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Gallage S, Ali A, Barragan Avila JE, Seymen N, Ramadori P, Joerke V, Zizmare L, Aicher D, Gopalsamy IK, Fong W, Kosla J, Focaccia E, Li X, Yousuf S, Sijmonsma T, Rahbari M, Kommoss KS, Billeter A, Prokosch S, Rothermel U, Mueller F, Hetzer J, Heide D, Schinkel B, Machauer T, Pichler B, Malek NP, Longerich T, Roth S, Rose AJ, Schwenck J, Trautwein C, Karimi MM, Heikenwalder M. A 5:2 intermittent fasting regimen ameliorates NASH and fibrosis and blunts HCC development via hepatic PPARα and PCK1. Cell Metab 2024; 36:1371-1393.e7. [PMID: 38718791 DOI: 10.1016/j.cmet.2024.04.015] [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: 04/15/2023] [Revised: 12/21/2023] [Accepted: 04/17/2024] [Indexed: 06/07/2024]
Abstract
The role and molecular mechanisms of intermittent fasting (IF) in non-alcoholic steatohepatitis (NASH) and its transition to hepatocellular carcinoma (HCC) are unknown. Here, we identified that an IF 5:2 regimen prevents NASH development as well as ameliorates established NASH and fibrosis without affecting total calorie intake. Furthermore, the IF 5:2 regimen blunted NASH-HCC transition when applied therapeutically. The timing, length, and number of fasting cycles as well as the type of NASH diet were critical parameters determining the benefits of fasting. Combined proteome, transcriptome, and metabolome analyses identified that peroxisome-proliferator-activated receptor alpha (PPARα) and glucocorticoid-signaling-induced PCK1 act co-operatively as hepatic executors of the fasting response. In line with this, PPARα targets and PCK1 were reduced in human NASH. Notably, only fasting initiated during the active phase of mice robustly induced glucocorticoid signaling and free-fatty-acid-induced PPARα signaling. However, hepatocyte-specific glucocorticoid receptor deletion only partially abrogated the hepatic fasting response. In contrast, the combined knockdown of Ppara and Pck1 in vivo abolished the beneficial outcomes of fasting against inflammation and fibrosis. Moreover, overexpression of Pck1 alone or together with Ppara in vivo lowered hepatic triglycerides and steatosis. Our data support the notion that the IF 5:2 regimen is a promising intervention against NASH and subsequent liver cancer.
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Affiliation(s)
- Suchira Gallage
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen.
| | - Adnan Ali
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jose Efren Barragan Avila
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Nogayhan Seymen
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, Denmark Hill, London, UK
| | - Pierluigi Ramadori
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen
| | - Vera Joerke
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Röntgenweg 13, 72076 Tübingen, Germany
| | - Laimdota Zizmare
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Röntgenweg 13, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - David Aicher
- University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen
| | - Indresh K Gopalsamy
- University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen
| | - Winnie Fong
- University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen
| | - Jan Kosla
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Enrico Focaccia
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Xin Li
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Suhail Yousuf
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Tjeerd Sijmonsma
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mohammad Rahbari
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Surgery, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Katharina S Kommoss
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Adrian Billeter
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Sandra Prokosch
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ulrike Rothermel
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Florian Mueller
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jenny Hetzer
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Danijela Heide
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Benjamin Schinkel
- University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen
| | - Tim Machauer
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Bernd Pichler
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Röntgenweg 13, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," Eberhard-Karls University of Tübingen, Tübingen, Germany; Department of Nuclear Medicine and Clinical Molecular Imaging, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Nisar P Malek
- University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen; Department Internal Medicine I, University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Thomas Longerich
- Institute of Pathology, Heidelberg University Hospital, Universitätsklinikum Heidelberg, Pathologisches Institut, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Susanne Roth
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Adam J Rose
- Nutrient Metabolism and Signalling Laboratory, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and Metabolism, Diabetes and Obesity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Johannes Schwenck
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Röntgenweg 13, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," Eberhard-Karls University of Tübingen, Tübingen, Germany; Department of Nuclear Medicine and Clinical Molecular Imaging, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Christoph Trautwein
- University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen; Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Röntgenweg 13, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Mohammad M Karimi
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, Denmark Hill, London, UK
| | - Mathias Heikenwalder
- German Cancer Research Center (DKFZ), Division of Chronic Inflammation and Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; University Tuebingen, Faculty of Medicine, Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Otfried-Müller-Straße 37, 72076 Tübingen; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," Eberhard-Karls University of Tübingen, Tübingen, Germany.
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Fu M, Lu S, Gong L, Zhou Y, Wei F, Duan Z, Xiang R, Gonzalez FJ, Li G. Intermittent fasting shifts the diurnal transcriptome atlas of transcription factors. Mol Cell Biochem 2024:10.1007/s11010-024-04928-y. [PMID: 38528297 DOI: 10.1007/s11010-024-04928-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/05/2024] [Indexed: 03/27/2024]
Abstract
Intermittent fasting remains a safe and effective strategy to ameliorate various age-related diseases, but its specific mechanisms are not fully understood. Considering that transcription factors (TFs) determine the response to environmental signals, here, we profiled the diurnal expression of 600 samples across four metabolic tissues sampled every 4 over 24 h from mice placed on five different feeding regimens to provide an atlas of TFs in biological space, time, and feeding regimen. Results showed that 1218 TFs exhibited tissue-specific and temporal expression profiles in ad libitum mice, of which 974 displayed significant oscillations at least in one tissue. Intermittent fasting triggered more than 90% (1161 in 1234) of TFs to oscillate somewhere in the body and repartitioned their tissue-specific expression. A single round of fasting generally promoted TF expression, especially in skeletal muscle and adipose tissues, while intermittent fasting mainly suppressed TF expression. Intermittent fasting down-regulated aging pathway and upregulated the pathway responsible for the inhibition of mammalian target of rapamycin (mTOR). Intermittent fasting shifts the diurnal transcriptome atlas of TFs, and mTOR inhibition may orchestrate intermittent fasting-induced health improvements. This atlas offers a reference and resource to understand how TFs and intermittent fasting may contribute to diurnal rhythm oscillation and bring about specific health benefits.
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Affiliation(s)
- Min Fu
- Department of Neurology, The Fourth Hospital of Changsha, Affiliated Changsha Hospital of Hunan Normal University, Changsha, 410006, Hunan, China
| | - Siyu Lu
- Key Laboratory of Hunan Province for Model Animal and Stem Cell Biology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China
- Center for Aging Biomedicine, National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Lijun Gong
- Key Laboratory of Hunan Province for Model Animal and Stem Cell Biology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China
- Center for Aging Biomedicine, National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yiming Zhou
- Key Laboratory of Hunan Province for Model Animal and Stem Cell Biology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China
- Center for Aging Biomedicine, National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Fang Wei
- Department of Neurology, The Fourth Hospital of Changsha, Affiliated Changsha Hospital of Hunan Normal University, Changsha, 410006, Hunan, China.
- Center for Aging Biomedicine, National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Zhigui Duan
- Center for Aging Biomedicine, National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Rong Xiang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 41001, Hunan, China
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guolin Li
- Key Laboratory of Hunan Province for Model Animal and Stem Cell Biology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China.
- Center for Aging Biomedicine, National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
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Sinha RA. Targeting nuclear receptors for NASH/MASH: From bench to bedside. LIVER RESEARCH 2024; 8:34-45. [PMID: 38544909 PMCID: PMC7615772 DOI: 10.1016/j.livres.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
The onset of metabolic dysfunction-associated steatohepatitis (MASH) or non-alcoholic steatohepatitis (NASH) represents a tipping point leading to liver injury and subsequent hepatic complications in the natural progression of what is now termed metabolic dysfunction-associated steatotic liver diseases (MASLD), formerly known as non-alcoholic fatty liver disease (NAFLD). With no pharmacological treatment currently available for MASH/NASH, the race is on to develop drugs targeting multiple facets of hepatic metabolism, inflammation, and pro-fibrotic events, which are major drivers of MASH. Nuclear receptors (NRs) regulate genomic transcription upon binding to lipophilic ligands and govern multiple aspects of liver metabolism and inflammation. Ligands of NRs may include hormones, lipids, bile acids, and synthetic ligands, which upon binding to NRs regulate the transcriptional activities of target genes. NR ligands are presently the most promising drug candidates expected to receive approval from the United States Food and Drug Administration as a pharmacological treatment for MASH. This review aims to cover the current understanding of NRs, including nuclear hormone receptors, non-steroid hormone receptors, circadian NRs, and orphan NRs, which are currently undergoing clinical trials for MASH treatment, along with NRs that have shown promising results in preclinical studies.
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Affiliation(s)
- Rohit A Sinha
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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4
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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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5
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Vishnevsky OV, Bocharnikov AV, Ignatieva EV. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks. Int J Mol Sci 2024; 25:1011. [PMID: 38256085 PMCID: PMC10816497 DOI: 10.3390/ijms25021011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments, multiple regression models were constructed, demonstrating a significant dependence of the peak scores on the presence in the peak sequences of not only highly significant target motifs but also less significant motifs corresponding to the binding sites of the partner transcription factors. A significant correlation was shown between the presence of the target motifs FOXA2 and the partner motifs HNF4G, which found experimental confirmation in the scientific literature, demonstrating the important contribution of the partner transcription factors to the binding of the target transcription factor to DNA and, consequently, their important contribution to the peak score.
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Affiliation(s)
- Oleg V. Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Andrey V. Bocharnikov
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Elena V. Ignatieva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
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Wang J, Wen Y, Zhao W, Zhang Y, Lin F, Ouyang C, Wang H, Yao L, Ma H, Zhuo Y, Huang H, Shi X, Feng L, Lin D, Jiang B, Li Q. Hepatic conversion of acetyl-CoA to acetate plays crucial roles in energy stress. eLife 2023; 12:RP87419. [PMID: 37902629 PMCID: PMC10615369 DOI: 10.7554/elife.87419] [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] [Indexed: 10/31/2023] Open
Abstract
Accumulating evidence indicates that acetate is increased under energy stress conditions such as those that occur in diabetes mellitus and prolonged starvation. However, how and where acetate is produced and the nature of its biological significance are largely unknown. We observed overproduction of acetate to concentrations comparable to those of ketone bodies in patients and mice with diabetes or starvation. Mechanistically, ACOT12 and ACOT8 are dramatically upregulated in the liver to convert free fatty acid-derived acetyl-CoA to acetate and CoA. This conversion not only provides a large amount of acetate, which preferentially fuels the brain rather than muscle, but also recycles CoA, which is required for sustained fatty acid oxidation and ketogenesis. We suggest that acetate is an emerging novel 'ketone body' that may be used as a parameter to evaluate the progression of energy stress.
