DOCSLIB.ORG

IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to Igg2b in BXD2 Mice

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to Igg2b in BXD2 Mice IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice This information is current as Huixian Hong, Min Gao, Qi Wu, PingAr Yang, Shanrun Liu, of October 2, 2021. Hao Li, Peter D. Burrows, Daniel Cua, Jake Y. Chen, Hui-Chen Hsu and John D. Mountz J Immunol published online 17 June 2020 http://www.jimmunol.org/content/early/2020/06/16/jimmun ol.2000280 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2020/06/16/jimmunol.200028 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 October 2, 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 © 2020 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published June 17, 2020, doi:10.4049/jimmunol.2000280 The Journal of Immunology IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice Huixian Hong,* Min Gao,† Qi Wu,* PingAr Yang,* Shanrun Liu,* Hao Li,‡ Peter D. Burrows,x Daniel Cua,{,1 Jake Y. Chen,† Hui-Chen Hsu,* and John D. Mountz*,‖ IL-23 promotes autoimmune disease, including Th17 CD4 T cell development and autoantibody production. In this study, we show that a deficiency of the p19 component of IL-23 in the autoimmune BXD2 (BXD2-p192/2) mouse leads to a shift of the follicular T helper cell program from follicular T helper (Tfh)–IL-17 to Tfh–IFN-g. Although the germinal center (GC) size and the number of GC B cells remained the same, BXD2-p192/2 mice exhibited a lower class-switch recombination (CSR) in the GC B cells, leading to lower serum levels of IgG2b. Single-cell transcriptomics analysis of GC B cells revealed that whereas Ifngr1, Il21r, and Il4r genes exhibited a synchronized expression pattern with Cxcr5 and plasma cell program genes, Il17ra exhibited a synchronized Downloaded from expression pattern with Cxcr4 and GC program genes. Downregulation of Ighg2b in BXD2-p192/2 GC B cells was associated with decreased expression of CSR-related novel base excision repair genes that were otherwise predominantly expressed by Il17ra+ GC B cells in BXD2 mice. Together, these results suggest that although IL-23 is dispensable for GC formation, it is essential to promote a population of Tfh–IL-17 cells. IL-23 acts indirectly on Il17ra+ GC B cells to facilitate CSR-related base excision repair genes during the dark zone phase of GC B cell development. The Journal of Immunology, 2020, 205: 000–000. http://www.jimmunol.org/ ollicular T helper (Tfh) cells have been reported to express transcription factor and the cytokine IL-21 are key initial events well-characterized transcription factors and different cy- that enable the establishment of the Tfh cell program and upreg- F tokines that define this Th cell subset as well as molecules ulation of adhesion molecules, leading to effective, long-term, that promote T–B cell interactions (1, 2). Upregulation of the Bcl6 and productive interactions between T and B cells in the ger- minal center (GC) (3–6). The spectrum of CD4+CXCR5+PD- 1+ICOS+CD40L+ Tfh cells has increased over the past several *Division of Clinical Immunology and Rheumatology, Department of Medicine, years to include multiple subpopulations (5, 7, 8). Although University of Alabama at Birmingham, Birmingham, AL; †Informatics Institute, ‡ classical Tfh cells produce IL-21, sublineages and pathogenic Tfh the University of Alabama at Birmingham, Birmingham, AL; Beth Israel Deaconess by guest on October 2, 2021 Medical Center, Harvard Medical School, Boston, MA; xDepartment of Microbiol- cells, including IFN-g–producing Tfh–IFN-g, IL-4–producing ogy, University of Alabama at Birmingham, Birmingham, AL; {Discovery Research, ‖ Tfh–IL-4, and IL-17–producing Tfh–IL-17, have been identified Merck Research Laboratory, Boston, MA; and Department of Medicine, Birmingham VA Medical center, Birmingham, AL in both humans and mice (9–11). In BXD2 autoimmune mice, 1Current address: Janssen Pharmaceuticals, Spring House, PA IL-17 was shown to contribute to spontaneous GC formation and autoantibody production by enhancing and prolonging the inter- ORCIDs: 0000-0002-5592-9349 (M.G.); 0000-0002-7201-4212 (S.L.); 0000-0002- 2171-8826 (H.L.); 0000-0002-5752-5647 (P.D.B.); 0000-0001-8829-7504 (J.Y.C.); action between Tfh cells and B cells through the desensitization of 0000-0002-0317-5725 (H.-C.H.). chemokine receptor responses through regulator of G-protein Received for publication March 16, 2020. Accepted for publication May 14, 2020. signaling (RGS) 13 and RGS16 (5, 12–15). Such a response + + This work was supported by the National Institutes of Health (R01-AI-071110, R01 promotes the migration arrest of CXCR4 - or CXCR5 -respond- AI134023, and P30-AR-048311 to J.D.M. and R01-AI-083705 to H.