DOCSLIB.ORG

Point Mutation Specific Antibodies in B-Cell and T-Cell Lymphomas And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Point Mutation Specific Antibodies in B-Cell and T-Cell Lymphomas And diagnostics Review Point Mutation Specific Antibodies in B-Cell and T-Cell Lymphomas and Leukemias: Targeting IDH2, KRAS, BRAF and Other Biomarkers RHOA, IRF8, MYD88, ID3, NRAS, SF3B1 and EZH2 Kunwar Singh 1,*,† , Sumanth Gollapudi 2,† , Sasha Mittal 2, Corinn Small 2, Jyoti Kumar 1 and Robert S. Ohgami 2,* 1 Department of Pathology, Stanford University, Stanford, CA 94063, USA; [email protected] 2 Department of Pathology, University of California, San Francisco, CA 94143, USA; [email protected] (S.G.); [email protected] (S.M.); [email protected] (C.S.) * Correspondence: [email protected] (K.S.); [email protected] (R.S.O.); Tel.: +1-347-856-7047 (K.S.); +1-415-514-8179 (R.S.O.) † These authors contributed equally. Abstract: B-cell and T-cell lymphomas and leukemias often have distinct genetic mutations that are diagnostically defining or prognostically significant. A subset of these mutations consists of specific point mutations, which can be evaluated using genetic sequencing approaches or point mutation Citation: Singh, K.; Gollapudi, S.; specific antibodies. Here, we describe genes harboring point mutations relevant to B-cell and T-cell Mittal, S.; Small, C.; Kumar, J.; malignancies and discuss the current availability of these targeted point mutation specific antibodies. Ohgami, R.S. Point Mutation Specific We also evaluate the possibility of generating novel antibodies against known point mutations Antibodies in B-Cell and T-Cell by computationally assessing for chemical and structural features as well as epitope antigenicity Lymphomas and Leukemias: of these targets. Our results not only summarize several genetic mutations and identify existing Targeting IDH2, KRAS, BRAF and point mutation specific antibodies relevant to hematologic malignancies, but also reveal potential Other Biomarkers RHOA, IRF8, underdeveloped targets which merit further study. MYD88, ID3, NRAS, SF3B1 and EZH2. Diagnostics 2021, 11, 600. https://doi.org/10.3390/ Keywords: single nucleotide polymorphisms; hematopathology; cancer; diagnostics; point mutation diagnostics11040600 specific antibodies; precision medicine Academic Editor: Chung-Che (Jeff) Chang 1. Introduction Received: 4 February 2021 In 2016, the World Health Organization (WHO) revised the fourth edition of the WHO Accepted: 24 March 2021 Classification of Tumours of Haematopoietic and Lymphoid Tissues based on new molecular and Published: 27 March 2021 morphological findings [1]. The revised criteria for numerous hematopoietic malignancies indicate that genetic mutations play a significant role in the diagnosis of these entities. Publisher’s Note: MDPI stays neutral Many of these mutations are well-defined recurrent point mutations in specific genes. with regard to jurisdictional claims in While such mutations can be detected using genetic sequencing methodologies, another published maps and institutional affil- strategy for identification is to develop antibodies that specifically target mutated sites in iations. proteins present within patient tissue samples [2,3]. Monoclonal or polyclonal antibodies can also be developed against these mutations by conjugating the relevant peptide to a carrier protein and injecting the peptide-protein complex into a host animal (Figure1). Many biotechnology companies produce antibodies that target commonly expressed Copyright: © 2021 by the authors. proteins but there is a paucity of antibodies available on the market that are designed Licensee MDPI, Basel, Switzerland. to target point mutations related to T-cell and B-cell malignancies. The ability to use This article is an open access article antibodies in hematologic malignancies would provide benefit both in research and clinical distributed under the terms and settings. Compared to next-generation sequencing (NGS) assays, in which results and conditions of the Creative Commons interpretation can take weeks to finalize, in situ immunohistochemistry (IHC) assays Attribution (CC BY) license (https:// are a sensitive and often more efficient approach. In order to expedite