Mouse Rint1 Conditional Knockout Project (CRISPR/Cas9)
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Gene Expression Imputation Across Multiple Brain Regions Provides Insights Into Schizophrenia Risk
VU Research Portal Gene expression imputation across multiple brain regions provides insights into schizophrenia risk iPSYCH-GEMS Schizophrenia Working Group; CommonMind Consortium; The Schizophrenia Working Group of the PsyUniversity of Copenhagenchiatric Genomics Consortium published in Nature Genetics 2019 DOI (link to publisher) 10.1038/s41588-019-0364-4 document version Publisher's PDF, also known as Version of record document license Article 25fa Dutch Copyright Act Link to publication in VU Research Portal citation for published version (APA) iPSYCH-GEMS Schizophrenia Working Group, CommonMind Consortium, & The Schizophrenia Working Group of the PsyUniversity of Copenhagenchiatric Genomics Consortium (2019). Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. Nature Genetics, 51(4), 659–674. https://doi.org/10.1038/s41588-019-0364-4 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 28. -
Rab18 Promotes Lipid Droplet (LD) Growth by Tethering the ER to Lds Through SNARE and NRZ Interactions
Published Online: 24 January, 2018 | Supp Info: http://doi.org/10.1083/jcb.201704184 Article Downloaded from jcb.rupress.org on August 7, 2018 Rab18 promotes lipid droplet (LD) growth by tethering the ER to LDs through SNARE and NRZ interactions Dijin Xu,1* Yuqi Li,1* Lizhen Wu,1* Ying Li,1 Dongyu Zhao,1 Jinhai Yu,1 Tuozhi Huang,1 Charles Ferguson,2 Robert G. Parton,2,3 Hongyuan Yang,4 and Peng Li1 1State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 2Institute for Molecular Bioscience and 3Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Australia 4School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia Lipid incorporation from endoplasmic reticulum (ER) to lipid droplet (LD) is important in controlling LD growth and intra- cellular lipid homeostasis. However, the molecular link mediating ER and LD cross talk remains elusive. Here, we identi- fied Rab18 as an important Rab guanosine triphosphatase in controlling LD growth and maturation.Rab18 deficiency resulted in a drastically reduced number of mature LDs and decreased lipid storage, and was accompanied by increased ER stress. Rab3GAP1/2, the GEF of Rab18, promoted LD growth by activating and targeting Rab18 to LDs. LD-associated Rab18 bound specifically to the ER-associated NAG-RINT1-ZW10 (NRZ) tethering complex and their associated SNAREs (Syntaxin18, Use1, BNIP1), resulting in the recruitment of ER to LD and the formation of direct ER–LD contact. Cells with defects in the NRZ/SNA RE complex function showed reduced LD growth and lipid storage. -
Identification of Rab18 As an Essential Host Factor for Bkpyv Infection Using a Whole Genome RNA 2 Interference Screen
bioRxiv preprint doi: https://doi.org/10.1101/157602; this version posted June 29, 2017. 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. 1 Identification of Rab18 as an Essential Host Factor for BKPyV Infection Using a Whole Genome RNA 2 Interference Screen 3 4 Linbo Zhaoa, Michael J. Imperialea,b,* 5 6 aDepartment of Microbiology and Immunology, bComprehensive Cancer Center, University of Michigan, 7 Ann Arbor, MI, 48109, USA 8 9 10 11 12 13 14 15 16 17 18 * Corresponding author. Department of Microbiology and Immunology, 1150 West Medical Center 19 Drive, 5724 Medical Science II, Ann Arbor, MI 48109-5620, USA. Tel. +1 (734) 763 9162. Fax: +1 (734) 20 764 3562. 21 E-mail addresses: [email protected] (L. Zhao); [email protected] (M.J. Imperiale). 22 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/157602; this version posted June 29, 2017. 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. 25 Abstract 26 27 BK polyomavirus (BKPyV) is a human pathogen first isolated in 1971. BKPyV infection is ubiquitous in the 28 human population, with over 80% of adults worldwide being seropositive for BKPyV. BKPyV infection is 29 usually asymptomatic; however, BKPyV reactivation in immunosuppressed transplant patients causes 30 two diseases, polyomavirus-associated nephropathy and hemorrhagic cystitis. -