-C.H.), U.S. ing cells and thereby is critical to enable prolonged interactions of Department of Veterans Affairs grants (I01BX004049 and 1I01BX000600 to J.D.M.), and the Lupus Research Alliance (a distinguished innovator award to J.D.M. and an GC B cells with other cells for GC B cell affinity maturation. alliance target identification award to H.-C.H.). Similarly, Tfh–IFN-g cells can promote the development of au- The single-cell RNA sequencing data presented in this article have been submitted to toreactive B cells outside the GC through the T-bet transcription the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/query/ program (16). Despite these previous insights, it is not clear if acc.cgi?acc=GSE145922) under accession number GSE145922. these different Tfh cytokines operate concomitantly or sequen- Address correspondence and reprint requests to Dr. John D. Mountz, Department of Medicine, Division of Clinical Immunology and Rheumatology, University of tially in different niches or stages of GC B cell development to Alabama at Birmingham, Shelby Interdisciplinary Biomed Research Building, facilitate pathogenic autoantibody formation. It is also unknown if Room SHEL 307, 1825 University Boulevard, Birmingham, AL 35294-2182. the functions of one lineage can be replaced by the others. E-mail address: [email protected] It is also perplexing that activation-induced cytidine deaminase The online version of this article contains supplemental material. (AID) expression and activity primarily occurs in the highly Abbreviations used in this article: Ad, adenovirus; AID, activation-induced cytidine proliferative CXCR4+ dark zone (DZ) GC B cells, leading to deaminase; B6, C57BL/6; contig, contiguous sequence of overlapping DNA fragments; CSR, class-switch recombination; DZ, dark zone; GC, germinal center; KEGG, Kyoto extensive somatic hypermutation (SHM) (17, 18). In contrast, Tfh Encyclopedia of Genes and Genomes; LZ, light zone; NEIL, nucleotide excision repair- cells interact primarily with CXCR5+ GC B cells in the light zone like; NHEJ, nonhomologous end joining; PALS, periarteriolar lymphatic sheath; PB, plasmablast; PNA, peanut agglutinin; POLD, DNA polymerase d; qRT-PCR, quantitative (LZ) for fine-tuning of selection and plasma B cell development RT-PCR; RF, rheumatoid factor; RGS, regulator of G-protein signaling; scRNA-seq, (19–21). We previously have shown that the spontaneous autore- single-cell RNA sequencing; SHM, somatic hypermutation; Tfh, follicular T helper; active GCs in BXD2 mice lead to the development of autoanti- UAB, University of Alabama at Birmingham; WT, wild type. bodies through the upregulation of AID, which promotes SHM Copyright Ó 2020 by The American Association of Immunologists, Inc. 0022-1767/20/$37.50 and class-switch recombination (CSR) (22, 23). www.jimmunol.org/cgi/doi/10.4049/jimmunol.2000280 2 IL-23 PROMOTES A COORDINATED B CELL GC PROGRAM In addition to AID, both SHM and CSR require Bcl6-directed 660 anti-GL7 (clone GL7), FITC anti–PD-1 (clone J43), and Alexa Fluor programs of both B cell survival (24) and DNA damage and re- 647 anti–IL-17A (clone eBio17B7). Peanut agglutinin (PNA) was conju- pair genes (25–27). For CSR, nonhomologous end joining (NHEJ) gated with biotin (Vector Laboratories, Burlingame, CA) and detected by Alexa Fluor 488–conjugated streptavidin (Invitrogen). Dead cells were first requires transcription initiating upstream of the IgH constant excluded from analysis with allophycocyanin–eFluor 780 Organic Via- region undergoing CSR, followed by AID-mediated dsDNA bility Dye (eBioscience). breaks and then double-stranded break repair, resulting in a syn- For cytokine-producing T cell analysis, cells were stimulated for 5 h with apse and joining of the two switch regions (28). Known classical PMA (50 ng/ml; Sigma-Aldrich) and ionomycin (750 ng/ml; Sigma- Aldrich) in the presence of GolgiPlug (BD Biosciences). Cells were NHEJ players include Ku70 (XRCC6), Ku80 (XRCC5), XRCC4, stained for surface markers and then fixed and permeabilized with Cytofix/ DNA ligase IV, and DNA-PKcs (29), whereas the nonclassical (or Cytoperm solution (BD Biosciences) before intracellular staining (5). alternative) NHEJ pathway uses XRCC1 and DNA ligase III Data were acquired using standard flow cytometry (LSR II; BD Biosci- for DNA end joining (30, 31). Other DNA damage/repair gene ences) and analyzed with FlowJo_v10 software. FACS sorting was performed families, including histone variants H2a and H3a, which encode using a FACSAria cell sorter (BD Biosciences).
