Hereditary Multiple Exostoses, Macrocephaly, Congenital Heart
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Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Specific Functions of Exostosin-Like 3 (EXTL3) Gene Products Shuhei Yamada
Yamada Cellular & Molecular Biology Letters (2020) 25:39 Cellular & Molecular https://doi.org/10.1186/s11658-020-00231-y Biology Letters REVIEW LETTER Open Access Specific functions of Exostosin-like 3 (EXTL3) gene products Shuhei Yamada Correspondence: shuheiy@meijo-u. ac.jp Abstract Department of Pathobiochemistry, Exostosin-like 3 EXTL3 Faculty of Pharmacy, Meijo ( ) encodes the glycosyltransferases responsible for the University, 150 Yagotoyama, biosynthesis of the backbone structure of heparan sulfate (HS), a sulfated Tempaku-ku, Nagoya 468-8503, polysaccharide that is ubiquitously distributed on the animal cell surface and in the Japan extracellular matrix. A lack of EXTL3 reduces HS levels and causes embryonic lethality, indicating its indispensable role in the biosynthesis of HS. EXTL3 has also been identified as a receptor molecule for regenerating islet-derived (REG) protein ligands, which have been shown to stimulate islet β-cell growth. REG proteins also play roles in keratinocyte proliferation and/or differentiation, tissue regeneration and immune defenses in the gut as well as neurite outgrowth in the central nervous system. Compared with the established function of EXTL3 as a glycosyltransferase in HS biosynthesis, the REG-receptor function of EXTL3 is not conclusive. Genetic diseases caused by biallelic mutations in the EXTL3 gene were recently reported to result in a neuro-immuno-skeletal dysplasia syndrome. EXTL3 is a key molecule for the biosynthesis of HS and may be involved in the signal transduction of REG proteins. Keywords: Exostosin-like 3 (EXTL3), Heparan sulfate (HS), Biosynthesis, Glycosaminoglycan, Regenerating islet-derived (REG) protein Introduction Hereditary multiple exostosis (HME), also known as multiple osteochondromas, is a rare disorder occurring in approximately 1 in 50,000 individuals [1, 2]. -
Gene Silencing of EXTL2 and EXTL3 As a Substrate Deprivation Therapy for Heparan Sulphate Storing Mucopolysaccharidoses
European Journal of Human Genetics (2010) 18, 194–199 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 $32.00 www.nature.com/ejhg ARTICLE Gene silencing of EXTL2 and EXTL3 as a substrate deprivation therapy for heparan sulphate storing mucopolysaccharidoses Xenia Kaidonis1,2, Wan Chin Liaw1, Ainslie Derrick Roberts1,3, Marleesa Ly1,3, Donald Anson1,3 and Sharon Byers*,1,2,3 Neurological pathology is characteristic of the mucopolysaccharidoses (MPSs) that store heparan sulphate (HS) glycosaminoglycan (gag) and has been proven to be refractory to systemic therapies. Substrate deprivation therapy (SDT) using general inhibitors of gag synthesis improves neurological function in mouse models of MPS, but is not specific to an MPS type. We have investigated RNA interference (RNAi) as a method of targeting SDT to the HS synthesising enzymes, EXTL2 and EXTL3. Multiple shRNA molecules specific to EXTL2 or EXTL3 were designed and validated in a reporter gene assay, with four out of six shRNA constructs reducing expression by over 90%. The three EXTL2-specific shRNA constructs reduced endogenous target gene expression by 68, 32 and 65%, and decreased gag synthesis by 46, 50 and 27%. One EXTL3-specific shRNA construct reduced endogenous target gene expression by 14% and gag synthesis by 39%. Lysosomal gag levels in MPS IIIA and MPS I fibroblasts were also reduced by EXTL2 and EXTL3-specific shRNA. Incorporation of shRNAs into a lentiviral expression system reduced gene expression, and one EXTL2-specific shRNA reduced gag synthesis. These results indicate that deprivation therapy through shRNA-mediated RNAi has potential as a therapy for HS-storing MPSs. -
A Genomic Approach to Delineating the Occurrence of Scoliosis in Arthrogryposis Multiplex Congenita