the diagnosis creativecommons.org/licenses/by/ 4.0/). and treatment of hematologic malignancies, a tiered system consisting of early IHC and Diagnostics 2021, 11, 600. https://doi.org/10.3390/diagnostics11040600 https://www.mdpi.com/journal/diagnostics Diagnostics 2021, 11, 600 2 of 14 Diagnostics 2021, 11, 600 follow up NGS is used in many clinical settings and has been proposed in some published2 of 14 studies [4]. However, a limitation to this rapid protocol, in certain settings, is the availability of mutation-specific antibodies. Figure 1. Example of a conventional targeted monoclonal and polyclonal antibody development process using conju- Figure 1. Example of a conventional targeted monoclonal and polyclonal antibody development process using conjugated gated peptides. peptides. In this study, we aim to describe both current and potential biomarker targets in T-cell Many biotechnology companies produce antibodies that target commonly expressed and B-cell neoplasms, highlighting several point mutations for their suitability in antibody proteins but there is a paucity of antibodies available on the market that are designed to development based on their predicted antigenicity in relation to multiple chemical and targetstructural point mutations parameters. related to T-cell and B-cell malignancies. The ability to use anti- bodies in hematologic malignancies would provide benefit both in research and clinical settings.2. Materials Compared and to Methods next-generation sequencing (NGS) assays, in which results and in- terpretation2.1. Target can Selection take weeks to finalize, in situ immunohistochemistry (IHC) assays are a sensitiveFor and our often study, more we efficient selected genesapproach. with In known order point to expedite mutations the thatdiagnosis have been and described treat- mentin of hematolymphoid hematologic malignancies, neoplasms a that tiered occur system at a minimumconsisting of frequency early IHC of and 10% follow within up each NGSdiagnostic is used in entity. many clinical We also settings included and mutations has been thatproposed influence in some diagnostic published or prognosticstudies [4]. subtypingHowever, baseda limitation on WHO to this criteria. rapid protocol, in certain settings, is the availability of mutation-specificAntibodies antibodies. for point mutations available on market or shared freely from research groupsIn this werestudy, identified we aim to using describe Biocompare both current (https://www.biocompare.com/ and potential biomarker targets, accessed in T- on cell 4and January B-cell 2021),neoplasms, web-based highlighting search engineseveral queries, point mutations and major for antibody their suitability vendor in websites an- tibody(i.e., development Millipore Sigma, based BioLegend, on their predicted and Abcam). antigenicity in relation to multiple chemical and structural parameters. 2.2. Peptide and Antibody Evaluation 2. MaterialsThe and potential Methods for point mutation specific antibody production of the selected genes 2.1.was Target assessed Selection by using peptide sequences from the associated proteins that contained theFor mutated our study, amino we acids,selected which genes were with identified known point using mutations NCBI’s GenBankthat have andbeen UniProt. de- scribedThe sequencesin hematolymphoid used for analysis neoplasms consisted that o ofccur the at targeted a minimum point frequency mutation site,of 10% the within 10 amino eachacids diagnostic upstream entity. and We the also 10 amino included acids mutations downstream that influence of the target, diagnostic resulting or inprognostic a 21-mer for subtypinganalysis. based Solubility on WHO was criteria. determined using the PepCalc calculator (https://pepcalc.com/, accessedAntibodies on 28for December point mutations 2020) by available Innovagen on market AB [5]. or Three shared crosslinkers freely from were research assessed groupsfor eachwere peptide identified regarding using Biocompare appropriate (https://www.biocompare.com/, conjugation chemistry to carrier accessed proteins on (KLH 4 Januaryor BSA); 2021), (1) web-based m-Maleimidobenzoyl-N-hydroxysuccinimide search engine queries, and major antibody ester vendor (MBS), websites (2) 