Load more

Recommended publications
  • Genome-Wide Analysis of 5-Hmc in the Peripheral Blood of Systemic Lupus Erythematosus Patients Using an Hmedip-Chip
    INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 35: 1467-1479, 2015 Genome-wide analysis of 5-hmC in the peripheral blood of systemic lupus erythematosus patients using an hMeDIP-chip WEIGUO SUI1*, QIUPEI TAN1*, MING YANG1, QIANG YAN1, HUA LIN1, MINGLIN OU1, WEN XUE1, JIEJING CHEN1, TONGXIANG ZOU1, HUANYUN JING1, LI GUO1, CUIHUI CAO1, YUFENG SUN1, ZHENZHEN CUI1 and YONG DAI2 1Guangxi Key Laboratory of Metabolic Diseases Research, Central Laboratory of Guilin 181st Hospital, Guilin, Guangxi 541002; 2Clinical Medical Research Center, the Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China Received July 9, 2014; Accepted February 27, 2015 DOI: 10.3892/ijmm.2015.2149 Abstract. Systemic lupus erythematosus (SLE) is a chronic, Introduction potentially fatal systemic autoimmune disease characterized by the production of autoantibodies against a wide range Systemic lupus erythematosus (SLE) is a typical systemic auto- of self-antigens. To investigate the role of the 5-hmC DNA immune disease, involving diffuse connective tissues (1) and modification with regard to the onset of SLE, we compared is characterized by immune inflammation. SLE has a complex the levels 5-hmC between SLE patients and normal controls. pathogenesis (2), involving genetic, immunologic and envi- Whole blood was obtained from patients, and genomic DNA ronmental factors. Thus, it may result in damage to multiple was extracted. Using the hMeDIP-chip analysis and valida- tissues and organs, especially the kidneys (3). SLE arises from tion by quantitative RT-PCR (RT-qPCR), we identified the a combination of heritable and environmental influences. differentially hydroxymethylated regions that are associated Epigenetics, the study of changes in gene expression with SLE.
    [Show full text]
  • Histone Variants: Deviants?
    Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Histone variants: deviants? Rohinton T. Kamakaka2,3 and Sue Biggins1 1Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 2UCT/National Institutes of Health, Bethesda, Maryland 20892, USA Histones are a major component of chromatin, the pro- sealing the two turns of DNA. The nucleosome filament tein–DNA complex fundamental to genome packaging, is then folded into a 30-nm fiber mediated in part by function, and regulation. A fraction of histones are non- nucleosome–nucleosome interactions, and this fiber is allelic variants that have specific expression, localiza- probably the template for most nuclear processes. Addi- tion, and species-distribution patterns. Here we discuss tional levels of compaction enable these fibers to be recent progress in understanding how histone variants packaged into the small volume of the nucleus. lead to changes in chromatin structure and dynamics to The packaging of DNA into nucleosomes and chroma- carry out specific functions. In addition, we review his- tin positively or negatively affects all nuclear processes tone variant assembly into chromatin, the structure of in the cell. While nucleosomes have long been viewed as the variant chromatin, and post-translational modifica- stable entities, there is a large body of evidence indicat- tions that occur on the variants. ing that they are highly dynamic (for review, see Ka- makaka 2003), capable of being altered in their compo- Supplemental material is available at http://www.genesdev.org. sition, structure, and location along the DNA. Enzyme Approximately two meters of human diploid DNA are complexes that either post-translationally modify the packaged into the cell’s nucleus with a volume of ∼1000 histones or alter the position and structure of the nucleo- µm3.
