DOCSLIB.ORG

NPM1C, Une Cible Dans Le Traitement Des Leucémies Aigues Myéloides Rita Hleihel

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
NPM1C, Une Cible Dans Le Traitement Des Leucémies Aigues Myéloides Rita Hleihel NPM1C, une cible dans le traitement des leucémies aigues myéloides Rita Hleihel To cite this version: Rita Hleihel. NPM1C, une cible dans le traitement des leucémies aigues myéloides. Médecine humaine et pathologie. Université Sorbonne Paris Cité, 2019. Français. NNT : 2019USPCC095. tel-03036805 HAL Id: tel-03036805 https://tel.archives-ouvertes.fr/tel-03036805 Submitted on 2 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Hleihel Rita – Thèse de doctorat - 2019 Thèse de doctorat de l’Université Sorbonne Paris Cité Préparée à l’Université Paris Diderot Ecole doctorale Hématologie, Oncogenèse, et Biothérapies U944 / Chaire d’Oncologie Cellulaire et Moléculaire NPM1c, une cible dans le traitement des leucémies aigues myéloïdes (LAM) Par RITA HLEIHEL Doctorat Hématologie et Oncologie Thèse co-dirigée par le Pr Ali BAZARBACHI et le Pr Hugues DE THE Présentée et soutenue publiquement à Paris le 11 Juillet 2019 Président du jury : François Sigaux MD, PhD Université Paris Diderot, Sorbonne Paris Cité Rapporteur : Claude Preudhomme, PhD CHU Lille, Lille, France Rapporteur: Eric Solary, MD, PhD Gustave Roussy, Villejuif, France Examinateur: Saverio Minucci, MD, PhD University of Milan, Italy Examinatrice: Hiba El Hajj, PhD American University of Beirut, Lebanon Directeur de thèse : Hugues de Thé, MD, PhD Collège de France Co-directeur de thèse: Ali Bazarbachi, MD, PhD American University of Beirut, Lebanon 1 Hleihel Rita – Thèse de doctorat - 2019 ACKNOWLEDGMENTS 2 Hleihel Rita – Thèse de doctorat - 2019 I would like to start by expressing my appreciation to all my thesis defense jury members, Dr François Sigaux, Dr Claude Preudhomme, Dr Eric Solary, Dr Saverio Minucci and Dr Hiba El Hajj, for putting the time and effort to serve on my committee. My deepest gratitude goes to Dr. Ali Bazarbachi and Dr Hugues de Thé for not only directing my work but also providing great role models and inspiration for me to grow as a scientist and an individual. I appreciate all the efforts and trust they put in me of which without I wouldn’t have been able to reach this point in my career. I am indebted to Dr. Hiba El Hajj who not only provided me with scientific support but also the much needed friendly atmosphere and emotional support in the lab. I cannot thank her enough for all her efforts and friendliness, without her my journey in Dr. Bazarbachi’s lab wouldn’t have been as pleasant. Dr. Marwan El Sabban has not been only a mentor, but also a friend and a confidant. I am very grateful for all the discussions I had with him. He was a friend like a father, but also fun and friendly like a brother, and a scientist who I can see has the features of a genius. I thank him for every word he said, for every argument we have had and for every time he supported me on a road full of pitfalls. Your science and your soul are unparalleled. The people in Dr. Sabban’s lab are not far from their mentor. They are among the most pleasant and the most helpful people I knew. Mohammad Harake, John Saliba, Jamal El Saghir, Layal Hajjar and the rest are not only members in Dr. Sabbans lab but also great friends. Iam very happy and grateful I have met. 3 Hleihel Rita – Thèse de doctorat - 2019 I want to extend my thanks to Dr. Zeina Dassouki and Dr. Margret Shirinian. Science only thrives when the medium allows, and I thank both of them for providing a great niche for scientific discussions in a most friendly possible environment. I have never felt so attached to people in my life as much as I felt towards my previous colleagues. I want to thank Martin Karam, Nadim Tawil, Lea Maalouf, Lama Hamadeh, and Sana El Sayed for the love and friendliness and beyond. These people cannot be described in words, they are just incredible and words fall short to describe them. Working with them felt like a feast. Seeing them every day made working in the lab the more exciting and rewarding experience I ever had. I love them beyond words. As I moved forward in my studies, I met incredible people that influenced me positively and marked themselves in my life. I particularly want to mention Maguy Hamieh, the shy sweetheart, the innocent, loving and caring person. She not only was a colleague but also a sister and a friend of whom I could rely on blindly and be sure she always got