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Regulation and Dysregulation of Chromosome Structure in Cancer
Regulation and Dysregulation of Chromosome Structure in Cancer The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Hnisz, Denes et al. “Regulation and Dysregulation of Chromosome Structure in Cancer.” Annual Review of Cancer Biology 2, 1 (March 2018): 21–40 © 2018 Annual Reviews As Published https://doi.org/10.1146/annurev-cancerbio-030617-050134 Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/117286 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike Detailed Terms http://creativecommons.org/licenses/by-nc-sa/4.0/ Regulation and dysregulation of chromosome structure in cancer Denes Hnisz1*, Jurian Schuijers1, Charles H. Li1,2, Richard A. Young1,2* 1 Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA 2 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA * Corresponding authors Corresponding Authors: Denes Hnisz Whitehead Institute for Biomedical Research 455 Main Street Cambridge, MA 02142 Tel: (617) 258-7181 Fax: (617) 258-0376 [email protected] Richard A. Young Whitehead Institute for Biomedical Research 455 Main Street Cambridge, MA 02142 Tel: (617) 258-5218 Fax: (617) 258-0376 [email protected] 1 Summary Cancer arises from genetic alterations that produce dysregulated gene expression programs. Normal gene regulation occurs in the context of chromosome loop structures called insulated neighborhoods, and recent studies have shown that these structures are altered and can contribute to oncogene dysregulation in various cancer cells. We review here the types of genetic and epigenetic alterations that influence neighborhood structures and contribute to gene dysregulation in cancer, present models for insulated neighborhoods associated with the most prominent human oncogenes, and discuss how such models may lead to further advances in cancer diagnosis and therapy. -
Universidade Estadual De Campinas Instituto De Biologia
UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA CAMPINAS 2016 1 VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA Dissertação apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Mestra em Biologia Funcional e Molecular na área de concentração de Bioquímica. Dissertation presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Functional and Molecular Biology, in the area of Biochemistry. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA E ORIENTADA PELO DANIEL MARTINS-DE-SOUZA. Orientador: Daniel Martins-de-Souza CAMPINAS 2016 2 Agência(s) de fomento e nº(s) de processo(s): CNPq, 151787/2F2014-0 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Saia-Cereda, Verônica Aparecida Monteiro, 1988- Sa21p O proteoma do corpo caloso da esquizofrenia / Verônica Aparecida Monteiro Saia Cereda. – Campinas, SP : [s.n.], 2016. Orientador: Daniel Martins de Souza. Dissertação (mestrado) – Universidade Estadual de Campinas, Instituto de Biologia. 1. Esquizofrenia. 2. Espectrometria de massas. 3. Corpo caloso. -
Sequencing-Based Computational Methods for Identifying Impactful Genomic Alterations in Cancers
Sequencing-based computational methods for identifying impactful genomic alterations in cancers by Isaac Charles Joseph A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Computational Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Lior Pachter, Chair Professor Joseph Costello Associate Professor Haiyan Huang Professor Anthony Joseph Fall 2016 Sequencing-based computational methods for identifying impactful genomic alterations in cancers Copyright 2016 by Isaac Charles Joseph 1 Abstract Sequencing-based computational methods for identifying impactful genomic alterations in cancers by Isaac Charles Joseph Doctor of Philosophy in Computational Biology University of California, Berkeley Professor Lior Pachter, Chair Recent advances in collecting sequencing data from tumors is promising for both immediate individual patient treatment and investigation of cancer mechanisms. A resultant central goal is identifying changes in tumors that are impactful towards these ends. Here, we develop two tools to identify