The Transcription Factor Osterix (SP7) Regulates Bmp6induced Human Osteoblast Differentiation
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PLZF Targets Developmental Enhancers for Activation During Osteogenic Differentiation of Human Mesenchymal Stem Cells
RESEARCH ARTICLE PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells Shuchi Agrawal Singh1,2,3*, Mads Lerdrup1,3, Ana-Luisa R Gomes1,3, Harmen JG van de Werken4,5,6, Jens Vilstrup Johansen1,3,7, Robin Andersson1,3,7, Albin Sandelin1,3,7, Kristian Helin8,9,10, Klaus Hansen1,3* 1Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; 2Department of Hematology, Cambridge Institute for Medical Research and Welcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom; 3Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; 4Department of Cell Biology, University Medical Center, Rotterdam, Netherlands; 5Cancer Computational Biology Center, University Medical Center, Rotterdam, Netherlands; 6Department of Urology, University Medical Center, Rotterdam, Netherlands; 7Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark; 8The Novo Nordisk Center for Stem Cell Biology, Faculty of Health and Medical Sciences University of Copenhagen, Copenhagen, Denmark; 9Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States; 10Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, United States *For correspondence: [email protected]; Abstract The PLZF transcription factor is essential for osteogenic differentiation of hMSCs; [email protected] (SAS); however, its regulation and molecular function during this process is not fully understood. Here, we [email protected] (KHA) revealed that the ZBTB16 locus encoding PLZF, is repressed by Polycomb (PcG) and H3K27me3 in Competing interests: The naive hMSCs. At the pre-osteoblast stage of differentiation, the locus lost PcG binding and authors declare that no H3K27me3, gained JMJD3 recruitment, and H3K27ac resulting in high expression of PLZF. -
V10a91-Tasheva Pgmkr
Molecular Vision 2004; 10:758-772 <http://www.molvis.org/molvis/v10/a91> ©2004 Molecular Vision Received 12 August 2004 | Accepted 7 October 2004 | Published 7 October 2004 Analysis of transcriptional regulation of the small leucine rich proteoglycans Elena S. Tasheva,1 Bernward Klocke,2 Gary W. Conrad1 1Kansas State University, Division of Biology, Manhattan, KS; 2Genomatix Software GmbH, München, Germany Purpose: Small leucine rich proteoglycans (SLRPs) constitute a family of secreted proteoglycans that are important for collagen fibrillogenesis, cellular growth, differentiation, and migration. Ten of the 13 known members of the SLRP gene family are arranged in tandem clusters on human chromosomes 1, 9, and 12. Their syntenic equivalents are on mouse chromosomes 1, 13, and 10, and rat chromosomes 13, 17, and 7. The purpose of this study was to determine whether there is evidence for control elements, which could regulate the expression of these clusters coordinately. Methods: Promoters were identified using a comparative genomics approach and Genomatix software tools. For each gene a set of human, mouse, and rat orthologous promoters was extracted from genomic sequences. Transcription factor (TF) binding site analysis combined with a literature search was performed using MatInspector and Genomatix’ BiblioSphere. Inspection for the presence of interspecies conserved scaffold/matrix attachment regions (S/MARs) was performed using ElDorado annotation lists. DNAseI hypersensitivity assay, chromatin immunoprecipitation (ChIP), and transient transfection experiments were used to validate the results from bioinformatics analysis. Results: Transcription factor binding site analysis combined with a literature search revealed co-citations between several SLRPs and TFs Runx2 and IRF1, indicating that these TFs have potential roles in transcriptional regulation of the SLRP family members. -
A Molecular and Genetic Analysis of Otosclerosis