Rare Mutations in RINT1 Predispose Carriers to Breast and Lynch Syndrome–Spectrum Cancers
Published OnlineFirst May 2, 2014; DOI: 10.1158/2159-8290.CD-14-0212 RESEARCH ARTICLE Rare Mutations in RINT1 Predispose Carriers to Breast and Lynch Syndrome–Spectrum Cancers Daniel J. Park 1 , K a y o k o Ta o 7 , Florence Le Calvez-Kelm 17 , Tu Nguyen-Dumont 1 , Nivonirina Robinot 17 , Fleur Hammet1 , Fabrice Odefrey 1 , Helen Tsimiklis 1 , Zhi L. Teo 1 , Louise B. Thingholm 1 , Erin L. Young 7 , Catherine Voegele 17 , Andrew Lonie 4 , Bernard J. Pope 2 , 4 , Terrell C. Roane 10 , Russell Bell 7 , Hao Hu 11 , Shankaracharya 11 , Chad D. Huff 11 , Jonathan Ellis 6 , Jun Li 6 , Igor V. Makunin 6 , Esther M. John 12 , 13 , Irene L. Andrulis 19 , Mary B. Terry 14 , Mary Daly 15 , Saundra S. Buys 9 , Carrie Snyder 16 , Henry T. Lynch 16 , Peter Devilee20 , Graham G. Giles 3 , 5 , John L. Hopper 3 , 21 , Bing-Jian Feng 8 , 9 , Fabienne Lesueur 17 , 18 , Sean V. Tavtigian 7 , Melissa C. Southey 1 , and David E. Goldgar 8 , 9 ABSTRACT Approximately half of the familial aggregation of breast cancer remains unex- plained. A multiple-case breast cancer family exome-sequencing study identifi ed three likely pathogenic mutations in RINT1 (NM_021930.4) not present in public sequencing data- bases: RINT1 c.343C>T (p.Q115X), c.1132_1134del (p.M378del), and c.1207G>T (p.D403Y). On the basis of this fi nding, a population-based case–control mutation-screening study was conducted that identifi ed 29 carriers of rare (minor allele frequency < 0.5%), likely pathogenic variants: 23 in 1,313 early-onset breast cancer cases and six in 1,123 frequency-matched controls [OR, 3.24; 95% confi - dence interval (CI), 1.29–8.17; P = 0.013]. -
On the Role of Chromosomal Rearrangements in Evolution
On the role of chromosomal rearrangements in evolution: Reconstruction of genome reshuffling in rodents and analysis of Robertsonian fusions in a house mouse chromosomal polymorphism zone by Laia Capilla Pérez A thesis submitted for the degree of Doctor of Philosophy in Animal Biology Supervisors: Dra. Aurora Ruiz-Herrera Moreno and Dr. Jacint Ventura Queija Institut de Biotecnologia i Biomedicina (IBB) Departament de Biologia Cel·lular, Fisiologia i Immunologia Departament de Biologia Animal, Biologia Vegetal i Ecologia Universitat Autònoma de Barcelona Supervisor Supervisor PhD candidate Aurora Ruiz-Herrera Moreno Jacint Ventura Queija Laia Capilla Pérez Bellaterra, 2015 A la mare Al pare Al mano “Visto a la luz de la evolución, la biología es, quizás, la ciencia más satisfactoria e inspiradora. Sin esa luz, se convierte en un montón de hechos varios, algunos de ellos interesantes o curiosos, pero sin formar ninguna visión conjunta.” Theodosius Dobzhansky “La evolución es tan creativa. Por eso tenemos jirafas.” Kurt Vonnegut This thesis was supported by grants from: • Ministerio de Economía y Competitividad (CGL2010-15243 and CGL2010- 20170). • Generalitat de Catalunya, GRQ 1057. • Ministerio de Economía y Competitividad. Beca de Formación de Personal Investigador (FPI) (BES-2011-047722). • Ministerio de Economía y Competitividad. Beca para la realización de estancias breves (EEBB-2011-07350). Covers designed by cintamontserrat.blogspot.com INDEX Abstract 15-17 Acronyms 19-20 1. GENERAL INTRODUCTION 21-60 1.1 Chromosomal rearrangements -
Evaluation of Rint1 As a Modifier of Intestinal Tumorigenesis and Cancer Risk