impactful changes at different levels. We develop both methods in the context of gliomas, a common form of brain cancer. Firstly, we develop and assess a tool for assessing the impact of fusion genes, a type of common mutation using RNA-sequencing data. We validate the tool by working with collaborators in The Cancer Genome Atlas. Secondly, we develop a tool for an overall assessment of patient outcome by integrating data from diverse sequencing platforms. We validate this tool using simulation, data from consortiums, and collaborators at UCSF. i To those that suffer It is you that have convinced me that there is something still worth fighting for in this world. -
ABSTRACT MITCHELL III, ROBERT DRAKE. Global Human Health
ABSTRACT MITCHELL III, ROBERT DRAKE. Global Human Health Risks for Arthropod Repellents or Insecticides and Alternative Control Strategies. (Under the direction of Dr. R. Michael Roe). Protein-coding genes and environmental chemicals. New paradigms for human health risk assessment of environmental chemicals emphasize the use of molecular methods and human-derived cell lines. In this study, we examined the effects of the insect repellent DEET (N, N-diethyl-m-toluamide) and the phenylpyrazole insecticide fipronil (fluocyanobenpyrazole) on transcript levels in primary human hepatocytes. These chemicals were tested individually and as a mixture. RNA-Seq showed that 100 µM DEET significantly increased transcript levels for 108 genes and lowered transcript levels for 64 genes and fipronil at 10 µM increased the levels of 2,246 transcripts and decreased the levels for 1,428 transcripts. Fipronil was 21-times more effective than DEET in eliciting changes, even though the treatment concentration was 10-fold lower for fipronil versus DEET. The mixture of DEET and fipronil produced a more than additive effect (levels increased for 3,017 transcripts and decreased for 2,087 transcripts). The transcripts affected in our treatments influenced various biological pathways and processes important to normal cellular functions. Long non-protein coding RNAs and environmental chemicals. While the synthesis and use of new chemical compounds is at an all-time high, the study of their potential impact on human health is quickly falling behind. We chose to examine the effects of two common environmental chemicals, the insect repellent DEET and the insecticide fipronil, on transcript levels of long non-protein coding RNAs (lncRNAs) in primary human hepatocytes. -
Annual Report
Greeks Helping Greeks ANNUAL REPORT 2019 About THI The Hellenic Initiative (THI) is a global, nonprofi t, secular institution mobilizing the Greek Diaspora and Philhellene community to support sustainable economic recovery and renewal for Greece and its people. Our programs address crisis relief through strong nonprofi t organizations, led by heroic Greeks that are serving their country. They also build capacity in a new generation of heroes, the business leaders and entrepreneurs with the skills and values to promote the long term growth of Hellas. THI Vision / Mission Statement Investing in the future of Greece through direct philanthropy and economic revitalization. We empower people to provide crisis relief, encourage entrepreneurs, and create jobs. We are The Hellenic Initiative (THI) – a global movement of the Greek Diaspora About the Cover Featuring the faces of our ReGeneration Interns. We, the members of the Executive Committee and the Board of Directors, wish to express to all of you, the supporters and friends of The Hellenic Initiative, our deepest gratitude for the trust and support you have given to our organization for the past seven years. Our mission is simple, to connect the Diaspora with Greece in ways which are valuable for Greece, and valuable for the Diaspora. One of the programs you will read about in this report is THI’s ReGeneration Program. In just 5 years since we launched ReGeneration, with the support of the Coca-Cola Co. and the Coca-Cola Foundation and 400 hiring partners, we have put over 1100 people to work in permanent well-paying jobs in Greece. -