A molecular and genetic analysis of otosclerosis Joanna Lauren Ziff Submitted for the degree of PhD University College London January 2014 1 Declaration I, Joanna Ziff, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Where work has been conducted by other members of our laboratory, this has been indicated by an appropriate reference. 2 Abstract Otosclerosis is a common form of conductive hearing loss. It is characterised by abnormal bone remodelling within the otic capsule, leading to formation of sclerotic lesions of the temporal bone. Encroachment of these lesions on to the footplate of the stapes in the middle ear leads to stapes fixation and subsequent conductive hearing loss. The hereditary nature of otosclerosis has long been recognised due to its recurrence within families, but its genetic aetiology is yet to be characterised. Although many familial linkage studies and candidate gene association studies to investigate the genetic nature of otosclerosis have been performed in recent years, progress in identifying disease causing genes has been slow. This is largely due to the highly heterogeneous nature of this condition. The research presented in this thesis examines the molecular and genetic basis of otosclerosis using two next generation sequencing technologies; RNA-sequencing and Whole Exome Sequencing. RNA–sequencing has provided human stapes transcriptomes for healthy and diseased stapes, and in combination with pathway analysis has helped identify genes and molecular processes dysregulated in otosclerotic tissue. Whole Exome Sequencing has been employed to investigate rare variants that segregate with otosclerosis in affected families, and has been followed by a variant filtering strategy, which has prioritised genes found to be dysregulated during RNA-sequencing. -
Large-Scale Serum Protein Biomarker Discovery in Duchenne Muscular Dystrophy
Large-scale serum protein biomarker discovery in Duchenne muscular dystrophy Yetrib Hathouta, Edward Brodyb, Paula R. Clemensc,d, Linda Cripee, Robert Kirk DeLisleb, Pat Furlongf, Heather Gordish- Dressmana, Lauren Hachea, Erik Henricsong, Eric P. Hoffmana, Yvonne Monique Kobayashih, Angela Lortsi, Jean K. Mahj, Craig McDonaldg, Bob Mehlerb, Sally Nelsonk, Malti Nikradb, Britta Singerb, Fintan Steeleb, David Sterlingb, H. Lee Sweeneyl, Steve Williamsb, and Larry Goldb,1 aResearch Center for Genetic Medicine, Children’s National Medical Center, Washington, DC 20012; bSomaLogic, Inc., Boulder, CO 80301; cNeurology Service, Department of Veteran Affairs Medical Center, Pittsburgh, PA 15240; dUniversity of Pittsburgh, Pittsburgh, PA 15213; eThe Heart Center, Nationwide Children’s Hospital, The Ohio State University, Columbus, OH 15213; fParent Project Muscular Dystrophy, Hackensack, NJ 07601; gDepartment of Physical Medicine and Rehabilitation, University of California Davis School of Medicine, Davis, CA 95618; hDepartment of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202; iThe Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229; jDepartment of Pediatrics, University of Calgary, Alberta Children’s Hospital, Calgary, AB, Canada T3B 6A8; kDivision of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, CO 80045; and lDepartment of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL 32610 Contributed -
A Single-Cell Transcriptomic Landscape of Primate Arterial Aging