1-ethyl-3-[3- (i.e., Milliporedimethylaminopropyl]carbodiimide Sigma, BioLegend, and Abcam). hydrochloride (EDC), and (3) activated EDC (aEDC). A main factor considered for crosslinker selection was the ability to bind to residues 2.2.without Peptide and reacting Antibody to nearby Evaluation side chains, which could lead to incorrect conjugation to the carrier protein. MBS is a crosslinker compound with a maleimide reactive group at one end andThe an potential ester group for onpoint the mutation other end. specific The maleimide antibody group production reacts with of the sulfhydryl selected groupsgenes to wasform assessed thioester by using linkages, peptide therefore sequences the 21-mer from shouldthe associated not contain proteins cysteine that residues. contained EDC the is a mutatedcarbodiimide, amino acids, and itswhich reactivity were toidentified carboxyl using groups NCBI’s leads GenBank to direct conjugation and UniProt. to aThe peptide’s se- quencesfree amineused for group. analysis As consisted a result, of the the side targeted chains point of aspartic mutation and site, glutamic the 10 amino acid residues,acids upstreamboth of and which the contain10 amino carboxylate acids downstream ions, can of react the with
Load more

Recommended publications
  • IRAK4 Gene Interleukin 1 Receptor Associated Kinase 4
    IRAK4 gene interleukin 1 receptor associated kinase 4 Normal Function The IRAK4 gene provides instructions for making a protein that plays an important role in innate immunity, which is the body's early, nonspecific response to foreign invaders ( pathogens). The IRAK-4 protein is part of a signaling pathway that is involved in early recognition of pathogens and the initiation of inflammation to fight infection. In particular, the IRAK-4 protein relays signals from proteins called Toll-like receptors and IL-1 receptor-related proteins. As one of the first lines of defense against infection, Toll-like receptors recognize patterns that are common to many pathogens, rather than recognizing specific pathogens, and stimulate a quick immune response. The IL-1 receptor and related proteins recognize immune system proteins called cytokines that signal the need for an immune response. The resulting signaling pathway triggers inflammation, a nonspecific immune response that helps fight infection. Health Conditions Related to Genetic Changes IRAK-4 deficiency At least 20 mutations in the IRAK4 gene have been identified in people with IRAK-4 deficiency, an immune system disorder that leads to recurrent invasive bacterial infections. These gene mutations lead to an abnormally short, nonfunctional IRAK-4 protein or no protein at all. The loss of functional IRAK-4 protein blocks the initiation of inflammation in response to pathogens or cytokines that would normally help fight the infections. Because the early immune response is insufficient, bacterial
    [Show full text]
  • Structural Effects of Point Mutations in Proteins Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier
    Structural effects of point mutations in proteins Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier To cite this version: Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier. Structural effects of point muta- tions in proteins. Proteins - Structure, Function and Bioinformatics, Wiley, 2018, 86 (8), pp.853-867. 10.1002/prot.25499. hal-01909365 HAL Id: hal-01909365 https://hal.sorbonne-universite.fr/hal-01909365 Submitted on 31 Oct 2018 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. Structural effects of point mutations in proteins Suvethigaa Shanthirabalan1, Jacques Chomilier2, Mathilde Carpentier1,2 1. Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France. 2. Sorbonne Université, CNRS, MNHN, IRD, IMPMC, BiBiP, Paris, France Corresponding author: [email protected] Mail: [email protected]; [email protected]; [email protected] Abstract A structural database of eleven families of chains differing by a single amino acid substitution has been built. Another structural dataset of 5 families with identical sequences has been used for comparison. The RMSD computed after a global superimposition of the mutated protein on each native one is smaller than the RMSD calculated among proteins of identical sequences.