    [Show full text]
  • Complex Interacts with WRN and Is Crucial to Regulate Its Response to Replication Fork Stalling
    Oncogene (2012) 31, 2809–2823 & 2012 Macmillan Publishers Limited All rights reserved 0950-9232/12 www.nature.com/onc ORIGINAL ARTICLE The RAD9–RAD1–HUS1 (9.1.1) complex interacts with WRN and is crucial to regulate its response to replication fork stalling P Pichierri, S Nicolai, L Cignolo1, M Bignami and A Franchitto Department of Environment and Primary Prevention, Istituto Superiore di Sanita`, Rome, Italy The WRN protein belongs to the RecQ family of DNA preference toward substrates that mimic structures helicases and is implicated in replication fork restart, but associated with stalled replication forks (Brosh et al., how its function is regulated remains unknown. We show 2002; Machwe et al., 2006) and WS cells exhibit that WRN interacts with the 9.1.1 complex, one of enhanced instability at common fragile sites, chromo- the central factors of the replication checkpoint. This somal regions especially prone to replication fork interaction is mediated by the binding of the RAD1 stalling (Pirzio et al., 2008). How WRN favors recovery subunit to the N-terminal region of WRN and is of stalled forks and prevents DNA breakage upon instrumental for WRN relocalization in nuclear foci and replication perturbation is not fully understood. It has its phosphorylation in response to replication arrest. We been suggested that WRN might facilitate replication also find that ATR-dependent WRN phosphorylation restart by either promoting recombination or processing depends on TopBP1, which is recruited by the 9.1.1 intermediates at stalled forks in a way that counteracts complex in response to replication arrest. Finally, we unscheduled recombination (Franchitto and Pichierri, provide evidence for a cooperation between WRN and 2004; Pichierri, 2007; Sidorova, 2008).
    [Show full text]
  • 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.
    [Show full text]
  • Consequences Resulting from the Loss of the NEIL1 DNA Glycosylase
    Crossing the oxidative DNA damage threshold - consequences resulting from the loss of the NEIL1 DNA glycosylase R. Stephen Lloyd Center for Research on Occupational and Environmental Toxicology and Department of Molecular & Medical Genetics Oregon Health & Science University DNA Repair & Related Transactions October 2001 Erling Seeberg Arthur Grollman Stephen Lloyd But…..we were not alone Sankar Mitra 3/2002 (NEH1) Susan Wallace 4/2002 (NEIL1) Mitra, Hazra, Izumi 7/2002 (NEIL2) Erling Seeberg 9/2002 (HFPG1) Akira Yasui 9/2002 (NEIL1) Arthur Grollman 1/2003 (NEIL1) Reaction Mechanism of DNA Glycosylase/AP Lyases *B δ− *B H H *B H NE NE CH δ+ E N H CH C C H H O O O O HO O O O O CH2 O CH2 O CH2 O CH2 protonated Schiff base intermediate O O O CH2 OH CH2 OH CH2 OH + H2N E 3' phosphate O H H N N O AH H H H δ-elimination :B- E OH E OH β-elimination trans α/β unsaturated aldehyde McCullough et al, 2001 Catalytic Mechanism Glycosylase/β, δ elimination catalyst Higher catalytic efficiency on single-stranded vs double-stranded DNA and S-phase expression ⇒ replication-associated and/or transcription-coupled repair (Dou et al, 2003) Stimulated by the hus1,Rad1, Rad9 (9-1-1 complex) Major Products of Oxidative Damage to DNA Bases Evans et al, 2004 Substrate Specificities of NEIL1 IR-damaged genomic DNA (Miral Dizdaroglu) Fapy A* and Fapy G Defined Oligodeoxynucleotides Thymine glycol (both 5S,6R*, and 5R,6S) 5-OH U (↑ proximity to ssb), 5-OH C me-FapyG DHT, DHU ↓ 8-oxoG oxidation spiroiminodihydantoin * ↑↑↑ guanidinohydantoin * ↑↑↑ * = Lack of recognition redundancy for: FapyA, 5S,6R TG, SP, GH May suggest a critical role for NEIL1 in maintenance of genomic integrity Radiation Sensitivity of neil1 si RNA Depleted Cells Rosenquist et al.