G C A T T A C G G C A T genes Article A Genomic Approach to Delineating the Occurrence of Scoliosis in Arthrogryposis Multiplex Congenita Xenia Latypova 1, Stefan Giovanni Creadore 2, Noémi Dahan-Oliel 3,4, Anxhela Gjyshi Gustafson 2, Steven Wei-Hung Hwang 5, Tanya Bedard 6, Kamran Shazand 2, Harold J. P. van Bosse 5 , Philip F. Giampietro 7,* and Klaus Dieterich 8,* 1 Grenoble Institut Neurosciences, Université Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, 38000 Grenoble, France; [email protected] 2 Shriners Hospitals for Children Headquarters, Tampa, FL 33607, USA; [email protected] (S.G.C.); [email protected] (A.G.G.); [email protected] (K.S.) 3 Shriners Hospitals for Children, Montreal, QC H4A 0A9, Canada; [email protected] 4 School of Physical & Occupational Therapy, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 2M1, Canada 5 Shriners Hospitals for Children, Philadelphia, PA 19140, USA; [email protected] (S.W.-H.H.); [email protected] (H.J.P.v.B.) 6 Alberta Congenital Anomalies Surveillance System, Alberta Health Services, Edmonton, AB T5J 3E4, Canada; [email protected] 7 Department of Pediatrics, University of Illinois-Chicago, Chicago, IL 60607, USA 8 Institut of Advanced Biosciences, Université Grenoble Alpes, Inserm, U1209, CHU Grenoble Alpes, 38000 Grenoble, France * Correspondence: [email protected] (P.F.G.); [email protected] (K.D.) Citation: Latypova, X.; Creadore, S.G.; Dahan-Oliel, N.; Gustafson, Abstract: Arthrogryposis multiplex congenita (AMC) describes a group of conditions characterized A.G.; Wei-Hung Hwang, S.; Bedard, by the presence of non-progressive congenital contractures in multiple body areas. -
The Tissue-Specific Transcriptomic Landscape of the Mid-Gestational Mouse Embryo Martin Werber1, Lars Wittler1, Bernd Timmermann2, Phillip Grote1,* and Bernhard G
© 2014. Published by The Company of Biologists Ltd | Development (2014) 141, 2325-2330 doi:10.1242/dev.105858 RESEARCH REPORT TECHNIQUES AND RESOURCES The tissue-specific transcriptomic landscape of the mid-gestational mouse embryo Martin Werber1, Lars Wittler1, Bernd Timmermann2, Phillip Grote1,* and Bernhard G. Herrmann1,3,* ABSTRACT mainly protein-coding genes. However, none of these datasets has Differential gene expression is a prerequisite for the formation of multiple provided an accurate representation of the transcriptome of the mouse cell types from the fertilized egg during embryogenesis. Understanding embryo. In particular, earlier studies using expression profiling did not the gene regulatory networks controlling cellular differentiation requires cover the complete set of protein coding genes or alternative transcripts the identification of crucial differentially expressed control genes and, or noncoding RNA genes. The latter have come into focus in recent ideally, the determination of the complete transcriptomes of each years, as noncoding genes are assumed to play important roles in gene individual cell type. Here, we have analyzed the transcriptomes of six regulation (for reviews, see Pauli et al., 2011; Rinn and Chang, 2012). major tissues dissected from mid-gestational (TS12) mouse embryos. Among the highly diverse class of noncoding genes, long Approximately one billion reads derived by RNA-seq analysis provided noncoding RNAs (lncRNAs) are thought to influence transcription extended transcript lengths, novel first exons and alternative transcripts by a wide range of mechanisms. For example, lncRNAs can interact of known genes. We have identified 1375 genes showing tissue-specific with chromatin-modifying protein complexes involved in gene expression, providing gene signatures for each of the six tissues. -
Variation in Protein Coding Genes Identifies Information Flow
bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number. -
A Network of Clinically and Functionally Relevant Genes Is Involved in The