    [Show full text]
  • Targeting Myddosome Signaling in Waldenström’S
    Author Manuscript Published OnlineFirst on August 20, 2018; DOI: 10.1158/1078-0432.CCR-17-3265 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. IRAK 1/4 Inhibition in Waldenström’s Ni, H. et al. Targeting Myddosome Signaling in Waldenström’s Macroglobulinemia with the Interleukin-1 Receptor- associated Kinase 1/4 Inhibitor R191 Haiwen Ni1,2,#, Fazal Shirazi2,#, Veerabhadran Baladandayuthapani3, Heather Lin3, Isere Kuiatse2, Hua Wang2, Richard J. Jones2, Zuzana Berkova2, Yasumichi Hitoshi4, Stephen M. Ansell5, Steven P. Treon6, Sheeba K. Thomas2, Hans C. Lee2, Zhiqiang Wang2, R. Eric Davis2, and Robert Z. Orlowski2,7,* 1Department of Hematology, The Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing, JangSu, China; 2Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX; 3Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX; 4Rigel, South San Francisco, CA; The 5Division of Hematology, Mayo Clinic, Rochester, MN; The 6Dana Farber Cancer Institute, Harvard Medical School, Boston, MA. 7Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX #Indicates that these authors contributed equally. Address correspondence to: Dr. Robert Z. Orlowski, The University of Texas MD Anderson Cancer Center, Department of Lymphoma and Myeloma, 1515 Holcombe Blvd., Unit 429, Houston, TX 77030-4009, E-mail: [email protected], Telephone 713-794-3234, Fax 713- 563-5067 Page 1 Downloaded from clincancerres.aacrjournals.org on September 24, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on August 20, 2018; DOI: 10.1158/1078-0432.CCR-17-3265 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
    [Show full text]
  • Carna Newsletter 2021.05.26
    画像：ファイル＞配置＞リンクから画像を選択＞画像を選択して右クリック＞画像を最前面に配置＞オブジェクト＞テキストの回り込み＞作成 Vol.10 Carna Newsletter 2021.05.26 Targeted Degradation of Non-catalytic Kinases New Drug Discovery Options The announcement that Kymera Therapeutics, a TLR/IL-1R signaling in several cell types, which company pioneering targeted protein degradation, indicates that the IRAK4 scaffolding function is entered into a strategic collaboration with Sanofi important in some cases2)3). to develop and commercialize first-in-class protein degrader therapies targeting IRAK4 in patients with immune-inflammatory diseases highlights the TLR growing interest in clinical applications of small IL-1R molecule mediated kinase degradation. Kymera received $150 million in cash up front and may cytosol 8 8 potentially receive at least $2 billion in this key D y strategic partnership, including sales milestones M 4 4 K K and royalty payments. A A R R I I 2 P 1 K Most of the protein degraders currently under K A A R I R development are heterobifunctional molecules I which contain one moiety that binds a desired target protein and another that binds an E3 ligase, P joined by a linker. Protein degrader-induced proximity results in ubiquitination of the target Fig.1. TLR and IL-1R Signaling in the Myddosome followed by its degradation by the proteasome. This transformative new modality is expected to open a new chapter in drug discovery targeting 【Allosteric regulatory function】 kinases for which the development of clinical Aside from scaffolding functions, allosteric inhibitors has been difficult. One such example is regulation is another non-catalytic function that IRAK4, which has a non-catalytic function activates binding partners by inducing a independent of kinase activity in addition to a conformational change.
    [Show full text]
  • Large Accumulation of Mrna and DNA Point Modi¢Cations in a Plant
    FEBS Letters 472 (2000) 14^16 FEBS 23560 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Large accumulation of mRNA and DNA point modi¢cationsprovided in by a Elsevier plant - Publisher Connector senescent tissue Maria Plaa;*, Anna Jofre¨a, Maria Martellb, Marisa Molinasa, Jordi Go¨mezb aLaboratori del Suro, Universitat de Girona, Campus Montilivi sn, E-17071 Girona, Spain bLiver Unit, Department of Medicine, Universitat Auto©noma de Barcelona, Hospital General Universitari Vall d'Hebron, E-08035 Barcelona, Spain Received 26 January 2000 Edited by Takashi Gojobori We investigated the frequency of cDNA modi¢cation in Abstract Although nucleic acids are the paradigm of genetic information conservation, they are inherently unstable molecules cork (phellem) compared to a normally growing young tissue that suffer intrinsic and environmental damage. Oxidative stress (root tip) using cork-oak (Quercus suber) as a model system. has been related to senescence and aging and, recently, it has For this purpose, we analyzed a population of Qs_hsp17 been shown that mutations accumulate at high frequency in mRNA sequences (reverse transcription PCR products form mitochondrial DNA with age. We investigated RNA and DNA position 32^401, AC AJ000691) in cork and in root tip tissue modifications in cork, a senescent plant tissue under high [6]. Cork (phellem) is an external layer of protective tissue, endogenous oxidative stress conditions. When compared to consisting of several layers of cells that deposit large amounts normally growing young tissue, cork revealed an unexpected of suberin and undergo programmed cell death. Due to phen- high frequency of point modifications in both cDNA (Pn = oxy radicals generated during suberin synthesis [7,8], cork 1/1784) and nuclear DNA (Pn = 1/1520).