    [Show full text]
  • Epigenetic Regulation of DNA Repair Genes and Implications for Tumor Therapy ⁎ ⁎ Markus Christmann , Bernd Kaina
    Mutation Research-Reviews in Mutation Research xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Mutation Research-Reviews in Mutation Research journal homepage: www.elsevier.com/locate/mutrev Review Epigenetic regulation of DNA repair genes and implications for tumor therapy ⁎ ⁎ Markus Christmann , Bernd Kaina Department of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany ARTICLE INFO ABSTRACT Keywords: DNA repair represents the first barrier against genotoxic stress causing metabolic changes, inflammation and DNA repair cancer. Besides its role in preventing cancer, DNA repair needs also to be considered during cancer treatment Genotoxic stress with radiation and DNA damaging drugs as it impacts therapy outcome. The DNA repair capacity is mainly Epigenetic silencing governed by the expression level of repair genes. Alterations in the expression of repair genes can occur due to tumor formation mutations in their coding or promoter region, changes in the expression of transcription factors activating or Cancer therapy repressing these genes, and/or epigenetic factors changing histone modifications and CpG promoter methylation MGMT Promoter methylation or demethylation levels. In this review we provide an overview on the epigenetic regulation of DNA repair genes. GADD45 We summarize the mechanisms underlying CpG methylation and demethylation, with de novo methyl- TET transferases and DNA repair involved in gain and loss of CpG methylation, respectively. We discuss the role of p53 components of the DNA damage response, p53, PARP-1 and GADD45a on the regulation of the DNA (cytosine-5)- methyltransferase DNMT1, the key enzyme responsible for gene silencing. We stress the relevance of epigenetic silencing of DNA repair genes for tumor formation and tumor therapy.
    [Show full text]
  • Tautomerization-Dependent Recognition and Excision of Oxidation Damage in Base-Excision DNA Repair
    Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair Chenxu Zhua,1, Lining Lua,1, Jun Zhangb,c,1, Zongwei Yuea, Jinghui Songa, Shuai Zonga, Menghao Liua,d, Olivia Stoviceke, Yi Qin Gaob,c,2, and Chengqi Yia,d,f,2 aState Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; bInstitute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; cBiodynamic Optical Imaging Center, Peking University, Beijing 100871, China; dPeking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; eUniversity of Chicago, Chicago, IL 60637; and fSynthetic and Functional Biomolecules Center, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China Edited by Suse Broyde, New York University, New York, NY, and accepted by Editorial Board Member Dinshaw J. Patel June 1, 2016 (received for review March 29, 2016) NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mamma- (FapyA and FapyG), spiroiminodihydantoin (Sp), and guanidino- lian genome against oxidized DNA bases. As the first enzymes in hydantoin (Gh) (23–27). Among these lesions, Tg is the most the base-excision repair pathway, glycosylases must recognize common pyrimidine base modification produced under oxidative the cognate substrates and catalyze their excision. Here we stress and ionizing radiation (28)—arising from oxidation of thy- present crystal structures of human NEIL1 bound to a range of mine and 5-methylcytosine—and is also a preferred substrate of duplex DNA. Together with computational and biochemical NEIL1 (3).
    [Show full text]
  • Identification of Molecular Targets in Head and Neck Squamous Cell Carcinomas Based on Genome-Wide Gene Expression Profiling
    1489-1497 7/11/07 18:41 Page 1489 ONCOLOGY REPORTS 18: 1489-1497, 2007 Identification of molecular targets in head and neck squamous cell carcinomas based on genome-wide gene expression profiling SATOYA SHIMIZU1,2, NAOHIKO SEKI2, TAKASHI SUGIMOTO2, SHIGETOSHI HORIGUCHI1, HIDEKI TANZAWA3, TOYOYUKI HANAZAWA1 and YOSHITAKA OKAMOTO1 Departments of 1Otorhinolaryngology, 2Functional Genomics and 3Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan Received May 21, 2007; Accepted June 28, 2007 Abstract. DNA amplifications activate oncogenes and are patients and metastases develop in 15-25% of patients (1). hallmarks of nearly all advanced cancers including head and Many factors, such as TNM stage, pathological grade and neck squamous cell carcinoma (HNSCC). Some oncogenes tumor site, influence the prognosis of HNSCC but are not show both DNA copy number gain and mRNA overexpression. sufficient to predict outcome. In addition, treatment often Chromosomal comparative genomic hybridization and oligo- results in impairment of functions such as speech and nucleotide microarrays were used to examine 8 HNSCC cell swallowing, cosmetic disfiguration and mental pain. These lines and a plot of gene expression levels relative to their inflictions significantly erode quality of life. To overcome this position on the chromosome was produced. Three highly situation, there is a need to find novel biomarkers that classify up-regulated genes, NT5C3, ANLN and INHBA, were patients into prognostic groups, to aid identification of high- identified on chromosome 7p14. These genes were subjected risk patients who may benefit from different treatments. to quantitative real-time RT-PCR on cDNA and genomic Comparative genomic hybridization (CGH) has facilitated DNA derived from 8 HNSCC cell lines.
