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Deregulated Gene Expression Pathways in Myelodysplastic Syndrome Hematopoietic Stem Cells
Leukemia (2010) 24, 756–764 & 2010 Macmillan Publishers Limited All rights reserved 0887-6924/10 $32.00 www.nature.com/leu ORIGINAL ARTICLE Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells A Pellagatti1, M Cazzola2, A Giagounidis3, J Perry1, L Malcovati2, MG Della Porta2,MJa¨dersten4, S Killick5, A Verma6, CJ Norbury7, E Hellstro¨m-Lindberg4, JS Wainscoat1 and J Boultwood1 1LRF Molecular Haematology Unit, NDCLS, John Radcliffe Hospital, Oxford, UK; 2Department of Hematology Oncology, University of Pavia Medical School, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; 3Medizinische Klinik II, St Johannes Hospital, Duisburg, Germany; 4Division of Hematology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden; 5Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK; 6Albert Einstein College of Medicine, Bronx, NY, USA and 7Sir William Dunn School of Pathology, University of Oxford, Oxford, UK To gain insight into the molecular pathogenesis of the the World Health Organization.6,7 Patients with refractory myelodysplastic syndromes (MDS), we performed global gene anemia (RA) with or without ringed sideroblasts, according to expression profiling and pathway analysis on the hemato- poietic stem cells (HSC) of 183 MDS patients as compared with the the French–American–British classification, were subdivided HSC of 17 healthy controls. The most significantly deregulated based on the presence or absence of multilineage dysplasia. In pathways in MDS include interferon signaling, thrombopoietin addition, patients with RA with excess blasts (RAEB) were signaling and the Wnt pathways. Among the most signifi- subdivided into two categories, RAEB1 and RAEB2, based on the cantly deregulated gene pathways in early MDS are immuno- percentage of bone marrow blasts. -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Association of PPP2R1A with Alzheimer's Disease and Specific
Neurobiology of Aging 81 (2019) 234e243 Contents lists available at ScienceDirect Neurobiology of Aging journal homepage: www.elsevier.com/locate/neuaging Association of PPP2R1A with Alzheimer’s disease and specific cognitive domains Justin Miron a,b,c, Cynthia Picard a,b,c, Anne Labonté a,b, Daniel Auld d, John Breitner a,b,c, Judes Poirier a,b,c,*, for the United Kingdom Brain Expression Consortium, for the PREVENT-AD research group a Douglas Hospital Research Centre, Montréal, Canada b Centre for the Studies on the Prevention of Alzheimer’s Disease, Montréal, Canada c McGill University, Montréal, Canada d McGill University and Génome Québec Innovation Centre, Montréal, Canada article info abstract Article history: In an attempt to identify novel genetic variants associated with sporadic Alzheimer’s disease (AD), a Received 26 February 2019 genome-wide association study was performed on a population isolate from Eastern Canada, referred to Received in revised form 19 June 2019 as the Québec Founder Population (QFP). In the QFP cohort, the rs10406151 C variant on chromosome 19 Accepted 23 June 2019 is associated with higher AD risk and younger age at AD onset in APOE4À individuals. After surveying the Available online 2 July 2019 region surrounding this intergenic polymorphism for brain cis-eQTL associations in BRAINEAC, we identified PPP2R1A as the most likely target gene modulated by the rs10406151 C variant. PPP2R1A Keywords: mRNA and protein levels are elevated in multiple regions from QFP autopsy-confirmed AD brains when Alzheimer’s disease Genome-wide association study compared with age-matched controls. Using an independent cohort of cognitively normal individuals fi Quebec Founder Population with a parental history of AD, we found that the rs10406151 C variant is signi cantly associated with APOE4 lower visuospatial and constructional performances. -
Temporal Proteomic Analysis of HIV Infection Reveals Remodelling of The
