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Lappa D, Meijnikman AS, Krautkramer KA, Olsson LM, Aydin Ö, Van Rijswijk AS, Acherman YIZ, De Brauw ML, Tremaroli V, Olofsson LE, Lundqvist A, Hjorth SA, Ji B, Gerdes VEA, Groen AK, Schwartz TW, Nieuwdorp M, Bäckhed F, Nielsen J. Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery. PLoS One 2023; 18:e0279335. [PMID: 36862673 PMCID: PMC9980823 DOI: 10.1371/journal.pone.0279335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/05/2022] [Indexed: 03/03/2023] Open
Abstract
Weight loss through bariatric surgery is efficient for treatment or prevention of obesity related diseases such as type 2 diabetes and cardiovascular disease. Long term weight loss response does, however, vary among patients undergoing surgery. Thus, it is difficult to identify predictive markers while most obese individuals have one or more comorbidities. To overcome such challenges, an in-depth multiple omics analyses including fasting peripheral plasma metabolome, fecal metagenome as well as liver, jejunum, and adipose tissue transcriptome were performed for 106 individuals undergoing bariatric surgery. Machine leaning was applied to explore the metabolic differences in individuals and evaluate if metabolism-based patients' stratification is related to their weight loss responses to bariatric surgery. Using Self-Organizing Maps (SOMs) to analyze the plasma metabolome, we identified five distinct metabotypes, which were differentially enriched for KEGG pathways related to immune functions, fatty acid metabolism, protein-signaling, and obesity pathogenesis. The gut metagenome of the most heavily medicated metabotypes, treated simultaneously for multiple cardiometabolic comorbidities, was significantly enriched in Prevotella and Lactobacillus species. This unbiased stratification into SOM-defined metabotypes identified signatures for each metabolic phenotype and we found that the different metabotypes respond differently to bariatric surgery in terms of weight loss after 12 months. An integrative framework that utilizes SOMs and omics integration was developed for stratifying a heterogeneous bariatric surgery cohort. The multiple omics datasets described in this study reveal that the metabotypes are characterized by a concrete metabolic status and different responses in weight loss and adipose tissue reduction over time. Our study thus opens a path to enable patient stratification and hereby allow for improved clinical treatments.
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Affiliation(s)
- Dimitra Lappa
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail: (DL); (JN)
| | - Abraham S. Meijnikman
- Department of Internal and Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Kimberly A. Krautkramer
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lisa M. Olsson
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ömrüm Aydin
- Department of Internal and Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | | | | | | | - Valentina Tremaroli
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Louise E. Olofsson
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Annika Lundqvist
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Siv A. Hjorth
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Boyang Ji
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Victor E. A. Gerdes
- Department of Internal and Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Internal Medicine, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Albert K. Groen
- Department of Internal and Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Pediatrics, Laboratory of Metabolic Diseases, University of Groningen, UMCG, Groningen, The Netherlands
| | - Thue W. Schwartz
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, Copenhagen N, Denmark
- * E-mail: (DL); (JN)
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2
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Meijnikman AS, Lappa D, Herrema H, Aydin O, Krautkramer KA, Tremaroli V, Olofsson LE, Lundqvist A, Bruin S, Acherman Y, Verheij J, Hjorth S, Gerdes VE, Schwartz TW, Groen AK, Bäckhed F, Nielsen J, Nieuwdorp M. A systems biology approach to study non-alcoholic fatty liver (NAFL) in women with obesity. iScience 2022; 25:104828. [PMID: 35992074 PMCID: PMC9382345 DOI: 10.1016/j.isci.2022.104828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/03/2021] [Accepted: 07/20/2022] [Indexed: 11/30/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is now the most frequent global chronic liver disease. Individuals with NAFLD exhibited an increased risk of all-cause mortality driven by extrahepatic cancers and liver and cardiovascular disease. Once the disease is established, women have a higher risk of disease progression and worse outcome. It is therefore critical to deepen the current knowledge on the pathophysiology of NAFLD in women. Here, we used a systems biology approach to investigate the contribution of different organs to this disease. We analyzed transcriptomics profiles of liver and adipose tissues, fecal metagenomes, and plasma metabolomes of 55 women with and without NAFLD. We observed differences in metabolites, expression of human genes, and gut microbial features between the groups and revealed that there is substantial crosstalk between these different omics sets. Multi-omics analysis of individuals with NAFLD may provide novel strategies to study the pathophysiology of NAFLD in humans. The gut microbiome is significantly different between women with and without NAFLD The NAFLD plasma metabolome is characterized by lipid and amino acids post prandial Women with NAFLD have distinct transcriptional profiles in liver and adipose tissue Women with NAFL have a different response upon MMT after massive weight loss
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Affiliation(s)