RESEARCH ARTICLE Evaluation of Rint1 as a modifier of intestinal tumorigenesis and cancer risk Karla L. Otterpohl¤, Karen A. Gould* Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America ¤ Current address: Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, United States of America * [email protected] a1111111111 Abstract a1111111111 a1111111111 The Rad50 Interacting Protein 1 (Rint1) influences cellular homeostasis through mainte- a1111111111 nance of endoplasmic reticulum, Golgi and centrosome integrity and regulation of vesicle a1111111111 transport, autophagy and the G2/M checkpoint. Rint1 has been postulated to function as a tumor suppressor as well as an oncogene, with its role depending perhaps upon the precise cellular and/or experimental context. In humans, heterozygosity for germline missense vari- ants in RINT1 have, in some studies, been associated with increased risk of both breast and OPEN ACCESS Lynch syndrome type cancers. However, it is not known if these germline variants represent Citation: Otterpohl KL, Gould KA (2017) Evaluation loss of function alleles or gain of function alleles. Based upon these findings, as well as our of Rint1 as a modifier of intestinal tumorigenesis initial consideration of Rint1 as a potential candidate for Mom5, a genetic modifier of intesti- and cancer risk. PLoS ONE 12(3): e0172247. Min/+ doi:10.1371/journal.pone.0172247 nal tumorigenesis in Apc mice, we sought to explicitly examine the impact of Rint1 on tumorigenesis in ApcMin/+ mice. However, heterozygosity for a knockout of Rint1 had no Editor: Alvaro Galli, CNR, ITALY impact on tumorigenesis in Rint1+/-; ApcMin/+ mice. -
The FEM R Package: Identification of Functional Epigenetic Modules
The FEM R package: Identification of Functional Epigenetic Modules Yinming Jiao and Andrew E. Teschendorff April 24, 2017 1 Summary This vignette provides examples of how to use the package FEM to identify interactome hotspots of differential promoter methylation and differential ex- pression, where an inverse association between promoter methylation and gene expression is assumed [1]. By \interactome hotspot" we mean a connected sub- network of the protein interaction network (PIN) with an exceptionally large average edge-weight density in relation to the rest of the network. The weight edges are constructed from the statistics of association of DNA methylation and gene expression with the phenotype of interest. Thus, the FEM algorithm can be viewed as a functional supervised algorithm, which uses a network of relations between genes (in our case a PPI network), to identify subnetworks where a significant number of genes are associated with a phenotype of interest (POI). We call these \hotspots" also Functional Epigenetic Modules (FEMs). Current functionality of FEM works for Illumina Infinium 450k data, how- ever, the structure is modular allowing easy application or generalization to DNA methylation data generated with other technologies. The FEM algorithm on Illumina 27k data was first presented in [2], with its extension to Illumina 450k data described in [1]. The module detection algorithm used is the spin- glass algorithm of [3]. The PIN used in this vignette includes only protein- protein interactions, derives from Pathway Commons [4] and is available from http://sourceforge.net/projects/funepimod/files under filename hprdAsigH*.Rd, but the user is allowed to specify his own network. -
Endometrial Cancer Gene Panels: Clinical Diagnostic Vs Research Germline DNA Testing Amanda B Spurdle1, Michael a Bowman1, Jannah Shamsani1 and Judy Kirk2
