphism. Here, we synthesize the current molecular knowledge on the impact of fasting on hepatic fatty acid oxidation and ketogenesis.
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Affiliation(s)
- Philip M M Ruppert
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5000 C Odense, Denmark
| | - Sander Kersten
- Nutrition, Metabolism, and Genomics Group, Division of Human Nutrition and Health, Wageningen University, 6708 WE Wageningen, The Netherlands; Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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Jin S, Meng J, Zhang C, Qi J, Wu H. Consistency of mouse models with human intracerebral hemorrhage: core targets and non-coding RNA regulatory axis. Aging (Albany NY) 2024; 16:1952-1967. [PMID: 38271077 PMCID: PMC10866413 DOI: 10.18632/aging.205473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/04/2023] [Indexed: 01/27/2024]
Abstract
Intracerebral hemorrhage (ICH) has a high mortality and disability rate. Numerous basic studies on pathogenesis and therapeutics have been performed in mice. However, the consistency of the experimental mouse model and the human ICH patient remains unclear. This has slowed progress in translational medicine. Furthermore, effective therapeutic targets and reliable regulatory networks for ICH are needed. Therefore, we determined the differentially expressed (DE) messenger RNAs (mRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs) before and after murine ICH and analyzed their regulatory relationships. Subsequently, data on mRNAs from human peripheral blood after ICH were obtained from the Gene Expression Omnibus database. The DE mRNAs after human ICH were compared with those of the mouse. Finally, we obtained seven genes with translational medicine research value and verified them in mice. Then the regulatory network of these genes was analyzed in humans. Similarly, species homologies of these regulatory pathways were identified. In conclusion, we found that the mouse ICH model mimics the human disease mainly in terms of chemokines and inflammatory factors. This has important implications for future research into the mechanisms of ICH injury and repair.
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Affiliation(s)
- Sinan Jin
- Department of Pathology, First Clinical Hospital, Harbin Medical University, Harbin 150001, China
| | - Jincheng Meng
- Department of Pathology, First Clinical Hospital, Harbin Medical University, Harbin 150001, China
| | - Chong Zhang
- Department of Pathology, First Clinical Hospital, Harbin Medical University, Harbin 150001, China
| | - Jiping Qi
- Department of Pathology, First Clinical Hospital, Harbin Medical University, Harbin 150001, China
| | - He Wu
- Department of Pathology, First Clinical Hospital, Harbin Medical University, Harbin 150001, China
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Saldarriaga OA, Wanninger TG, Arroyave E, Gosnell J, Krishnan S, Oneka M, Bao D, Millian DE, Kueht ML, Moghe A, Jiao J, Sanchez JI, Spratt H, Beretta L, Rao A, Burks JK, Stevenson HL. Heterogeneity in intrahepatic macrophage populations and druggable target expression in patients with steatotic liver disease-related fibrosis. JHEP Rep 2024; 6:100958. [PMID: 38162144 PMCID: PMC10757256 DOI: 10.1016/j.jhepr.2023.100958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 01/03/2024] Open
Abstract
Background & Aims Clinical trials for reducing fibrosis in steatotic liver disease (SLD) have targeted macrophages with variable results. We evaluated intrahepatic macrophages in patients with SLD to determine if activity scores or fibrosis stages influenced phenotypes and expression of druggable targets, such as CCR2 and galectin-3. Methods Liver biopsies from controls or patients with minimal or advanced fibrosis were subject to gene expression analysis using nCounter to determine differences in macrophage-related genes (n = 30). To investigate variability among individual patients, we compared additional biopsies by staining them with multiplex antibody panels (CD68/CD14/CD16/CD163/Mac387 or CD163/CCR2/galectin-3/Mac387) followed by spectral imaging and spatial analysis. Algorithms that utilize deep learning/artificial intelligence were applied to create cell cluster plots, phenotype profile maps, and to determine levels of protein expression (n = 34). Results Several genes known to be pro-fibrotic (e.g. CD206, TREM2, CD163, and ARG1) showed either no significant differences or significantly decreased with advanced fibrosis. Although marked variability in gene expression was observed in individual patients with cirrhosis, several druggable targets and their ligands (e.g. CCR2, CCR5, CCL2, CCL5, and LGALS3) were significantly increased when compared to patients with minimal fibrosis. Antibody panels identified populations that were significantly increased (e.g. Mac387+), decreased (e.g. CD14+), or enriched (e.g. interactions of Mac387) in patients that had progression of disease or advanced fibrosis. Despite heterogeneity in patients with SLD, several macrophage phenotypes and druggable targets showed a positive correlation with increasing NAFLD activity scores and fibrosis stages. Conclusions Patients with SLD have markedly varied macrophage- and druggable target-related gene and protein expression in their livers. Several patients had relatively high expression, while others were like controls. Overall, patients with more advanced disease had significantly higher expression of CCR2 and galectin-3 at both the gene and protein levels. Impact and implications Appreciating individual differences within the hepatic microenvironment of patients with SLD may be paramount to developing effective treatments. These results may explain why such a small percentage of patients have responded to macrophage-targeting therapies and provide additional support for precision medicine-guided treatment of chronic liver diseases.
