The Role of Long Non‑Coding RNA H19 in Breast Cancer (Review)
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis
Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Castaño-Betancourt, M. C., D. S. Evans, Y. F. M. Ramos, C. G. Boer, S. Metrustry, Y. Liu, W. den Hollander, et al. 2016. “Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis.” PLoS Genetics 12 (10): e1006260. doi:10.1371/journal.pgen.1006260. http://dx.doi.org/10.1371/journal.pgen.1006260. Published Version doi:10.1371/journal.pgen.1006260 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:29408344 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 RESEARCH ARTICLE Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis Martha C. Castaño-Betancourt1☯, Dan S. Evans2☯, Yolande F. M. Ramos3☯, Cindy G. Boer1☯, Sarah Metrustry4, Youfang Liu5, Wouter den Hollander3, Jeroen van Rooij1, Virginia B. Kraus6, Michelle S. Yau7, Braxton D. Mitchell7,8, Kenneth Muir9, Albert Hofman10,11, Michael Doherty12, Sally Doherty12, Weiya Zhang12, Robert Kraaij1, Fernando Rivadeneira1, Elizabeth Barrett-Connor13, Rose A. Maciewicz14, Nigel Arden15, Rob G. H. H. Nelissen16, Margreet Kloppenburg17, Joanne M. Jordan5, Michael C. Nevitt18, Eline P. Slagboom3, Deborah J. Hart4, Floris Lafeber19, Unnur Styrkarsdottir20, 21 22,23 4 a11111 Eleftheria Zeggini , Evangelos Evangelou , Tim D. Spector , Andre G. Uitterlinden1,10, Nancy E. Lane18,24³, Ingrid Meulenbelt3³, Ana M. -
Ectopic Protein Interactions Within BRD4–Chromatin Complexes Drive Oncogenic Megadomain Formation in NUT Midline Carcinoma
Ectopic protein interactions within BRD4–chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma Artyom A. Alekseyenkoa,b,1, Erica M. Walshc,1, Barry M. Zeea,b, Tibor Pakozdid, Peter Hsic, Madeleine E. Lemieuxe, Paola Dal Cinc, Tan A. Incef,g,h,i, Peter V. Kharchenkod,j, Mitzi I. Kurodaa,b,2, and Christopher A. Frenchc,2 aDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; bDepartment of Genetics, Harvard Medical School, Boston, MA 02115; cDepartment of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; dDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115; eBioinfo, Plantagenet, ON, Canada K0B 1L0; fDepartment of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136; gBraman Family Breast Cancer Institute, University of Miami Miller School of Medicine, Miami, FL 33136; hInterdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136; iSylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136; and jHarvard Stem Cell Institute, Cambridge, MA 02138 Contributed by Mitzi I. Kuroda, April 6, 2017 (sent for review February 7, 2017; reviewed by Sharon Y. R. Dent and Jerry L. Workman) To investigate the mechanism that drives dramatic mistargeting of and, in the case of MYC, leads to differentiation in culture (2, 3). active chromatin in NUT midline carcinoma (NMC), we have Similarly, small-molecule BET inhibitors such as JQ1, which identified protein interactions unique to the BRD4–NUT fusion disengage BRD4–NUT from chromatin, diminish megadomain- oncoprotein compared with wild-type BRD4. -
Epigenetic Regulators in Neuroblastoma: Brg1, a Future Therapeutic Target
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en EPIGENETIC REGULATORS IN NEUROBLASTOMA: BRG1, A FUTURE THERAPEUTIC TARGET PhD thesis presented by Luz Jubierre Zapater To obtain the degree of PhD for the Universitat Autónoma de Barcelona (UAB) PhD thesis carried out at the Translational Research in Child and Adolescent Cancer Laboratory, at Vall d’Hebron Research Institute (VHIR), under the supervision of Dr. Miguel F. Segura and Dr. Soledad Gallego Thesis affiliated to the Department of Biochemistry and Molecular Biology from the UAB, in the PhD program of Biochemistry, Molecular Biology and Biomedicine, under the tutoring of Dr. José Miguel Lizcano Universidad Autónoma de Barcelona, Septiembre 5th 2017 Dr. Miguel F. Segura Dr. Soledad Gallego (Director) (Director) Luz Jubierre Zapater (Student) 2017 Is this the real life? Is this just fantasy? Caught in a landslide No escape from reality; Open your eyes Look up to the skies and see Bohemian Rhapsody, Queen To my Mom To my Dad To Adri ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS Acknowledgement Desde que escribí la primera palabra en el libro de mi vida mucha gente se ha cruzado en mi camino para dejar su huella en él. -