1 1 Temporal proteomic analysis of HIV infection reveals 2 remodelling of the host phosphoproteome 3 by lentiviral Vif variants 4 5 Edward JD Greenwood 1,2,*, Nicholas J Matheson1,2,*, Kim Wals1, Dick JH van den Boomen1, 6 Robin Antrobus1, James C Williamson1, Paul J Lehner1,* 7 1. Cambridge Institute for Medical Research, Department of Medicine, University of 8 Cambridge, Cambridge, CB2 0XY, UK. 9 2. These authors contributed equally to this work. 10 *Correspondence: [email protected]; [email protected]; [email protected] 11 12 Abstract 13 Viruses manipulate host factors to enhance their replication and evade cellular restriction. 14 We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a 15 comprehensive time course analysis of >6,500 viral and cellular proteins during HIV 16 infection. To enable specific functional predictions, we categorized cellular proteins regulated 17 by HIV according to their patterns of temporal expression. We focussed on proteins depleted 18 with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be 19 necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the 20 B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). 21 Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent 22 hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. 23 The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral 2 24 lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and 25 conserved Vif function. -
Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. X, NO. X, MONTHXXX 20XX 1 Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations Davide Chicco, Fernando Palluzzi, and Marco Masseroli Abstract—Biomolecular controlled annotations have become pivotal in computational biology, because they allow scientists to analyze large amounts of biological data to better understand their test results, and to infer new knowledge. Yet, biomolecular annotation databases are incomplete by definition, like our knowledge of biology, and may contain errors and inconsistent information. In this context, machine-learning algorithms able to predict and prioritize new biomolecular annotations are both effective and efficient, especially if compared with the time-consuming trials of biological validation. To limit the possibility that these techniques predict obvious and trivial high-level features, and to help prioritizing their results, we introduce here a new element that can improve the accuracy and relevance of the results of an annotation prediction and prioritization pipeline. We propose a novelty indicator able to state the level of ”newness” (or ”originality”) of the annotations predicted for a specific gene to Gene Ontology terms, and to help prioritizing the most novel and interesting annotations predicted. We performed a thorough biological functional analysis of the prioritized annotations predicted with high accuracy by using this indicator and our previously proposed prediction algorithms. The relevance -
Patterning and Gastrulation Defects Caused by the Tw18 Lethal Are Due
© 2017. Published by The Company of Biologists Ltd | Biology Open (2017) 6, 752-764 doi:10.1242/bio.023200 RESEARCH ARTICLE Patterning and gastrulation defects caused by the tw18 lethal are due to loss of Ppp2r1a Lisette Lange1,2,‡, Matthias Marks1,*,‡, Jinhua Liu1, Lars Wittler1, Hermann Bauer1, Sandra Piehl1, Gabriele Bläß1, Bernd Timmermann3 and Bernhard G. Herrmann1,4,§ ABSTRACT t haplotypes, to date only one t lethal, tw5, has been identified and The mouse t haplotype, a variant 20 cM genomic region on characterized at the molecular level (Sugimoto et al., 2012). The t w18 Chromosome 17, harbors 16 embryonic control genes identified by lethal t and related t lethals of the same complementation group 4 9 recessive lethal mutations isolated from wild mouse populations. Due (t , t ) were described about 50 years ago (Bennett and Dunn, 1960; to technical constraints so far only one of these, the tw5 lethal, has Moser and Gluecksohn-Waelsch, 1967). They cause strong been cloned and molecularly characterized. Here we report the gastrulation defects with striking overgrowth of the primitive molecular isolation of the tw18 lethal. Embryos carrying the tw18 lethal streak (PS) and bulging of cells into the amniotic cavity, die from major gastrulation defects commencing with primitive streak commencing on the seventh and prominent on the eighth to ninth formation at E6.5. We have used transcriptome and marker gene day of gestation, followed by embryonic death one day later. In analyses to describe the molecular etiology of the tw18 phenotype. We contrast, normal development requires the ingression of epiblast show that both WNT and Nodal signal transduction are impaired in the cells at the PS, epithelial-to-mesenchymal transition (EMT) and mutant epiblast, causing embryonic patterning defects and failure of migration of single mesodermal cells in between the epiblast and the primitive streak and mesoderm formation. -