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Affiliation(s)
- Omar A. Saldarriaga
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Timothy G. Wanninger
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Esteban Arroyave
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Joseph Gosnell
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Santhoshi Krishnan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Morgan Oneka
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel Bao
- School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Daniel E. Millian
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael L. Kueht
- Department of Surgery, University of Texas Medical Branch, Galveston, TX, USA
| | - Akshata Moghe
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Jingjing Jiao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jessica I. Sanchez
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heidi Spratt
- Department of Biostatistics and Data Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Departmen of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, Rice University, Ann Arbor, MI, USA
| | - Jared K. Burks
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Martinez-Lopez S, Angel-Gomis E, Sanchez-Ardid E, Pastor-Campos A, Picó J, Gomez-Hurtado I. The 3Rs in Experimental Liver Disease. Animals (Basel) 2023; 13:2357. [PMID: 37508134 PMCID: PMC10376896 DOI: 10.3390/ani13142357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Patients with cirrhosis present multiple physiological and immunological alterations that play a very important role in the development of clinically relevant secondary complications to the disease. Experimentation in animal models is essential to understand the pathogenesis of human diseases and, considering the high prevalence of liver disease worldwide, to understand the pathophysiology of disease progression and the molecular pathways involved, due to the complexity of the liver as an organ and its relationship with the rest of the organism. However, today there is a growing awareness about the sensitivity and suffering of animals, causing opposition to animal research among a minority in society and some scientists, but also about the attention to the welfare of laboratory animals since this has been built into regulations in most nations that conduct animal research. In 1959, Russell and Burch published the book "The Principles of Humane Experimental Technique", proposing that in those experiments where animals were necessary, everything possible should be done to try to replace them with non-sentient alternatives, to reduce to a minimum their number, and to refine experiments that are essential so that they caused the least amount of pain and distress. In this review, a comprehensive summary of the most widely used techniques to replace, reduce, and refine in experimental liver research is offered, to assess the advantages and weaknesses of available experimental liver disease models for researchers who are planning to perform animal studies in the near future.
