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Berdnikovs S, Newcomb DC, Hartert TV. How early life respiratory viral infections impact airway epithelial development and may lead to asthma. Front Pediatr 2024; 12:1441293. [PMID: 39156016 PMCID: PMC11327159 DOI: 10.3389/fped.2024.1441293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/20/2024] Open
Abstract
Childhood asthma is a common chronic disease of the airways that results from host and environment interactions. Most risk factor studies of asthma point to the first year of life as a susceptibility window of mucosal exposure that directly impacts the airway epithelium and airway epithelial cell development. The development of the airway epithelium, which forms a competent barrier resulting from coordinated interactions of different specialized cell subsets, occurs during a critical time frame in normal postnatal development in the first year of life. Understanding the normal and aberrant developmental trajectory of airway epithelial cells is important in identifying pathways that may contribute to barrier dysfunction and asthma pathogenesis. Respiratory viruses make first contact with and infect the airway mucosa. Human rhinovirus (HRV) and respiratory syncytial virus (RSV) are mucosal pathogens that are consistently identified as asthma risk factors. Respiratory viruses represent a unique early life exposure, different from passive irritant exposures which injure the developing airway epithelium. To replicate, respiratory viruses take over the host cell transcriptional and translational processes and exploit host cell energy metabolism. This takeover impacts the development and differentiation processes of airway epithelial cells. Therefore, delineating the mechanisms through which early life respiratory viral infections alter airway epithelial cell development will allow us to understand the maturation and heterogeneity of asthma and develop tools tailored to prevent disease in specific children. This review will summarize what is understood about the impact of early life respiratory viruses on the developing airway epithelium and define critical gaps in our knowledge.
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Affiliation(s)
- Sergejs Berdnikovs
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Dawn C. Newcomb
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Tina V. Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
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2
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Chatziparasidis G, Bush A, Chatziparasidi MR, Kantar A. Airway epithelial development and function: A key player in asthma pathogenesis? Paediatr Respir Rev 2023; 47:51-61. [PMID: 37330410 DOI: 10.1016/j.prrv.2023.04.005] [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: 02/05/2023] [Revised: 04/07/2023] [Accepted: 04/25/2023] [Indexed: 06/19/2023]
Abstract
Though asthma is a common and relatively easy to diagnose disease, attempts at primary or secondary prevention, and cure, have been disappointing. The widespread use of inhaled steroids has dramatically improved asthma control but has offered nothing in terms of altering long-term outcomes or reversing airway remodeling and impairment in lung function. The inability to cure asthma is unsurprising given our limited understanding of the factors that contribute to disease initiation and persistence. New data have focused on the airway epithelium as a potentially key factor orchestrating the different stages of asthma. In this review we summarize for the clinician the current evidence on the central role of the airway epithelium in asthma pathogenesis and the factors that may alter epithelial integrity and functionality.
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Affiliation(s)
- Grigorios Chatziparasidis
- Paediatric Respiratory Unit, IASO Hospital, Larissa, Thessaly, Greece; Faculty of Nursing, Thessaly University, Greece.
| | - Andrew Bush
- National Heart and Lung Institute, Royal Brompton & Harefield NHS Foundation Trust, London, UK
| | | | - Ahmad Kantar
- Pediatric Asthma and Cough Centre, Instituti Ospedalieri Bergamaschi, University and Research Hospitals, Bergamo, Italy
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3
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Ghorbaninejad M, Asadzadeh-Aghdaei H, Baharvand H, Meyfour A. Intestinal organoids: A versatile platform for modeling gastrointestinal diseases and monitoring epigenetic alterations. Life Sci 2023; 319:121506. [PMID: 36858311 DOI: 10.1016/j.lfs.2023.121506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023]
Abstract
Considering the significant limitations of conventional 2D cell cultures and tissue in vitro models, creating intestinal organoids has burgeoned as an ideal option to recapitulate the heterogeneity of the native intestinal epithelium. Intestinal organoids can be developed from either tissue-resident adult stem cells (ADSs) or pluripotent stem cells (PSCs) in both forms induced PSCs and embryonic stem cells. Here, we review current advances in the development of intestinal organoids that have led to a better recapitulation of the complexity, physiology, morphology, function, and microenvironment of the intestine. We discuss current applications of intestinal organoids with an emphasis on disease modeling. In particular, we point out recent studies on SARS-CoV-2 infection in human intestinal organoids. We also discuss the less explored application of intestinal organoids in epigenetics by highlighting the role of epigenetic modifications in intestinal development, homeostasis, and diseases, and subsequently the power of organoids in mirroring the regulatory role of epigenetic mechanisms in these conditions and introducing novel predictive/diagnostic biomarkers. Finally, we propose 3D organoid models to evaluate the effects of novel epigenetic drugs (epi-drugs) on the treatment of GI diseases where epigenetic mechanisms play a key role in disease development and progression, particularly in colorectal cancer treatment and epigenetically acquired drug resistance.
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Affiliation(s)
- Mahsa Ghorbaninejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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4
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Premadasa LS, Lee E, McDew-White M, Alvarez X, Jayakumar S, Ling B, Okeoma CM, Byrareddy SN, Kulkarni S, Mohan M. Cannabinoid enhancement of lncRNA MMP25-AS1/MMP25 interaction reduces neutrophil infiltration and intestinal epithelial injury in HIV/SIV infection. JCI Insight 2023; 8:e167903. [PMID: 37036007 PMCID: PMC10132162 DOI: 10.1172/jci.insight.167903] [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: 12/09/2022] [Accepted: 02/16/2023] [Indexed: 04/11/2023] Open
Abstract
Intestinal epithelial barrier dysfunction, a hallmark of HIV/SIV infection, persists despite viral suppression by combination antiretroviral therapy (cART). Emerging evidence suggests a critical role for long noncoding RNAs (lncRNAs) in maintaining epithelial homeostasis. We simultaneously profiled lncRNA/mRNA expression exclusively in colonic epithelium (CE) of SIV-infected rhesus macaques (RMs) administered vehicle (VEH) or Δ-9-tetrahydrocannabinol (THC). Relative to controls, fewer lncRNAs were up- or downregulated in CE of THC/SIV compared with VEH/SIV RMs. Importantly, reciprocal expression of the natural antisense lncRNA MMP25-AS1 (up 2.3-fold) and its associated protein-coding gene MMP25 (attracts neutrophils by inactivating alpha-1 anti-trypsin/SERPINA1) (down 2.2-fold) was detected in CE of THC/SIV RMs. Computational analysis verified 2 perfectly matched complementary regions and an energetically stable (normalized binding free energy = -0.2626) MMP25-AS1/MMP25 duplex structure. MMP25-AS1 overexpression blocked IFN-γ-induced MMP25 mRNA and protein expression in vitro. Elevated MMP25 protein expression in CE of VEH/SIV but not THC/SIV RMs was associated with increased infiltration by myeloperoxidase/CD11b++ neutrophils (transendothelial migration) and epithelial CD47 (transepithelial migration) expression. Interestingly, THC administered in combination with cART increased MMP25-AS1 and reduced MMP25 mRNA/protein expression in jejunal epithelium of SIV-infected RMs. Our findings demonstrate that MMP25-AS1 is a potentially unique epigenetic regulator of MMP25 and that low-dose THC can reduce neutrophil infiltration and intestinal epithelial injury potentially by downregulating MMP25 expression through modulation of MMP25-AS1.