ARTICLE https://doi.org/10.1038/s41467-020-15997-0 OPEN A single-cell transcriptomic landscape of primate arterial aging Weiqi Zhang 1,2,3,4,5,13, Shu Zhang6,7,13, Pengze Yan3,8,13, Jie Ren7,9,13, Moshi Song3,5,8, Jingyi Li2,3,8, Jinghui Lei4, Huize Pan2,3, Si Wang3,5,8, Xibo Ma3,10, Shuai Ma2,3,8, Hongyu Li2,3, Fei Sun2,3, Haifeng Wan3,5,11, ✉ ✉ ✉ Wei Li 3,5,11, Piu Chan4, Qi Zhou3,5,11, Guang-Hui Liu 2,3,4,5,8 , Fuchou Tang 6,7,9,12 & Jing Qu 3,5,11 Our understanding of how aging affects the cellular and molecular components of the vas- 1234567890():,; culature and contributes to cardiovascular diseases is still limited. Here we report a single-cell transcriptomic survey of aortas and coronary arteries in young and old cynomolgus monkeys. Our data define the molecular signatures of specialized arteries and identify eight markers discriminating aortic and coronary vasculatures. Gene network analyses characterize tran- scriptional landmarks that regulate vascular senility and position FOXO3A, a longevity- associated transcription factor, as a master regulator gene that is downregulated in six subtypes of monkey vascular cells during aging. Targeted inactivation of FOXO3A in human vascular endothelial cells recapitulates the major phenotypic defects observed in aged monkey arteries, verifying FOXO3A loss as a key driver for arterial endothelial aging. Our study provides a critical resource for understanding the principles underlying primate arterial aging and contributes important clues to future treatment of age-associated vascular disorders. 1 CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Acemannan Stimulates Bone Sialoprotein, Osteocalcin, Osteopon- Tin and Osteonectin Expression in Periodontal Ligament Cells in V
Original Article บ ท วิ ท ย า ก า ร Acemannan Stimulates Bone Sialoprotein, Osteocalcin, Osteopon- tin and Osteonectin Expression in Periodontal Ligament Cells in Vitro Pintu-on Chantarawaratit1,2,4, Polkit Sangvanich3 and Pasutha Thunyakitpisal2,4 1Department of Orthodontics, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand 2Dental Biomaterials Program, Graduate School, Chulalongkorn University, Bangkok, Thailand 3Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand 4Research Unit of Herbal Medicine and Natural Products of Dental Application, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand Correspondence to: Pasutha Thunyakitpisal, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, 34, Henri-Dunant Rd, Patumwan, Bangkok 10330, Thailand Email: [email protected] Abstract The periodontium is composed of both soft and hard tissues, thus hard tissue regeneration is one of the most important processes in periodontal regeneration. Bone sialoprotein, osteocalcin, osteopontin and osteonectin are non- collagenous matrix proteins which play vital roles in the mineralization of hard tissue. Recent studies have demonstrated that acemannan, a polysaccharide extracted from Aloe vera gel, upregulated the expression of proteins involved in hard tissue regeneration. This study investigated effect of acemannan on bone sialoprotein, osteocalcin, osteopontin and osteonectin expression in human periodontal ligament cells. Primary periodontal ligament cells were isolated from impacted third molars and then treated with acemannan in vitro. The mRNA expression of bone sialoprotein and osteocalcin and the protein levels of osteopontin and osteonectin were determined using reverse transcription-polymerase chain reaction and western blot analysis, respectively. One-way analysis of variance and Dunnett multiple comparisons were performed to analyze the data. -
Microarray Analysis of Bone Marrow Lesions in Osteoarthritis
ARD Online First, published on July 13, 2017 as 10.1136/annrheumdis-2017-211396 Basic and translational research Ann Rheum Dis: first published as 10.1136/annrheumdis-2017-211396 on 13 July 2017. Downloaded from EXTENDED REPORT Microarray analysis of bone marrow lesions in osteoarthritis demonstrates upregulation of genes implicated in osteochondral turnover, neurogenesis and inflammation Anasuya Kuttapitiya,1 Lena Assi,1 Ken Laing,1 Caroline Hing,2 Philip Mitchell,2 Guy Whitley,3 Abiola Harrison,1 Franklyn A Howe,3 Vivian Ejindu,2 Christine Heron,2 Nidhi Sofat1 ► Additional material is ABSTRACT affecting the knees in up to 37% of adults over published online only. To view Objective Bone marrow lesions (BMLs) are well 60.1 Pain is a major symptom for people with OA, please visit the journal online described in osteoarthritis (OA) using MRI and are with 16.7% of US adults aged 45 years and above (http:// dx. doi. org/ 10. 