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Affiliation(s)
- Jinyang Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yaxin Wen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Wentao Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Furong Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Cong Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Huihui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Lizheng Yao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Huanhuan Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yue Zhuo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Huiying Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xiulin Shi
- Department of Endocrinology and Diabetes, Xiamen Diabetes Institute, Fujian Province Key Laboratory of Translational Research for Diabetes, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Liubin Feng
- High-Field NMR Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Donghai Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Bin Jiang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Qinxi Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
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Abstract
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
- Department of Physics, University of Maryland, College Park, Maryland, USA;
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, Maryland, USA;
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
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Kitamoto T, Accili D. Unraveling the mysteries of hepatic insulin signaling: deconvoluting the nuclear targets of insulin. Endocr J 2023; 70:851-866. [PMID: 37245960 DOI: 10.1507/endocrj.ej23-0150] [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] [Indexed: 05/30/2023] Open
Abstract
Over 100 years have passed since insulin was first administered to a diabetic patient. Since then great strides have been made in diabetes research. It has determined where insulin is secreted from, which organs it acts on, how it is transferred into the cell and is delivered to the nucleus, how it orchestrates the expression pattern of the genes, and how it works with each organ to maintain systemic metabolism. Any breakdown in this system leads to diabetes. Thanks to the numerous researchers who have dedicated their lives to cure diabetes, we now know that there are three major organs where insulin acts to maintain glucose/lipid metabolism: the liver, muscles, and fat. The failure of insulin action on these organs, such as insulin resistance, result in hyperglycemia and/or dyslipidemia. The primary trigger of this condition and its association among these tissues still remain to be uncovered. Among the major organs, the liver finely tunes the glucose/lipid metabolism to maintain metabolic flexibility, and plays a crucial role in glucose/lipid abnormality due to insulin resistance. Insulin resistance disrupts this tuning, and selective insulin resistance arises. The glucose metabolism loses its sensitivity to insulin, while the lipid metabolism maintains it. The clarification of its mechanism is warranted to reverse the metabolic abnormalities due to insulin resistance. This review will provide a brief historical review for the progress of the pathophysiology of diabetes since the discovery of insulin, followed by a review of the current research clarifying our understanding of selective insulin resistance.
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Affiliation(s)
- Takumi Kitamoto
- Department of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba 260-8670, Japan
| | - Domenico Accili
- Department of Medicine and Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
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9
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Wang J, Zhao X, Zhou R, Wang M, Xiang W, You Z, Li M, Tang R, Zheng J, Li J, Zhu L, Gao J, Li H, Pang R, Zhang A. Gut microbiota and transcriptome dynamics in every-other-day fasting are associated with neuroprotection in rats with spinal cord injury. Front Microbiol 2023; 14:1206909. [PMID: 37577426 PMCID: PMC10417830 DOI: 10.3389/fmicb.2023.1206909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Every-other-day fasting (EODF) is a classical intermittent fasting (IF) mode with neuroprotective effects that promotes motor function recovery after spinal cord injury (SCI) in rats. However, its dynamic effects on the gut microbiota and spinal cord transcriptome remain unknown. Methods In this study, 16S rRNA sequencing and RNA-seq analysis were used to investigate the effects of ad libitum (AL) and EODF dietary modes on the structural characteristics of rat gut microbiota in rats and the spinal cord transcriptome at various time points after SCI induction. Results Our results showed that both dietary modes affected the bacterial community composition in SCI rats, with EODF treatment inducing and suppressing dynamic changes in the abundances of potentially anti-inflammatory and pro-inflammatory bacteria. Furthermore, the differentially expressed genes (DEGs) enriched after EODF intervention in SCI rats were associated with various biological events, including immune inflammatory response, cell differentiation, protein modification, neural growth, and apoptosis. In particular, significant spatiotemporal differences were apparent in the DEGs associated with neuroprotection between the EODF and AL interventions. These DGEs were mainly focused on days 1, 3, and 7 after SCI. The relative abundance of certain genera was significantly correlated with DEGs associated with neuroprotective effects in the EODF-SCI group. Discussion Our results showed that EODF treatment may exert neuroprotective effects by modulating the transcriptome expression profile following SCI in rats. Furthermore, gut microbiota may be partially involved in mediating these effects.
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Affiliation(s)
- Junyu Wang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaohua Zhao
- Department of Rehabilitation Medicine, General Hospital of Western Theater Command, Chengdu, China
- Department of Rehabilitation Medicine, The People’s Hospital of Tongliang District, Chongqing, China
| | - Ruihan Zhou
- Department of Rehabilitation Medicine, General Hospital of Western Theater Command, Chengdu, China
| | - Meiyu Wang
- Rehabilitation and Wellness Care Centre, Tian Fu College of Swufe, Chengdu, China
| | - Wu Xiang
- Department of Rehabilitation Medicine, General Hospital of Western Theater Command, Chengdu, China
| | - Zilong You
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Min Li
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Ruiling Tang
- Department of Rehabilitation Medicine, General Hospital of Western Theater Command, Chengdu, China
| | - Jingqi Zheng
- Department of Rehabilitation Medicine, General Hospital of Western Theater Command, Chengdu, China
| | - Jiayu Li
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li Zhu
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Jiaxin Gao
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Huaqiang Li
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rizhao Pang
- Department of Rehabilitation Medicine, The People’s Hospital of Tongliang District, Chongqing, China
| | - Anren Zhang
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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10
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Sen D, Maniyadath B, Chowdhury S, Kaur A, Khatri S, Chakraborty A, Mehendale N, Nadagouda S, Sandra U, Kamat SS, Kolthur-Seetharam U. Metabolic regulation of CTCF expression and chromatin association dictates starvation response in mice and flies. iScience 2023; 26:107128. [PMID: 37416476 PMCID: PMC10320512 DOI: 10.1016/j.isci.2023.107128] [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: 09/08/2022] [Revised: 05/16/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Coordinated temporal control of gene expression is essential for physiological homeostasis, especially during metabolic transitions. However, the interplay between chromatin architectural proteins and metabolism in regulating transcription is less understood. Here, we demonstrate a conserved bidirectional interplay between CTCF (CCCTC-binding factor) expression/function and metabolic inputs during feed-fast cycles. Our results indicate that its loci-specific functional diversity is associated with physiological plasticity in mouse hepatocytes. CTCF differential expression and long non-coding RNA-Jpx mediated changes in chromatin occupancy, unraveled its paradoxical yet tuneable functions, which are governed by metabolic inputs. We illustrate the key role of CTCF in controlling temporal cascade of transcriptional response, with effects on hepatic mitochondrial energetics and lipidome. Underscoring the evolutionary conservation of CTCF-dependent metabolic homeostasis, CTCF knockdown in flies abrogated starvation resistance. In summary, we demonstrate the interplay between CTCF and metabolic inputs that highlights the coupled plasticity of physiological responses and chromatin function.
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Affiliation(s)
- Devashish Sen
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Babukrishna Maniyadath
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Shreyam Chowdhury
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Arshdeep Kaur
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Subhash Khatri
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Arnab Chakraborty
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Neelay Mehendale
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Snigdha Nadagouda
- Tata Institute of Fundamental Research- Hyderabad (TIFR-H), Hyderabad, Telangana 500046, India
| | - U.S. Sandra
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
- Tata Institute of Fundamental Research- Hyderabad (TIFR-H), Hyderabad, Telangana 500046, India
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11
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Radushkevitz-Frishman T, Charni-Natan M, Goldstein I. Dynamic chromatin accessibility during nutritional iron overload reveals a BMP6-independent induction of cell cycle genes. J Nutr Biochem 2023:109407. [PMID: 37336330 DOI: 10.1016/j.jnutbio.2023.109407] [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: 01/30/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Iron is essential to organism physiology as it participates in numerous biological processes including oxygen transport, respiration and erythropoiesis. Although iron is critical to physiology, excess iron is toxic to cells and tissues due to generation of reactive oxygen species. Therefore, well-kept iron homeostasis is a mainstay of proper cell and organ function. Iron overload disorders, caused by nutritional or genetic factors, contribute to many pathologies such as diabetes, non-alcoholic steatohepatitis and hepatocellular carcinoma. The liver is not only vulnerable to the effects of iron overload, it is also the major organ controlling iron homeostasis. During iron overload, Bone Morphogenic Protein (BMP) levels increase and initiate a hepatic response aimed at lowering iron levels. The transcriptional effects of iron overload are not well-characterized and the underlining enhancer regulation is uncharted. Here, we profiled the liver's transcriptome and chromatin accessibility following nutritional iron overload. We found marked changes in gene expression and enhancer accessibility following iron overload. Surprisingly, 16% of genes induced following iron overload participate in propagating the cell cycle. Induction of cell cycle genes was independent of BMP. Genome-wide enhancer landscape profiling revealed hundreds of enhancers with altered activity following iron overload. Characterization of transcription factor motifs and footprints in iron-regulated enhancers showed a role for the Activator Protein 1 (AP-1) transcription factor in promoting cell cycle-related transcription. In summary, we found that the transcriptional program at play during iron overload is bifurcated in which BMP signaling controls iron homeostasis genes while an AP-1-driven program controls cell cycle genes.
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Affiliation(s)
- Talia Radushkevitz-Frishman
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. 229 Herzl St., Rehovot 7610001, Israel
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. 229 Herzl St., Rehovot 7610001, Israel
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. 229 Herzl St., Rehovot 7610001, Israel.
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12
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Wortham M, Liu F, Harrington AR, Fleischman JY, Wallace M, Mulas F, Mallick M, Vinckier NK, Cross BR, Chiou J, Patel NA, Sui Y, McGrail C, Jun Y, Wang G, Jhala US, Schüle R, Shirihai OS, Huising MO, Gaulton KJ, Metallo CM, Sander M. Nutrient regulation of the islet epigenome controls adaptive insulin secretion. J Clin Invest 2023; 133:e165208. [PMID: 36821378 PMCID: PMC10104905 DOI: 10.1172/jci165208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
Adaptation of the islet β cell insulin-secretory response to changing insulin demand is critical for blood glucose homeostasis, yet the mechanisms underlying this adaptation are unknown. Here, we have shown that nutrient-stimulated histone acetylation plays a key role in adapting insulin secretion through regulation of genes involved in β cell nutrient sensing and metabolism. Nutrient regulation of the epigenome occurred at sites occupied by the chromatin-modifying enzyme lysine-specific demethylase 1 (Lsd1) in islets. β Cell-specific deletion of Lsd1 led to insulin hypersecretion, aberrant expression of nutrient-response genes, and histone hyperacetylation. Islets from mice adapted to chronically increased insulin demand exhibited shared epigenetic and transcriptional changes. Moreover, we found that genetic variants associated with type 2 diabetes were enriched at LSD1-bound sites in human islets, suggesting that interpretation of nutrient signals is genetically determined and clinically relevant. Overall, these studies revealed that adaptive insulin secretion involves Lsd1-mediated coupling of nutrient state to regulation of the islet epigenome.