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Affiliation(s)
- Lakmini S. Premadasa
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Eunhee Lee
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Marina McDew-White
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Xavier Alvarez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Sahana Jayakumar
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Binhua Ling
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Chioma M. Okeoma
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, New York, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Smita Kulkarni
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Mahesh Mohan
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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5
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Beiderman M, Ashkenazy A, Segal E, Motiei M, Salomon A, Sadan T, Fixler D, Popovtzer R. Optimization of Gold Nanorod Features for the Enhanced Performance of Plasmonic Nanocavity Arrays. ACS OMEGA 2021; 6:29071-29077. [PMID: 34746596 PMCID: PMC8567385 DOI: 10.1021/acsomega.1c04301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Nanoplasmonic biosensors incorporating noble metal nanocavity arrays are widely used for the detection of various biomarkers. Gold nanorods (GNRs) have unique properties that can enhance spectroscopic detection capabilities of such nanocavity-based biosensors. However, the contribution of the physical properties of multiple GNRs to resonance enhancement of gold nanocavity arrays requires further characterization and elucidation. In this work, we study how GNR aspect ratio (AR) and surface area (SA) modify the plasmonic resonance spectrum of a gold triangular nanocavity array by both simulations and experiments. The finite integration technique (FIT) simulated the extinction spectrum of the gold nanocavity array with 300 nm periodicity onto which the GNRs of different ARs and SAs are placed. Simulations showed that matching of the GNRs longitudinal peak, which is affected by AR, to the nanocavity array's spectrum minima can optimize signal suppression and shifting. Moreover, increasing SA of the matched GNRs increased the spectral variations of the array. Experiments confirmed that GNRs conjugated to a gold triangular nanocavity array of 300 nm periodicity caused spectrum suppression and redshift. Our findings demonstrate that tailoring of the GNR AR and SA parameters to nanoplasmonic arrays has the potential to greatly improve spectral variations for enhanced plasmonic biosensing.
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Affiliation(s)
- Marianna Beiderman
- Faculty
of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Ariel Ashkenazy
- Faculty
of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Elad Segal
- Department
of Chemistry, Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Menachem Motiei
- Faculty
of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Adi Salomon
- Department
of Chemistry, Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Sadan
- Faculty
of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Dror Fixler
- Faculty
of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Rachela Popovtzer
- Faculty
of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
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6
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Abstract
The interaction between the gut and its eventual trillions of microbe inhabitants during microbial colonization, represents a critical time period for establishing the overall health and wellbeing of an individual. The gut microbiome represents a diverse community of microbes that are critical for many physiological roles of the host including host metabolism. These processes are controlled by a fine-tuned chemical cross talk between the host and microbiota. Although the exact mechanisms behind this cross talk remains elusive, microbiota induced epigenetic mechanisms like DNA methylation and histone modifications may be key. This review presents our perspective on the epigenome as a mediator for host-microbiota cross talk, as well as methodology to study epigenetics, the role of dysbiosis in disease, and how the gut microbiome-host axis may be used in personal medicine.
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7
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Guibourdenche M, El Khayat El Sabbouri H, Djekkoun N, Khorsi-Cauet H, Bach V, Anton PM, Gay-Quéheillard J. Programming of intestinal homeostasis in male rat offspring after maternal exposure to chlorpyrifos and/or to a high fat diet. Sci Rep 2021; 11:11420. [PMID: 34075131 PMCID: PMC8169651 DOI: 10.1038/s41598-021-90981-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Alteration of programming of the intestinal wall maturation may be responsible for non-communicable chronic diseases in adulthood. It may originate from prenatal exposure of mothers to deleterious environmental factors such as pesticides or western diet. This work was undertaken to determine whether disturbances of the digestive tract function and of innate immunity of offspring at adulthood could be due to maternal exposure to a pesticide, chlorpyrifos (CPF) and a High Fat Diet (HFD) starting 4 months before gestation and lasting until weaning of offspring. Fifty-one male Wistar rats coming from 4 groups of dams exposed to CPF, HFD, both and control were followed from birth to 8 weeks of age. They were fed standard chow and received no treatment. The maternal pesticide exposure slows down fetal and postnatal weight gain without histological injuries of the gut mucosa. CPF or HFD both induced modifications of tight junctions and mucins genes expressions without inducing an increase in epithelial permeability or an inflammatory state. Co-exposure to both CPF and HFD did not exacerbate the effects observed with each factor separately. Despite the lack of direct contact except through breast milk until weaning, CPF or HFD maternal exposure have demonstrated preliminary gut barrier impacts on offspring.