STRIPAK Directs PP2A Activity Toward MAP4K4 to Promote Oncogenic Transformation
bioRxiv preprint doi: https://doi.org/10.1101/823096; this version posted October 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation Jong Wook Kim1,2,7,8*, Christian Berrios2,4*, Miju Kim1,2*, Amy E. Schade2,4*, Guillaume Adelmant5, Huwate Yeerna7, Emily Damato1, Amanda Balboni Iniguez1,6, Selene K. Swanson9, Laurence Florens9, Michael P. Washburn9.10, Kim Stegmaier1,6, Nathaniel S. Gray5, Pablo Tamayo7,8, Ole Gjoerup2, Jarrod A. Marto5, James A. DeCaprio2,3,4,†, William C. Hahn1, 2, 3,† 1Broad Institute of Harvard and MIT, Cambridge MA. 2Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA. 3Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston MA. 4Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA. 5Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston MA. 6Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston MA. 7Division of Medical Genetics, School of Medicine, UC San Diego, CA. 8Moores Cancer Center, University of California, San Diego, CA. 9Stowers Institute for Medical Research, Kansas City, MO 64110 10Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160 * These authors contributed equally to the work. †Co-senior authors 1 bioRxiv preprint doi: https://doi.org/10.1101/823096; this version posted October 29, 2019. -
CD25 and Protein Phosphatase 2A Cooperate to Enhance IL-2R Signaling in Human Regulatory T Cells
CD25 and Protein Phosphatase 2A Cooperate to Enhance IL-2R Signaling in Human Regulatory T Cells This information is current as Ying Ding, Aixin Yu, George C. Tsokos and Thomas R. of September 30, 2021. Malek J Immunol published online 13 May 2019 http://www.jimmunol.org/content/early/2019/05/10/jimmun ol.1801570 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2019/05/10/jimmunol.180157 Material 0.DCSupplemental http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 30, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2019 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published May 13, 2019, doi:10.4049/jimmunol.1801570 The Journal of Immunology CD25 and Protein Phosphatase 2A Cooperate to Enhance IL-2R Signaling in Human Regulatory T Cells Ying Ding,* Aixin Yu,* George C. Tsokos,† and Thomas R. Malek*,‡ Low-dose IL-2 therapy is a direct approach to boost regulatory T cells (Tregs) and promote immune tolerance in autoimmune patients. -
STRIP1, a Core Component of STRIPAK Complexes, Is PNAS PLUS Essential for Normal Mesoderm Migration in the Mouse Embryo
STRIP1, a core component of STRIPAK complexes, is PNAS PLUS essential for normal mesoderm migration in the mouse embryo Hisham Bazzia,b,c,1, Ekaterina Sorokab,c, Heather L. Alcorna, and Kathryn V. Andersona,1 aDevelopmental Biology Program, Sloan Kettering Institute, New York, NY 10065; bDepartment of Dermatology and Venereology, University Hospital of Cologne, 50937 Cologne, Germany; and cCologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany Edited by Brigid L. M. Hogan, Duke University Medical Center, Durham, NC, and approved November 10, 2017 (received for review August 1, 2017) Regulated mesoderm migration is necessary for the proper mor- E-cadherin is essential for mesoderm migration (9, 10). In the phogenesis and organ formation during embryonic development. chick, directional migration of the nascent mesoderm appears Cell migration and its dependence on the cytoskeleton and signaling to depend on chemorepulsion by FGF and Wnt3a ligands expressed machines have been studied extensively in cultured cells; in at the primitive streak (11), but it is not clear whether the same contrast, remarkably little is known about the mechanisms that signals operate in the mouse. The ability of mesoderm cells to mi- regulate mesoderm cell migration in vivo. Here, we report the grate depends on a complete reorganization of the actin cytoskel- identification and characterization of a mouse mutation in striatin- eton, and motility depends on the WAVE complex and the small Strip1 interacting protein 1 ( ) that disrupts migration of the meso- GTPase RAC1 (12, 13). derm after the gastrulation epithelial-to-mesenchymal transition Experiments in cell culture recently implicated the striatin- (EMT). -
Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors
University of Cincinnati Date: 12/20/2010 I, Arturo R Maldonado , hereby submit this original work as part of the requirements for the degree of Doctor of Philosophy in Developmental Biology. It is entitled: Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors Student's name: Arturo R Maldonado This work and its defense approved by: Committee chair: Jeffrey Whitsett Committee member: Timothy Crombleholme, MD Committee member: Dan Wiginton, PhD Committee member: Rhonda Cardin, PhD Committee member: Tim Cripe 1297 Last Printed:1/11/2011 Document Of Defense Form Molecular Targeting and Enhancing Anticancer Efficacy of Oncolytic HSV-1 to Midkine Expressing Tumors A dissertation submitted to the Graduate School of the University of Cincinnati College of Medicine in partial fulfillment of the requirements for the degree of DOCTORATE OF PHILOSOPHY (PH.D.) in the Division of Molecular & Developmental Biology 2010 By Arturo Rafael Maldonado B.A., University of Miami, Coral Gables, Florida June 1993 M.D., New Jersey Medical School, Newark, New Jersey June 1999 Committee Chair: Jeffrey A. Whitsett, M.D. Advisor: Timothy M. Crombleholme, M.D. Timothy P. Cripe, M.D. Ph.D. Dan Wiginton, Ph.D. Rhonda D. Cardin, Ph.D. ABSTRACT Since 1999, cancer has surpassed heart disease as the number one cause of death in the US for people under the age of 85. Malignant Peripheral Nerve Sheath Tumor (MPNST), a common malignancy in patients with Neurofibromatosis, and colorectal cancer are midkine- producing tumors with high mortality rates. In vitro and preclinical xenograft models of MPNST were utilized in this dissertation to study the role of midkine (MDK), a tumor-specific gene over- expressed in these tumors and to test the efficacy of a MDK-transcriptionally targeted oncolytic HSV-1 (oHSV). -
Inhibition of Protein Phosphatase 2A Radiosensitizes Pancreatic Cancers by Modulating CDC25C/CDK1 and Homologous Recombination Repair
Author Manuscript Published OnlineFirst on June 18, 2013; DOI: 10.1158/1078-0432.CCR-13-0788 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Inhibition of protein phosphatase 2A radiosensitizes pancreatic cancers by modulating CDC25C/CDK1 and homologous recombination repair Dongping Wei1, Leslie A. Parsels2, David Karnak1, Mary A. Davis1, Joshua D. Parsels2, Lili Zhao3, Jonathan Maybaum2, Theodore S. Lawrence1, Yi Sun1, and Meredith A. Morgan1 Department of Radiation Oncology1, Department of Pharmacology2, University of Michigan Medical School; Department of Biostatistics3, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI 48109 Running title: Radiosensitization by PP2A inhibition Grant support: This work was funded by NIH Grants R01CA163895 (to MM), R01CA156744 (to YS), P50CA130810 (to TSL), and an Alfred B. Taubman Scholarship (to TSL). Requests for reprints: Meredith A. Morgan, Department of Radiation Oncology, University of Michigan Medical School, Room 4326B Medical Sciences I, Ann Arbor, MI, 48109-5637, Phone: 734-647-5928, Fax: 734-763-1581, e-mail: [email protected] Disclosure of potential conflicts of interest: None. Acknowledgements: Key words: pancreatic cancer, protein phosphatase 2A, radiosensitization, homologous recombination repair Abbreviations: DSB, DNA double-strand break; RER, radiation enhancement ratio; HRR, homologous recombination repair; IR, ionizing radiation; PBT, Phosphate Buffered Saline with 0.2% Triton X-100; PP2A, protein phosphatase 2A; SF, surviving fraction; TV, tumor volume 1 Downloaded from clincancerres.aacrjournals.org on September 26, 2021. © 2013 American Association for Cancer Research. Author Manuscript Published OnlineFirst on June 18, 2013; DOI: 10.1158/1078-0432.CCR-13-0788 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.