- Abraham S. Meijnikman
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
- Corresponding author
| | - Dimitra Lappa
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Hilde Herrema
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Omrum Aydin
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
| | - Kimberly A. Krautkramer
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Louise E. Olofsson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Annika Lundqvist
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sjoerd Bruin
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
| | - Yair Acherman
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
| | - Joanne Verheij
- Department of Pathology, UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Siv Hjorth
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Victor E.A. Gerdes
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
| | - Thue W. Schwartz
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Albert K. Groen
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Heath and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Corresponding author
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
- Corresponding author
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3
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Haws SA, Yu D, Ye C, Wille CK, Nguyen LC, Krautkramer KA, Tomasiewicz JL, Yang SE, Miller BR, Liu WH, Igarashi K, Sridharan R, Tu BP, Cryns VL, Lamming DW, Denu JM. Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence. Mol Cell 2020; 78:210-223.e8. [PMID: 32208170 PMCID: PMC7191556 DOI: 10.1016/j.molcel.2020.03.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/05/2020] [Accepted: 02/28/2020] [Indexed: 12/12/2022]
Abstract
S-adenosylmethionine (SAM) is the methyl-donor substrate for DNA and histone methyltransferases that regulate epigenetic states and subsequent gene expression. This metabolism-epigenome link sensitizes chromatin methylation to altered SAM abundance, yet the mechanisms that allow organisms to adapt and protect epigenetic information during life-experienced fluctuations in SAM availability are unknown. We identified a robust response to SAM depletion that is highlighted by preferential cytoplasmic and nuclear mono-methylation of H3 Lys 9 (H3K9) at the expense of broad losses in histone di- and tri-methylation. Under SAM-depleted conditions, H3K9 mono-methylation preserves heterochromatin stability and supports global epigenetic persistence upon metabolic recovery. This unique chromatin response was robust across the mouse lifespan and correlated with improved metabolic health, supporting a significant role for epigenetic adaptation to SAM depletion in vivo. Together, these studies provide evidence for an adaptive response that enables epigenetic persistence to metabolic stress.
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Affiliation(s)
- Spencer A Haws
- Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Deyang Yu
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA; Department of Medicine, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular & Environmental Toxicology Center, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Cunqi Ye
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Coral K Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Long C Nguyen
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Kimberly A Krautkramer
- Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jay L Tomasiewicz
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Shany E Yang
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA; Department of Medicine, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Blake R Miller
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA; Department of Medicine, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Wallace H Liu
- Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent L Cryns
- Department of Medicine, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular & Environmental Toxicology Center, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA; University of Wisconsin Carbone Cancer Center, Madison, WI 53792, USA
| | - Dudley W Lamming
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA; Department of Medicine, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular & Environmental Toxicology Center, SMPH, University of Wisconsin-Madison, Madison, WI 53705, USA; University of Wisconsin Carbone Cancer Center, Madison, WI 53792, USA
| | - John M Denu
- Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
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4
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Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife 2018; 7:37816. [PMID: 30039798 PMCID: PMC6085123 DOI: 10.7554/elife.37816] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/12/2018] [Indexed: 12/18/2022] Open
Abstract
The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated type 1 diabetes (T1D) development in male NOD mice. The single course had deep and persistent effects on the intestinal microbiome, leading to altered cecal, hepatic, and serum metabolites. The exposure elicited sex-specific effects on chromatin states in the ileum and liver and perturbed ileal gene expression, altering normal maturational patterns. The global signature changes included specific genes controlling both innate and adaptive immunity. Microbiome analysis revealed four taxa each that potentially protect against or accelerate T1D onset, that were linked in a network model to specific differences in ileal gene expression. This simplified animal model reveals multiple potential pathways to understand pathogenesis by which early-life gut microbiome perturbations alter a global suite of intestinal responses, contributing to the accelerated and enhanced T1D development.