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Affiliation(s)
- Marion Guibourdenche
- PériTox, Périnatalité & Risques Toxiques, UMR-I 01, UPJV/INERIS, Université Picardie Jules Verne, CURS, Présidence UPJV, Chemin du Thil, 80025, Amiens, France.,Institut Polytechnique UniLaSalle, Université d'Artois, ULR 7519, 19 rue Pierre Waguet, BP 30313, 60026, Beauvais, France
| | - Hiba El Khayat El Sabbouri
- PériTox, Périnatalité & Risques Toxiques, UMR-I 01, UPJV/INERIS, Université Picardie Jules Verne, CURS, Présidence UPJV, Chemin du Thil, 80025, Amiens, France
| | - Narimane Djekkoun
- PériTox, Périnatalité & Risques Toxiques, UMR-I 01, UPJV/INERIS, Université Picardie Jules Verne, CURS, Présidence UPJV, Chemin du Thil, 80025, Amiens, France
| | - Hafida Khorsi-Cauet
- PériTox, Périnatalité & Risques Toxiques, UMR-I 01, UPJV/INERIS, Université Picardie Jules Verne, CURS, Présidence UPJV, Chemin du Thil, 80025, Amiens, France
| | - Véronique Bach
- PériTox, Périnatalité & Risques Toxiques, UMR-I 01, UPJV/INERIS, Université Picardie Jules Verne, CURS, Présidence UPJV, Chemin du Thil, 80025, Amiens, France
| | - Pauline M Anton
- Institut Polytechnique UniLaSalle, Université d'Artois, ULR 7519, 19 rue Pierre Waguet, BP 30313, 60026, Beauvais, France
| | - Jérôme Gay-Quéheillard
- PériTox, Périnatalité & Risques Toxiques, UMR-I 01, UPJV/INERIS, Université Picardie Jules Verne, CURS, Présidence UPJV, Chemin du Thil, 80025, Amiens, France.
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8
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Ostrop J, Zwiggelaar RT, Terndrup Pedersen M, Gerbe F, Bösl K, Lindholm HT, Díez-Sánchez A, Parmar N, Radetzki S, von Kries JP, Jay P, Jensen KB, Arrowsmith C, Oudhoff MJ. A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. Front Cell Dev Biol 2021; 8:618552. [PMID: 33575256 PMCID: PMC7872100 DOI: 10.3389/fcell.2020.618552] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Intestinal organoids are an excellent model to study epithelial biology. Yet, the selection of analytical tools to accurately quantify heterogeneous organoid cultures remains limited. Here, we developed a semi-automated organoid screening method, which we applied to a library of highly specific chemical probes to identify epigenetic regulators of intestinal epithelial biology. The role of epigenetic modifiers in adult stem cell systems, such as the intestinal epithelium, is still undefined. Based on this resource dataset, we identified several targets that affected epithelial cell differentiation, including HDACs, EP300/CREBBP, LSD1, and type I PRMTs, which were verified by complementary methods. For example, we show that inhibiting type I PRMTs, which leads enhanced epithelial differentiation, blocks the growth of adenoma but not normal organoid cultures. Thus, epigenetic probes are powerful tools to study intestinal epithelial biology and may have therapeutic potential.
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Affiliation(s)
- Jenny Ostrop
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Rosalie T. Zwiggelaar
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Marianne Terndrup Pedersen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - François Gerbe
- Cancer Biology Department, Institute of Functional Genomics, University of Montpellier, Montpellier, France
| | - Korbinian Bösl
- Department of Bioinformatics, Computational Biological Unit, University of Bergen, Bergen, Norway
| | - Håvard T. Lindholm
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Silke Radetzki
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Jens Peter von Kries
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Philippe Jay
- Cancer Biology Department, Institute of Functional Genomics, University of Montpellier, Montpellier, France
| | - Kim B. Jensen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Menno J. Oudhoff
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
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Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium. Nat Rev Gastroenterol Hepatol 2021; 18:7-23. [PMID: 33024279 PMCID: PMC7997278 DOI: 10.1038/s41575-020-00357-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2020] [Indexed: 12/19/2022]
Abstract
The intestinal epithelium serves the unique and critical function of harvesting dietary nutrients, while simultaneously acting as a cellular barrier separating tissues from the luminal environment and gut microbial ecosystem. Two salient features of the intestinal epithelium enable it to perform these complex functions. First, cells within the intestinal epithelium achieve a wide range of specialized identities, including different cell types and distinct anterior-posterior patterning along the intestine. Second, intestinal epithelial cells are sensitive and responsive to the dynamic milieu of dietary nutrients, xenobiotics and microorganisms encountered in the intestinal luminal environment. These diverse identities and responsiveness of intestinal epithelial cells are achieved in part through the differential transcription of genes encoded in their shared genome. Here, we review insights from mice and other vertebrate models into the transcriptional regulatory mechanisms underlying intestinal epithelial identity and microbial responsiveness, including DNA methylation, chromatin accessibility, histone modifications and transcription factors. These studies are revealing that most transcription factors involved in intestinal epithelial identity also respond to changes in the microbiota, raising both opportunities and challenges to discern the underlying integrative transcriptional regulatory networks.
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10
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Verzi MP, Shivdasani RA. Epigenetic regulation of intestinal stem cell differentiation. Am J Physiol Gastrointest Liver Physiol 2020; 319:G189-G196. [PMID: 32628072 PMCID: PMC7500269 DOI: 10.1152/ajpgi.00084.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To fulfill the lifelong need to supply diverse epithelial cells, intestinal stem cells (ISCs) rely on executing accurate transcriptional programs. This review addresses the mechanisms that control those programs. Genes that define cell behaviors and identities are regulated principally through thousands of dispersed enhancers, each individually <1 kb long and positioned from a few to hundreds of kilobases away from transcription start sites, upstream or downstream from coding genes or within introns. Wnt, Notch, and other epithelial control signals feed into these cis-regulatory DNA elements, which are also common loci of polymorphisms and mutations that confer disease risk. Cell-specific gene activity requires promoters to interact with the correct combination of signal-responsive enhancers. We review the current state of knowledge in ISCs regarding active enhancers, the nucleosome modifications that may enable appropriate and hinder inappropriate enhancer-promoter contacts, and the roles of lineage-restricted transcription factors.