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Affiliation(s)
- Sebastian Martinez-Lopez
- Instituto ISABIAL, Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain
- Departamento de Medicina Clínica, Universidad Miguel Hernández, 03550 Sant Joan, Spain
| | - Enrique Angel-Gomis
- Instituto ISABIAL, Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain
- Departamento de Medicina Clínica, Universidad Miguel Hernández, 03550 Sant Joan, Spain
| | - Elisabet Sanchez-Ardid
- CIBERehd, Instituto de Salud Carlos III, 28220 Madrid, Spain
- Servicio de Patología Digestiva, Institut de Recerca IIB-Sant Pau, Hospital de Santa Creu i Sant Pau, 08025 Barcelona, Spain
| | - Alberto Pastor-Campos
- Oficina de Investigación Responsable, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Joanna Picó
- Instituto ISABIAL, Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain
| | - Isabel Gomez-Hurtado
- Instituto ISABIAL, Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain
- Departamento de Medicina Clínica, Universidad Miguel Hernández, 03550 Sant Joan, Spain
- CIBERehd, Instituto de Salud Carlos III, 28220 Madrid, Spain
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Delbès AS, Quiñones M, Gobet C, Castel J, Denis RGP, Berthelet J, Weger BD, Challet E, Charpagne A, Metairon S, Piccand J, Kraus M, Rohde BH, Bial J, Wilson EM, Vedin LL, Minniti ME, Pedrelli M, Parini P, Gachon F, Luquet S. Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior. SCIENCE ADVANCES 2023; 9:eadf2982. [PMID: 37196091 DOI: 10.1126/sciadv.adf2982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
The synchronization of circadian clock depends on a central pacemaker located in the suprachiasmatic nuclei. However, the potential feedback of peripheral signals on the central clock remains poorly characterized. To explore whether peripheral organ circadian clocks may affect the central pacemaker, we used a chimeric model in which mouse hepatocytes were replaced by human hepatocytes. Liver humanization led to reprogrammed diurnal gene expression and advanced the phase of the liver circadian clock that extended to muscle and the entire rhythmic physiology. Similar to clock-deficient mice, liver-humanized mice shifted their rhythmic physiology more rapidly to the light phase under day feeding. Our results indicate that hepatocyte clocks can affect the central pacemaker and offer potential perspectives to apprehend pathologies associated with altered circadian physiology.
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Affiliation(s)
- Anne-Sophie Delbès
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Mar Quiñones
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
- Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
- CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Cédric Gobet
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Julien Castel
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Raphaël G P Denis
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, Paris 75014, France
| | - Jérémy Berthelet
- Université Paris Cité, CNRS, Unité Epigenetique et Destin Cellulaire, Paris F-75013, France
| | - Benjamin D Weger
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Etienne Challet
- Institute for Cellular and Integrative Neurosciences, CNRS and University of Strasbourg, Strasbourg, France
| | - Aline Charpagne
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Sylviane Metairon
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Julie Piccand
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Marine Kraus
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Bettina H Rohde
- Eurofins Genomics Europe Sequencing GmbH, European Genome and Diagnostics Centre, Konstanz, Germany
| | | | | | - Lise-Lotte Vedin
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Mirko E Minniti
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Matteo Pedrelli
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
- Medical Unit Endocrinology, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Paolo Parini
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
- Medical Unit Endocrinology, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Frédéric Gachon
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Serge Luquet
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
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9
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Saldarriaga OA, Krishnan S, Wanninger TG, Oneka M, Rao A, Bao D, Arroyave E, Gosnell J, Kueht M, Moghe A, Millian D, Jiao J, Sanchez JI, Spratt H, Beretta L, Stevenson HL. Patients with fibrosis from non-alcoholic steatohepatitis have heterogeneous intrahepatic macrophages and therapeutic targets. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.16.23285924. [PMID: 36865099 PMCID: PMC9980226 DOI: 10.1101/2023.02.16.23285924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Background and Aims In clinical trials for reducing fibrosis in NASH patients, therapeutics that target macrophages have had variable results. We evaluated intrahepatic macrophages in patients with non-alcoholic steatohepatitis to determine if fibrosis influenced phenotypes and expression of CCR2 and Galectin-3. Approach & Results We used nCounter to analyze liver biopsies from well-matched patients with minimal (n=12) or advanced (n=12) fibrosis to determine which macrophage-related genes would be significantly different. Known therapy targets (e.g., CCR2 and Galectin-3) were significantly increased in patients with cirrhosis.However, several genes (e.g., CD68, CD16, and CD14) did not show significant differences, and CD163, a marker of pro-fibrotic macrophages was significantly decreased with cirrhosis. Next, we analyzed patients with minimal (n=6) or advanced fibrosis (n=5) using approaches that preserved hepatic architecture by multiplex-staining with anti-CD68, Mac387, CD163, CD14, and CD16. Spectral data were analyzed using deep learning/artificial intelligence to determine percentages and spatial relationships. This approach showed patients with advanced fibrosis had increased CD68+, CD16+, Mac387+, CD163+, and CD16+CD163+ populations. Interaction of CD68+ and Mac387+ populations was significantly increased in patients with cirrhosis and enrichment of these same phenotypes in individuals with minimal fibrosis correlated with poor outcomes. Evaluation of a final set of patients (n=4) also showed heterogenous expression of CD163, CCR2, Galectin-3, and Mac387, and significant differences were not dependent on fibrosis stage or NAFLD activity. Conclusions Approaches that leave hepatic architecture intact, like multispectral imaging, may be paramount to developing effective treatments for NASH. In addition, understanding individual differences in patients may be required for optimal responses to macrophage-targeting therapies.