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Affiliation(s)
- Matthew Wortham
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Fenfen Liu
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Austin R. Harrington
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Johanna Y. Fleischman
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Martina Wallace
- Department of Bioengineering, UCSD, La Jolla, California, USA
| | - Francesca Mulas
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Medhavi Mallick
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Nicholas K. Vinckier
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Benjamin R. Cross
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Joshua Chiou
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Nisha A. Patel
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Yinghui Sui
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Carolyn McGrail
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Yesl Jun
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Gaowei Wang
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Ulupi S. Jhala
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Roland Schüle
- Department of Urology, University of Freiburg Medical Center, Freiburg, Germany
| | - Orian S. Shirihai
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Mark O. Huising
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, and Physiology and Membrane Biology, School of Medicine, UCD, Davis, California, USA
| | - Kyle J. Gaulton
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | | | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
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13
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Kersten S. The impact of fasting on adipose tissue metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159262. [PMID: 36521736 DOI: 10.1016/j.bbalip.2022.159262] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/20/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Fasting and starvation were common occurrences during human evolution and accordingly have been an important environmental factor shaping human energy metabolism. Humans can tolerate fasting reasonably well through adaptative and well-orchestrated time-dependent changes in energy metabolism. Key features of the adaptive response to fasting are the breakdown of liver glycogen and muscle protein to produce glucose for the brain, as well as the gradual depletion of the fat stores, resulting in the release of glycerol and fatty acids into the bloodstream and the production of ketone bodies in the liver. In this paper, an overview is presented of our current understanding of the effects of fasting on adipose tissue metabolism. Fasting leads to reduced uptake of circulating triacylglycerols by adipocytes through inhibition of the activity of the rate-limiting enzyme lipoprotein lipase. In addition, fasting stimulates the degradation of stored triacylglycerols by activating the key enzyme adipose triglyceride lipase. The mechanisms underlying these events are discussed, with a special interest in insights gained from studies on humans. Furthermore, an overview is presented of the effects of fasting on other metabolic pathways in the adipose tissue, including fatty acid synthesis, glucose uptake, glyceroneogenesis, autophagy, and the endocrine function of adipose tissue.
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Affiliation(s)
- Sander Kersten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University, the Netherlands.
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14
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Zhao Y, Li S, Chen Y, Wang Y, Wei Y, Zhou T, Zhang Y, Yang Y, Chen L, Liu Y, Hu C, Zhou B, Ding Q. Histone phosphorylation integrates the hepatic glucagon-PKA-CREB gluconeogenesis program in response to fasting. Mol Cell 2023; 83:1093-1108.e8. [PMID: 36863348 DOI: 10.1016/j.molcel.2023.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/08/2022] [Accepted: 02/04/2023] [Indexed: 03/04/2023]
Abstract
The glucagon-PKA signal is generally believed to control hepatic gluconeogenesis via the CREB transcription factor. Here we uncovered a distinct function of this signal in directly stimulating histone phosphorylation for gluconeogenic gene regulation in mice. In the fasting state, CREB recruited activated PKA to regions near gluconeogenic genes, where PKA phosphorylated histone H3 serine 28 (H3S28ph). H3S28ph, recognized by 14-3-3ζ, promoted recruitment of RNA polymerase II and transcriptional stimulation of gluconeogenic genes. In contrast, in the fed state, more PP2A was found near gluconeogenic genes, which counteracted PKA by dephosphorylating H3S28ph and repressing transcription. Importantly, ectopic expression of phosphomimic H3S28 efficiently restored gluconeogenic gene expression when liver PKA or CREB was depleted. These results together highlight a different functional scheme in regulating gluconeogenesis by the glucagon-PKA-CREB-H3S28ph cascade, in which the hormone signal is transmitted to chromatin for rapid and efficient gluconeogenic gene activation.
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Affiliation(s)
- Yongxu Zhao
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Shuang Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhao Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuchen Wang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuda Wei
- Department of Clinical Laboratory, Linyi People's Hospital, Xuzhou Medical University, Shandong 276000, China
| | - Tingting Zhou
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuwei Zhang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuanyuan Yang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lanlan Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Liu
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng Hu
- Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ben Zhou
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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15
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Caratti G, Desgeorges T, Juban G, Stifel U, Fessard A, Koenen M, Caratti B, Théret M, Skurk C, Chazaud B, Tuckermann JP, Mounier R. Macrophagic AMPKα1 orchestrates regenerative inflammation induced by glucocorticoids. EMBO Rep 2023; 24:e55363. [PMID: 36520372 PMCID: PMC9900347 DOI: 10.15252/embr.202255363] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Macrophages are key cells after tissue damage since they mediate both acute inflammatory phase and regenerative inflammation by shifting from pro-inflammatory to restorative cells. Glucocorticoids (GCs) are the most potent anti-inflammatory hormone in clinical use, still their actions on macrophages are not fully understood. We show that the metabolic sensor AMP-activated protein kinase (AMPK) is required for GCs to induce restorative macrophages. GC Dexamethasone activates AMPK in macrophages and GC receptor (GR) phosphorylation is decreased in AMPK-deficient macrophages. Loss of AMPK in macrophages abrogates the GC-induced acquisition of their repair phenotype and impairs GC-induced resolution of inflammation in vivo during post-injury muscle regeneration and acute lung injury. Mechanistically, two categories of genes are impacted by GC treatment in macrophages. Firstly, canonical cytokine regulation by GCs is not affected by AMPK loss. Secondly, AMPK-dependent GC-induced genes required for the phenotypic transition of macrophages are co-regulated by the transcription factor FOXO3, an AMPK substrate. Thus, beyond cytokine regulation, GR requires AMPK-FOXO3 for immunomodulatory actions in macrophages, linking their metabolic status to transcriptional control in regenerative inflammation.
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Affiliation(s)
- Giorgio Caratti
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Thibaut Desgeorges
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Gaëtan Juban
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Ulrich Stifel
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Aurélie Fessard
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Mascha Koenen
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
- Present address:
Laboratory of Molecular MetabolismThe Rockefeller UniversityNew YorkNYUSA
| | - Bozhena Caratti
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Marine Théret
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
- Present address:
Department of Medical GeneticsSchool of Biomedical Engineering and the Biomedical Research CentreVancouverBCCanada
| | - Carsten Skurk
- Department of CardiologyCharité Universitätsmedizin BerlinBerlinGermany
- Franklin/German Centre for Cardiovascular Research (DZHK), Partner Site Berlin/Institute of Health (BIH)BerlinGermany
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
| | - Jan P Tuckermann
- Institute of Comparative Molecular EndocrinologyUniversität UlmUlmGermany
| | - Rémi Mounier
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217Université de LyonLyonFrance
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16
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Vandewalle J, Garcia B, Timmermans S, Vanderhaeghen T, Van Wyngene L, Eggermont M, Dufoor H, Van Dender C, Halimi F, Croubels S, Herpain A, Libert C. Hepatic Peroxisome Proliferator-Activated Receptor Alpha Dysfunction in Porcine Septic Shock. Cells 2022; 11:cells11244080. [PMID: 36552845 PMCID: PMC9777423 DOI: 10.3390/cells11244080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Despite decades of research, sepsis remains one of the most urgent unmet medical needs. Mechanistic investigations into sepsis have mainly focused on targeting inflammatory pathways; however, recent data indicate that sepsis should also be seen as a metabolic disease. Targeting metabolic dysregulations that take place in sepsis might uncover novel therapeutic opportunities. The role of peroxisome proliferator-activated receptor alpha (PPARɑ) in liver dysfunction during sepsis has recently been described, and restoring PPARɑ signaling has proven to be successful in mouse polymicrobial sepsis. To confirm that such therapy might be translated to septic patients, we analyzed metabolic perturbations in the liver of a porcine fecal peritonitis model. Resuscitation with fluids, vasopressor, antimicrobial therapy and abdominal lavage were applied to the pigs in order to mimic human clinical care. By using RNA-seq, we detected downregulated PPARɑ signaling in the livers of septic pigs and that reduced PPARɑ levels correlated well with disease severity. As PPARɑ regulates the expression of many genes involved in fatty acid oxidation, the reduced expression of these target genes, concomitant with increased free fatty acids in plasma and ectopic lipid deposition in the liver, was observed. The results obtained with pigs are in agreement with earlier observations seen in mice and support the potential of targeting defective PPARɑ signaling in clinical research.
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Affiliation(s)
- Jolien Vandewalle
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
- Correspondence: (J.V.); (C.L.)
| | - Bruno Garcia
- Experimental Laboratory of Intensive Care, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Department of Intensive Care, Centre Hospitalier Universitaire de Lille, 59000 Lille, France
| | - Steven Timmermans
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
| | - Tineke Vanderhaeghen
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
| | - Lise Van Wyngene
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
| | - Melanie Eggermont
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
| | - Hester Dufoor
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
| | - Céline Van Dender
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
| | - Fëllanza Halimi
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Siska Croubels
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Antoine Herpain
- Experimental Laboratory of Intensive Care, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Department of Intensive Care, Erasme University Hospital—HUB, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Department of Intensive Care, St.-Pierre University Hospital, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Claude Libert
- VIB Center for Inflammation Research, VIB, 9052 Ghent, Belgium
- Department for Biomedical Molecular Biology, Faculty of Sciences, Ghent University, 9052 Ghent, Belgium
- Correspondence: (J.V.); (C.L.)
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17
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Yoon JY, Kim JY, Kim HJ, Ka NL, Lee SH, Lee MO. LncRNA Ctcflos modulates glucocorticoid receptor-mediated induction of hepatic phosphoenolpyruvate carboxykinase in mice. Life Sci 2022; 312:121254. [PMID: 36470542 DOI: 10.1016/j.lfs.2022.121254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/16/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Jae-Yeun Yoon
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Ju-Yeon Kim
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Hyeon-Ji Kim
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea; Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Na-Lee Ka
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea; Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sang-Heon Lee
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Mi-Ock Lee
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea; Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea; Bio-MAX institute, Seoul National University, Seoul, Republic of Korea.
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18
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Luzete-Monteiro E, Zaret KS. Structures and consequences of pioneer factor binding to nucleosomes. Curr Opin Struct Biol 2022; 75:102425. [PMID: 35863165 PMCID: PMC9976633 DOI: 10.1016/j.sbi.2022.102425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022]
Abstract
Pioneer transcription factors are able to bind a partially exposed motif on the surface of a nucleosome, enabling the proteins to target sites in silent regions of chromatin that have been compacted by linker histone. The targeting of nucleosomal DNA by pioneer factors has been observed in vitro and in vivo, where binding can promote local nucleosome exposure that allows other transcription factors, nucleosome remodelers, and histone modifiers to engage the chromatin and elicit gene activation or further repression. Pioneer factors thereby establish new gene expression programs during cell fate changes that occur during embryonic development, regeneration, and cancer. Here, we review recent biophysical studies that reveal the structural features and strategies used by pioneer factors to accomplish nucleosome binding and the consequential changes to nucleosomes that can lead to DNA accessibility.