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Affiliation(s)
- Michael P. Verzi
- 1Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey,2Cancer Institute of New Jersey and Human Genetics Institute of New Jersey, Piscataway, New Jersey
| | - Ramesh A. Shivdasani
- 3Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts,4Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts,5Harvard Stem Cell Institute, Cambridge, Massachusetts
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11
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MacDonald EA, Rose RA, Quinn TA. Neurohumoral Control of Sinoatrial Node Activity and Heart Rate: Insight From Experimental Models and Findings From Humans. Front Physiol 2020; 11:170. [PMID: 32194439 PMCID: PMC7063087 DOI: 10.3389/fphys.2020.00170] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/13/2020] [Indexed: 12/22/2022] Open
Abstract
The sinoatrial node is perhaps one of the most important tissues in the entire body: it is the natural pacemaker of the heart, making it responsible for initiating each-and-every normal heartbeat. As such, its activity is heavily controlled, allowing heart rate to rapidly adapt to changes in physiological demand. Control of sinoatrial node activity, however, is complex, occurring through the autonomic nervous system and various circulating and locally released factors. In this review we discuss the coupled-clock pacemaker system and how its manipulation by neurohumoral signaling alters heart rate, considering the multitude of canonical and non-canonical agents that are known to modulate sinoatrial node activity. For each, we discuss the principal receptors involved and known intracellular signaling and protein targets, highlighting gaps in our knowledge and understanding from experimental models and human studies that represent areas for future research.
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Affiliation(s)
- Eilidh A. MacDonald
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - Robert A. Rose
- Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - T. Alexander Quinn
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax, NS, Canada
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12
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Li J, Luo J, Zhang Y, Tang C, Wang J, Chen C. Silencing of soluble epoxide hydrolase 2 gene reduces H 2O 2-induced oxidative damage in rat intestinal epithelial IEC-6 cells via activating PI3K/Akt/GSK3β signaling pathway. Cytotechnology 2020; 72:23-36. [PMID: 31907700 PMCID: PMC7002799 DOI: 10.1007/s10616-019-00354-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 11/03/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022] Open
Abstract
Oxidative stress plays a vital role in the occurrence and development of intestinal injury. Soluble epoxide hydrolase 2 gene (EPHX2) is a class of hydrolytic enzymes. We aim to explore the effects and molecular mechanism of siEPHX2 on H2O2-induced oxidative damage in rat intestinal epithelial IEC-6 cells. IEC-6 cells were transfected with EPHX2-siRNA and control si RNA plasmids by lipofectamine™ 2000 transfection reagent. The transfected samples were treated with H2O2 (50, 100, 200, 300, 400, and 500 µmol/L) for 12, 24, and 48 h, respectively. Cell viability was determined by cell counting kit-8 (CCK-8). Lactate dehydrogenase (LDH), malondialdehyde (MDA), and superoxide dismutase (SOD) were assessed by respective detection kits. Mitochondrial membrane potential (MMP), cell apoptosis and reactive oxygen species (ROS) and the levels of factors were determined by flow cytometer, quantitative real-time PCR (qRT-PCR) and western blot assays, respectively. We found that the IC50 of H2O2 was 200 µmol/L at 24 h, and the transfection of siEHPX2 in H2O2-induced IEC-6 cells significantly promoted the cell viability, SOD activity and MMP rate, and reduced the rates of ROS and apoptosis as well as LDH and MDA contents. siEHPX2 up-regulated the B-cell lymphoma-2 (Bcl-2) level and down-regulated the levels of fibroblast-associated (Fas), Fas ligand (Fasl), Bcl-2 associated X protein (Bax), and Caspase-3. Moreover, the phosphorylation levels of phosphoinositide 3 kinase (PI3K), protein kinase B (Akt), and glycogen synthase kinase3β (GSK3β) were up-regulated. We proved that siEPHX2 had a protective effect on H2O2-induced oxidative damage in IEC-6 cells through activating PI3K/Akt/GSK3β signaling pathway.
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Affiliation(s)
- Jun Li
- Department of Gastrointestinal Surgery, Hunan Provincial People's Hospital, No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan, China
| | - Jihui Luo
- Department of Surgical Oncology, Chenzhou No.1 People's Hospital, Chenzhou, China
| | - Yang Zhang
- Department of Burn Plastic Surgery, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Chunming Tang
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Jiang Wang
- Department of Gastrointestinal Surgery, Hunan Provincial People's Hospital, No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan, China
| | - Chaowu Chen
- Department of Gastrointestinal Surgery, Hunan Provincial People's Hospital, No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan, China.
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13
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Link-Lenczowski P, Jastrzębska M, Chwalenia K, Pierzchalska M, Leja-Szpak A, Bonior J, Pierzchalski P, Jaworek J. A switch of N-glycosylation of proteome and secretome during differentiation of intestinal epithelial cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118555. [PMID: 31499077 DOI: 10.1016/j.bbamcr.2019.118555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 12/24/2022]
Abstract
The maintenance of homeostasis of the intestinal epithelium depends on the complex process of epithelial cells differentiation, which repeatedly continues throughout the entire life. Many studies suggest, that cellular differentiation is regulated by glycosylation, or at least that changes of the latter are the hallmark of the process. The detailed description and understanding of this relationship are important in the context of gastrointestinal tract disease, including cancer. Here we employ a broadly used in vitro model of intestinal cell differentiation to track the glycosylation changes in details. We analyzed the glycoproteome- and glycosecretome-derived N-glycomes of undifferentiated Caco-2 adenocarcinoma cells and Caco-2-derived enterocyte-like cells. We used HILIC-HPLC and MALDI-ToF-MS approach together with exoglycosidases digestions to describe qualitative and quantitative N-glycosylation changes upon differentiation. Derived glycan traits analysis revealed, that differentiation results in substantial upregulation of sialylation of glycoproteome and increment of fucosylation within glycosecretome. This was also clearly visible when we analyzed the abundances of individual glycan species. Moreover, we observed the characteristic shift within oligomannose N-glycans, suggesting the augmentation of mannose trimming, resulting in downregulation of H8N2 and upregulation of H5N2 glycan. This was supported by elevated expression of Golgi alpha-mannosidases (especially MAN1C1). We hypothesize, that intensified mannose trimming at the initial steps of N-glycosylation pathway during differentiation, together with the remodeling of the expression of key glycosyltransferases leads to increased diversity of N-glycans and enhanced fucosylation and sialylation of complex structures. Finally, we propose H4N5F1 glycan as a potential biomarker of intestinal epithelial cell differentiation.