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10
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Yan A, Zhao Y, Zhang L, Liang X, Zhang X, Liang F, Nian S, Li X, Sun Z, Li K, Zhao YF. β-Hydroxybutyrate upregulates FGF21 expression through inhibition of histone deacetylases in hepatocytes. Open Life Sci 2022; 17:856-864. [PMID: 36045720 PMCID: PMC9372706 DOI: 10.1515/biol-2022-0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
Fibroblast growth factor 21 (FGF21) is secreted by hepatocytes as a peptide hormone to regulate glucose and lipid metabolism. FGF21 promotes hepatic ketogenesis and increases ketone body utilization in starvation. Histones are the target molecules of nutrients in regulating hepatic metabolic homeostasis. However, the effect of ketone bodies on FGF21 expression and the involvement of histones in it is not clear yet. The present study observed the effects of β-hydroxybutyrate (β-OHB), the main physiological ketone body, on FGF21 expression in human hepatoma HepG2 cells in vitro and in mice in vivo, and the role of histone deacetylases (HDACs) in β-OHB-regulated FGF21 expression was investigated. The results showed that β-OHB significantly upregulated FGF21 gene expression and increased FGF21 protein levels while it inhibited HDACs’ activity in HepG2 cells. HDACs’ inhibition by entinostat upregulated FGF21 expression and eliminated β-OHB-stimulated FGF21 expression in HepG2 cells. Intraperitoneal injections of β-OHB in mice resulted in the elevation of serum β-OHB and the inhibition of hepatic HDACs’ activity. Meanwhile, hepatic FGF21 expression and serum FGF21 levels were significantly increased in β-OHB-treated mice compared with the control. It is suggested that β-OHB upregulates FGF21 expression through inhibition of HDACs’ activity in hepatocytes.
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Affiliation(s)
- Aili Yan
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Yanyan Zhao
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Lijun Zhang
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Xiangyan Liang
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Xiaochun Zhang
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Fenli Liang
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Shen Nian
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Xinhua Li
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Zhuo Sun
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
| | - Ke Li
- Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, 710021, China
| | - Yu-Feng Zhao
- Institute of Basic Medical Sciences, Xi'an Medical University, Xi'an, 710021, China
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11
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Liu G, Wang L, Wess J, Dean A. Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors. Nucleic Acids Res 2022; 50:9195-9211. [PMID: 36018801 PMCID: PMC9458430 DOI: 10.1093/nar/gkac707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
Enhancers establish proximity with distant target genes to regulate temporospatial gene expression and specify cell identity. Lim domain binding protein 1 (LDB1) is a conserved and widely expressed protein that functions as an enhancer looping factor. Previous studies in erythroid cells and neuronal cells showed that LDB1 forms protein complexes with different transcription factors to regulate cell-specific gene expression. Here, we show that LDB1 regulates expression of liver genes by occupying enhancer elements and cooperating with hepatic transcription factors HNF4A, FOXA1, TCF7 and GATA4. Using the glucose transporter SLC2A2 gene, encoding GLUT2, as an example, we find that LDB1 regulates gene expression by mediating enhancer-promoter interactions. In vivo, we find that LDB1 deficiency in primary mouse hepatocytes dysregulates metabolic gene expression and changes the enhancer landscape. Conditional deletion of LDB1 in adult mouse liver induces glucose intolerance. However, Ldb1 knockout hepatocytes show improved liver pathology under high-fat diet conditions associated with increased expression of genes related to liver fatty acid metabolic processes. Thus, LDB1 is linked to liver metabolic functions under normal and obesogenic conditions.