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Affiliation(s)
- Edgar Luzete-Monteiro
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104-4544
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA
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19
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Reinisch I, Klymiuk I, Michenthaler H, Moyschewitz E, Galhuber M, Krstic J, Domingo M, Zhang F, Karbiener M, Vujić N, Kratky D, Schreiber R, Schupp M, Lenihan-Geels G, Schulz TJ, Malli R, Madl T, Prokesch A. p53 Regulates a miRNA-Fructose Transporter Axis in Brown Adipose Tissue Under Fasting. Front Genet 2022; 13:913030. [PMID: 35734423 PMCID: PMC9207587 DOI: 10.3389/fgene.2022.913030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022] Open
Abstract
Active thermogenic adipocytes avidly consume energy substrates like fatty acids and glucose to maintain body temperature upon cold exposure. Despite strong evidence for the involvement of brown adipose tissue (BAT) in controlling systemic energy homeostasis upon nutrient excess, it is unclear how the activity of brown adipocytes is regulated in times of nutrient scarcity. Therefore, this study aimed to scrutinize factors that modulate BAT activity to balance thermogenic and energetic needs upon simultaneous fasting and cold stress. For an unbiased view, we performed transcriptomic and miRNA sequencing analyses of BAT from acutely fasted (24 h) mice under mild cold exposure. Combining these data with in-depth bioinformatic analyses and in vitro gain-of-function experiments, we define a previously undescribed axis of p53 inducing miR-92a-1-5p transcription that is highly upregulated by fasting in thermogenic adipocytes. p53, a fasting-responsive transcription factor, was previously shown to control genes involved in the thermogenic program and miR-92a-1-5p was found to negatively correlate with human BAT activity. Here, we identify fructose transporter Slc2a5 as one direct downstream target of this axis and show that fructose can be taken up by and metabolized in brown adipocytes. In sum, this study delineates a fasting-induced pathway involving p53 that transactivates miR-92a-1-5p, which in turn decreases Slc2a5 expression, and suggests fructose as an energy substrate in thermogenic adipocytes.
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Affiliation(s)
- Isabel Reinisch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Ingeborg Klymiuk
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Helene Michenthaler
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Elisabeth Moyschewitz
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Markus Galhuber
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Jelena Krstic
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Magnus Domingo
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | | | - Nemanja Vujić
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Renate Schreiber
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria
- BioHealth Graz, Graz, Austria
| | - Michael Schupp
- Cardiovascular Metabolic Renal (CMR)- Research Center, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt- Universität zu Berlin, Berlin, Germany
| | - Georgia Lenihan-Geels
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Tim J. Schulz
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Roland Malli
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Andreas Prokesch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
- *Correspondence: Andreas Prokesch,
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20
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Fan L, Sweet DR, Fan EK, Prosdocimo DA, Madera A, Jiang Z, Padmanabhan R, Haldar SM, Vinayachandran V, Jain MK. Transcription factors KLF15 and PPARδ cooperatively orchestrate genome-wide regulation of lipid metabolism in skeletal muscle. J Biol Chem 2022; 298:101926. [PMID: 35413288 PMCID: PMC9190004 DOI: 10.1016/j.jbc.2022.101926] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022] Open
Abstract
Skeletal muscle dynamically regulates systemic nutrient homeostasis through transcriptional adaptations to physiological cues. In response to changes in the metabolic environment (e.g., alterations in circulating glucose or lipid levels), networks of transcription factors and coregulators are recruited to specific genomic loci to fine-tune homeostatic gene regulation. Elucidating these mechanisms is of particular interest as these gene regulatory pathways can serve as potential targets to treat metabolic disease. The zinc-finger transcription factor Krüppel-like factor 15 (KLF15) is a critical regulator of metabolic homeostasis; however, its genome-wide distribution in skeletal muscle has not been previously identified. Here, we characterize the KLF15 cistrome in vivo in skeletal muscle and find that the majority of KLF15 binding is localized to distal intergenic regions and associated with genes related to circadian rhythmicity and lipid metabolism. We also identify critical interdependence between KLF15 and the nuclear receptor PPARδ in the regulation of lipid metabolic gene programs. We further demonstrate that KLF15 and PPARδ colocalize genome-wide, physically interact, and are dependent on one another to exert their transcriptional effects on target genes. These findings reveal that skeletal muscle KLF15 plays a critical role in metabolic adaptation through its direct actions on target genes and interactions with other nodal transcription factors such as PPARδ.
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Affiliation(s)
- Liyan Fan
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - David R Sweet
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Erica K Fan
- University of Pittsburgh School of Medicine, Department of Physical Medicine and Rehabilitation, Pittsburgh, Pennsylvania, USA
| | - Domenick A Prosdocimo
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA; The Webb Law Firm, Pittsburgh, Pennsylvania, USA
| | - Annmarie Madera
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Zhen Jiang
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
| | - Roshan Padmanabhan
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA; Department of Medicine, Division of Cardiology, University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Vinesh Vinayachandran
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.
| | - Mukesh K Jain
- Case Cardiovascular Research Institute, Case Western Reserve University, and Harrington Heart and Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.
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21
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Luo K, Zhong J, Safi A, Hong LK, Tewari AK, Song L, Reddy TE, Ma L, Crawford GE, Hartemink AJ. Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data. Genome Res 2022; 32:1183-1198. [PMID: 35609992 PMCID: PMC9248881 DOI: 10.1101/gr.272203.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/06/2022] [Indexed: 11/24/2022]
Abstract
Over a thousand different transcription factors (TFs) bind with varying occupancy across the human genome. Chromatin immunoprecipitation (ChIP) can assay occupancy genome-wide, but only one TF at a time, limiting our ability to comprehensively observe the TF occupancy landscape, let alone quantify how it changes across conditions. We developed TF occupancy profiler (TOP), a Bayesian hierarchical regression framework, to profile genome-wide quantitative occupancy of numerous TFs using data from a single chromatin accessibility experiment (DNase- or ATAC-seq). TOP is supervised, and its hierarchical structure allows it to predict the occupancy of any sequence-specific TF, even those never assayed with ChIP. We used TOP to profile the quantitative occupancy of hundreds of sequence-specific TFs at sites throughout the genome and examined how their occupancies changed in multiple contexts: in approximately 200 human cell types, through 12 h of exposure to different hormones, and across the genetic backgrounds of 70 individuals. TOP enables cost-effective exploration of quantitative changes in the landscape of TF binding.
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Affiliation(s)
- Kaixuan Luo
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jianling Zhong
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Linda K Hong
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Timothy E Reddy
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Biostatistics and Bioinformatics, Durham, North Carolina 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Li Ma
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA
- Department of Statistical Science, Duke University, Durham, North Carolina 27708, USA
| | - Gregory E Crawford
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Alexander J Hartemink
- Computational Biology & Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
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22
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Strickland BA, Ansari SA, Dantoft W, Uhlenhaut NH. How to tame your genes: mechanisms of inflammatory gene repression by glucocorticoids. FEBS Lett 2022; 596:2596-2616. [PMID: 35612756 DOI: 10.1002/1873-3468.14409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/24/2022] [Accepted: 05/18/2022] [Indexed: 01/08/2023]
Abstract
Glucocorticoids (GCs) are widely used therapeutic agents to treat a broad range of inflammatory conditions. Their functional effects are elicited by binding to the glucocorticoid receptor (GR), which regulates transcription of distinct gene networks in response to ligand. However, the mechanisms governing various aspects of undesired side effects versus beneficial immunomodulation upon GR activation remain complex and incompletely understood. In this review, we discuss emerging models of inflammatory gene regulation by GR, highlighting GR's regulatory specificity conferred by context-dependent changes in chromatin architecture and transcription factor or co-regulator dynamics. GR controls both gene activation and repression, with the repression mechanism being central to favorable clinical outcomes. We describe current knowledge about 3D genome organization and its role in spatiotemporal transcriptional control by GR. Looking beyond, we summarize the evidence for dynamics in gene regulation by GR through cooperative convergence of epigenetic modifications, transcription factor crosstalk, molecular condensate formation and chromatin looping. Further characterizing these genomic events will reframe our understanding of mechanisms of transcriptional repression by GR.
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Affiliation(s)
- Benjamin A Strickland
- Metabolic Programming, Technische Universitaet Muenchen (TUM), School of Life Sciences Weihenstephan, ZIEL - Institute for Food and Health, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Suhail A Ansari
- Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Widad Dantoft
- Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - N Henriette Uhlenhaut
- Metabolic Programming, Technische Universitaet Muenchen (TUM), School of Life Sciences Weihenstephan, ZIEL - Institute for Food and Health, Gregor-Mendel-Str. 2, 85354, Freising, Germany.,Institute for Diabetes and Endocrinology (IDE), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
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23
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Goldberg D, Charni-Natan M, Buchshtab N, Bar-Shimon M, Goldstein I. Hormone-controlled cooperative binding of transcription factors drives synergistic induction of fasting-regulated genes. Nucleic Acids Res 2022; 50:5528-5544. [PMID: 35556130 PMCID: PMC9177981 DOI: 10.1093/nar/gkac358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/22/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
During fasting, hepatocytes produce glucose in response to hormonal signals. Glucagon and glucocorticoids are principal fasting hormones that cooperate in regulating glucose production via gluconeogenesis. However, how these hormone signals are integrated and interpreted to a biological output is unknown. Here, we use genome-wide profiling of gene expression, enhancer dynamics and transcription factor (TF) binding in primary mouse hepatocytes to uncover the mode of cooperation between glucagon and glucocorticoids. We found that compared to a single treatment with each hormone, a dual treatment directs hepatocytes to a pro-gluconeogenic gene program by synergistically inducing gluconeogenic genes. The cooperative mechanism driving synergistic gene expression is based on ‘assisted loading’ whereby a glucagon-activated TF (cAMP responsive element binding protein; CREB) leads to enhancer activation which facilitates binding of the glucocorticoid receptor (GR) upon glucocorticoid stimulation. Glucagon does not only activate single enhancers but also activates enhancer clusters, thereby assisting the loading of GR also across enhancer units within the cluster. In summary, we show that cells integrate extracellular signals by an enhancer-specific mechanism: one hormone-activated TF activates enhancers, thereby assisting the loading of a TF stimulated by a second hormone, leading to synergistic gene induction and a tailored transcriptional response to fasting.
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Affiliation(s)
- Dana Goldberg
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. POB 12, Rehovot 7610001, Israel
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. POB 12, Rehovot 7610001, Israel
| | - Nufar Buchshtab
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. POB 12, Rehovot 7610001, Israel
| | - Meirav Bar-Shimon
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. POB 12, Rehovot 7610001, Israel
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. POB 12, Rehovot 7610001, Israel
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24
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Hunter AL, Poolman TM, Kim D, Gonzalez FJ, Bechtold DA, Loudon ASI, Iqbal M, Ray DW. HNF4A modulates glucocorticoid action in the liver. Cell Rep 2022; 39:110697. [PMID: 35443180 PMCID: PMC9380254 DOI: 10.1016/j.celrep.2022.110697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 01/24/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022] Open
Abstract
The glucocorticoid receptor (GR) is a nuclear receptor critical to the regulation of energy metabolism and inflammation. The actions of GR are dependent on cell type and context. Here, we demonstrate the role of liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver specificity of GR action. In mouse liver, the HNF4A motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodeled, with loss and gain of GR recruitment evident. Loss of chromatin accessibility at HNF4A-marked sites associates with loss of GR binding at weak GRE motifs. GR binding and chromatin accessibility are gained at sites characterized by strong GRE motifs, which show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is indicated by an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver.