Towards Personalized Medicine in Psychiatry: Focus on Suicide
TOWARDS PERSONALIZED MEDICINE IN PSYCHIATRY: FOCUS ON SUICIDE Daniel F. Levey Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy in the Program of Medical Neuroscience, Indiana University April 2017 ii Accepted by the Graduate Faculty, Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Andrew J. Saykin, Psy. D. - Chair ___________________________ Alan F. Breier, M.D. Doctoral Committee Gerry S. Oxford, Ph.D. December 13, 2016 Anantha Shekhar, M.D., Ph.D. Alexander B. Niculescu III, M.D., Ph.D. iii Dedication This work is dedicated to all those who suffer, whether their pain is physical or psychological. iv Acknowledgements The work I have done over the last several years would not have been possible without the contributions of many people. I first need to thank my terrific mentor and PI, Dr. Alexander Niculescu. He has continuously given me advice and opportunities over the years even as he has suffered through my many mistakes, and I greatly appreciate his patience. The incredible passion he brings to his work every single day has been inspirational. It has been an at times painful but often exhilarating 5 years. I need to thank Helen Le-Niculescu for being a wonderful colleague and mentor. I learned a lot about organization and presentation working alongside her, and her tireless work ethic was an excellent example for a new graduate student. I had the pleasure of working with a number of great people over the years. Mikias Ayalew showed me the ropes of the lab and began my understanding of the power of algorithms. -
The Role of GRHL2 and Epigenetic Remodeling in Epithelial–Mesenchymal Plasticity in Ovarian Cancer Cells
ARTICLE https://doi.org/10.1038/s42003-019-0506-3 OPEN The role of GRHL2 and epigenetic remodeling in epithelial–mesenchymal plasticity in ovarian cancer cells Vin Yee Chung 1, Tuan Zea Tan 1, Jieru Ye1, Rui-Lan Huang2, Hung-Cheng Lai2, Dennis Kappei 1,3, 1234567890():,; Heike Wollmann4, Ernesto Guccione4 & Ruby Yun-Ju Huang1,5 Cancer cells exhibit phenotypic plasticity during epithelial–mesenchymal transition (EMT) and mesenchymal–epithelial transition (MET) involving intermediate states. To study genome-wide epigenetic remodeling associated with EMT plasticity, we integrate the ana- lyses of DNA methylation, ChIP-sequencing of five histone marks (H3K4me1, H3K4me3, H3K27Ac, H3K27me3 and H3K9me3) and transcriptome profiling performed on ovarian cancer cells with different epithelial/mesenchymal states and on a knockdown model of EMT suppressor Grainyhead-like 2 (GRHL2). We have identified differentially methylated CpG sites associated with EMT, found at promoters of epithelial genes and GRHL2 binding sites. GRHL2 knockdown results in CpG methylation gain and nucleosomal remodeling (reduction in permissive marks H3K4me3 and H3K27ac; elevated repressive mark H3K27me3), resembling the changes observed across progressive EMT states. Epigenetic-modifying agents such as 5-azacitidine, GSK126 and mocetinostat further reveal cell state-dependent plasticity upon GRHL2 overexpression. Overall, we demonstrate that epithelial genes are subject to epigenetic control during intermediate phases of EMT/MET involving GRHL2. 1 Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore. 2 Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, 11031 Taipei, Taiwan. 3 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore. -
(12) Patent Application Publication (10) Pub. No.: US 2016/0264934 A1 GALLOURAKIS Et Al