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Affiliation(s)
- Xue-Song Zhang
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Jackie Li
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Kimberly A Krautkramer
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Michelle Badri
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Center for Data Science, New York University, New York, United States
| | - Thomas Battaglia
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Timothy C Borbet
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Hyunwook Koh
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Sandy Ng
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Rachel A Sibley
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Yuanyuan Li
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Wimal Pathmasiri
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Shawn Jindal
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Robin R Shields-Cutler
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Ben Hillmann
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Gabriel A Al-Ghalith
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Victoria E Ruiz
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Alexandra Livanos
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Angélique B van 't Wout
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Nabeetha Nagalingam
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Arlin B Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, United States
| | - Susan Jenkins Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Dan Knights
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - John M Denu
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Kelly V Ruggles
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Richard Bonneau
- Center for Data Science, New York University, New York, United States
| | - R Anthony Williamson
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Marcus Rauch
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Martin J Blaser
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Department of Microbiology, New York Uniersity Langone Medical Center, New York, United States
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5
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Krautkramer KA, Dhillon RS, Denu JM, Carey HV. Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin. Transl Res 2017; 189:30-50. [PMID: 28919341 PMCID: PMC5659875 DOI: 10.1016/j.trsl.2017.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/14/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023]
Abstract
The mammalian gut microbiota has been linked to host developmental, immunologic, and metabolic outcomes. This collection of trillions of microbes inhabits the gut and produces a myriad of metabolites, which are measurable in host circulation and contribute to the pathogenesis of human diseases. The link between endogenous metabolite availability and chromatin regulation is a well-established and active area of investigation; however, whether microbial metabolites can elicit similar effects is less understood. In this review, we focus on seminal and recent research that establishes chromatin regulatory roles for both endogenous and microbial metabolites. We also highlight key physiologic and disease settings where microbial metabolite-host chromatin interactions have been established and/or may be pertinent.
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Affiliation(s)
- Kimberly A Krautkramer
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis.
| | - Rashpal S Dhillon
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis; Morgridge Institute for Research, Madison, Wis
| | - Hannah V Carey
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, Wis
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6
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Abstract
Mammals and their gut microbial communities share extensive and tightly coordinated co-metabolism of dietary substrates. A large number of microbial metabolites have been detected in host circulation and tissues and, in many cases, are linked to host metabolic, developmental, and immunological states. The presence of these metabolites in host tissues intersects with regulation of the host's epigenetic machinery. Although it is established that the host's epigenetic machinery is sensitive to levels of endogenous metabolites, the roles for microbial metabolites in epigenetic regulation are just beginning to be elucidated. This review focuses on eukaryotic chromatin regulation by endogenous and gut microbial metabolites and how these regulatory events may impact host developmental and metabolic phenotypes.
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Affiliation(s)
- Kimberly A Krautkramer
- From the Wisconsin Institute for Discovery, Morgridge Institute for Research, and the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53715 and
| | - Federico E Rey
- the Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - John M Denu
- From the Wisconsin Institute for Discovery, Morgridge Institute for Research, and the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53715 and
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7
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Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, Keller MP, Attie AD, Rey FE, Denu JM. Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Mol Cell 2016; 64:982-992. [PMID: 27889451 DOI: 10.1016/j.molcel.2016.10.025] [Citation(s) in RCA: 323] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 09/22/2016] [Accepted: 10/18/2016] [Indexed: 02/07/2023]
Abstract
Histone-modifying enzymes regulate transcription and are sensitive to availability of endogenous small-molecule metabolites, allowing chromatin to respond to changes in environment. The gut microbiota produces a myriad of metabolites that affect host physiology and susceptibility to disease; however, the underlying molecular events remain largely unknown. Here we demonstrate that microbial colonization regulates global histone acetylation and methylation in multiple host tissues in a diet-dependent manner: consumption of a "Western-type" diet prevents many of the microbiota-dependent chromatin changes that occur in a polysaccharide-rich diet. Finally, we demonstrate that supplementation of germ-free mice with short-chain fatty acids, major products of gut bacterial fermentation, is sufficient to recapitulate chromatin modification states and transcriptional responses associated with colonization. These findings have profound implications for understanding the complex functional interactions between diet, gut microbiota, and host health.