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Affiliation(s)
- Guoyou Liu
- Correspondence may also be addressed to Guoyou Liu. Tel: +1 301 435 9396;
| | - Lei Wang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jürgen Wess
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- To whom correspondence should be addressed. Tel: +1 301 496 6068;
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12
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Abstract
As medical and pharmacological technology advances, new and complex modalities of disease treatment that are more personalized and targeted are being developed. Often these modalities must be validated in the presence of critical components of the human biological system. Given the incongruencies between murine and human biology, as well as the human-tropism of certain drugs and pathogens, the selection of animal models that accurately recapitulate the intricacies of the human biological system becomes more salient for disease modeling and preclinical testing. Immunodeficient mice engrafted with functional human tissues (so-called humanized mice), which allow for the study of physiologically relevant disease mechanisms, have thus become an integral aspect of biomedical research. This review discusses the recent advancements and applications of humanized mouse models on human immune system and liver humanization in modeling human diseases, as well as how they can facilitate translational medicine.
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Affiliation(s)
- Weijian Ye
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; ,
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13
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Wang H, Jiang H, Cheng XW. Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments. PeerJ 2022; 10:e12846. [PMID: 35186462 PMCID: PMC8833225 DOI: 10.7717/peerj.12846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/07/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Atherosclerosis emerges as a result of multiple dynamic cell processes including endothelial damage, inflammatory and immune cell infiltration, foam cell formation, plaque rupture, and thrombosis. Animal experiments have indicated that cathepsins (CTSs) mediate the antigen transmission and inflammatory response involved in the atherosclerosis process, but the specific signal pathways and target cells of the CTSs involved in atherosclerosis are unknown. METHODS We used the GEO query package to download the dataset GSE28829 from the Gene Expression Omnibus (GEO) and filtered the data to check the standardization of the samples through the box chart. We then used the 'limma' package to analyze between-group differences and selected the corresponding differentially expressed genes of CTSs from the protein-protein interaction (PPI) network constructed with the STRING database, and then visualized the CTS-target genes. The best matching pathway and target cells were verified by a male mouse ligation experiment, single-sample GSEA (ssGSEA) analysis, and vitro experiment. RESULTS There were 275 differentially expressed genes (DEGs) selected from the GSE28829 dataset, and the DEGs were identified mainly in the PPI network; 58 core genes (APOE, CD74, CP, AIF1, etc.) target three selected CTS family members (CTSS, CTSB, and CTSC). After the enriched analysis, 15 CTS-target genes were markedly enriched in the phagosome signaling pathway. The mouse experiment results revealed that the percentages and numbers of monocytes and neutrophils and the number of CD68+ cells in CTSS deficiency (CatS-/-) group were lower than those in the wildtype (CatS+/+) group. CTSS mediating phagosome via macrophage were further verified by ssGSEA analysis and vitro experiment. CONCLUSIONS CTSS are the main target molecules in the CTS family that are involved in atherosclerosis. The molecule participate in the progression of atherosclerosis by mediating the phagosome via macrophage.