Modern Pathology (2017) 30, 1048–1068 1048 © 2017 USCAP, Inc All rights reserved 0893-3952/17 $32.00 Endometrial cancer gene panels: clinical diagnostic vs research germline DNA testing Amanda B Spurdle1, Michael A Bowman1, Jannah Shamsani1 and Judy Kirk2 1Molecular Cancer Epidemiology Laboratory, Genetics and Computational Biology Division, Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia and 2Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney Medical School, University of Sydney, Centre for Cancer Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia Endometrial cancer is the most common gynecological cancer, but is nevertheless uncommon enough to have value as a signature cancer for some hereditary cancer syndromes. Commercial multigene testing panels include up to 13 different genes annotated for germline DNA testing of patients with endometrial cancer. Many other genes have been reported as relevant to familial endometrial cancer from directed genome-wide sequencing studies or multigene panel testing, or research. This review assesses the evidence supporting association with endometrial cancer risk for 32 genes implicated in hereditary endometrial cancer, and presents a summary of rare germline variants in these 32 genes detected by analysis of quasi-population-based endometrial cancer patients from The Cancer Genome Atlas project. This comprehensive investigation has led to the conclusion that convincing evidence currently exists to support clinical testing of only six of these genes for diagnosis of hereditary endometrial cancer. Testing of endometrial cancer patients for the remaining genes should be considered in the context of research studies, as a means to better establish the level of endometrial cancer risk, if any, associated with genetic variants that are deleterious to gene or protein function. -
Download Special Issue
BioMed Research International Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Disease 2016 Guest Editors: Tao Huang, Lei Chen, Jiangning Song, Mingyue Zheng, Jialiang Yang, and Zhenguo Zhang Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Disease 2016 BioMed Research International Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Disease 2016 GuestEditors:TaoHuang,LeiChen,JiangningSong, Mingyue Zheng, Jialiang Yang, and Zhenguo Zhang Copyright © 2016 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Disease 2016 Tao Huang, Lei Chen, Jiangning Song, Mingyue Zheng, Jialiang Yang, and Zhenguo Zhang Volume 2016, Article ID 6585069, 2 pages New Trends of Digital Data Storage in DNA Pavani Yashodha De Silva and Gamage Upeksha Ganegoda Volume 2016, Article ID 8072463, 14 pages Analyzing the miRNA-Gene Networks to Mine the Important miRNAs under Skin of Human and Mouse Jianghong Wu, Husile Gong, Yongsheng Bai, and Wenguang Zhang Volume 2016, Article ID 5469371, 9 pages Differential Regulatory Analysis Based on Coexpression Network in Cancer Research Junyi -
(12) Patent Application Publication (10) Pub. No.: US 2010/0267569 A1 Salmon Et Al
US 2010O267569A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0267569 A1 Salmon et al. (43) Pub. Date: Oct. 21, 2010 (54) COMPOSITIONS, METHODS AND KITS FOR (30) Foreign Application Priority Data THE DAGNOSS OF CARRIERS OF MUTATIONS IN THE BRCA1 AND BRCA2 Jul. 8, 2007 (IL) .......................................... 184478 GENES AND EARLY DAGNOSS OF CANCEROUS DISORDERS ASSOCATED Publication Classification WITH MUTATIONS IN BRCA1 AND BRCA2 GENES (51) Int. Cl. CI2O I/68 (2006.01) (75) Inventors: Asher Salmon, Jerusalem (IL); C40B 40/06 (2006.01) Tamar Peretz, Jerusalem (IL) C40B 30/00 (2006.01) GOIN 33/53 (2006.01) Correspondence Address: GOIN 33/50 (2006.01) KEVIN D. MCCARTHY ROACH BROWN MCCARTHY & GRUBER, P.C. (52) U.S. Cl. .................... 506/7; 435/6:506/16:435/7.1; 424 MAIN STREET, 1920 LIBERTY BUILDING 435/7.92; 436/86 BUFFALO, NY 14202 (US) (73) Assignee: Hadasit Medical Research (57) ABSTRACT Services and Development Ltd., The present invention relates to diagnostic compositions Jerusalem (IL) methods and kits for the detection of carriers of mutations in Appl. No.: 12/668,154 the BRCA1 and BRCA2 genes. The detection is based on the (21) use of detecting nucleic acids oramino acid based molecules, (22) PCT Fled: Jul. 8, 2008 specific for determination of the expression of at least six marker genes of the invention, in a test sample. The invention (86) PCT NO.: PCT/ILO8/OO934 thereby provides methods compositions and kits for the diag nosis of cancerous disorders associated with mutations in the S371 (c)(1), BRCA1 and BRCA2 genes, specifically, of ovarian and breast (2), (4) Date: Apr. -