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Affiliation(s)
- Kimberly A Krautkramer
- Wisconsin Institute for Discovery, Madison, WI 53715, USA; Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health - Madison, Madison, WI 53706, USA
| | - Julia H Kreznar
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Kymberleigh A Romano
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Eugenio I Vivas
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | | | - Mary E Rabaglia
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA.
| | - John M Denu
- Wisconsin Institute for Discovery, Madison, WI 53715, USA; Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health - Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA.
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8
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Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN, Denu JM. Reader domain specificity and lysine demethylase-4 family function. Nat Commun 2016; 7:13387. [PMID: 27841353 PMCID: PMC5114558 DOI: 10.1038/ncomms13387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022] Open
Abstract
The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
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Affiliation(s)
- Zhangli Su
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
| | - Jin-Hee Lee
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Kimberly E. Stephens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Kimberly A. Krautkramer
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy J. Thorpe
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Melissa D. Boersma
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Vyacheslav I. Kuznetsov
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | | | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - George N. Phillips
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
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9
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Rensvold JW, Krautkramer KA, Dowell JA, Denu JM, Pagliarini DJ. Iron Deprivation Induces Transcriptional Regulation of Mitochondrial Biogenesis. J Biol Chem 2016; 291:20827-20837. [PMID: 27497435 DOI: 10.1074/jbc.m116.727701] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 01/31/2023] Open
Abstract
Mitochondria are essential organelles that adapt to stress and environmental changes. Among the nutrient signals that affect mitochondrial form and function is iron, whose depletion initiates a rapid and reversible decrease in mitochondrial biogenesis through unclear means. Here we demonstrate that, unlike the canonical iron-induced alterations to transcript stability, loss of iron dampens the transcription of genes encoding mitochondrial proteins with no change to transcript half-life. Using mass spectrometry, we demonstrate that these transcriptional changes are accompanied by dynamic alterations to histone acetylation and methylation levels that are largely reversible upon readministration of iron. Moreover, histone deacetylase inhibition abrogates the decreased histone acetylation observed upon iron deprivation and restores normal transcript levels at genes encoding mitochondrial proteins. Collectively, we demonstrate that deprivation of an essential nutrient induces transcriptional repression of organellar biogenesis involving epigenetic alterations.
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Affiliation(s)
| | - Kimberly A Krautkramer
- the Department of Biomolecular Chemistry and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, and
| | - James A Dowell
- the Department of Biomolecular Chemistry and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, and
| | - John M Denu
- From the Morgridge Institute for Research, Madison, Wisconsin 53715, the Department of Biomolecular Chemistry and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, and
| | - David J Pagliarini
- From the Morgridge Institute for Research, Madison, Wisconsin 53715, the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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10
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Yu W, Denu RA, Krautkramer KA, Grindle KM, Yang DT, Asimakopoulos F, Hematti P, Denu JM. Loss of SIRT3 Provides Growth Advantage for B Cell Malignancies. J Biol Chem 2015; 291:3268-79. [PMID: 26631723 DOI: 10.1074/jbc.m115.702076] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Indexed: 12/16/2022] Open
Abstract
B cell malignancies comprise a diverse group of cancers that proliferate in lymph nodes, bone marrow, and peripheral blood. SIRT3 (sirtuin 3) is the major deacetylase within the mitochondrial matrix that promotes aerobic metabolism and controls reactive oxygen species (ROS) by deacetylating and activating isocitrate dehydrogenase 2 (IDH2) and superoxide dismutase 2 (SOD2). There is controversy as to whether SIRT3 acts as an oncogene or a tumor suppressor, and here we investigated its role in B cell malignancies. In mantle cell lymphoma patient samples, we found that lower SIRT3 protein expression was associated with worse overall survival. Further, SIRT3 protein expression was reduced in chronic lymphocytic leukemia primary samples and malignant B cell lines compared to primary B cells from healthy donors. This lower level of expression correlated with hyperacetylation of IDH2 and SOD2 mitochondrial proteins, lowered enzymatic activities, and higher ROS levels. Overexpression of SIRT3 decreased proliferation and diminished the Warburg-like phenotype in SIRT3-deficient cell lines, and this effect is largely dependent on deacetylation of IDH2 and SOD2. Lastly, depletion of SIRT3 from malignant B cell lines resulted in greater susceptibility to treatment with an ROS scavenger but did not result in greater sensitivity to inhibition of the hypoxia-inducible factor-1α pathway, suggesting that loss of SIRT3 increases proliferation via ROS-dependent but hypoxia-inducible factor-1α-independent mechanisms. Our study suggests that SIRT3 acts as a tumor suppressor in B cell malignancies, and activating the SIRT3 pathway might represent a novel therapeutic approach for treating B cell malignancies.