my back. I appreciate her and I cherish the time we spend together. In these few recent years I also met Dr. Abdo Akkouche who had a positive impact to my career and development through interesting discussions and collegiality and collaboration. He is a person I am happy to work with and share the time I spend in the lab in a most productive and meaningful fashion. I want to thank the members of the labs of Dr. Hugues de Thé, Dr. Ali Bazarbachi, and Dr. Hiba El Hajj for the interaction and collegiality. I particularly want to mention Hala Skayneh and Batoul Jishi who lately witnessed all my ups and downs. These two adorable girls boosted my mood and made each day in the lab a 4 Hleihel Rita – Thèse de doctorat - 2019 better one. I want to thank them for all the love and support that they have showered upon me. Hala, Batoul, I was and I will always be there for you. I also want to thank CJ and Caroline from Dr. Hugues’ lab who, despite the distance from Lebanon to France, were close colleagues and friends. I learned a lot from them. I want to thank my friends: Berthe and Jessica Hayar, Fatima Ghamlouch, Farah Gamlouch, Dr Ghina Rammal, Assil Fahs, Dr. Hassan Zalzali, Mohammad Harajli. These people are the best kind of friends, the kind that makes a person feel lucky to be present in a certain place at a certain time to meet them and get to know them and become friends with them. I can’t express how lucky I feel to have them in my life. I am grateful for the core facilities of both the American University of Beirut, Saint-Louis Hospital-France and College de France, for providing all the necessary and much needed equipment and expertise. I also want to thank the administrative staff of AUB-FM and Saint-Louis hospital in particular Ms. Rana Habli and Ms. Soniah Raharinosy for their efforts, making tedious administrative work seem doable and for doing it in the friendliest way. Finally, the greatest appreciation of all goes to those that were not with me in the lab but were with me in every single step I make, every decision I take supporting me and loving me unconditionally. My brother SAMI is God’s gift to me, an angel disguised in a man’s form. I love him beyond the capacity of my heart to love. In this light I also want to thank my number one supporter, JOSEPH, the person I chose to be my partner in life which turned to be the best decision I made my entire life. He not only accepted me, but also accepted all the long working hours, all 5 Hleihel Rita – Thèse de doctorat - 2019 the missed holidays, and all the time I could be spending with him, putting me and my career ahead of everything else. I thank him for being who he is and for showing me that love overcomes everything. I thank my mother ELHAM, my father SLEIMAN and my sisters, DARINE, LARA and ALINE for being the people sitting in the first rows to cheer for me at every achievement and trial. They saw my broken side and helped it mend. I can’t thank them enough. Their families, are my families, my nieces (LEA, LINE, RITA- MARIA, CLARA, RITA and ELMA) and nephews (TONY and CHARBEL) are my own kids, they make life happier, and they show me that no matter how things get hard, I can always laugh and forget my exhaustion or sadness during the times I spend with them. 6 Hleihel Rita – Thèse de doctorat - 2019 ABSTRACT 7 Hleihel Rita – Thèse de doctorat - 2019 Acute myeloid leukemia (AML) is a genetically heterogeneous disease. Despite improvements in understanding the biology of AML, survival rates remain quite low. Prognosis of AML patients largely depends on acquired cytogenetic and molecular abnormalities. Nucleophosmin-1 (NPM1) is an essential gene encoding for a nucleocytoplasmic shuttling protein mainly localized to the nucleolus. Among several functions, NPM1 plays major roles in stabilization of the p14ARF tumor suppressor protein, regulation of ribosome biogenesis, control of centrosome duplication, response to stress stimuli and P53 activation. NPM1 is one of the most frequently mutated genes in AML accounting for around one third of patients (NPM1c AML). In mutant NPM1c proteins, critical tryptophan residues in the C-terminus are lost and a de novo nuclear export signal is created. This leads to ectopic and aberrant accumulation of NPM1c, along with normal NPM1, in the cytoplasm of AML blasts, thus playing a major role in leukemogenesis. The promyelocytic leukemia protein (PML) tumor suppressor organizes nuclear bodies (NB) domains that control proteolysis and P53-driven senescence.