US 20160264934A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0264934 A1 GALLOURAKIS et al. (43) Pub. Date: Sep. 15, 2016 (54) METHODS FOR MODULATING AND Publication Classification ASSAYING MI6AIN STEM CELL POPULATIONS (51) Int. Cl. CI2N5/0735 (2006.01) (71) Applicants: THE GENERAL, HOSPITAL AOIN I/02 (2006.01) CORPORATION, Boston, MA (US); CI2O I/68 (2006.01) The Regents of the University of GOIN 33/573 (2006.01) California, Oakland, CA (US) CI2N 5/077 (2006.01) CI2N5/0793 (2006.01) (72) Inventors: Cosmas GIALLOURAKIS, Boston, (52) U.S. Cl. MA (US); Alan C. MULLEN, CPC ............ CI2N5/0606 (2013.01); CI2N5/0657 Brookline, MA (US); Yi XING, (2013.01); C12N5/0619 (2013.01); C12O Torrance, CA (US) I/6888 (2013.01); G0IN33/573 (2013.01); A0IN I/0226 (2013.01); C12N 2501/72 (73) Assignees: THE GENERAL, HOSPITAL (2013.01); C12N 2506/02 (2013.01); C12O CORPORATION, Boston, MA (US); 2600/158 (2013.01); C12Y 201/01062 The Regents of the University of (2013.01); C12Y 201/01 (2013.01) California, Oakland, CA (US) (57) ABSTRACT (21) Appl. No.: 15/067,780 The present invention generally relates to methods, assays and kits to maintain a human stem cell population in an (22) Filed: Mar 11, 2016 undifferentiated state by inhibiting the expression or function of METTL3 and/or METTL4, and mA fingerprint methods, assays, arrays and kits to assess the cell state of a human stem Related U.S. Application Data cell population by assessing mA levels (e.g. mA peak inten (60) Provisional application No. -
Cornelia De Lange Syndrome-Associated Mutations Cause a DNA Damage Signalling and Repair Defect
ARTICLE https://doi.org/10.1038/s41467-021-23500-6 OPEN Cornelia de Lange syndrome-associated mutations cause a DNA damage signalling and repair defect Gabrielle Olley1, Madapura M. Pradeepa 1,2, Graeme R. Grimes1, Sandra Piquet3, Sophie E. Polo 3, ✉ ✉ David R. FitzPatrick1, Wendy A. Bickmore 1 & Charlene Boumendil 1,4 Cornelia de Lange syndrome is a multisystem developmental disorder typically caused by mutations in the gene encoding the cohesin loader NIPBL. The associated phenotype is 1234567890():,; generally assumed to be the consequence of aberrant transcriptional regulation. Recently, we identified a missense mutation in BRD4 associated with a Cornelia de Lange-like syndrome that reduces BRD4 binding to acetylated histones. Here we show that, although this mutation reduces BRD4-occupancy at enhancers it does not affect transcription of the pluripotency network in mouse embryonic stem cells. Rather, it delays the cell cycle, increases DNA damage signalling, and perturbs regulation of DNA repair in mutant cells. This uncovers a role for BRD4 in DNA repair pathway choice. Furthermore, we find evidence of a similar increase in DNA damage signalling in cells derived from NIPBL-deficient individuals, suggesting that defective DNA damage signalling and repair is also a feature of typical Cornelia de Lange syndrome. 1 MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, UK. 2 Blizard institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK. 3 Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, ✉ Paris, France. 4 Université de Paris, CNRS, Institut Jacques Monod, Paris, France. -
Role of Gigaxonin in the Regulation of Intermediate Filaments: a Study Using Giant Axonal Neuropathy Patient-Derived Induced Pluripotent Stem Cell-Motor Neurons
Role of Gigaxonin in the Regulation of Intermediate Filaments: a Study Using Giant Axonal Neuropathy Patient-Derived Induced Pluripotent Stem Cell-Motor Neurons Bethany Johnson-Kerner Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2013 © 2012 Bethany Johnson-Kerner All rights reserved Abstract Role of Gigaxonin in the Regulation of Intermediate Filaments: a Study Using Giant Axonal Neuropathy Patient-Derived Induced Pluripotent Stem Cell-Motor Neurons Bethany Johnson-Kerner Patients with giant axonal neuropathy (GAN) exhibit loss of motor and sensory function and typically live for less than 30 years. GAN is caused by autosomal recessive mutations leading to low levels of gigaxonin, a ubiquitously-expressed cytoplasmic protein whose cellular roles are poorly understood. GAN pathology is characterized by aggregates of intermediate filaments (IFs) in multiple tissues. Disorganization of the neuronal intermediate