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Affiliation(s)
- A Louise Hunter
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Toryn M Poolman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, UK
| | - Donghwan Kim
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Bechtold
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Andrew S I Loudon
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Mudassar Iqbal
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - David W Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, UK; NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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25
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Loft A, Schmidt SF, Caratti G, Stifel U, Havelund J, Sekar R, Kwon Y, Sulaj A, Chow KK, Alfaro AJ, Schwarzmayr T, Rittig N, Svart M, Tsokanos FF, Maida A, Blutke A, Feuchtinger A, Møller N, Blüher M, Nawroth P, Szendrödi J, Færgeman NJ, Zeigerer A, Tuckermann J, Herzig S. A macrophage-hepatocyte glucocorticoid receptor axis coordinates fasting ketogenesis. Cell Metab 2022; 34:473-486.e9. [PMID: 35120589 DOI: 10.1016/j.cmet.2022.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 09/30/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022]
Abstract
Fasting metabolism and immunity are tightly linked; however, it is largely unknown how immune cells contribute to metabolic homeostasis during fasting in healthy subjects. Here, we combined cell-type-resolved genomics and computational approaches to map crosstalk between hepatocytes and liver macrophages during fasting. We identified the glucocorticoid receptor (GR) as a key driver of fasting-induced reprogramming of the macrophage secretome including fasting-suppressed cytokines and showed that lack of macrophage GR impaired induction of ketogenesis during fasting as well as endotoxemia. Mechanistically, macrophage GR suppressed the expression of tumor necrosis factor (TNF) and promoted nuclear translocation of hepatocyte GR to activate a fat oxidation/ketogenesis-related gene program, cooperatively induced by GR and peroxisome proliferator-activated receptor alpha (PPARα) in hepatocytes. Together, our results demonstrate how resident liver macrophages directly influence ketogenesis in hepatocytes, thereby also outlining a strategy by which the immune system can set the metabolic tone during inflammatory disease and infection.
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Affiliation(s)
- Anne Loft
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany; Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense 5230, Denmark; Center for Functional Genomics and Tissue Plasticity (ATLAS), SDU, Odense 5230, Denmark
| | - Søren Fisker Schmidt
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany; Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense 5230, Denmark; Center for Functional Genomics and Tissue Plasticity (ATLAS), SDU, Odense 5230, Denmark.
| | - Giorgio Caratti
- Institute for Comparative Molecular Endocrinology, Universität Ulm, Ulm 89081, Germany
| | - Ulrich Stifel
- Institute for Comparative Molecular Endocrinology, Universität Ulm, Ulm 89081, Germany
| | - Jesper Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense 5230, Denmark
| | - Revathi Sekar
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Yun Kwon
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Alba Sulaj
- German Center for Diabetes Research, Neuherberg 85764, Germany; Department of Endocrinology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Kan Kau Chow
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Ana Jimena Alfaro
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Nikolaj Rittig
- Department of Internal Medicine and Endocrinology (Multilateral Environmental Agreement) and Medical Research Laboratory, Aarhus University Hospital, Aarhus C 8000, Denmark; Steno Diabetes Center Aarhus, Aarhus University, Hedeager 3, 2nd Floor, 8200 Aarhus N, Denmark
| | - Mads Svart
- Department of Internal Medicine and Endocrinology (Multilateral Environmental Agreement) and Medical Research Laboratory, Aarhus University Hospital, Aarhus C 8000, Denmark; Steno Diabetes Center Aarhus, Aarhus University, Hedeager 3, 2nd Floor, 8200 Aarhus N, Denmark
| | - Foivos-Filippos Tsokanos
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Adriano Maida
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Andreas Blutke
- Research Unit Analytical Pathology, Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Niels Møller
- Department of Internal Medicine and Endocrinology (Multilateral Environmental Agreement) and Medical Research Laboratory, Aarhus University Hospital, Aarhus C 8000, Denmark
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig 04103, Germany
| | - Peter Nawroth
- Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Department of Endocrinology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Julia Szendrödi
- Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Department of Endocrinology and Clinical Chemistry, Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), Odense 5230, Denmark
| | - Anja Zeigerer
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Jan Tuckermann
- Institute for Comparative Molecular Endocrinology, Universität Ulm, Ulm 89081, Germany.
| | - Stephan Herzig
- Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg 85764, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg 69120, Germany; Molecular Metabolic Control, Technical University Munich, Munich 80333, Germany; German Center for Diabetes Research, Neuherberg 85764, Germany.
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Transcriptional Regulation of Hepatic Autophagy by Nuclear Receptors. Cells 2022; 11:cells11040620. [PMID: 35203271 PMCID: PMC8869834 DOI: 10.3390/cells11040620] [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: 01/23/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 02/04/2023] Open
Abstract
Autophagy is an adaptive self-eating process involved in degradation of various cellular components such as carbohydrates, lipids, proteins, and organelles. Its activity plays an essential role in tissue homeostasis and systemic metabolism in response to diverse challenges, including nutrient depletion, pathogen invasion, and accumulations of toxic materials. Therefore, autophagy dysfunctions are intimately associated with many human diseases such as cancer, neurodegeneration, obesity, diabetes, infection, and aging. Although its acute post-translational regulation is well described, recent studies have also shown that autophagy can be controlled at the transcriptional and post-transcriptional levels. Nuclear receptors (NRs) are in general ligand-dependent transcription factors consisting of 48 members in humans. These receptors extensively control transcription of a variety of genes involved in development, metabolism, and inflammation. In this review, we discuss the roles and mechanisms of NRs in an aspect of transcriptional regulation of hepatic autophagy, and how the NR-driven autophagy pathway can be harnessed to treat various liver diseases.
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Hierarchical regulation of autophagy during adipocyte differentiation. PLoS One 2022; 17:e0250865. [PMID: 35081114 PMCID: PMC8791469 DOI: 10.1371/journal.pone.0250865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/05/2021] [Indexed: 11/19/2022] Open
Abstract
We previously showed that some adipogenic transcription factors such as CEBPB and PPARG directly and indirectly regulate autophagy gene expression in adipogenesis. The order and effect of these events are undetermined. In this study, we modeled the gene expression, DNA-binding of transcriptional regulators, and histone modifications during adipocyte differentiation and evaluated the effect of the regulators on gene expression in terms of direction and magnitude. Then, we identified the overlap of the transcription factors and co-factors binding sites and targets. Finally, we built a chromatin state model based on the histone marks and studied their relation to the factors’ binding. Adipogenic factors differentially regulated autophagy genes as part of the differentiation program. Co-regulators associated with specific transcription factors and preceded them to the regulatory regions. Transcription factors differed in the binding time and location, and their effect on expression was either localized or long-lasting. Adipogenic factors disproportionately targeted genes coding for autophagy-specific transcription factors. In sum, a hierarchical arrangement between adipogenic transcription factors and co-factors drives the regulation of autophagy during adipocyte differentiation.
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Ray DW. Circadian Rhythm and Nuclear Receptors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:143-153. [PMID: 36107317 DOI: 10.1007/978-3-031-11836-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
All life of Earth has evolved mechanisms to track time. This permits anticipation of predictable changes in light/dark, and in most cases also directs fed/fasted cycles, and sleep/wake. The nuclear receptors enjoy a close relationship with the molecular machinery of the clock. Some play a core role within the circadian machinery, other respond to ligands which oscillate in concentration, and physical cross-talk between clock transcription factors, eg cryptochromes, and multiple nuclear receptors also enable coupling of nuclear receptor function to time of day. Essential processes including inflammation, and energy metabolism are strongly regulated by both the circadian machinery, and rhythmic behaviour, and also by multiple members of the nuclear receptor family. An emerging theme is reciprocal regulation of key processes by different members of the nuclear receptor family, for example NR1D1/2, and NR1F1, in regulation of the core circadian clock transcription factor BMAL1.
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Varticovski L, Stavreva DA, McGowan A, Raziuddin R, Hager GL. Endocrine disruptors of sex hormone activities. Mol Cell Endocrinol 2022; 539:111415. [PMID: 34339825 PMCID: PMC8762672 DOI: 10.1016/j.mce.2021.111415] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022]
Abstract
Sex hormones, such as androgens, estrogens and progestins are naturally occurring compounds that tightly regulate endocrine systems in a variety of living organisms. Uncontrolled environmental exposure to these hormones or their biological and synthetic mimetics has been widely documented. Furthermore, water contaminants penetrate soil to affect flora, fauna and ultimately humans. Because endocrine systems evolved to respond to very small changes in hormone levels, the low levels found in the environment cannot be ignored. The combined actions of sex hormones with glucocorticoids and other nuclear receptors disruptors creates additional level of complexity including the newly described "dynamic assisted loading" mechanism. We reviewed the extensive literature pertaining to world-wide detection of these disruptors and created a detailed Table on the development and current status of methods used for their analysis.
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Affiliation(s)
- L Varticovski
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - D A Stavreva
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A McGowan
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - R Raziuddin
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - G L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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30
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Rong B, Wu Q, Saeed M, Sun C. Gut microbiota-a positive contributor in the process of intermittent fasting-mediated obesity control. ACTA ACUST UNITED AC 2021; 7:1283-1295. [PMID: 34786501 PMCID: PMC8567329 DOI: 10.1016/j.aninu.2021.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/12/2021] [Accepted: 09/25/2021] [Indexed: 12/12/2022]
Abstract
Historically, intermittent fasting (IF) has been considered as an effective strategy for controlling the weight of athletes before competition. Along with excellent insight into its application in various spaces by numerous studies, increasing IF-mediated positive effects have been reported, including anti-aging, neuroprotection, especially obesity control. Recently, the gut microbiota has been considered as an essential manipulator for host energy metabolism and its structure has been reported to be sensitive to dietary structure and habits, indicating that there is a potential and strong association between IF and gut microbiota. In this paper, we focus on the crosstalk between these symbionts and energy metabolism during IF which hold the promise to optimize host energy metabolism at various physical positions, including adipose tissue, liver and intestines, and further improve milieu internal homeostasis. Moreover, this paper also discusses the positive function of a potential recommendatory strain (Akkermansia muciniphila) based on the observational data for IF-mediated alternated pattern of gut microbiota and a hopefully regulatory pathway (circadian rhythm) for gut microbiota in IF-involved improvement on host energy metabolism. Finally, this review addresses the limitation and perspective originating from these studies, such as the association with tissue-specific bio-clock and single strain research, which may continuously reveal novel viewpoints and mechanisms to understand the energy metabolism and develop new strategies for treating obesity, diabetes, and metabolic disorders.