Load more

Recommended publications
  • Transcriptome-Wide Profiling of Cerebral Cavernous Malformations
    www.nature.com/scientificreports OPEN Transcriptome-wide Profling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures Santhilal Subhash 2,8, Norman Kalmbach3, Florian Wegner4, Susanne Petri4, Torsten Glomb5, Oliver Dittrich-Breiholz5, Caiquan Huang1, Kiran Kumar Bali6, Wolfram S. Kunz7, Amir Samii1, Helmut Bertalanfy1, Chandrasekhar Kanduri2* & Souvik Kar1,8* Cerebral cavernous malformations (CCMs) are low-fow vascular malformations in the brain associated with recurrent hemorrhage and seizures. The current treatment of CCMs relies solely on surgical intervention. Henceforth, alternative non-invasive therapies are urgently needed to help prevent subsequent hemorrhagic episodes. Long non-coding RNAs (lncRNAs) belong to the class of non-coding RNAs and are known to regulate gene transcription and involved in chromatin remodeling via various mechanism. Despite accumulating evidence demonstrating the role of lncRNAs in cerebrovascular disorders, their identifcation in CCMs pathology remains unknown. The objective of the current study was to identify lncRNAs associated with CCMs pathogenesis using patient cohorts having 10 CCM patients and 4 controls from brain. Executing next generation sequencing, we performed whole transcriptome sequencing (RNA-seq) analysis and identifed 1,967 lncRNAs and 4,928 protein coding genes (PCGs) to be diferentially expressed in CCMs patients. Among these, we selected top 6 diferentially expressed lncRNAs each having signifcant correlative expression with more than 100 diferentially expressed PCGs. The diferential expression status of the top lncRNAs, SMIM25 and LBX2-AS1 in CCMs was further confrmed by qRT-PCR analysis. Additionally, gene set enrichment analysis of correlated PCGs revealed critical pathways related to vascular signaling and important biological processes relevant to CCMs pathophysiology.
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [Show full text]
  • An Integrative Systems Genetics Approach Reveals Potential Causal Genes and Pathways Related to Obesity Lisette J
    Kogelman et al. Genome Medicine (2015) 7:105 DOI 10.1186/s13073-015-0229-0 RESEARCH Open Access An integrative systems genetics approach reveals potential causal genes and pathways related to obesity Lisette J. A. Kogelman1, Daria V. Zhernakova2, Harm-Jan Westra3,4,5, Susanna Cirera1, Merete Fredholm1, Lude Franke2 and Haja N. Kadarmideen1* Abstract Background: Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about the transcriptome, and may reveal novel genes affecting complex diseases. Integration of genomic and transcriptomic variation (expression quantitative trait loci [eQTL] mapping) has identified causal variants that affect complex diseases. We integrated transcriptomic data from adipose tissue and genomic data from a porcine model to investigate the mechanisms involved in obesity using a systems genetics approach. Methods: Using a selective gene expression profiling approach, we selected 36 animals based on a previously created genomic Obesity Index for RNA sequencing of subcutaneous adipose tissue. Differential expression analysis was performed using the Obesity Index as a continuous variable in a linear model. eQTL mapping was then performed to integrate 60 K porcine SNP chip data with the RNA sequencing data. Results were restricted based on genome-wide significant single nucleotide polymorphisms, detected differentially expressed genes, and previously detected co-expressed gene modules. Further data integration was performed by detecting co-expression patterns among eQTLs and integration with protein data. Results: Differential expression analysis of RNA sequencing data revealed 458 differentially expressed genes.