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Affiliation(s)
- Paweł Link-Lenczowski
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Kraków, Poland.
| | - Martyna Jastrzębska
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Kraków, Poland
| | - Katarzyna Chwalenia
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Kraków, Poland; Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Małgorzata Pierzchalska
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Kraków, Poland
| | - Anna Leja-Szpak
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Kraków, Poland
| | - Joanna Bonior
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Kraków, Poland
| | - Piotr Pierzchalski
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Kraków, Poland
| | - Jolanta Jaworek
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Kraków, Poland
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14
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Ganz J, Melancon E, Wilson C, Amores A, Batzel P, Strader M, Braasch I, Diba P, Kuhlman JA, Postlethwait JH, Eisen JS. Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development. Dev Biol 2019; 455:473-484. [PMID: 31394080 DOI: 10.1016/j.ydbio.2019.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/05/2019] [Accepted: 08/01/2019] [Indexed: 12/15/2022]
Abstract
Intestinal tract development is a coordinated process involving signaling among the progenitors and developing cells from all three germ layers. Development of endoderm-derived intestinal epithelium has been shown to depend on epigenetic modifications, but whether that is also the case for intestinal tract cell types from other germ layers remains unclear. We found that functional loss of a DNA methylation machinery component, ubiquitin-like protein containing PHD and RING finger domains 1 (uhrf1), leads to reduced numbers of ectoderm-derived enteric neurons and severe disruption of mesoderm-derived intestinal smooth muscle. Genetic chimeras revealed that Uhrf1 functions both cell-autonomously in enteric neuron precursors and cell-non-autonomously in surrounding intestinal cells, consistent with what is known about signaling interactions between these cell types that promote one another's development. Uhrf1 recruits the DNA methyltransferase Dnmt1 to unmethylated DNA during replication. Dnmt1 is also expressed in enteric neurons and smooth muscle progenitors. dnmt1 mutants have fewer enteric neurons and disrupted intestinal smooth muscle compared to wildtypes. Because dnmt1;uhrf1 double mutants have a similar phenotype to dnmt1 and uhrf1 single mutants, Dnmt1 and Uhrf1 must function together during enteric neuron and intestinal muscle development. This work shows that genes controlling epigenetic modifications are important to coordinate intestinal tract development, provides the first demonstration that these genes influence development of the ENS, and advances uhrf1 and dnmt1 as potential new Hirschsprung disease candidates.
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Affiliation(s)
- Julia Ganz
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Ellie Melancon
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Catherine Wilson
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Angel Amores
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Peter Batzel
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Marie Strader
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Ingo Braasch
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Parham Diba
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Julie A Kuhlman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - John H Postlethwait
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Judith S Eisen
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA.
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15
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Vymetalkova V, Vodicka P, Vodenkova S, Alonso S, Schneider-Stock R. DNA methylation and chromatin modifiers in colorectal cancer. Mol Aspects Med 2019; 69:73-92. [PMID: 31028771 DOI: 10.1016/j.mam.2019.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 12/15/2022]
Abstract
Colorectal carcinogenesis is a multistep process involving the accumulation of genetic alterations over time that ultimately leads to disease progression and metastasis. Binding of transcription factors to gene promoter regions alone cannot explain the complex regulation pattern of gene expression during this process. It is the chromatin structure that allows for a high grade of regulatory flexibility for gene expression. Posttranslational modifications on histone proteins such as acetylation, methylation, or phosphorylation determine the accessibility of transcription factors to DNA. DNA methylation, a chemical modification of DNA that modulates chromatin structure and gene transcription acts in concert with these chromatin conformation alterations. Another epigenetic mechanism regulating gene expression is represented by small non-coding RNAs. Only very recently epigenetic alterations have been included in molecular subtype classification of colorectal cancer (CRC). In this chapter, we will provide examples of the different epigenetic players, focus on their role for epithelial-mesenchymal transition and metastatic processes and discuss their prognostic value in CRC.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00, Pilsen, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00, Pilsen, Czech Republic
| | - Sona Vodenkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Sergio Alonso
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, (IGTP-PMPPC), Campus Can Ruti, 08916, Badalona, Barcelona, Spain
| | - Regine Schneider-Stock
- Experimental Tumorpathology, Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Universitätsstrasse 22, 91054, Erlangen, Germany.
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16
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Intestinal Epithelial Organoids as Tools to Study Epigenetics in Gut Health and Disease. Stem Cells Int 2019; 2019:7242415. [PMID: 30809264 PMCID: PMC6369455 DOI: 10.1155/2019/7242415] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/15/2019] [Indexed: 11/30/2022] Open
Abstract
The intestinal epithelium forms the inner layer of the human intestine and serves a wide range of diverse functions. Its constant exposure to a vast amount of complex microbiota highlights the critical interface that this single-cell layer forms between the host and our environment. Importantly, the well-documented contribution of environmental factors towards the functional development of the human intestinal epithelium directly implies epigenetic mechanisms in orchestrating this complex interplay. The development of intestinal epithelial organoid culture systems that can be generated from human tissue provides researchers with unpresented opportunities to study functional aspects of human intestinal epithelial pathophysiology. In this brief review, we summarise existing evidence for the role of epigenetics in regulating intestinal epithelial cell function and highlight the great potential for human gut organoids as translational research tools to investigate these mechanisms in vitro.
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Sawant-Basak A, Rodrigues AD, Lech M, Doyonnas R, Kasaian M, Prasad B, Tsamandouras N. Physiologically Relevant, Humanized Intestinal Systems to Study Metabolism and Transport of Small Molecule Therapeutics. Drug Metab Dispos 2018; 46:1581-1587. [PMID: 30126862 DOI: 10.1124/dmd.118.082784] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/16/2018] [Indexed: 01/15/2023] Open
Abstract
Intestinal disposition of small molecules involves interplay of drug metabolizing enzymes (DMEs), transporters, and host-microbiome interactions, which has spurred the development of in vitro intestinal models derived from primary tissue sources. Such models have been bioengineered from intestinal crypts, mucosal extracts, induced pluripotent stem cell (iPSC)-derived organoids, and human intestinal tissue. This minireview discusses the utility and limitations of these human-derived models in support of small molecule drug metabolism and disposition. Enteroids from human intestinal crypts, organoids derived from iPSCs using growth factors or small molecule compounds, and enterocytes extracted from mucosal scrapings show key absorptive cell morphology while are limited in quantitative applications due to the lack of accessibility to the apical compartment, the lack of monolayers, or low expression of key DMEs, transporters, and nuclear hormone receptors. Despite morphogenesis to epithelial cells, similar challenges have been reported by more advanced technologies that have explored the impact of flow and mechanical stretch on proliferation and differentiation of Caco-2 cells. Most recently, bioengineered human intestinal epithelial or ileal cells have overcome many of the challenges, as the DME and transporter expression pattern resembles that of native intestinal tissue. Engineering advances may improve such models to support longer-term applications and meet end-user needs. Biochemical characterization and transcriptomic, proteomic, and functional endpoints of emerging novel intestinal models, when referenced to native human tissue, can provide greater confidence and increased utility in drug discovery and development.