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Affiliation(s)
- Wei Yu
- From the Wisconsin Institute for Discovery and the Department of Biomolecular Chemistry
| | - Ryan A Denu
- the Medical Scientist Training Program, and the Departments of Medicine and
| | - Kimberly A Krautkramer
- From the Wisconsin Institute for Discovery and the Department of Biomolecular Chemistry, the Medical Scientist Training Program, and
| | | | - David T Yang
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705 and
| | - Fotis Asimakopoulos
- the Departments of Medicine and the University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53792
| | - Peiman Hematti
- the Departments of Medicine and the University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53792
| | - John M Denu
- From the Wisconsin Institute for Discovery and the Department of Biomolecular Chemistry, the University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53792
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11
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Krautkramer KA, Reiter L, Denu JM, Dowell JA. Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. J Proteome Res 2015; 14:3252-62. [PMID: 26120868 DOI: 10.1021/acs.jproteome.5b00245] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Histone post-translational modifications (PTMs) are important regulators of chromatin structure and gene expression. Quantitative analysis of histone PTMs by mass spectrometry remains extremely challenging due to the complex and combinatorial nature of histone PTMs. The most commonly used mass spectrometry-based method for high-throughput histone PTM analysis is data-dependent acquisition (DDA). However, stochastic precursor selection and dependence on MS1 ions for quantification impede comprehensive interrogation of histone PTM states using DDA methods. To overcome these limitations, we utilized a data-independent acquisition (DIA) workflow that provides superior run-to-run consistency and postacquisition flexibility in comparison to DDA methods. In addition, we developed a novel DIA-based methodology to quantify isobaric, co-eluting histone peptides that lack unique MS2 transitions. Our method enabled deconvolution and quantification of histone PTMs that are otherwise refractory to quantitation, including the heavily acetylated tail of histone H4. Using this workflow, we investigated the effects of the histone deacetylase inhibitor SAHA (suberoylanilide hydroxamic acid) on the global histone PTM state of human breast cancer MCF7 cells. A total of 62 unique histone PTMs were quantified, revealing novel SAHA-induced changes in acetylation and methylation of histones H3 and H4.
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Affiliation(s)
| | - Lukas Reiter
- §BiognoSYS AG, Wagistrasse 25, CH-8952 Schlieren, Switzerland
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12
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Abstract
Histone post-translational modifications regulate transcription and other DNA-templated functions. This process is dynamically regulated by specific modifying enzymes whose activities require metabolites that either serve as cosubstrates or act as activators/inhibitors. Therefore, metabolism can influence histone modification by changing local concentrations of key metabolites. Physiologically, the epigenetic response to metabolism is important for nutrient sensing and environment adaption. In pathologic states, the connection between metabolism and histone modification mediates epigenetic abnormality in complex disease. In this review, we summarize recent studies of the molecular mechanisms involved in metabolic regulation of histone modifications and discuss their biological significance.