    [Show full text]
  • A Study of Alterations in DNA Epigenetic Modifications (5Mc and 5Hmc) and Gene Expression Influenced by Simulated Microgravity I
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital Repository @ Iowa State University Genome Informatics Facility Publications Genome Informatics Facility 1-28-2016 A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells Basudev Chowdhury Purdue University Arun S. Seetharam Iowa State University, [email protected] Zhiping Wang Indiana University School of Medicine Yunlong Liu Indiana University School of Medicine Amy C. Lossie Purdue University See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/genomeinformatics_pubs Part of the Bioinformatics Commons, Genetics Commons, and the Genomics Commons Recommended Citation Chowdhury, Basudev; Seetharam, Arun S.; Wang, Zhiping; Liu, Yunlong; Lossie, Amy C.; Thimmapuram, Jyothi; and Irudayaraj, Joseph, "A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells" (2016). Genome Informatics Facility Publications. 4. https://lib.dr.iastate.edu/genomeinformatics_pubs/4 This Article is brought to you for free and open access by the Genome Informatics Facility at Iowa State University Digital Repository. It has been accepted for inclusion in Genome Informatics Facility Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells Abstract Cells alter their gene expression in response to exposure to various environmental changes. Epigenetic mechanisms such as DNA methylation are believed to regulate the alterations in gene expression patterns.
    [Show full text]
  • Loss of the Deubiquitinase USP36 Destabilizes the RNA Helicase
    ARTICLE cro Loss of the deubiquitinase USP36 destabilizes the RNA helicase DHX33 and causes preimplantation lethality in mice Received for publication, March 27, 2017, and in revised form, December 19, 2017 Published, Papers in Press, December 22, 2017, DOI 10.1074/jbc.M117.788430 Julia M. Fraile‡, Diana Campos-Iglesias‡, Francisco Rodríguez‡, Aurora Astudillo§, Roser Vilarrasa-Blasi¶, Nuria Verdaguer-Dot¶, Miguel A. Pradoʈ, Joao A. Pauloʈ, Steven P. Gygiʈ, José I. Martín-Subero¶, X José M. P. Freije‡**1, and Carlos López-Otín‡**2 From the ‡Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006-Oviedo, Spain, the §Servicio de Anatomía Patológica, Hospital Universitario Central de Asturias, 33006-Oviedo, Spain, the ¶Departamento de Anatomía Patológica, Farmacología y Microbiología, Universitat de Barcelona, IDIBAPS, 08036-Barcelona, Spain, the ʈDepartment of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, and the **Centro de Investigación Biomédica en Red de Cáncer, Spain Edited by Eric R. Fearon Downloaded from Deubiquitinases are proteases with a wide functional diversity uitin chains to target proteins (1–4). There are six families of that profoundly impact multiple biological processes. Among DUBs grouped according to sequence and structural similari- them, the ubiquitin-specific protease 36 (USP36) has been ties: ubiquitin-specific proteases (USPs), ubiquitin carboxyl- implicated in the regulation of nucleolar activity. However, its terminal hydrolases, ovarian-tumor proteases, Machado-Jo- http://www.jbc.org/ functional relevance in vivo has not yet been fully described. seph disease protein domain proteases (MJDs), JAMM/MPN Here, we report the generation of an Usp36-deficient mouse domain-associated metallopeptidases (JAMMs), and monocyte model to examine the function of this enzyme.
    [Show full text]
  • Altered Nucleophosmin Transport in Acute Myeloid Leukaemia with Mutated NPM1: Molecular Basis and Clinical Implications
    Leukemia (2009) 23, 1731–1743 & 2009 Macmillan Publishers Limited All rights reserved 0887-6924/09 $32.00 www.nature.com/leu REVIEW Altered nucleophosmin transport in acute myeloid leukaemia with mutated NPM1: molecular basis and clinical implications B Falini1, N Bolli1,5, A Liso2, MP Martelli1, R Mannucci3, S Pileri4 and I Nicoletti3 1The Institute of Haematology, University of Perugia, IBiT Foundation, Fondazione IRCCS Biotecnologie nel Trapianto, Perugia, Italy; 2Institute of Haematology, University of Foggia, Foggia, Italy; 3Institute of Internal Medicine, University of Perugia, Perugia, Italy and 4Unit of Haematopathology, Policlinico S. Orsola, University of Bologna, Bologna, Italy Nucleophosmin (NPM1) is a highly conserved nucleo-cytoplas- n. NM_001037738) with a distinct C-terminus; it accounts for mic shuttling protein that shows a restricted nucleolar localiza- minimal nucleophosmin content in tissues. NPM1 (B23.1) and tion. Mutations of NPM1 gene leading to aberrant cytoplasmic NPM1.2 (B23.2) have different subcellular distribution patterns:5 dislocation of nucleophosmin (NPMc þ ) occurs in about one 6,7 third of acute myeloid leukaemia (AML) patients that exhibit NPM1 protein is localized only in the nucleolus and NPM1.2 8 distinctive biological and clinical features. We discuss the mainly in the nucleoplasm. A third variant (accession number latest advances in the molecular basis of nucleophosmin traffic NM_199185) lacks an alternate in-frame exon compared with under physiological conditions, describe the molecular ab- variant 1, resulting in a shorter protein whose functions and normalities underlying altered transport of nucleophosmin in expression pattern are unknown. NPM1-mutated AML and present evidences supporting the view that cytoplasmic nucleophosmin is a critical event for leukae- Experiments on NPM1/B23 migration in interspecies (chick- mogenesis.