filament (nIF) network is a feature of several neurodegenerative disorders, including amyotrophic lateral sclerosis, Parkinson’s disease and axonal Charcot-Marie-Tooth disease. In GAN such changes are often striking: peripheral nerve biopsies show enlarged axons with accumulations of neurofilaments; so called “giant axons.” Interestingly, IFs also accumulate in other cell types in patients. These include desmin in muscle fibers, GFAP (glial fibrillary acidic protein) in astrocytes, and vimentin in multiple cell types including primary cultures of biopsied fibroblasts. These findings suggest that gigaxonin may be a master regulator of IFs, and understanding its function(s) could shed light on GAN as well as the numerous other diseases in which IFs accumulate. -
Osteoarthritis: Genetics and Phenotypes in All Their Complexity Cindy Germaine Boer
Osteoarthritis: genetics and phenotypes in all their complexity Cindy Germaine Boer The works described in this thesis was conducted at the department of Internal Medicine at the Erasmus MC University Medical Center Rotterdam, the Netherlands. The Rotterdam study is funded by Erasmus MC University Medical Center and Erasmus University Rotterdam; the Netherlands Organization for Scientific Research (NWO); the Netherlands Organization for Health Research and Development (ZonMW); the Research institute for Diseases in the elderly (RIDE); the Dutch Ministry of Education, Culture and Science; the Dutch Ministry of Health, Welfare and sports; the European Commission (DG XII); and the municipality of Rotterdam. ISBN: 978-94-6416-105-2 Cover Design: Cindy G. Boer Design: Cindy G. Boer and Ridderprint Illustrations: Cindy G. Boer Layout and printing: Ridderprint © Cindy Germaine Boer | 2020 All rights reserved. No part of this book may be reproduced, stored in a retrieval system or transmitted in any form or by any means, without prior written permission of the author, or, the scientific journal in which parts of the book have been published. Osteoarthriti s: geneti cs and phenotypes in all their complexity Artrose: geneti ca en fenotypen in al hun complexiteit Proefschrift ter verkrijging van de graad van doctor aan de Erasmus Universiteit Rott erdam op gezag van de rector magnifi cus Prof. Dr. R.C.M.E. Engels en volgens besluit van het College voor Promoti es. De openbare verdediging zal plaatsvinden op dinsdag 15 december 2020 om 13:30 uur Door Cindy Germaine Boer geboren te Sliedrecht Promotiecommissie Promotor: Prof. Dr. A.G. Uitterlinden Overige Leden: Prof. -
Inbred Mouse Strains Expression in Primary Immunocytes Across
Downloaded from http://www.jimmunol.org/ by guest on September 28, 2021 Daphne is online at: average * The Journal of Immunology published online 29 September 2014 from submission to initial decision 4 weeks from acceptance to publication Sara Mostafavi, Adriana Ortiz-Lopez, Molly A. Bogue, Kimie Hattori, Cristina Pop, Daphne Koller, Diane Mathis, Christophe Benoist, The Immunological Genome Consortium, David A. Blair, Michael L. Dustin, Susan A. Shinton, Richard R. Hardy, Tal Shay, Aviv Regev, Nadia Cohen, Patrick Brennan, Michael Brenner, Francis Kim, Tata Nageswara Rao, Amy Wagers, Tracy Heng, Jeffrey Ericson, Katherine Rothamel, Adriana Ortiz-Lopez, Diane Mathis, Christophe Benoist, Taras Kreslavsky, Anne Fletcher, Kutlu Elpek, Angelique Bellemare-Pelletier, Deepali Malhotra, Shannon Turley, Jennifer Miller, Brian Brown, Miriam Merad, Emmanuel L. Gautier, Claudia Jakubzick, Gwendalyn J. Randolph, Paul Monach, Adam J. Best, Jamie Knell, Ananda Goldrath, Vladimir Jojic, J Immunol http://www.jimmunol.org/content/early/2014/09/28/jimmun ol.1401280 Koller, David Laidlaw, Jim Collins, Roi Gazit, Derrick J. Rossi, Nidhi Malhotra, Katelyn Sylvia, Joonsoo Kang, Natalie A. Bezman, Joseph C. Sun, Gundula Min-Oo, Charlie C. Kim and Lewis L. Lanier Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2014/09/28/jimmunol.140128 0.DCSupplemental Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2014 by The American Association of Immunologists, Inc. -