    [Show full text]
  • A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
    Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase.
    [Show full text]
  • Targeting the Mitochondria for the Treatment of MLH1-Deficient Disease !
    Targeting the mitochondria for the treatment of MLH1-deficient disease ! A thesis submitted in partial fulfillment of the requirements of the Degree of Doctor of Philosophy at the University of London Dr. Sukaina Rashid Clinical Research Fellow Centre for Molecular Oncology Barts Cancer Institute Queen Mary University of London EC1M 6BQ UK ! ! ! 1! Declaration!! I, Sukaina Rashid confirm that the research included within this thesis is my own work or that where it has been carried out in collaboration with, or supported by others, that this is duly acknowledged below and my contribution indicated. Previously published material is also acknowledged below. I attest that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge break any UK law, infringe any third party’s copyright or other Intellectual Property Right, or contain any confidential material. I accept that the College has the right to use plagiarism detection software to check the electronic version of the thesis. I confirm that this thesis has not been previously submitted for the award of a degree by this or any other university. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. Signature: Date: 14/9/2016 ! 2! Supervisors!! Primary Supervisor: Dr Sarah Martin Senior Lecturer, Deputy Centre Lead, Centre for Molecular Oncology, Barts Cancer Institute. Secondary Supervisor: Dr Michelle Lockley Clinical Senior Lecturer Centre Lead and Honorary Consultant in Medical Oncology, Centre for Molecular Oncology, Barts Cancer Institute.
    [Show full text]
  • Dsir2 and Dmp53 Interact to Mediate Aspects of CR-Dependent Life Span
    β-catenin-mediated hair growth induction effect of 3,4,5-tri-O-caffeoylquinic acid 著者（英） Meriem Bejaoui, Myra Orlina VILLAREAL, Hiroko ISODA journal or Aging publication title volume 11 number 12 page range 4216-4237 year 2019-06 権利 Bejaoui et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. URL http://hdl.handle.net/2241/00157702 doi: 10.18632/aging.102048 Creative Commons : 表示 http://creativecommons.org/licenses/by/3.0/deed.ja www.aging-us.com AGING 2019, Vol. 11, No. 12 Research Paper β-catenin-mediated hair growth induction effect of 3,4,5-tri-O- caffeoylquinic acid Meriem Bejaoui1, Myra O. Villareal1,2,3, Hiroko Isoda1,2,3 1School of Integrative and Global Majors (SIGMA), University of Tsukuba, Tsukuba City, 305-8572 Japan 2Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba City, 305-8572 Japan 3Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba City, 305- 8572 Japan Correspondence to: Hiroko Isoda; email: [email protected] Keywords: 3,4,5-tri-O-caffeoylquinic acid (TCQA), β-catenin, dermal papilla, anagen, Wnt/β-catenin pathway Received: April 23, 2018 Accepted: June 17, 2019 Published: June 29, 2019 Copyright: Bejaoui et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
    [Show full text]
  • The Role of Histone Variants in the Epithelial-To-Mesenchymal Transition
    cells Review The Role of Histone Variants in the Epithelial-To-Mesenchymal Transition Imtiaz Nisar Lone 1, Burcu Sengez 1,2 , Ali Hamiche 3, Stefan Dimitrov 1,4 and Hani Alotaibi 1,2,* 1 Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; [email protected] (I.N.L.); [email protected] (B.S.); [email protected] (S.D.) 2 Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey 3 Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67400 Illkirch, France; [email protected] 4 Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé-Allée des Alpes, 38700 La Tronche, France * Correspondence: [email protected]; Tel.: +90-232-299-4100 (ext. 5071) Received: 18 October 2020; Accepted: 14 November 2020; Published: 17 November 2020 Abstract: The epithelial-to-mesenchymal transition (EMT) is a physiological process activated during early embryogenesis, which continues to shape tissues and organs later on. It is also hijacked by tumor cells during metastasis. The regulation of EMT has been the focus of many research groups culminating in the last few years and resulting in an elaborate transcriptional network buildup. However, the implication of epigenetic factors in the control of EMT is still in its infancy. Recent discoveries pointed out that histone variants, which are key epigenetic players, appear to be involved in EMT control. This review summarizes the available data on histone variants’ function in EMT that would contribute to a better understanding of EMT itself and EMT-related diseases.
    [Show full text]