    [Show full text]
  • Tau Modulates Mrna Transcription, Alternative Polyadenylation Profiles of Hnrnps, Chromatin Remodeling and Spliceosome Complexes
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.16.452616; this version posted July 16, 2021. 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 4.0 International license. 1 Tau modulates mRNA transcription, alternative 2 polyadenylation profiles of hnRNPs, chromatin remodeling 3 and spliceosome complexes 4 5 Montalbano Mauro1,2, Elizabeth Jaworski3, Stephanie Garcia1,2, Anna Ellsworth1,2, 6 Salome McAllen1,2, Andrew Routh3,4 and Rakez Kayed1,2†. 7 8 1 Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, 9 77555, USA 10 2 Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, 11 Galveston, Texas, 77555, USA 12 3 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 13 77555, USA 14 4Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 15 Galveston, TX, USA 16 † To whom correspondence should be addressed 17 18 Corresponding Author 19 Rakez Kayed, PhD 20 University of Texas Medical Branch 21 Medical Research Building Room 10.138C 22 301 University Blvd 23 Galveston, TX 77555-1045 24 Phone: 409.772.0138 25 Fax: 409.747.0015 26 e-mail: [email protected] 27 28 Running Title: Tau modulates transcription and alternative polyadenilation processes 29 30 Keywords: Tau, Transcriptomic, Alternative Polyadenilation,
    [Show full text]
  • Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Fall 2010 Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Renuka Nayak University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Computational Biology Commons, and the Genomics Commons Recommended Citation Nayak, Renuka, "Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress" (2010). Publicly Accessible Penn Dissertations. 1559. https://repository.upenn.edu/edissertations/1559 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1559 For more information, please contact [email protected]. Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Abstract Genes interact in networks to orchestrate cellular processes. Here, we used coexpression networks based on natural variation in gene expression to study the functions and interactions of human genes. We asked how these networks change in response to stress. First, we studied human coexpression networks at baseline. We constructed networks by identifying correlations in expression levels of 8.9 million gene pairs in immortalized B cells from 295 individuals comprising three independent samples. The resulting networks allowed us to infer interactions between biological processes. We used the network to predict the functions of poorly-characterized human genes, and provided some experimental support. Examining genes implicated in disease, we found that IFIH1, a diabetes susceptibility gene, interacts with YES1, which affects glucose transport. Genes predisposing to the same diseases are clustered non-randomly in the network, suggesting that the network may be used to identify candidate genes that influence disease susceptibility.
    [Show full text]
  • Whole-Exome Sequencing in Familial Parkinson Disease
    Supplementary Online Content Farlow JL, Robak LA, Hetrick K, et al. Whole-exome sequencing in familial Parkinson disease. JAMA Neurol. Published online November 23, 2015. doi:10.1001/jamaneurol.2015.3266. eMethods. Supplemental Methods eFigure 1. Pedigrees of Discovery Cohort Families A-I eFigure 2. Pedigrees of Discovery Cohort Families J-Q eFigure 3. Pedigrees of Discovery Cohort Families R-Z eFigure 4. Pedigrees of Discovery Cohort Families AA-AF eTable 1. Single-Nucleotide Variants Identified in the Filtered Genes With GO Annotation eTable 2. Primer Sequences for Sanger Sequencing Verification of Identified Variants of Interest This supplementary material has been provided by the authors to give readers additional information about their work. © 2015 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 eMethods. Supplemental Methods Whole exome sequencing Discovery cohort. All members of each family were sequenced at the same center (44 samples/15 families at the Center for Inherited Disease Research [CIDR], and 53 samples/18 families at the HudsonAlpha Institute for Biotechnology). One family with 4 members was sequenced at both centers (eMethods). The Agilent SureSelect 50Mb Human All Exon Kit (CIDR) and Nimblegen 44.1Mb SeqCap EZ Exome Capture version 2.0 (HudsonAlpha) were used for capture, and the Illumina HiSeq 2000 system was used for 100bp paired-end sequencing. Samples were aligned to the human genome (build hg19) using Burrows Wheeler Aligner1. The Genome Analysis Toolkit (GATK)2 was used for local realignment, base quality score recalibration, and multi-sample variant calling (Unified Genotyper) for the samples sequenced at CIDR and HudsonAlpha separately.