Dissecting the Genetic Basis of Convergent Complex Traits Based on Molecular
Dissecting the Genetic Basis of Convergent Complex Traits Based on Molecular Homoplasy by Rui Wang Graduate Program in Bioinformatics and Genome Technology Duke University Date:_______________________ Approved: ___________________________ Erich D. Jarvis, Supervisor ___________________________ Gregory A. Wray ___________________________ Alexander Hartemink ___________________________ Paul Magwene ___________________________ Sridhar Raghavachari Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate Program in Bioinformatics and Genome Technology in the Graduate School of Duke University 2011 ABSTRACT Dissecting the Genetic Basis of Convergent Complex Traits Based on Molecular Homoplasy by Rui Wang Graduate Program in Bioinformatics and Genome Technology Duke University Date:_______________________ Approved: ___________________________ Erich D. Jarvis, Supervisor ___________________________ Gregory A. Wray ___________________________ Alexander Hartemink ___________________________ Paul Magwene ___________________________ Sridhar Raghavachari An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate Program in Bioinformatics and Genome Technology in the Graduate School of Duke University 2011 Copyright by Rui Wang 2011 Abstract The goal of my thesis is to understand the genetics of a complex behavioral trait, vocal learning, which serves as a critical substrate for human spoken language. With the available genomes of 23 mammals, I developed a novel approach based on molecular homoplasy to reveal Single Non‐random Amino Acids Patterns (SNAAPs) that are associated with convergent traits, a task that proved intractable for standard approaches, e.g. dN/dS analyses. Of 73 genes I identified in mammalian vocal learners, ~25% function in neural connectivity, auditory or speech processing. Remarkably, these include a group of 6 genes from the ROBO1 axon guidance pathway. -
Adrenal GIPR Expression and Chromosome 19Q13 Microduplications in GIP-Dependent Cushing’S Syndrome
Adrenal GIPR expression and chromosome 19q13 microduplications in GIP-dependent Cushing’s syndrome Anne-Lise Lecoq, … , Jérôme Bouligand, Peter Kamenický JCI Insight. 2017;2(18):e92184. https://doi.org/10.1172/jci.insight.92184. Research Article Endocrinology GIP-dependent Cushing’s syndrome is caused by ectopic expression of glucose-dependent insulinotropic polypeptide receptor (GIPR) in cortisol-producing adrenal adenomas or in bilateral macronodular adrenal hyperplasias. Molecular mechanisms leading to ectopic GIPR expression in adrenal tissue are not known. Here we performed molecular analyses on adrenocortical adenomas and bilateral macronodular adrenal hyperplasias obtained from 14 patients with GIP- dependent adrenal Cushing’s syndrome and one patient with GIP-dependent aldosteronism. GIPR expression in all adenoma and hyperplasia samples occurred through transcriptional activation of a single allele of the GIPR gene. While no abnormality was detected in proximal GIPR promoter methylation, we identified somatic duplications in chromosome region 19q13.32 containing the GIPR locus in the adrenocortical lesions derived from 3 patients. In 2 adenoma samples, the duplicated 19q13.32 region was rearranged with other chromosome regions, whereas a single tissue sample with hyperplasia had a 19q duplication only. We demonstrated that juxtaposition with cis-acting regulatory sequences such as glucocorticoid response elements in the newly identified genomic environment drives abnormal expression of the translocated GIPR allele in adenoma cells. Altogether, our results provide insight into the molecular pathogenesis of GIP- dependent Cushing’s syndrome, occurring through monoallelic transcriptional activation of GIPR driven in some adrenal lesions by structural variations. Find the latest version: https://jci.me/92184/pdf RESEARCH ARTICLE Adrenal GIPR expression and chromosome 19q13 microduplications in GIP-dependent Cushing’s syndrome Anne-Lise Lecoq,1,2,3 Constantine A.