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Affiliation(s)
- Aarti Sawant-Basak
- Pfizer Worldwide Research & Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (A.S.-B.); Pfizer Worldwide Research & Development, PDM, Eastern Point Road, Groton, 06340 (A.D.R.); Pfizer Worldwide Research & Development, Inflammation and Immunology, 1 Portland Street, Cambridge, MA 02139 (M.L., M.K.); Pfizer Worldwide Research & Development, Discovery Sciences, Eastern Point Road, Groton, 06340 (R.D.); Assistant Professor, Department of Pharmaceutics, UWRAPT H268, Health Science Building, Seattle (B.P.); Pfizer Worldwide Research & Development, Early Clinical Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (N.T.).
| | - A David Rodrigues
- Pfizer Worldwide Research & Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (A.S.-B.); Pfizer Worldwide Research & Development, PDM, Eastern Point Road, Groton, 06340 (A.D.R.); Pfizer Worldwide Research & Development, Inflammation and Immunology, 1 Portland Street, Cambridge, MA 02139 (M.L., M.K.); Pfizer Worldwide Research & Development, Discovery Sciences, Eastern Point Road, Groton, 06340 (R.D.); Assistant Professor, Department of Pharmaceutics, UWRAPT H268, Health Science Building, Seattle (B.P.); Pfizer Worldwide Research & Development, Early Clinical Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (N.T.)
| | - Matthew Lech
- Pfizer Worldwide Research & Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (A.S.-B.); Pfizer Worldwide Research & Development, PDM, Eastern Point Road, Groton, 06340 (A.D.R.); Pfizer Worldwide Research & Development, Inflammation and Immunology, 1 Portland Street, Cambridge, MA 02139 (M.L., M.K.); Pfizer Worldwide Research & Development, Discovery Sciences, Eastern Point Road, Groton, 06340 (R.D.); Assistant Professor, Department of Pharmaceutics, UWRAPT H268, Health Science Building, Seattle (B.P.); Pfizer Worldwide Research & Development, Early Clinical Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (N.T.)
| | - Regis Doyonnas
- Pfizer Worldwide Research & Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (A.S.-B.); Pfizer Worldwide Research & Development, PDM, Eastern Point Road, Groton, 06340 (A.D.R.); Pfizer Worldwide Research & Development, Inflammation and Immunology, 1 Portland Street, Cambridge, MA 02139 (M.L., M.K.); Pfizer Worldwide Research & Development, Discovery Sciences, Eastern Point Road, Groton, 06340 (R.D.); Assistant Professor, Department of Pharmaceutics, UWRAPT H268, Health Science Building, Seattle (B.P.); Pfizer Worldwide Research & Development, Early Clinical Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (N.T.)
| | - Marion Kasaian
- Pfizer Worldwide Research & Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (A.S.-B.); Pfizer Worldwide Research & Development, PDM, Eastern Point Road, Groton, 06340 (A.D.R.); Pfizer Worldwide Research & Development, Inflammation and Immunology, 1 Portland Street, Cambridge, MA 02139 (M.L., M.K.); Pfizer Worldwide Research & Development, Discovery Sciences, Eastern Point Road, Groton, 06340 (R.D.); Assistant Professor, Department of Pharmaceutics, UWRAPT H268, Health Science Building, Seattle (B.P.); Pfizer Worldwide Research & Development, Early Clinical Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (N.T.)
| | - Bhagwat Prasad
- Pfizer Worldwide Research & Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (A.S.-B.); Pfizer Worldwide Research & Development, PDM, Eastern Point Road, Groton, 06340 (A.D.R.); Pfizer Worldwide Research & Development, Inflammation and Immunology, 1 Portland Street, Cambridge, MA 02139 (M.L., M.K.); Pfizer Worldwide Research & Development, Discovery Sciences, Eastern Point Road, Groton, 06340 (R.D.); Assistant Professor, Department of Pharmaceutics, UWRAPT H268, Health Science Building, Seattle (B.P.); Pfizer Worldwide Research & Development, Early Clinical Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (N.T.)
| | - Nikolaos Tsamandouras
- Pfizer Worldwide Research & Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (A.S.-B.); Pfizer Worldwide Research & Development, PDM, Eastern Point Road, Groton, 06340 (A.D.R.); Pfizer Worldwide Research & Development, Inflammation and Immunology, 1 Portland Street, Cambridge, MA 02139 (M.L., M.K.); Pfizer Worldwide Research & Development, Discovery Sciences, Eastern Point Road, Groton, 06340 (R.D.); Assistant Professor, Department of Pharmaceutics, UWRAPT H268, Health Science Building, Seattle (B.P.); Pfizer Worldwide Research & Development, Early Clinical Development, Clinical Pharmacology, 1 Portland Street, Cambridge, MA 02139 (N.T.)