NCCN: Genetic/Familial High-Risk Assessment: Breast and Ovarian
NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) Genetic/Familial High-Risk Assessment: Breast and Ovarian Version 3.2019 — January 18, 2019 NCCN.org Continue Version 3.2019, 01/18/19 © 2019 National Comprehensive Cancer Network® (NCCN®), All rights reserved. NCCN Guidelines® and this illustration may not be reproduced in any form without the express written permission of NCCN. NCCN Guidelines Index NCCN Guidelines Version 3.2019 Table of Contents Genetic/Familial High-Risk Assessment: Breast and Ovarian Discussion *Mary B. Daly, MD, PhD/Chair † Catherine Klein, MD † Þ Holly J. Pederson, MD Fox Chase Cancer Center University of Colorado Cancer Center Case Comprehensive Cancer Center/ University Hospitals Seidman Cancer Center *Robert Pilarski, MS, CGC/Vice-chair ∆ Wendy Kohlmann, MS, CGC ∆ and Cleveland Clinic Taussig Cancer Institute The Ohio State University Comprehensive Huntsman Cancer Institute Cancer Center - James Cancer Hospital at the University of Utah Gwen Reiser, MS, CGC ∆ and Solove Research Institute Fred & Pamela Buffett Cancer Center Allison W. Kurian, MD, MSc † Þ ∆ Michael P. Berry, MD ¶ Stanford Cancer Institute Kristen Mahoney Shannon, MS, CGC † ∆ St. Jude Children’s Research Hospital/ Massachusetts General Hospital The University of Tennessee Health Christine Laronga, MD ¶ Cancer Center Science Center Moffitt Cancer Center Premal Thaker, MD Ω Saundra S. Buys, MD ‡ Þ † Jennifer K. Litton, MD † Siteman Cancer Center at Barnes- Huntsman Cancer Institute The University of Texas Jewish Hospital and Washington at the University of Utah MD Anderson Cancer Center University School of Medicine Susan Friedman, DVM ¥ Lisa Madlensky, PhD, CGC ∆ Kala Visvanathan, MD, MHS † Þ FORCE: Facing Our Risk of Cancer UC San Diego Moores Cancer Center The Sidney Kimmel Comprehensive Empowered Cancer Center at Johns Hopkins Julie S. -
DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines
DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Sun, Shuying, Sunny Tian, Karina Bertelsmann, Linda Yu, and Shuying Sun. “DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines.” Cancer Informatics (September 2016): 1. © 2016 the authors, publisher and licensee Libertas Academica Limited As Published http://dx.doi.org/10.4137/cin.s40300 Publisher Libertas Academica, Ltd. Version Final published version Citable link http://hdl.handle.net/1721.1/108129 Terms of Use Creative Commons Attribution-NonCommercial 3.0 Unported Detailed Terms https://creativecommons.org/licenses/by-nc/3.0/ DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines Sunny Tian1, Karina Bertelsmann2, Linda Yu3 and Shuying Sun4 1Massachusetts Institute of Technology, Cambridge, MA, USA. 2Clear Creek High School, League City, TX, USA. 3St. John’s School, Houston, TX, USA. 4Department of Mathematics, Texas State University, San Marcos, TX, USA. Supplementary Issue: Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes (A) ABSTR ACT: Heterogeneous DNA methylation patterns are linked to tumor growth. In order to study DNA methylation heterogeneity patterns for breast cancer cell lines, we comparatively study four metrics: variance, I2 statistic, entropy, and methylation state. Using the categorical metric methylation state, we select the two most heterogeneous states to identify genes that directly affect tumor suppressor genes and high- or moderate-risk breast cancer genes. Utilizing the Gene Set Enrichment Analysis software and the ConsensusPath Database visualization tool, we generate integrated gene networks to study biological relations of heterogeneous genes.