Oncogene (2005) 24, 869–879 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc A network of clinically and functionally relevant genes is involved in the reversion of the tumorigenic phenotype of MDA-MB-231 breast cancer cells after transfer of human chromosome 8 Susanne Seitz*,1, Renate Frege1, Anja Jacobsen2,Jo¨ rg Weimer2, Wolfgang Arnold3, Clarissa von Haefen4, Dieter Niederacher5, Rita Schmutzler6, Norbert Arnold2 and Siegfried Scherneck1 1Department of Tumor Genetics, Max Delbrueck Center for Molecular Medicine, Robert Roessle Str. 10, 13125 Berlin, Germany; 2Oncology Laboratory, Gynecology and Obstetrics Clinic, University Hospital Schleswig-Holstein Campus Kiel, Michalisstr. 16, 24105 Kiel, Germany; 3atugen AG, Wiltbergstr. 50, 13125 Berlin, Germany; 4Department of Hematology, Oncology and Tumor Immunology, Charite-Campus Berlin-Buch, Humboldt University, Lindenberger Weg 80, 13125 Berlin-Buch, Germany; 5Department of Gynecology and Obstetrics, University of Duesseldorf, Moorenstr. 5, 40225 Duesseldorf, Germany; 6Department of Molecular Gynecology and Oncology, Gynecology and Obstetrics Clinic, Kerpener Str. 34, 50931 Ko¨ln, Germany Several investigations have supposed that tumor suppres- and 17p are detected frequently in more than 20–25% of sor genes might be located on human chromosome 8. We primary BC, suggesting the presence of tumor suppres- used microcell-mediated transfer of chromosome 8 into sor genes (TSG) in these regions of the genome MDA-MB-231 breast cancer cells and generated inde- (Lerebours and Lidereau, 2002). The regions of LOH pendent hybrids with strongly reduced tumorigenic in BC are usually large and complex and it is difficult to potential. Loss of the transferred chromosome results in identify candidate genes relying on allelic loss alone. -
The Pathogenic Roles of Heparan Sulfate Deficiency in Hereditary Multiple Exostoses
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Matrix Biol Manuscript Author . Author manuscript; Manuscript Author available in PMC 2019 October 01. Published in final edited form as: Matrix Biol. 2018 October ; 71-72: 28–39. doi:10.1016/j.matbio.2017.12.011. The pathogenic roles of heparan sulfate deficiency in Hereditary Multiple Exostoses Maurizio Pacifici Translational Research Program in Pediatric Orthopaedics, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 Abstract Heparan sulfate (HS) is an essential component of cell surface and matrix proteoglycans (HS-PGs) that include syndecans and perlecan. Because of their unique structural features, the HS chains are able to specifically interact with signaling proteins–including bone morphogenetic proteins (BMPs)-via their HS-binding domain, regulating protein availability, distribution and action on target cells. Hereditary Multiple Exostoses (HME) is a rare pediatric disorder linked to germline heterozygous loss-of-function mutations in EXT1 or EXT2 that encode Golgi-resident glycosyltransferases responsible for HS synthesis, resulting in a systemic HS deficiency. HME is characterized by cartilaginous/bony tumors-called osteochondromas or exostoses- that form within perichondrium in long bones, ribs and other elements. This review examines most recent studies in HME, framing them in the context of classic studies. New findings show that the spectrum of EXT mutations is larger than previously realized and the clinical complications of HME extend beyond the skeleton. Osteochondroma development requires a somatic “second hit” that would complement the germline EXT mutation to further decrease HS production and/levels at perichondrial sites of osteochondroma induction. Cellular studies have shown that the steep decreases in local HS levels: derange the normal homeostatic signaling pathways keeping perichondrium mesenchymal; cause excessive BMP signaling; and provoke ectopic chondrogenesis and osteochondroma formation. -
EXTL3 Mutations Cause Skeletal Dysplasia, Immune Deficiency, and Developmental Delay
EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Volpi, S., Y. Yamazaki, P. M. Brauer, E. van Rooijen, A. Hayashida, A. Slavotinek, H. Sun Kuehn, et al. 2017. “EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay.” The Journal of Experimental Medicine 214 (3): 623-637. doi:10.1084/ jem.20161525. http://dx.doi.org/10.1084/jem.20161525. Published Version doi:10.1084/jem.20161525 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:34492076 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Brief Definitive Report EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay Stefano Volpi,1 Yasuhiro Yamazaki,3 Patrick M. Brauer,5 Ellen van Rooijen,6 Atsuko Hayashida,7 Anne Slavotinek,10 Hye Sun Kuehn,4 Maja Di Rocco,2 Carlo Rivolta,12 Ileana Bortolomai,14,22 Likun Du,8 Kerstin Felgentreff,8 Lisa Ott de Bruin,8 Kazutaka Hayashida,7 George Freedman,11 Genni Enza Marcovecchio,14 Kelly Capuder,8 Prisni Rath,15 Nicole Luche,8 Elliott J. Hagedorn,6 Antonella Buoncompagni,1 Beryl Royer-Bertrand,12,13 Silvia Giliani,16 Pietro Luigi Poliani,17 Luisa Imberti,18 Kerry Dobbs,3 Fabienne E. Poulain,19 Alberto Martini,1 John Manis,9 Robert J. -
UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent Permalink https://escholarship.org/uc/item/7m04f0b0 Author Buchholz, Kyle Stephen Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Kyle Stephen Buchholz Committee in Charge: Professor Jeffrey Omens, Chair Professor Andrew McCulloch, Co-Chair Professor Ju Chen Professor Karen Christman Professor Robert Ross Professor Alexander Zambon 2016 Copyright Kyle Stephen Buchholz, 2016 All rights reserved Signature Page The Dissertation of Kyle Stephen Buchholz is approved and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2016 iii Dedication To my beautiful wife, Rhia. iv Table of Contents Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Table of Contents ................................................................................................................ v List of Figures ................................................................................................................... -
Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. -
The Link Between Heparan Sulfate and Hereditary Bone Disease: Finding a Function for the EXT Family of Putative Tumor Suppressor Proteins
The link between heparan sulfate and hereditary bone disease: finding a function for the EXT family of putative tumor suppressor proteins Gillian Duncan, … , Craig McCormick, Frank Tufaro J Clin Invest. 2001;108(4):511-516. https://doi.org/10.1172/JCI13737. Perspective Although genetic linkage analysis is a vital tool for identifying disease genes, further study is often hindered by the lack of a known function for the corresponding gene products. In the case of hereditary multiple exostoses (HME), a dominantly inherited genetic disorder characterized by the formation of multiple cartilaginous tumors, extensive genetic analyses of affected families linked HME to mutations in two members of a novel family of putative tumor suppressor genes, EXT1 and EXT2. The biological function of the corresponding proteins, exostosin-1 (EXT1) and exostosin-2 (EXT2), has emerged in part by way of a serendipitous discovery made in the study of herpes simplex virology, which revealed that the pathogenesis of HME is linked to a defect in heparan sulfate (HS) biosynthesis. Biochemical analysis shows that EXT1 and EXT2 are type II transmembrane glycoproteins and form a Golgi-localized hetero-oligomeric complex that catalyzes the polymerization of HS. In this Perspective we will review the identification and characterization of the EXT family, with a particular focus on the biology of the EXT proteins in vivo, and we will explore their possible role(s) in both normal bone development and the formation of exostoses. Hereditary multiple exostoses Hereditary multiple exostoses (HME), an autosomal dominant bone disorder, is the most common type of benign bone tumor, with an estimated occurrence of 1 in 50,000–100,000 in […] Find the latest version: https://jci.me/13737/pdf PERSPECTIVE SERIES Heparan sulfate proteoglycans Renato V.