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18
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Identification of an episignature of human colorectal cancer associated with obesity by genome-wide DNA methylation analysis. Int J Obes (Lond) 2018; 43:176-188. [PMID: 29717273 DOI: 10.1038/s41366-018-0065-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/17/2018] [Accepted: 02/07/2018] [Indexed: 01/26/2023]
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19
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Buoncervello M, Romagnoli G, Buccarelli M, Fragale A, Toschi E, Parlato S, Lucchetti D, Macchia D, Spada M, Canini I, Sanchez M, Falchi M, Musella M, Biffoni M, Belardelli F, Capone I, Sgambato A, Vitiani LR, Gabriele L. IFN-α potentiates the direct and immune-mediated antitumor effects of epigenetic drugs on both metastatic and stem cells of colorectal cancer. Oncotarget 2018; 7:26361-73. [PMID: 27028869 PMCID: PMC5041985 DOI: 10.18632/oncotarget.8379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/02/2016] [Indexed: 01/29/2023] Open
Abstract
Epigenetic alterations, including dysregulated DNA methylation and histone modifications, govern the progression of colorectal cancer (CRC). Cancer cells exploit epigenetic regulation to control cellular pathways, including apoptotic and metastatic signals. Since aberrations in epigenome can be pharmacologically reversed by DNA methyltransferase and histone deacetylase inhibitors, epigenetics in combination with standard agents are currently envisaged as a new therapeutic frontier in cancer, expected to overcome drug resistance associated with current treatments. In this study, we challenged this idea and demonstrated that the combination of azacitidine and romidepsin with IFN-α owns a high therapeutic potential, targeting the most aggressive cellular components of CRC, such as metastatic cells and cancer stem cells (CSCs), via tight control of key survival and death pathways. Moreover, the antitumor efficacy of this novel pharmacological approach is associated with induction of signals of immunogenic cell death. Of note, a previously undisclosed key role of IFN-α in inducing both antiproliferative and pro-apoptotic effects on CSCs of CRC was also found. Overall, these findings open a new frontier on the suitability of IFN-α in association with epigenetics as a novel and promising therapeutic approach for CRC management.
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Affiliation(s)
- Maria Buoncervello
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giulia Romagnoli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mariachiara Buccarelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Fragale
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Elena Toschi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Stefania Parlato
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Donatella Lucchetti
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Daniele Macchia
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Spada
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Irene Canini
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Sanchez
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome, Italy
| | - Mario Falchi
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Martina Musella
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mauro Biffoni
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Filippo Belardelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Imerio Capone
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandro Sgambato
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lucia Ricci Vitiani
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Gabriele
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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20
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Katzenmaier EM, Kloor M, Gabius HJ, Gebert J, Kopitz J. Analyzing epigenetic control of galectin expression indicates silencing of galectin-12 by promoter methylation in colorectal cancer. IUBMB Life 2017; 69:962-970. [PMID: 29098769 DOI: 10.1002/iub.1690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/07/2017] [Indexed: 12/24/2022]
Abstract
Galectins, a class of lectins with specificity for ß-galactoside containing glycoconjugates, modulate several cellular processes that are involved in the control of normal cell growth, differentiation, cell-cell, and cell matrix interactions. Pathological alterations of the galectin expression pattern have been implicated in the development and progression of cancer. We therefore analyzed epigenetic mechanisms for control of galectin expression in 9 colorectal cancer (CRC) cell lines. Our data demonstrate that expression of galectins-1, -2, -7, -8, and -9 can be regulated by histone acetylation in CRC cell lines. In addition, the same set of galectins was also found to be modulated by DNA methylation. Of particular note, galectin-12 is silenced in all tested CRC cell lines but known to be re-expressed upon butyrate-induced differentiation and present in normal colonic mucosa. Loss of galectin-12 expression in undifferentiated CRC cells is associated with promoter hypermethylation and for the first time we provide detailed methylation analysis of the promoter region. In CRC tumor tissue, galectin-12 expression was downregulated in 66% of CRC tissue specimens as compared to adjacent normal tissue hinting to a possible tumor-suppressing function in CRC. © 2017 IUBMB Life, 69(12):962-970, 2017.
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Affiliation(s)
- Eva-Maria Katzenmaier
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center), Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center), Heidelberg, Germany
| | - Hans-Joachim Gabius
- Faculty of Veterinary Medicine, Institute of Physiological Chemistry, Ludwig-Maximilians-University, Munich, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center), Heidelberg, Germany
| | - Juergen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center), Heidelberg, Germany
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21
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Schleimer RP, Berdnikovs S. Etiology of epithelial barrier dysfunction in patients with type 2 inflammatory diseases. J Allergy Clin Immunol 2017; 139:1752-1761. [PMID: 28583447 DOI: 10.1016/j.jaci.2017.04.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022]
Abstract
Epithelial barriers of the skin, gastrointestinal tract, and airway serve common critical functions, such as maintaining a physical barrier against environmental insults and allergens and providing a tissue interface balancing the communication between the internal and external environments. We now understand that in patients with allergic disease, regardless of tissue location, the homeostatic balance of the epithelial barrier is skewed toward loss of differentiation, reduced junctional integrity, and impaired innate defense. Importantly, epithelial dysfunction characterized by these traits appears to pre-date atopy and development of allergic disease. Despite our growing appreciation of the centrality of barrier dysfunction in initiation of allergic disease, many important questions remain to be answered regarding mechanisms disrupting normal barrier function. Although our external environment (proteases, allergens, and injury) is classically thought of as a principal contributor to barrier disruption associated with allergic sensitization, there is a need to better understand contributions of the internal environment (hormones, diet, and circadian clock). Systemic drivers of disease, such as alterations of the endocrine system, metabolism, and aberrant control of developmental signaling, are emerging as new players in driving epithelial dysfunction and allergic predisposition at various barrier sites. Identifying such central mediators of epithelial dysfunction using both systems biology tools and causality-driven laboratory experimentation will be essential in building new strategic interventions to prevent or reverse the process of barrier loss in allergic patients.
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Affiliation(s)
- Robert P Schleimer
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Sergejs Berdnikovs
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Ill.