Protein Kinase A-Mediated Septin7 Phosphorylation Disrupts Septin Filaments and Ciliogenesis
cells Article Protein Kinase A-Mediated Septin7 Phosphorylation Disrupts Septin Filaments and Ciliogenesis Han-Yu Wang 1,2, Chun-Hsiang Lin 1, Yi-Ru Shen 1, Ting-Yu Chen 2,3, Chia-Yih Wang 2,3,* and Pao-Lin Kuo 1,2,4,* 1 Department of Obstetrics and Gynecology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; [email protected] (H.-Y.W.); [email protected] (C.-H.L.); [email protected] (Y.-R.S.) 2 Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; [email protected] 3 Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan 4 Department of Obstetrics and Gynecology, National Cheng-Kung University Hospital, Tainan 704, Taiwan * Correspondence: [email protected] (C.-Y.W.); [email protected] (P.-L.K.); Tel.: +886-6-2353535 (ext. 5338); (C.-Y.W.)+886-6-2353535 (ext. 5262) (P.-L.K.) Abstract: Septins are GTP-binding proteins that form heteromeric filaments for proper cell growth and migration. Among the septins, septin7 (SEPT7) is an important component of all septin filaments. Here we show that protein kinase A (PKA) phosphorylates SEPT7 at Thr197, thus disrupting septin filament dynamics and ciliogenesis. The Thr197 residue of SEPT7, a PKA phosphorylating site, was conserved among different species. Treatment with cAMP or overexpression of PKA catalytic subunit (PKACA2) induced SEPT7 phosphorylation, followed by disruption of septin filament formation. Constitutive phosphorylation of SEPT7 at Thr197 reduced SEPT7-SEPT7 interaction, but did not affect SEPT7-SEPT6-SEPT2 or SEPT4 interaction. -
2021 Western Medical Research Conference
Abstracts J Investig Med: first published as 10.1136/jim-2021-WRMC on 21 December 2020. Downloaded from Genetics I Purpose of Study Genomic sequencing has identified a growing number of genes associated with developmental brain disorders Concurrent session and revealed the overlapping genetic architecture of autism spectrum disorder (ASD) and intellectual disability (ID). Chil- 8:10 AM dren with ASD are often identified first by psychologists or neurologists and the extent of genetic testing or genetics refer- Friday, January 29, 2021 ral is variable. Applying clinical whole genome sequencing (cWGS) early in the diagnostic process has the potential for timely molecular diagnosis and to circumvent the diagnostic 1 PROSPECTIVE STUDY OF EPILEPSY IN NGLY1 odyssey. Here we report a pilot study of cWGS in a clinical DEFICIENCY cohort of young children with ASD. RJ Levy*, CH Frater, WB Galentine, MR Ruzhnikov. Stanford University School of Medicine, Methods Used Children with ASD and cognitive delays/ID Stanford, CA were referred by neurologists or psychologists at a regional healthcare organization. Medical records were used to classify 10.1136/jim-2021-WRMC.1 probands as 1) ASD/ID or 2) complex ASD (defined as 1 or more major malformations, abnormal head circumference, or Purpose of Study To refine the electroclinical phenotype of dysmorphic features). cWGS was performed using either epilepsy in NGLY1 deficiency via prospective clinical and elec- parent-child trio (n=16) or parent-child-affected sibling (multi- troencephalogram (EEG) findings in an international cohort. plex families; n=3). Variants were classified according to Methods Used We performed prospective phenotyping of 28 ACMG guidelines. -
The Licit and the Illicit in Archaeological and Heritage Discourses
CHALLENGING THE DICHOTOMY EDIT ED BY LES FIELD CRISTÓBAL GNeccO JOE WATKINS CHALLENGING THE DICHOTOMY • The Licit and the Illicit in Archaeological and Heritage Discourses TUCSON The University of Arizona Press www.uapress.arizona.edu © 2016 by The Arizona Board of Regents Open-access edition published 2020 ISBN-13: 978-0-8165-3130-1 (cloth) ISBN-13: 978-0-8165-4169-0 (open-access e-book) The text of this book is licensed under the Creative Commons Atrribution- NonCommercial-NoDerivsatives 4.0 (CC BY-NC-ND 4.0), which means that the text may be used for non-commercial purposes, provided credit is given to the author. For details go to http://creativecommons.org/licenses/by-nc-nd/4.0/. Cover designed by