1136/ 1 annrheumdis- 2017- 211396). associated with pain, but little is known about their reporting pain as a predominant problem. pathological characteristics and gene expression. We Pain in OA is thought to arise from several 1 Institute for Infection & evaluated BMLs using novel tissue analysis tools to gain structures within the arthritic joint, including the Immunity, St George's, a deeper understanding of their cellular and molecular synovium (from which prostaglandins, leukot- University of London, London, UK expression. rienes and inflammatory mediators are released), 2St George's University Methods We recruited 98 participants, 72 with joint effusions, joint capsule involvement, tendon Hospitals NHS Foundation Trust, advanced OA requiring total knee replacement (TKR), 12 and muscle weakness that all contribute to pain London, UK 3 3 with mild OA and 14 non-OA controls. -
CHAPTER 41 Target Genes: Bone Proteins 719
CHAPTER 41 Target Genes: Bone Proteins 719 45. Bellows CG, Reimers SM, Heersche JN 1999 Expression of 61. Price PA, Williamson MK, Lothringer JW 1981 Origin of the mRNAs for type-I collagen, bone sialoprotein, osteocalcin, vitamin K-dependent bone protein found in plasma and its and osteopontin at different stages of osteoblastic differentia- clearance by kidney and bone. J Biol Chem 256:12760–12766. tion and their regulation by 1,25-dihydroxyvitamin D3. Cell 62. Ducy P, Desbois C, Boyce B, Pinero G, Story B, Dunstan C, Tissue Res 297:249–259. Smith E, Bonadio J, Goldstein S, Gundberg C, Bradley A, 46. Broess M, Riva A, Gerstenfeld LC 1995 Inhibitory effects of Karsenty G 1996 Increased bone formation in osteocalcin- 1,25(OH)2 vitamin D3 on collagen type I, osteopontin, and deficient mice. Nature 382:448–452. osteocalcin gene expression in chicken osteoblasts. J Cell 63. Chenu C, Colucci S, Grano M, Zigrino P, Barattolo R, Biochem 57:440–451. Zambonin G, Baldini N, Vergnaud P, Delmas PD, Zallone AZ 47. Yoon K, Buenaga R, Rodan GA, Prince CW, Butler WT 1994 Osteocalcin induces chemotaxis, secretion of matrix pro- 1987 Tissue specificity and developmental expression of teins, and calcium-mediated intracellular signaling in human rat osteopontin. Biochem Biophys Res Commun 148: osteoclast-like cells. J Cell Biol 127:1149–1158. 1129–1136. 64. Watts NB 1999 Clinical utility of biochemical markers of bone 48. Beresford JN, Joyner CJ, Devlin C, Triffitt JT 1994 The effects remodeling. Clin Chem 45:1359–1368. of dexamethasone and 1,25-dihydroxyvitamin D3 on osteogenic 65. -
Method for Predicting the Occurence of Lung Metastasis in Breast Cancer Patients
(19) TZZ ¥ __T (11) EP 2 253 721 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 24.11.2010 Bulletin 2010/47 C12Q 1/68 (2006.01) (21) Application number: 10175619.5 (22) Date of filing: 26.02.2008 (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • Lidereau, Rosette HR HU IE IS IT LI LT LU LV MC MT NL NO PL PT 92230, Gennevilliers (FR) RO SE SI SK TR • Driouch, Keltouma Designated Extension States: 93260, Les Lilas (FR) AL BA MK RS • Landemaine, Thomas 92100, Boulogne-Billancourt (FR) (30) Priority: 26.02.2007 EP 07300823 (74) Representative: Catherine, Alain et al (62) Document number(s) of the earlier application(s) in Cabinet Harlé & Phélip accordance with Art. 76 EPC: 7 rue de Madrid 08709219.3 / 2 115 170 75008 Paris (FR) (71) Applicants: Remarks: • INSERM (Institut National de la Santé et de la This application was filed on 07-09-2010 as a Recherche Medicale) divisional application to the application mentioned 75013 Paris (FR) under INID code 62. • Centre Rene Huguenin 92210 Saint-Cloud (FR) (54) Method for predicting the occurence of lung metastasis in breast cancer patients (57) The present invention relates to the prognosis tasis in one or more tissue or organ of patients affected of the progression of breast cancer in a patient, and more with a breast cancer. particularly to the prediction of the occurrence of metas- EP 2 253 721 A1 Printed by Jouve, 75001 PARIS (FR) EP 2 253 721 A1 Description FIELD OF THE INVENTION 5 [0001] The present invention relates to the prognosis of the progression of breast cancer in a patient, and more particularly to the prediction of the occurrence of metastasis in one or more tissue or organ of patients affected with a breast cancer. -