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Affiliation(s)
- Hailong Wang
- Department of Cardiology and Hypertension, Yanbian University Hospital, Yanji, Jilin, China,Department of Community Health & Geriatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haiying Jiang
- Department of Department of Physiology and Pathophysiology, Jiaxing University Medical College, Jiaxing, Zhejiang, China
| | - Xian Wu Cheng
- Department of Cardiology and Hypertension, Yanbian University Hospital, Yanji, Jilin, China,Department of Community Health & Geriatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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14
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Schlezinger JJ, Hyötyläinen T, Sinioja T, Boston C, Puckett H, Oliver J, Heiger-Bernays W, Webster TF. Perfluorooctanoic acid induces liver and serum dyslipidemia in humanized PPARα mice fed an American diet. Toxicol Appl Pharmacol 2021; 426:115644. [PMID: 34252412 DOI: 10.1016/j.taap.2021.115644] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/06/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are pervasive in the environment resulting in nearly universal detection in people. Human serum PFAS concentrations are strongly associated with increased serum low-density lipoprotein cholesterol (LDL-C), and growing evidence suggests an association with serum triacylglycerides (TG). Here, we tested the hypothesis that perfluorooctanoic acid (PFOA) dysregulates liver and serum triacylglycerides in human peroxisome proliferator activated receptor α (hPPARα)-expressing mice fed an American diet. Mice were exposed to PFOA (3.5 mg/L) in drinking water for 6 weeks resulting in a serum concentration of 48 ± 9 μg/ml. In male and female hPPARα mice, PFOA increased total liver TG and TG substituted with saturated and monounsaturated fatty acids. Lack of expression of PPARα alone also increased total liver TG, and PFOA treatment had little effect on liver TG in PPARα null mice. In hPPARα mice, PFOA neither significantly increased nor decreased serum TG; however, there was a modest increase in TG associated with very low-density cholesterol particles in both sexes. Intriguingly, in female PPARα null mice, PFOA significantly increased serum TG, with a similar trend in males. PFOA also modified fatty acid and TG homeostasis-related gene expression in liver, in a hPPARα-dependent manner, but not in adipose. The results of our study and others reveal the importance of context (serum concentration and genotype) in determining the effect of PFOA on lipid homeostasis.
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Affiliation(s)
- J J Schlezinger
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA.
| | - T Hyötyläinen
- MTM Research Centre, School of Science and Technology, Örebro University, Örebro 702 81, Sweden
| | - T Sinioja
- MTM Research Centre, School of Science and Technology, Örebro University, Örebro 702 81, Sweden
| | - C Boston
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - H Puckett
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - J Oliver
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - W Heiger-Bernays
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - T F Webster
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
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15
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Lu H, Zhang J, Chen YE, Garcia-Barrio MT. Integration of Transformative Platforms for the Discovery of Causative Genes in Cardiovascular Diseases. Cardiovasc Drugs Ther 2021; 35:637-654. [PMID: 33856594 DOI: 10.1007/s10557-021-07175-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2021] [Indexed: 12/11/2022]
Abstract
Cardiovascular diseases are the leading cause of morbidity and mortality worldwide. Genome-wide association studies (GWAS) are powerful epidemiological tools to find genes and variants associated with cardiovascular diseases while follow-up biological studies allow to better understand the etiology and mechanisms of disease and assign causality. Improved methodologies and reduced costs have allowed wider use of bulk and single-cell RNA sequencing, human-induced pluripotent stem cells, organoids, metabolomics, epigenomics, and novel animal models in conjunction with GWAS. In this review, we feature recent advancements relevant to cardiovascular diseases arising from the integration of genetic findings with multiple enabling technologies within multidisciplinary teams to highlight the solidifying transformative potential of this approach. Well-designed workflows integrating different platforms are greatly improving and accelerating the unraveling and understanding of complex disease processes while promoting an effective way to find better drug targets, improve drug design and repurposing, and provide insight towards a more personalized clinical practice.
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Affiliation(s)
- Haocheng Lu
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA
| | - Jifeng Zhang
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA.,Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA. .,Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA.
| | - Minerva T Garcia-Barrio
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA.
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16
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Morral N, Liu S, Conteh AM, Chu X, Wang Y, Dong XC, Liu Y, Linnemann AK, Wan J. Aberrant gene expression induced by a high fat diet is linked to H3K9 acetylation in the promoter-proximal region. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194691. [PMID: 33556624 DOI: 10.1016/j.bbagrm.2021.194691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/22/2021] [Accepted: 01/30/2021] [Indexed: 12/13/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease, with an estimated global prevalence of 1 in 4 individuals. Aberrant transcriptional control of gene expression is central to the pathophysiology of metabolic diseases. However, the molecular mechanisms leading to gene dysregulation are not well understood. Histone modifications play important roles in the control of transcription. Acetylation of histone 3 at lysine 9 (H3K9ac) is associated with transcriptional activity and is implicated in transcript elongation by controlling RNA polymerase II (RNAPII) pause-release. Hence, changes in this histone modification may shed information on novel pathways linking transcription control and metabolic dysfunction. Here, we carried out genome-wide analysis of H3K9ac in the liver of mice fed a control or a high-fat diet (an animal model of NAFLD), and asked whether this histone mark associates with changes in gene expression. We found that over 70% of RNAPII peaks in promoter-proximal regions overlapped with H3K9ac, consistent with a role of H3K9ac in the regulation of transcription. When comparing high-fat with control diet, approximately 17% of the differentially expressed genes were associated with changes in H3K9ac in their promoters, showing a strong correlation between changes in H3K9ac signal and gene expression. Overall, our data indicate that in response to a high-fat diet, dysregulated gene expression of a subset of genes may be attributable to changes in transcription elongation driven by H3K9ac. Our results point at an added mechanism of gene regulation that may be important in the development of metabolic diseases.