    [Show full text]
  • Universidad Autónoma De Madrid
    Universidad Autónoma de Madrid Departamento de Bioquímica Identification of the substrates of the protease MT1-MMP in TNFα- stimulated endothelial cells by quantitative proteomics. Analysis of their potential use as biomarkers in inflammatory bowel disease. Agnieszka A. Koziol Tesis doctoral Madrid, 2013 2 Departamento de Bioquímica Facultad de Medicina Universidad Autónoma de Madrid Identification of the substrates of the protease MT1-MMP in TNFα- stimulated endothelial cells by quantitative proteomics. Analysis of their potential use as biomarkers in inflammatory bowel disease. Memoria presentada por Agnieszka A. Koziol licenciada en Ciencias Biológicas para optar al grado de Doctor. Directora: Dra Alicia García Arroyo Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid, 2013 3 4 ACKNOWLEDGEMENTS - ACKNOWLEDGEMENTS - First and foremost I would like to express my sincere gratitude to my supervisor Dr. Alicia García Arroyo for giving me the great opportunity to study under her direction. Her encouragement, guidance and support from the beginning to the end, enabled me to develop and understand the subject. Her feedback to this manuscript, critical reading and corrections was inappreciable to finish this dissertation. Next, I would like to express my gratitude to those who helped me substantially along the way. To all members of MMPs’ lab, for their interest in the project, teaching me during al these years and valuable contribution at the seminary discussion. Without your help it would have not been possible to do some of those experiments. Thank you all for creating a nice atmosphere at work and for being so good friends in private. I would like to also thank all of the collaborators and technical units for their support and professionalism.
    [Show full text]
  • An Integrative Systems Genetics Approach Reveals Potential Causal Genes and Pathways Related to Obesity
    An integrative systems genetics approach reveals potential causal genes and pathways related to obesity The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Kogelman, Lisette J. A., Daria V. Zhernakova, Harm-Jan Westra, Susanna Cirera, Merete Fredholm, Lude Franke, and Haja N. Kadarmideen. 2015. “An integrative systems genetics approach reveals potential causal genes and pathways related to obesity.” Genome Medicine 7 (1): 105. doi:10.1186/s13073-015-0229-0. http:// dx.doi.org/10.1186/s13073-015-0229-0. Published Version doi:10.1186/s13073-015-0229-0 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:23473972 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 Kogelman et al. Genome Medicine (2015) 7:105 DOI 10.1186/s13073-015-0229-0 RESEARCH Open Access An integrative systems genetics approach reveals potential causal genes and pathways related to obesity Lisette J. A. Kogelman1, Daria V. Zhernakova2, Harm-Jan Westra3,4,5, Susanna Cirera1, Merete Fredholm1, Lude Franke2 and Haja N. Kadarmideen1* Abstract Background: Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about the transcriptome, and may reveal novel genes affecting complex diseases.
    [Show full text]
  • Identifies Differentially Methylated Regions from Iron-Deficient Rat Hippocampus David E
    Condon et al. BMC Bioinformatics (2018) 19:31 DOI 10.1186/s12859-018-2037-1 SOFTWARE Open Access Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus David E. Condon1, Phu V. Tran2, Yu-Chin Lien3, Jonathan Schug1, Michael K. Georgieff2, Rebecca A. Simmons3 and Kyoung-Jae Won1,4* Abstract Background: Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. Results: We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data. Conclusions: Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays. Keywords: Epigenetics, DNA Methylation, WGBS, Differentially Methylated regions (DMR), RRBS, Bisulfite sequencing Background somatically heritable mark that is generally associated with DNA methylation plays a critical role in gene regulation transcriptional repression [10]. Aberrant methylation has [1].
    [Show full text]