Page 1 of 76 Diabetes Diabetes Publish Ahead of Print, Published Online September 14, 2020
Page 1 of 76 Diabetes Peters, Annette; Helmholtz Center Munich German Research Center for Environmental Health, Epidemiology Institute Waldenberger, Melanie; Helmholtz Center Munich German Research Center for Environmental Health, Molecular Epidemiology Diabetes Publish Ahead of Print, published online September 14, 2020 Diabetes Page 2 of 76 Deciphering the Plasma Proteome of Type 2 Diabetes Mohamed A. Elhadad1,2,3 MSc., Christian Jonasson4,5 PhD, Cornelia Huth2,6 PhD, Rory Wilson1,2 MSc, Christian Gieger1,2,6 PhD, Pamela Matias1,2,3 MSc, Harald Grallert1,2,6 PhD, Johannes Graumann7,8 PhD, Valerie Gailus-Durner9 PhD, Wolfgang Rathmann6,10 MD, Christine von Toerne11 PhD, Stefanie M. Hauck11 PhD, Wolfgang Koenig3,12,13 MD, FRCP, FESC, FACC, FAHA, Moritz F. Sinner3,14 MD, MPH, Tudor I Oprea15,16,17 MD, PhD, Karsten Suhre18 PhD, Barbara Thorand2,6 PhD, Kristian Hveem4,5 PhD, Annette Peters2,3,6,19 PhD, Melanie Waldenberger1,2,3 PhD 1. Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany. 2. Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany 3. German Research Center for Cardiovascular Disease (DZHK), Partner site Munich Heart Alliance, Germany 4. K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, NTNU - Norwegian University of Science and Technology, Trondheim, Norway 5. HUNT Research Center, Department of Public Health, NTNU - Norwegian University of Science and Technology, Levanger, Norway 6. German Center for Diabetes Research (DZD), München-Neuherberg, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany 7. Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, Bad Nauheim 61231, Germany 8. -
2598 Biomineralization of Bone: a Fresh View of the Roles of Non-Collagen
[Frontiers in Bioscience 16, 2598-2621, June 1, 2011] Biomineralization of bone: a fresh view of the roles of non-collagenous proteins Jeffrey Paul Gorski1 1Center of Excellence in the Study of Musculoskeletal and Dental Tissues and Dept. of Oral Biology, Sch. Of Dentistry, Univ. of Missouri-Kansas City, Kansas City, MO 64108 TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Proposed mechanisms of mineral nucleation in bone 3.1. Biomineralization Foci 3.2. Calcospherulites 3.3. Matrix vesicles 4. The role of individual non-collagenous proteins 4.1. Bone Sialoprotein 4.2. Noggin 4.3. Chordin 4.4. Osteopontin 4.5. Osteopontin, bone sialoprotein, and DMP1 form individual complexes with MMPs 4.6. Bone acidic glycoprotein-75 4.7. Dentin matrix protein1 4.8. Osteocalcin 4.9. Fetuin (alpha2HS-glycoprotein) 4.10. Periostin 4.11. Tissue nonspecific alkaline phosphatase 4.12. Phospho 1 phosphatase 4.13. Ectonucleotide pyrophosphatase/phosphodiesterase 4.14. Biological effects of hydroxyapatite on bone matrix proteins 4.15. Sclerostin 4.16. Tenascin C 4.17. Phosphate-regulating neutral endopeptidase (PHEX) 4.18. Matrix extracellular phosphoglycoprotein (MEPE, OF45) 4.19. Functional importance of proteolysis in activation of transglutaminase and PCOLCE 4.20. Neutral proteases in bone 5. Summary and Perspective 6. Acknowledgements 7. References 1. ABSTRACT The impact of genetics has dramatically affected nteractions which act in positive and negative ways to our understanding of the functions of non-collagenous regulate the process of bone mineralization. Several new proteins. Specifically, mutations and knockouts have examples from the author’s laboratory are provided defined their cellular spectrum of actions.