Leigh McDonald Publication of this book is made possible in part by the Wenner-Gren Foundation. Library of Congress Cataloging-in-Publication Data Names: Field, Les W., editor. | Gnecco, Cristóbal, editor. | Watkins, Joe, 1951– editor. Title: Challenging the dichotomy : the licit and the illicit in archaeological and heritage discourses / edited by Les Field, Cristóbal Gnecco, and Joe Watkins. Description: Tucson : The University of Arizona Press, 2016. | Includes bibliographical references and index. Identifiers: LCCN 2016007488 | ISBN 9780816531301 (cloth : alk. paper) Subjects: LCSH: Archaeology. | Archaeology and state. | Cultural property—Protection. Classification: LCC CC65 .C47 2016 | DDC 930.1—dc23 LC record available at https:// lccn.loc.gov/2016007488 An electronic version of this book is freely available, thanks to the support of libraries working with Knowledge Unlatched. KU is a collaborative initiative designed to make high quality books Open Access for the public good. -
List of Attendees
Second Stavros Niarchos Foundation International Conference on Philanthropy The Role of Philanthropy within a Social Welfare Society June 27-28, 2013 Divani Apollon Palace & Spa, Athens, Greece List of Attendees Name Organization Title Afroditi Veloudaki Prolepsis Program Director Aggeliki Hatzi Aggeliki Papadopoulou KIKPE Secretary Aggeliki Sandi Network for Children's Rights Aggelos Delivorrias Benaki Museum Director Aglaia Vasilopoulou Agni Dimopoulou - Greek Childrens Village in Filyro Secretary of the Board Datsiou Agoritsa KEPEP Karditsas Director Chantzopoulou Aimilia Geroulanou Benaki Museum Alessandra Pani IFAD/BFS Focal Point for Communication, Visibility and Fundraising Alex Theodoridis Boroume Co-Founder Alexandra Chaini Real News Alexandra Choli Metavallon Founder / Executive Director Alexandra Sarlis Alexandros Lighthouse for the Blind of Greece Head of Development and Despotopoulos International Relations Alexandros Athens Information Technology Communications Director Kambouroglou Alexandros Moraitakis Name Organization Title Alexandros Taxildaris Association for People with President Mobility Problems and Friends Perpato Alexia Divani Alexia Kotsopoulou AWOG Representative Alexia Raphael Stavros Niarchos Foundation Intern Aliki Martinou Mazigia to Paidi Aliki Mitsakou Aliki Tserketzoglou Galilee Palliative Care Unit Amalia Delicari Stavros Niarchos Foundation Associate Program Officer Amalia Zeppou Municipality of Athens Amvrosios Holy Metropolis of Kalavryta and Metropolitan Bishop Aegialia Anastasia Andritsou British -
Adhesion-Dependent Mechanisms Regulating Mitosis
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1523 Adhesion-dependent mechanisms regulating mitosis DEEPESH KUMAR GUPTA ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6206 ISBN 978-91-513-0531-8 UPPSALA urn:nbn:se:uu:diva-368422 2019 Dissertation presented at Uppsala University to be publicly examined in B42 Biomedical Center, Biomedical Center Husargatn 3, Uppsala, Friday, 1 February 2019 at 09:15 for the degree of Doctor of Philosophy (Faculty of Medicine). The examination will be conducted in English. Faculty examiner: Senior Scientist Kaisa Haglund (Oslo University Hospital). Abstract Gupta, D. K. 2019. Adhesion-dependent mechanisms regulating mitosis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1523. 51 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0531-8. Integrin-mediated cell adhesion is required for normal cell cycle progression during G1-S transition and for the completion of cytokinesis. Cancer cells have ability to grow anchorage- independently, but the underlying mechanisms and the functional significance for cancer development are unclear. The current thesis describes new data on the adhesion-linked molecular mechanisms regulating cytokinesis and centrosomes. Non-adherent fibroblast failed in the last step of the cytokinesis process, the abscission. This was due to lack of CEP55-binding of ESCRT-III and its associated proteins to the midbody (MB) in the intercellular bridge (ICB), which in turn correlated with too early disappearance of PLK1 and the consequent premature CEP55 accumulation. Integrin-induced FAK activity was found to be an important upstream step in the regulation of PLK1 and cytokinetic abscission. Under prolonged suspension culture, the MB disappeared but septin filaments kept the ICB in the ingressed state. -