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Affiliation(s)
- Bohan Rong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qiong Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Pathophysiology, Qinghai University Medical College, Xining, Qinghai, China
| | - Muhammad Saeed
- Faculty of Animal Production & Technology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Chao Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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31
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Bengtsen M, Winje IM, Eftestøl E, Landskron J, Sun C, Nygård K, Domanska D, Millay DP, Meza-Zepeda LA, Gundersen K. Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle. PLoS Genet 2021; 17:e1009907. [PMID: 34752468 PMCID: PMC8604348 DOI: 10.1371/journal.pgen.1009907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 11/19/2021] [Accepted: 10/23/2021] [Indexed: 01/04/2023] Open
Abstract
Muscle cells have different phenotypes adapted to different usage, and can be grossly divided into fast/glycolytic and slow/oxidative types. While most muscles contain a mixture of such fiber types, we aimed at providing a genome-wide analysis of the epigenetic landscape by ChIP-Seq in two muscle extremes, the fast/glycolytic extensor digitorum longus (EDL) and slow/oxidative soleus muscles. Muscle is a heterogeneous tissue where up to 60% of the nuclei can be of a different origin. Since cellular homogeneity is critical in epigenome-wide association studies we developed a new method for purifying skeletal muscle nuclei from whole tissue, based on the nuclear envelope protein Pericentriolar material 1 (PCM1) being a specific marker for myonuclei. Using antibody labelling and a magnetic-assisted sorting approach, we were able to sort out myonuclei with 95% purity in muscles from mice, rats and humans. The sorting eliminated influence from the other cell types in the tissue and improved the myo-specific signal. A genome-wide comparison of the epigenetic landscape in EDL and soleus reflected the differences in the functional properties of the two muscles, and revealed distinct regulatory programs involving distal enhancers, including a glycolytic super-enhancer in the EDL. The two muscles were also regulated by different sets of transcription factors; e.g. in soleus, binding sites for MEF2C, NFATC2 and PPARA were enriched, while in EDL MYOD1 and SIX1 binding sites were found to be overrepresented. In addition, more novel transcription factors for muscle regulation such as members of the MAF family, ZFX and ZBTB14 were identified. Complex tissues like skeletal muscle contain a variety of cells which confound the analysis of each cell type when based on homogenates, thus only about half of the cell nuclei in muscles reside inside the muscle cells. We here describe a labelling and sorting technique that allowed us to study the epigenetic landscape in purified muscle cell nuclei leaving the other cell types out. Differences between a fast/glycolytic and a slow/oxidative muscle were studied. While all skeletal muscle fibers have a similar make up and basic function, they differ in their physiology and the way they are used. Thus, some fibers are fast contracting but fatigable, and are used for short lasting explosive tasks such as sprinting. Other fibers are slow and are used for more prolonged tasks such as standing or long distance running. Since fiber type correlate with metabolic profile these features can also be related to metabolic diseases. We here show that the epigenetic landscape differed in gene loci corresponding to the differences in functional properties, and revealed that the two types are enriched in different gene regulatory networks. Exercise can alter muscle phenotype, and the epigenetic landscape might be related to how plastic different properties are.
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Affiliation(s)
- Mads Bengtsen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Einar Eftestøl
- Department of Biosciences, University of Oslo, Oslo, Norway
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Chengyi Sun
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kamilla Nygård
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Department of Pathology, University of Oslo, Oslo, Norway
| | - Douglas P. Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Leonardo A. Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Bruno NE, Nwachukwu JC, Hughes DC, Srinivasan S, Hawkins R, Sturgill D, Hager GL, Hurst S, Sheu SS, Bodine SC, Conkright MD, Nettles KW. Activation of Crtc2/Creb1 in skeletal muscle enhances weight loss during intermittent fasting. FASEB J 2021; 35:e21999. [PMID: 34748223 DOI: 10.1096/fj.202100171r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/11/2022]
Abstract
The Creb-Regulated Transcriptional Coactivator (Crtc) family of transcriptional coregulators drive Creb1-mediated transcription effects on metabolism in many tissues, but the in vivo effects of Crtc2/Creb1 transcription on skeletal muscle metabolism are not known. Skeletal muscle-specific overexpression of Crtc2 (Crtc2 mice) induced greater mitochondrial activity, metabolic flux capacity for both carbohydrates and fats, improved glucose tolerance and insulin sensitivity, and increased oxidative capacity, supported by upregulation of key metabolic genes. Crtc2 overexpression led to greater weight loss during alternate day fasting (ADF), selective loss of fat rather than lean mass, maintenance of higher energy expenditure during the fast and reduced binge-eating during the feeding period. ADF downregulated most of the mitochondrial electron transport genes, and other regulators of mitochondrial function, that were substantially reversed by Crtc2-driven transcription. Glucocorticoids acted with AMPK to drive atrophy and mitophagy, which was reversed by Crtc2/Creb1 signaling. Crtc2/Creb1-mediated signaling coordinates metabolic adaptations in skeletal muscle that explain how Crtc2/Creb1 regulates metabolism and weight loss.
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Affiliation(s)
- Nelson E Bruno
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David C Hughes
- Section for Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Sathish Srinivasan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Richard Hawkins
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Stephen Hurst
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Shey-Shing Sheu
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sue C Bodine
- Section for Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Michael D Conkright
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
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33
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Kitamoto T, Kuo T, Okabe A, Kaneda A, Accili D. An integrative transcriptional logic model of hepatic insulin resistance. Proc Natl Acad Sci U S A 2021; 118:e2102222118. [PMID: 34732569 PMCID: PMC8609333 DOI: 10.1073/pnas.2102222118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 12/27/2022] Open
Abstract
Abnormalities of lipid/lipoprotein and glucose metabolism are hallmarks of hepatic insulin resistance in type 2 diabetes. The former antedate the latter, but the latter become progressively refractory to treatment and contribute to therapeutic failures. It's unclear whether the two processes share a common pathogenesis and what underlies their progressive nature. In this study, we investigated the hypothesis that genes in the lipid/lipoprotein pathway and those in the glucose metabolic pathway are governed by different transcriptional regulatory logics that affect their response to physiologic (fasting/refeeding) as well as pathophysiologic cues (insulin resistance and hyperglycemia). To this end, we obtained genomic and transcriptomic maps of the key insulin-regulated transcription factor, FoxO1, and integrated them with those of CREB, PPAR-α, and glucocorticoid receptor. We found that glucose metabolic genes are primarily regulated by promoter and intergenic enhancers in a fasting-dependent manner, while lipid genes are regulated through fasting-dependent intron enhancers and fasting-independent enhancerless introns. Glucose genes also showed a remarkable transcriptional resiliency (i.e., the ability to compensate following constitutive FoxO1 ablation through an enrichment of active marks at shared PPAR-α/FoxO1 regulatory elements). Unexpectedly, insulin resistance and hyperglycemia were associated with a "spreading" of FoxO1 binding to enhancers and the emergence of unique target sites. We surmise that this unusual pattern correlates with the progressively intractable nature of hepatic insulin resistance. This transcriptional logic provides an integrated model to interpret the combined lipid and glucose abnormalities of type 2 diabetes.
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Affiliation(s)
- Takumi Kitamoto
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032;
- Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Taiyi Kuo
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Domenico Accili
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
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34
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PAQR9 regulates hepatic ketogenesis and fatty acid oxidation during fasting by modulating protein stability of PPARα. Mol Metab 2021; 53:101331. [PMID: 34474167 PMCID: PMC8452888 DOI: 10.1016/j.molmet.2021.101331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The cycle of feeding and fasting is fundamental to life and closely coordinated with changes of metabolic programs. During extended starvation, ketogenesis coupled with fatty acid oxidation in the liver supplies ketone bodies to extrahepatic tissues as the major form of fuel. In this study, we demonstrated that PAQR9, a member of the progesterone and adipoQ receptor family, has a regulatory role on hepatic ketogenesis. METHODS We analyzed the phenotype of Paqr9-deleted mice. We also used biochemical methods to investigate the interaction of PAQR9 with PPARα and HUWE1, an E3 ubiquitin ligase. RESULTS The expression of Paqr9 was decreased during fasting partly depending on PPARγ. The overall phenotype of the mice was not altered by Paqr9 deletion under normal chow feeding. However, fasting-induced ketogenesis and fatty acid oxidation were attenuated by Paqr9 deletion. Mechanistically, Paqr9 deletion decreased protein stability of PPARα via enhancing its poly-ubiquitination. PAQR9 competed with HUWE1 for interaction with PPARα, thus preventing ubiquitin-mediated degradation of PPARα. CONCLUSION Our study reveals that PAQR9 impacts starvation-mediated metabolic changes in the liver via post-translational regulation of PPARα.
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Hunter AL, Pelekanou CE, Barron NJ, Northeast RC, Grudzien M, Adamson AD, Downton P, Cornfield T, Cunningham PS, Billaud JN, Hodson L, Loudon ASI, Unwin RD, Iqbal M, Ray DW, Bechtold DA. Adipocyte NR1D1 dictates adipose tissue expansion during obesity. eLife 2021; 10:e63324. [PMID: 34350828 PMCID: PMC8360653 DOI: 10.7554/elife.63324] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
The circadian clock component NR1D1 (REVERBα) is considered a dominant regulator of lipid metabolism, with global Nr1d1 deletion driving dysregulation of white adipose tissue (WAT) lipogenesis and obesity. However, a similar phenotype is not observed under adipocyte-selective deletion (Nr1d1Flox2-6:AdipoqCre), and transcriptional profiling demonstrates that, under basal conditions, direct targets of NR1D1 regulation are limited, and include the circadian clock and collagen dynamics. Under high-fat diet (HFD) feeding, Nr1d1Flox2-6:AdipoqCre mice do manifest profound obesity, yet without the accompanying WAT inflammation and fibrosis exhibited by controls. Integration of the WAT NR1D1 cistrome with differential gene expression reveals broad control of metabolic processes by NR1D1 which is unmasked in the obese state. Adipocyte NR1D1 does not drive an anticipatory daily rhythm in WAT lipogenesis, but rather modulates WAT activity in response to alterations in metabolic state. Importantly, NR1D1 action in adipocytes is critical to the development of obesity-related WAT pathology and insulin resistance.