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Affiliation(s)
- Jing Fan
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Kimberly A. Krautkramer
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Jessica L. Feldman
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
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13
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Krautkramer KA, Linnemann AK, Fontaine DA, Whillock AL, Harris TW, Schleis GJ, Truchan NA, Marty-Santos L, Lavine JA, Cleaver O, Kimple ME, Davis DB. Tcf19 is a novel islet factor necessary for proliferation and survival in the INS-1 β-cell line. Am J Physiol Endocrinol Metab 2013; 305:E600-10. [PMID: 23860123 PMCID: PMC3761170 DOI: 10.1152/ajpendo.00147.2013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recently, a novel type 1 diabetes association locus was identified at human chromosome 6p31.3, and transcription factor 19 (TCF19) is a likely causal gene. Little is known about Tcf19, and we now show that it plays a role in both proliferation and apoptosis in insulinoma cells. Tcf19 is expressed in mouse and human islets, with increasing mRNA expression in nondiabetic obesity. The expression of Tcf19 is correlated with β-cell mass expansion, suggesting that it may be a transcriptional regulator of β-cell mass. Increasing proliferation and decreasing apoptotic cell death are two strategies to increase pancreatic β-cell mass and prevent or delay diabetes. siRNA-mediated knockdown of Tcf19 in the INS-1 insulinoma cell line, a β-cell model, results in a decrease in proliferation and an increase in apoptosis. There was a significant reduction in the expression of numerous cell cycle genes from the late G1 phase through the M phase, and cells were arrested at the G1/S checkpoint. We also observed increased apoptosis and susceptibility to endoplasmic reticulum (ER) stress after Tcf19 knockdown. There was a reduction in expression of genes important for the maintenance of ER homeostasis (Bip, p58(IPK), Edem1, and calreticulin) and an increase in proapoptotic genes (Bim, Bid, Nix, Gadd34, and Pdia2). Therefore, Tcf19 is necessary for both proliferation and survival and is a novel regulator of these pathways.
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Affiliation(s)
- Kimberly A Krautkramer
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin, Madison, Wisconsin
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Davis DB, Lavine JA, Suhonen JI, Krautkramer KA, Rabaglia ME, Sperger JM, Fernandez LA, Yandell BS, Keller MP, Wang IM, Schadt EE, Attie AD. FoxM1 is up-regulated by obesity and stimulates beta-cell proliferation. Mol Endocrinol 2010; 24:1822-34. [PMID: 20660304 DOI: 10.1210/me.2010-0082] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
beta-Cell mass expansion is one mechanism by which obese animals compensate for insulin resistance and prevent diabetes. FoxM1 is a transcription factor that can regulate the expression of multiple cell cycle genes and is necessary for the maintenance of adult beta-cell mass, beta-cell proliferation, and glucose homeostasis. We hypothesized that FoxM1 is up-regulated by nondiabetic obesity and initiates a transcriptional program leading to beta-cell proliferation. We performed gene expression analysis on islets from the nondiabetic C57BL/6 Leptin(ob/ob) mouse, the diabetic BTBR Leptin(ob/ob) mouse, and an F2 Leptin(ob/ob) population derived from these strains. We identified obesity-driven coordinated up-regulation of islet Foxm1 and its target genes in the nondiabetic strain, correlating with beta-cell mass expansion and proliferation. This up-regulation was absent in the diabetic strain. In the F2 Leptin(ob/ob) population, increased expression of Foxm1 and its target genes segregated with higher insulin and lower glucose levels. We next studied the effects of FOXM1b overexpression on isolated mouse and human islets. We found that FoxM1 stimulated mouse and human beta-cell proliferation by activating many cell cycle phases. We asked whether FOXM1 expression is also responsive to obesity in human islets by collecting RNA from human islet donors (body mass index range: 24-51). We found that the expression of FOXM1 and its target genes is positively correlated with body mass index. Our data suggest that beta-cell proliferation occurs in adult obese humans in an attempt to expand beta-cell mass to compensate for insulin resistance, and that the FoxM1 transcriptional program plays a key role in this process.
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Affiliation(s)
- Dawn Belt Davis
- Department of Medicine, University of Wisconsin, Madison, WI, USA.
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