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Affiliation(s)
- Núria Morral
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States of America.
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Abass M Conteh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Xiaona Chu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Yue Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - X Charlie Dong
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Amelia K Linnemann
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States of America; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States of America
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Wang X, Li G, Guo C, Zhang J, Kong J, He J, Li F, Liu Y, Yang Y, Lu Z, Liu J. Ethyl 2-[2,3,4-Trimethoxy-6-(1-Octanoyl)Phenyl] Acetate (TMPA) Ameliorates Lipid Accumulation by Disturbing the Combination of LKB1 with Nur77 and Activating the AMPK Pathway in HepG2 Cells and Mice Primary Hepatocytes. Diabetes Metab Syndr Obes 2021; 14:4165-4177. [PMID: 34629883 PMCID: PMC8495146 DOI: 10.2147/dmso.s321246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/30/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The AMP-activated protein kinase alpha (AMPKα) pathway has widely been considered a key factor in energy metabolism. Ethyl 2-[2,3,4-trimethoxy-6-(1-octanoyl)phenyl] acetate (TMPA) is a novel AMPK agonist, which influences the stability of Nuclear Receptor Subfamily 4, Group A, Member 1 (Nur77)-serine-threonine kinase 11 (LKB1) in the nucleus. A recent study has determined that TMPA can ameliorate the reduction of insulin resistance in type II db/db mice. However, the role of TMPA in hepatocyte lipid metabolism has not been elucidated. OBJECTIVE To investigate whether TMPA could ameliorate liver lipid accumulation under the stimulation of free fatty acids (FFAs) in vitro. METHODS We evaluated differences of Nur77 and AMPK pathway in mice fed a high-fat diet and those fed a normal diet. In vitro, TMPA was added to HepG2 cells and primary hepatocytes before FFAs stimulation. Oil red O staining, Nile red staining were used to evaluate lipid deposition. Western blot and immunofluorescence were used to quantify related proteins. RESULTS Nur77, AMPKα, LKB1, 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), acetyl-CoA carboxylase phosphorylation (p-ACC), and carnitine palmitoyltransferase 1 (CPT1A) showed significant differences in vivo. Under the intervention of TMPA, HepG2 cells and primary hepatocytes showed considerable amelioration of lipid deposition and improved the expression of phosphorylated (p)-AMPKα (p-AMPKα), p-LKB1, p-ACC, and CPT1A. Furthermore, Western blotting and immunofluorescence studies indicated that LKB1 dramatically increased expression in the cytoplasm but decreased in the nucleus. Further, AMPKα phosphorylation (p-AMPKα) also showed a higher expression in cytoplasm instead of the nucleus. CONCLUSION TMPA ameliorated lipid accumulation by influencing the stability of Nur77-LKB1 in vitro.
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Affiliation(s)
- Xiaoyu Wang
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Guangbing Li
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
| | - Changfa Guo
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong University, Cheeloo College of Medicine, Jinan, Shandong, People’s Republic of China
| | - Jiayao Zhang
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Junjie Kong
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
| | - Jingyi He
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
| | - Feiyu Li
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Yong Liu
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Yang Yang
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Ziwen Lu
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Jun Liu
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China
- Correspondence: Jun Liu Department of Hepatobiliary Surgery and Center of Organ Transplantation, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, People’s Republic of China Email
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