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Affiliation(s)
- Ann Louise Hunter
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Charlotte E Pelekanou
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Nichola J Barron
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Rebecca C Northeast
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Magdalena Grudzien
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Antony D Adamson
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Polly Downton
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Thomas Cornfield
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - Peter S Cunningham
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - Andrew SI Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Richard D Unwin
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Mudassar Iqbal
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - David W Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - David A Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
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Garcia DA, Fettweis G, Presman DM, Paakinaho V, Jarzynski C, Upadhyaya A, Hager GL. Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model. Nucleic Acids Res 2021; 49:6605-6620. [PMID: 33592625 DOI: 10.1093/nar/gkab072] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs-one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Institute of Biomedicine, University of Eastern Finland, Kuopio, PO Box 1627, FI-70211 Kuopio, Finland
| | - Christopher Jarzynski
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
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Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis. Blood 2021; 137:1327-1339. [PMID: 33512425 DOI: 10.1182/blood.2020005780] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/05/2020] [Indexed: 11/20/2022] Open
Abstract
While constitutive CCCTC-binding factor (CTCF)-binding sites are needed to maintain relatively invariant chromatin structures, such as topologically associating domains, the precise roles of CTCF to control cell-type-specific transcriptional regulation remain poorly explored. We examined CTCF occupancy in different types of primary blood cells derived from the same donor to elucidate a new role for CTCF in gene regulation during blood cell development. We identified dynamic, cell-type-specific binding sites for CTCF that colocalize with lineage-specific transcription factors. These dynamic sites are enriched for single-nucleotide polymorphisms that are associated with blood cell traits in different linages, and they coincide with the key regulatory elements governing hematopoiesis. CRISPR-Cas9-based perturbation experiments demonstrated that these dynamic CTCF-binding sites play a critical role in red blood cell development. Furthermore, precise deletion of CTCF-binding motifs in dynamic sites abolished interactions of erythroid genes, such as RBM38, with their associated enhancers and led to abnormal erythropoiesis. These results suggest a novel, cell-type-specific function for CTCF in which it may serve to facilitate interaction of distal regulatory emblements with target promoters. Our study of the dynamic, cell-type-specific binding and function of CTCF provides new insights into transcriptional regulation during hematopoiesis.
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Korenfeld N, Finkel M, Buchshtab N, Bar-Shimon M, Charni-Natan M, Goldstein I. Fasting Hormones Synergistically Induce Amino Acid Catabolism Genes to Promote Gluconeogenesis. Cell Mol Gastroenterol Hepatol 2021; 12:1021-1036. [PMID: 33957303 PMCID: PMC8346669 DOI: 10.1016/j.jcmgh.2021.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/10/2022]
Abstract
BACKGROUND & AIMS Gluconeogenesis from amino acids (AAs) maintains glucose homeostasis during fasting. Although glucagon is known to regulate AA catabolism, the contribution of other hormones to it and the scope of transcriptional regulation dictating AA catabolism are unknown. We explored the role of the fasting hormones glucagon and glucocorticoids in transcriptional regulation of AA catabolism genes and AA-dependent gluconeogenesis. METHODS We tested the RNA expression of AA catabolism genes and glucose production in primary mouse hepatocytes treated with fasting hormones (glucagon, corticosterone) and feeding hormones (insulin, fibroblast growth factor 19). We analyzed genomic data of chromatin accessibility and chromatin immunoprecipitation in mice and primary mouse hepatocytes. We performed chromatin immunoprecipitation in livers of fasted mice to show binding of cAMP responsive element binding protein (CREB) and the glucocorticoid receptor (GR). RESULTS Fasting induced the expression of 31 genes with various roles in AA catabolism. Of them, 15 were synergistically induced by co-treatment of glucagon and corticosterone. Synergistic gene expression relied on the activity of both CREB and GR and was abolished by treatment with either insulin or fibroblast growth factor 19. Enhancers adjacent to synergistically induced genes became more accessible and were bound by CREB and GR on fasting. Akin to the gene expression pattern, gluconeogenesis from AAs was synergistically induced by glucagon and corticosterone in a CREB- and GR-dependent manner. CONCLUSIONS Transcriptional regulation of AA catabolism genes during fasting is widespread and is driven by glucagon (via CREB) and corticosterone (via GR). Glucose production in hepatocytes is also synergistically augmented, showing that glucagon alone is insufficient in fully activating gluconeogenesis.
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Affiliation(s)
- Noga Korenfeld
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Finkel
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Nufar Buchshtab
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Meirav Bar-Shimon
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition. Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem, Rehovot, Israel.
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Abstract
Mammals undergo regular cycles of fasting and feeding that engage dynamic transcriptional responses in metabolic tissues. Here we review advances in our understanding of the gene regulatory networks that contribute to hepatic responses to fasting and feeding. The advent of sequencing and -omics techniques have begun to facilitate a holistic understanding of the transcriptional landscape and its plasticity. We highlight transcription factors, their cofactors, and the pathways that they impact. We also discuss physiological factors that impinge on these responses, including circadian rhythms and sex differences. Finally, we review how dietary modifications modulate hepatic gene expression programs.
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Affiliation(s)
- Lara Bideyan
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Rohith Nagari
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Biological Chemistry, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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40
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Xiao Y, Kim M, Lazar MA. Nuclear receptors and transcriptional regulation in non-alcoholic fatty liver disease. Mol Metab 2020; 50:101119. [PMID: 33220489 PMCID: PMC8324695 DOI: 10.1016/j.molmet.2020.101119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND As a result of a sedentary lifestyle and excess food consumption in modern society, non-alcoholic fatty liver disease (NAFLD) characterized by fat accumulation in the liver is becoming a major disease burden. Non-alcoholic steatohepatitis (NASH) is an advanced form of NAFLD characterized by inflammation and fibrosis that can lead to hepatocellular carcinoma and liver failure. Nuclear receptors (NRs) are a family of ligand-regulated transcription factors that closely control multiple aspects of metabolism. Their transcriptional activity is modulated by various ligands, including hormones and lipids. NRs serve as potential pharmacological targets for NAFLD/NASH and other metabolic diseases. SCOPE OF REVIEW In this review, we provide a comprehensive overview of NRs that have been studied in the context of NAFLD/NASH with a focus on their transcriptional regulation, function in preclinical models, and studies of their clinical utility. MAJOR CONCLUSIONS The transcriptional regulation of NRs is context-dependent. During the dynamic progression of NAFLD/NASH, NRs play diverse roles in multiple organs and different cell types in the liver, which highlights the necessity of targeting NRs in a stage-specific and cell-type-specific manner to enhance the efficacy and safety of treatment methods.
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Affiliation(s)
- Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mindy Kim
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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41
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Præstholm SM, Correia CM, Grøntved L. Multifaceted Control of GR Signaling and Its Impact on Hepatic Transcriptional Networks and Metabolism. Front Endocrinol (Lausanne) 2020; 11:572981. [PMID: 33133019 PMCID: PMC7578419 DOI: 10.3389/fendo.2020.572981] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Glucocorticoids (GCs) and the glucocorticoid receptor (GR) are important regulators of development, inflammation, stress response and metabolism, demonstrated in various diseases including Addison's disease, Cushing's syndrome and by the many side effects of prolonged clinical administration of GCs. These conditions include severe metabolic challenges in key metabolic organs like the liver. In the liver, GR is known to regulate the transcription of key enzymes in glucose and lipid metabolism and contribute to the regulation of circadian-expressed genes. Insights to the modes of GR regulation and the underlying functional mechanisms are key for understanding diseases and for the development of improved clinical uses of GCs. The activity and function of GR is regulated at numerous levels including ligand availability, interaction with heat shock protein (HSP) complexes, expression of GR isoforms and posttranslational modifications. Moreover, recent genomics studies show functional interaction with multiple transcription factors (TF) and coregulators in complex transcriptional networks controlling cell type-specific gene expression by GCs. In this review we describe the different regulatory steps important for GR activity and discuss how different TF interaction partners of GR selectively control hepatic gene transcription and metabolism.
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Affiliation(s)
| | | | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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42
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Huang SSY, Makhlouf M, AbouMoussa EH, Ruiz Tejada Segura ML, Mathew LS, Wang K, Leung MC, Chaussabel D, Logan DW, Scialdone A, Garand M, Saraiva LR. Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting. Mol Metab 2020; 40:101038. [PMID: 32526449 PMCID: PMC7339127 DOI: 10.1016/j.molmet.2020.101038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/24/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Fasting regimens can promote health, mitigate chronic immunological disorders, and improve age-related pathophysiological parameters in animals and humans. Several ongoing clinical trials are using fasting as a potential therapy for various conditions. Fasting alters metabolism by acting as a reset for energy homeostasis, but the molecular mechanisms underlying the beneficial effects of short-term fasting (STF) are not well understood, particularly at the systems or multiorgan level. METHODS We performed RNA-sequencing in nine organs from mice fed ad libitum (0 h) or subjected to fasting five times (2-22 h). We applied a combination of multivariate analysis, differential expression analysis, gene ontology, and network analysis for an in-depth understanding of the multiorgan transcriptome. We used literature mining solutions, LitLab™ and Gene Retriever™, to identify the biological and biochemical terms significantly associated with our experimental gene set, which provided additional support and meaning to the experimentally derived gene and inferred protein data. RESULTS We cataloged the transcriptional dynamics within and between organs during STF and discovered differential temporal effects of STF among organs. Using gene ontology enrichment analysis, we identified an organ network sharing 37 common biological pathways perturbed by STF. This network incorporates the brain, liver, interscapular brown adipose tissue, and posterior-subcutaneous white adipose tissue; hence, we named it the brain-liver-fats organ network. Using Reactome pathways analysis, we identified the immune system, dominated by T cell regulation processes, as a central and prominent target of systemic modulations during STF in this organ network. The changes we identified in specific immune components point to the priming of adaptive immunity and parallel the fine-tuning of innate immune signaling. CONCLUSIONS Our study provides a comprehensive multiorgan transcriptomic profiling of mice subjected to multiple periods of STF and provides new insights into the molecular modulators involved in the systemic immunotranscriptomic changes that occur during short-term energy loss.
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Affiliation(s)
| | | | | | - Mayra L Ruiz Tejada Segura
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Marchioninistraße 25, 81377, München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | | | - Kun Wang
- Sidra Medicine, PO Box 26999, Doha, Qatar.
| | | | | | - Darren W Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Marchioninistraße 25, 81377, München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | | | - Luis R Saraiva
- Sidra Medicine, PO Box 26999, Doha, Qatar; Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA, 19104, USA.
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Abstract
The circadian clock protein REVERBα is proposed to be a key regulator of liver metabolism. We now show that REVERBα action is critically dependent on metabolic state. Using transgenic mouse models, we show that the true role of REVERBα is to buffer against aberrant responses to metabolic perturbation, rather than confer rhythmic regulation to programs of lipid synthesis and storage, as has been thought previously. Thus, in the case of liver metabolism, the clock does not so much drive rhythmic processes, as provide protection against mistimed feeding cues. Understanding how the clock is coupled to metabolism is critical for understanding metabolic disease and the impacts of circadian disruptors such as shift work and 24-h lifestyles. The nuclear receptor REVERBα is a core component of the circadian clock and proposed to be a dominant regulator of hepatic lipid metabolism. Using antibody-independent ChIP-sequencing of REVERBα in mouse liver, we reveal a high-confidence cistrome and define direct target genes. REVERBα-binding sites are highly enriched for consensus RORE or RevDR2 motifs and overlap with corepressor complex binding. We find no evidence for transcription factor tethering and DNA-binding domain-independent action. Moreover, hepatocyte-specific deletion of Reverbα drives only modest physiological and transcriptional dysregulation, with derepressed target gene enrichment limited to circadian processes. Thus, contrary to previous reports, hepatic REVERBα does not repress lipogenesis under basal conditions. REVERBα control of a more extensive transcriptional program is only revealed under conditions of metabolic perturbation (including mistimed feeding, which is a feature of the global Reverbα−/− mouse). Repressive action of REVERBα in the liver therefore serves to buffer against metabolic challenge, rather than drive basal rhythmicity in metabolic activity.