Ongoing Human Chromosome End Extension Revealed by Analysis of Bionano and Nanopore Data Received: 4 May 2018 Haojing Shao , Chenxi Zhou , Minh Duc Cao & Lachlan J
www.nature.com/scientificreports OPEN Ongoing human chromosome end extension revealed by analysis of BioNano and nanopore data Received: 4 May 2018 Haojing Shao , Chenxi Zhou , Minh Duc Cao & Lachlan J. M. Coin Accepted: 22 October 2018 The majority of human chromosome ends remain incompletely assembled due to their highly repetitive Published: xx xx xxxx structure. In this study, we use BioNano data to anchor and extend chromosome ends from two European trios as well as two unrelated Asian genomes. At least 11 BioNano assembled chromosome ends are structurally divergent from the reference genome, including both missing sequence and extensions. These extensions are heritable and in some cases divergent between Asian and European samples. Six out of nine predicted extension sequences from NA12878 can be confrmed and flled by nanopore data. We identify two multi-kilobase sequence families both enriched more than 100- fold in extension sequence (p-values < 1e-5) whose origins can be traced to interstitial sequence on ancestral primate chromosome 7. Extensive sub-telomeric duplication of these families has occurred in the human lineage subsequent to divergence from chimpanzees. Te genome sequence of chromosome ends in the reference human genome remains incompletely assembled. In the latest draf of the human genome1 21 out of 48 chromosome ends were incomplete; amongst which fve chromosome ends (13p, 14p, 15p, 21p, 22p) are completely unknown and the remaining chromosome ends are capped with 10–110 kb of unknown sequence. Tere are many interesting observations in the chromosome end regions which remain unexplained, such as the observed increase in genetic divergence between Chimpanzee and Humans towards the chromosome ends2. -
Transcriptomics Analysis and Its Applications in Cancer
Transcriptomics analysis and its applications in cancer Alejandra Cervera Taboada Research Program in Systems Oncology Research Programs Unit Biochemistry and Developmental Biology Medicum Faculty of Medicine University of Helsinki Finland Academic dissertation To be publicly discussed, with the permission of the Faculty of Medicine of the University of Helsinki, on the 14th of December 2020, at 15 o’clock. The defence is open for audience through remote access. Helsinki 2020 Supervisor Sampsa Hautaniemi, DTech, Professor Research Program in Systems Oncology Research Programs Unit Biochemistry and Developmental Biology Medicum Faculty of Medicine University of Helsinki Helsinki, Finland Reviewers appointed by the Faculty Rolf Skotheim, PhD Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet Oslo, Norway Joaquin Dopazo, PhD, Director Clinical Bioinformatics Area Fundación Progreso y Salud Universidad de Valencia Sevilla, Spain Opponent appointed by the Faculty Carla Daniela Robles Espinoza, PhD International Laboratory for Human Genome Research, National Autonomous University of Mexico Juriquilla, Mexico Faculty of Medicine Doctoral Programme in Biomedicine ISBN 978-951-51-6865-8 (paperback) ISBN 978-951-51-6866-5 (PDF) http://ethesis.helsinki.fi Unigrafia Oy Helsinki 2020 The Faculty of Medicine uses the Urkund system (plagiarism recognition) to exam- ine all doctoral dissertations. "We reveal ourselves in the metaphors we choose for depicting the cosmos in miniature." - Stephen Jay Gould To Antonio, Abstract Cancer is a collection of diseases that combined are one of the leading causes of deaths worldwide. Although great strides have been made in finding cures for certain cancers, the heterogeneity caused by both the tissue in which cancer originates and the mutations acquired in the cell’s DNA results in unsuccessful treatments for some patients.