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22
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Epigenetic modification of TLE1 induce abnormal differentiation in diabetic mice intestinal epithelium. Mol Cell Biochem 2017; 438:85-96. [PMID: 28744818 DOI: 10.1007/s11010-017-3116-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 07/15/2017] [Indexed: 12/20/2022]
Abstract
The intestinal epithelium cells (IECs) in diabetes mellitus (DM) patients have been proven to be abnormally differentiated. During the differentiation of IECs, epigenetic modification acts as an important regulator. In this study, we aimed to examine the epigenetic alteration of Transducin-like Enhancer of Split 1 (TLE1), a multitask transcriptional co-repressor, contributing to the differentiation homeostasis in IECs of DM mice. The IECs of type 2 diabetic mice model were isolated and collected. Methylation states of whole genomic DNA promoter regions were investigated by microarray. Methylated-specific PCR was used to detect the methylation state of TLE1 promoter in DM mice IECs. The expression of TLE1, Hes1, and differentiated cell markers were measured through real-time PCR, Western blots, and immunohistochemistry; by transfection assay, TLE1 or Hes1 was independently down-regulated in intestinal epithelium cell line, IEC-6. Subsequent modulation on TLE1, Hes1, and differentiated intestinal cell markers were detected. Global gene promoter regions in DM intestinal epithelium were less methylated comparing to normal control. The expression of TLE1 was significantly increased via hypomethylated activation in DM mice IECs. Hes1 was significantly suppressed and the terminal cell markers abnormally expressed in DM mice IECs (P < 0.05). Inhibition or induction on the abundance of TLE1 in IEC-6 cell line resulted in the corresponding dysregulation of Hes1 and intestinal epithelium differentiation (P < 0.05). Demethylation of TLE1 promoter region activates the self-expression in diabetic mice IECs. Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice.
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23
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Rogler G. Resolution of inflammation in inflammatory bowel disease. Lancet Gastroenterol Hepatol 2017; 2:521-530. [PMID: 28606878 DOI: 10.1016/s2468-1253(17)30031-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 12/14/2022]
Abstract
Treatment of inflammatory bowel disease at present mainly targets mediators of inflammation to stop or suppress pro-inflammatory processes. Typical examples are steroids, suppression of T cells by thioguanine nucleotides, or antibodies against cytokines such as tumour necrosis factor, interleukin 12, or interleukin 23. In addition to suppression of inflammation, development of therapeutic strategies that support resolution of inflammation or that actively resolve inflammation might be desirable. Resolution of inflammation is now seen as an active process involving specific mediators (eg, lipid mediators or specific cytokines) that is mandatory to restore organ function and completely shut down inflammation. The molecular pathways involved in resolution of inflammation have been investigated in recent years and could be adopted in treatment strategies for inflammatory bowel disease. Among these approaches are anti-integrin strategies and means to produce or locally increase restitution or resolution factors, such as restoration of the activity of transforming growth factor-β by anti-SMAD7 antisense oligonucleotides. The potential role of inflammation-resolving lipid mediators (eg, resolvins), however, still warrants further study and clinical development. This Review focuses on the specific role of active resolution of inflammation in inflammatory bowel disease pathophysiology. Potential therapeutic targets based on these pathways are also discussed.
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Affiliation(s)
- Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland.
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Woo V, Alenghat T. Host-microbiota interactions: epigenomic regulation. Curr Opin Immunol 2017; 44:52-60. [PMID: 28103497 DOI: 10.1016/j.coi.2016.12.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/02/2016] [Accepted: 12/08/2016] [Indexed: 12/14/2022]
Abstract
The coevolution of mammalian hosts and their commensal microbiota has led to the development of complex symbiotic relationships between resident microbes and mammalian cells. Epigenomic modifications enable host cells to alter gene expression without modifying the genetic code, and therefore represent potent mechanisms by which mammalian cells can transcriptionally respond, transiently or stably, to environmental cues. Advances in genome-wide approaches are accelerating our appreciation of microbial influences on host physiology, and increasing evidence highlights that epigenomics represent a level of regulation by which the host integrates and responds to microbial signals. In particular, bacterial-derived short chain fatty acids have emerged as one clear link between how the microbiota intersects with host epigenomic pathways. Here we review recent findings describing crosstalk between the microbiota and epigenomic pathways in multiple mammalian cell populations. Further, we discuss interesting links that suggest that the scope of our understanding of epigenomic regulation in the host-microbiota relationship is still in its infancy.
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Affiliation(s)
- Vivienne Woo
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Theresa Alenghat
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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26
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Elliott EN, Sheaffer KL, Kaestner KH. The 'de novo' DNA methyltransferase Dnmt3b compensates the Dnmt1-deficient intestinal epithelium. eLife 2016; 5:e12975. [PMID: 26808831 PMCID: PMC4786433 DOI: 10.7554/elife.12975] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/25/2016] [Indexed: 12/11/2022] Open
Abstract
Dnmt1 is critical for immediate postnatal intestinal development, but is not required for the survival of the adult intestinal epithelium, the only rapidly dividing somatic tissue for which this has been shown. Acute Dnmt1 deletion elicits dramatic hypomethylation and genomic instability. Recovery of DNA methylation state and intestinal health is dependent on the de novo methyltransferase Dnmt3b. Ablation of both Dnmt1 and Dnmt3b in the intestinal epithelium is lethal, while deletion of either Dnmt1 or Dnmt3b has no effect on survival. These results demonstrate that Dnmt1 and Dnmt3b cooperate to maintain DNA methylation and genomic integrity in the intestinal epithelium.
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Affiliation(s)
- Ellen N Elliott
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Karyn L Sheaffer
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Klaus H Kaestner
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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Uenoyama Y, Tomikawa J, Inoue N, Goto T, Minabe S, Ieda N, Nakamura S, Watanabe Y, Ikegami K, Matsuda F, Ohkura S, Maeda KI, Tsukamura H. Molecular and Epigenetic Mechanism Regulating Hypothalamic Kiss1 Gene Expression in Mammals. Neuroendocrinology 2016; 103:640-9. [PMID: 26964105 DOI: 10.1159/000445207] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/02/2016] [Indexed: 11/19/2022]
Abstract
After the discovery of hypothalamic kisspeptin encoded by the Kiss1 gene, the central mechanism regulating gonadotropin-releasing hormone (GnRH) secretion, and hence gonadotropin secretion, is gradually being unraveled. This has increased our understanding of the central mechanism regulating puberty and subsequent reproductive performance in mammals. Recently, emerging evidence has indicated the molecular and epigenetic mechanism regulating hypothalamic Kiss1 gene expression. Here we compile data regarding DNA and histone modifications in the Kiss1 promoter region and provide a hypothetic scheme of the molecular and epigenetic mechanism regulating Kiss1 gene expression in two populations of hypothalamic kisspeptin neurons, which govern puberty and subsequent reproductive performance via GnRH/gonadotropin secretion.
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Affiliation(s)
- Yoshihisa Uenoyama
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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