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44
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Gyllensten U, Bosdotter Enroth S, Stålberg K, Sundfeldt K, Enroth S. Preoperative Fasting and General Anaesthesia Alter the Plasma Proteome. Cancers (Basel) 2020; 12:cancers12092439. [PMID: 32867270 PMCID: PMC7564209 DOI: 10.3390/cancers12092439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/22/2020] [Accepted: 08/26/2020] [Indexed: 01/15/2023] Open
Abstract
Background: Blood plasma collected at time of surgery is an excellent source of patient material for investigations into disease aetiology and for the discovery of novel biomarkers. Previous studies on limited sets of proteins and patients have indicated that pre-operative fasting and anaesthesia can affect protein levels, but this has not been investigated on a larger scale. These effects could produce erroneous results in case-control studies if samples are not carefully matched. Methods: The proximity extension assay (PEA) was used to characterize 983 unique proteins in a total of 327 patients diagnosed with ovarian cancer and 50 age-matched healthy women. The samples were collected either at time of initial diagnosis or before surgery under general anaesthesia. Results: 421 of the investigated proteins (42.8%) showed statistically significant differences in plasma abundance levels comparing samples collected at time of diagnosis or just before surgery under anaesthesia. Conclusions: The abundance levels of the plasma proteome in samples collected before incision, i.e., after short-time fasting and under general anaesthesia differs greatly from levels in samples from awake patients. This emphasizes the need for careful matching of the pre-analytical conditions of samples collected from controls to cases at time of surgery in the discovery as well as clinical use of protein biomarkers.
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Affiliation(s)
- Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory (SciLifeLab) Uppsala, Box 815, Uppsala University, SE-751 08 Uppsala, Sweden;
| | | | - Karin Stålberg
- Department of Women’s and Children’s Health, Uppsala University, SE-751 85 Uppsala, Sweden;
| | - Karin Sundfeldt
- Department of Obstetrics and Gynaecology, Institute of Clinical Sciences, Sahlgrenska Academy at Gothenburg University, SE-416 85 Gothenburg, Sweden;
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory (SciLifeLab) Uppsala, Box 815, Uppsala University, SE-751 08 Uppsala, Sweden;
- Correspondence: ; Tel.: +46-18-4714913
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45
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Abstract
Primary hepatocytes are a vital tool in various biomedical research disciplines, serving as an ex vivo model for liver physiology. Obtaining high yields of viable primary mouse hepatocytes is technically challenging, limiting their use. Here, we present an improved protocol based on the classic two-step collagenase perfusion technique. The liver is washed by perfusion, hepatocytes are dissociated by collagenase, separated from other cells, and cultured. This protocol was optimized to significantly reduce procedure duration and improve hepatocyte yield and viability.
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Affiliation(s)
- Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
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46
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Regulation of MYO18B mRNA by a network of C19MC miRNA-520G, IFN-γ, CEBPB, p53 and bFGF in hepatocellular carcinoma. Sci Rep 2020; 10:12371. [PMID: 32704163 PMCID: PMC7378193 DOI: 10.1038/s41598-020-69179-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
MYO18B has been proposed to contribute to the progression of hepatocellular carcinoma (HCC). However, the signals that govern MYO18B transcription are not known. Here we show that, a network of C19MC miRNA-520G, IFN-γ, CEBPB and p53 transcriptional-defects promote MYO18B mRNA expression in HCCs. IFN-γ by itself suppresses MYO18B transcription, but promotes it when miRNA-520G is stably overexpressed. Similarly, CEBPB-liver-enriched activator protein (LAP) isoform overexpression suppresses MYO18B transcription but promotes transcription when the cells are treated with IFN-γ. Furthermore, miR-520G together with mutant-p53 promotes MYO18B transcription. Conversely, bFGF suppresses MYO18B mRNA irrespective of CEBPB, miR-520G overexpression or IFN-γ treatment. Finally high MYO18B expression reflects poor prognosis while high MYL5 or MYO1B expression reflects better survival of HCC patients. Thus, we identified a network of positive and negative regulators of MYO18B mRNA expression which reflects the survival of HCC patients.
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47
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Cebola I. Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1480. [PMID: 32020788 DOI: 10.1002/wsbm.1480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
Metabolic diseases such as nonalcoholic fatty liver disease (NAFLD) result from complex interactions between intrinsic and extrinsic factors, including genetics and exposure to obesogenic environments. These risk factors converge in aberrant gene expression patterns in the liver, which are underlined by altered cis-regulatory networks. In homeostasis and in disease states, liver cis-regulatory networks are established by coordinated action of liver-enriched transcription factors (TFs), which define enhancer landscapes, activating broad gene programs with spatiotemporal resolution. Recent advances in DNA sequencing have dramatically expanded our ability to map active transcripts, enhancers and TF cistromes, and to define the 3D chromatin topology that contains these elements. Deployment of these technologies has allowed investigation of the molecular processes that regulate liver development and metabolic homeostasis. Moreover, genomic studies of NAFLD patients and NAFLD models have demonstrated that the liver undergoes pervasive regulatory rewiring in NAFLD, which is reflected by aberrant gene expression profiles. We have therefore achieved an unprecedented level of detail in the understanding of liver cis-regulatory networks, particularly in physiological conditions. Future studies should aim to map active regulatory elements with added levels of resolution, addressing how the chromatin landscapes of different cell lineages contribute to and are altered in NAFLD and NAFLD-associated metabolic states. Such efforts would provide additional clues into the molecular factors that trigger this disease. This article is categorized under: Biological Mechanisms > Metabolism Biological Mechanisms > Regulatory Biology Laboratory Methods and Technologies > Genetic/Genomic Methods.
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Affiliation(s)
- Inês Cebola
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, UK
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48
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Jin S, Zhang L, Nie Q. scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles. Genome Biol 2020; 21:25. [PMID: 32014031 PMCID: PMC6996200 DOI: 10.1186/s13059-020-1932-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Simultaneous measurements of transcriptomic and epigenomic profiles in the same individual cells provide an unprecedented opportunity to understand cell fates. However, effective approaches for the integrative analysis of such data are lacking. Here, we present a single-cell aggregation and integration (scAI) method to deconvolute cellular heterogeneity from parallel transcriptomic and epigenomic profiles. Through iterative learning, scAI aggregates sparse epigenomic signals in similar cells learned in an unsupervised manner, allowing coherent fusion with transcriptomic measurements. Simulation studies and applications to three real datasets demonstrate its capability of dissecting cellular heterogeneity within both transcriptomic and epigenomic layers and understanding transcriptional regulatory mechanisms.
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Affiliation(s)
- Suoqin Jin
- Department of Mathematics, University of California, Irvine, CA 92697 USA
| | - Lihua Zhang
- Department of Mathematics, University of California, Irvine, CA 92697 USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697 USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA 92697 USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697 USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697 USA
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49
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Kinouchi K, Magnan C, Ceglia N, Liu Y, Cervantes M, Pastore N, Huynh T, Ballabio A, Baldi P, Masri S, Sassone-Corsi P. Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle. Cell Rep 2019; 25:3299-3314.e6. [PMID: 30566858 DOI: 10.1016/j.celrep.2018.11.077] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 09/08/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
The circadian clock operates as intrinsic time-keeping machinery to preserve homeostasis in response to the changing environment. While food is a known zeitgeber for clocks in peripheral tissues, it remains unclear how lack of food influences clock function. We demonstrate that the transcriptional response to fasting operates through molecular mechanisms that are distinct from time-restricted feeding regimens. First, fasting affects core clock genes and proteins, resulting in blunted rhythmicity of BMAL1 and REV-ERBα both in liver and skeletal muscle. Second, fasting induces a switch in temporal gene expression through dedicated fasting-sensitive transcription factors such as GR, CREB, FOXO, TFEB, and PPARs. Third, the rhythmic genomic response to fasting is sustainable by prolonged fasting and reversible by refeeding. Thus, fasting imposes specialized dynamics of transcriptional coordination between the clock and nutrient-sensitive pathways, thereby achieving a switch to fasting-specific temporal gene regulation.
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Affiliation(s)
- Kenichiro Kinouchi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Christophe Magnan
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Nicholas Ceglia
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Yu Liu
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Nunzia Pastore
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tuong Huynh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ballabio
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy
| | - Pierre Baldi
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, Irvine, CA 92697, USA.
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50
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Quagliarini F, Mir AA, Balazs K, Wierer M, Dyar KA, Jouffe C, Makris K, Hawe J, Heinig M, Filipp FV, Barish GD, Uhlenhaut NH. Cistromic Reprogramming of the Diurnal Glucocorticoid Hormone Response by High-Fat Diet. Mol Cell 2019; 76:531-545.e5. [PMID: 31706703 DOI: 10.1016/j.molcel.2019.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 08/02/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022]
Abstract
The glucocorticoid receptor (GR) is a potent metabolic regulator and a major drug target. While GR is known to play integral roles in circadian biology, its rhythmic genomic actions have never been characterized. Here we mapped GR's chromatin occupancy in mouse livers throughout the day and night cycle. We show how GR partitions metabolic processes by time-dependent target gene regulation and controls circulating glucose and triglycerides differentially during feeding and fasting. Highlighting the dominant role GR plays in synchronizing circadian amplitudes, we find that the majority of oscillating genes are bound by and depend on GR. This rhythmic pattern is altered by high-fat diet in a ligand-independent manner. We find that the remodeling of oscillatory gene expression and postprandial GR binding results from a concomitant increase of STAT5 co-occupancy in obese mice. Altogether, our findings highlight GR's fundamental role in the rhythmic orchestration of hepatic metabolism.
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Affiliation(s)
- Fabiana Quagliarini
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Ashfaq Ali Mir
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Kinga Balazs
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried (Munich), Germany
| | - Kenneth Allen Dyar
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Celine Jouffe
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Konstantinos Makris
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Johann Hawe
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Department of Informatics, Boltzmannstr. 3, 85748 Garching, Technische Universitaet Muenchen (TUM), Munich, Germany
| | - Fabian Volker Filipp
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; School of Life Sciences Weihenstephan, Maximus-von-Imhof-Forum 3, 85354 Freising, Technische Universitaet Muenchen (TUM), Munich, Germany
| | - Grant Daniel Barish
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Nina Henriette Uhlenhaut
- Institute for Diabetes and Obesity (IDO), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Ingolstaedter Landstr. 1, 85764 Neuherberg (Munich), Germany; Metabolic Programming, School of Life Sciences Weihenstephan, Gregor Mendel Str. 2, 85354 Freising, Technische Universitaet Muenchen (TUM), Munich, Germany.
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