    [Show full text]
  • Point Mutations Underlying NF1 and NF2 and Increased Risk of Malignancy
    Central Annals of Otolaryngology and Rhinology Mini Review *Corresponding author Andrea L.O. Hebb, MSc, PhD, RN, Maritime Lateral Skull Base Clinic, Otolaryngology, Neurosurgery and the Point Mutations Underlying NF1 Stereotactic Radiotherapy Group QEII Health Science Centre, Halifax, Canada; Email: [email protected] and NF2 and Increased Risk of Submitted: 12 February 2020 Accepted: 25 February 2020 Published: 27 February 2020 Malignancy ISSN: 2379-948X Copyright 1 2 3,4 3,4 Myles Davidson , Haupt TS , Morris DP , Shoman NM , © 2020 Davidson M, et al. 2,4 1,2,4 Walling SA , and Hebb ALO * OPEN ACCESS 1Department of Psychology, Saint Mary’s University, Canada 2Division of Neurosurgery, Dalhousie University, Canada Keywords 3 Division of Otolaryngology, Dalhousie University, Canada • Neurofibromatosis 4 Maritime Lateral Skull Base Clinic, Otolaryngology, Neurosurgery and the Stereotactic • Missense mutation Radiotherapy Group QEII Health Science Centre, Canada • Frameshift mutation • Nonsense mutation Abstract • KRAS gene • Colorectal cancer Neurofibromatosis Type-1 and Neurofibromatosis Type-2 are autosomal dominant • Acoustic neuroma tumor suppressor disorders that result from inherited or spontaneous mutations in • Vestibular schwannoma their respective genes. Neurofibromatosis Type-1 has been attributed to a non-sense • Meningioma mutation in chromosome 17 and Neurofibromatosis Type-2 a point mutation in its gene on chromosome 22. The following discussion briefly reviews point and frameshift mutations and explores the relationship between point mutations and development of malignancies in patients with Neurofibromatosis Type-1 and Neurofibromatosis Type-2. INTRODUCTION producing phenylalanine hydroxylase, the majority of which are missense mutations [4]. A point mutation is the change of one base for another in the DNA sequence.
    [Show full text]
  • Supplementary Material
    BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Page 1 / 45 SUPPLEMENTARY MATERIAL Appendix A1: Neuropsychological protocol. Appendix A2: Description of the four cases at the transitional stage. Table A1: Clinical status and center proportion in each batch. Table A2: Complete output from EdgeR. Table A3: List of the putative target genes. Table A4: Complete output from DIANA-miRPath v.3. Table A5: Comparison of studies investigating miRNAs from brain samples. Figure A1: Stratified nested cross-validation. Figure A2: Expression heatmap of miRNA signature. Figure A3: Bootstrapped ROC AUC scores. Figure A4: ROC AUC scores with 100 different fold splits. Figure A5: Presymptomatic subjects probability scores. Figure A6: Heatmap of the level of enrichment in KEGG pathways. Kmetzsch V, et al. J Neurol Neurosurg Psychiatry 2021; 92:485–493. doi: 10.1136/jnnp-2020-324647 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Appendix A1. Neuropsychological protocol The PREV-DEMALS cognitive evaluation included standardized neuropsychological tests to investigate all cognitive domains, and in particular frontal lobe functions. The scores were provided previously (Bertrand et al., 2018). Briefly, global cognitive efficiency was evaluated by means of Mini-Mental State Examination (MMSE) and Mattis Dementia Rating Scale (MDRS). Frontal executive functions were assessed with Frontal Assessment Battery (FAB), forward and backward digit spans, Trail Making Test part A and B (TMT-A and TMT-B), Wisconsin Card Sorting Test (WCST), and Symbol-Digit Modalities test.
    [Show full text]
  • Supplementary Material DNA Methylation in Inflammatory Pathways Modifies the Association Between BMI and Adult-Onset Non- Atopic
    Supplementary Material DNA Methylation in Inflammatory Pathways Modifies the Association between BMI and Adult-Onset Non- Atopic Asthma Ayoung Jeong 1,2, Medea Imboden 1,2, Akram Ghantous 3, Alexei Novoloaca 3, Anne-Elie Carsin 4,5,6, Manolis Kogevinas 4,5,6, Christian Schindler 1,2, Gianfranco Lovison 7, Zdenko Herceg 3, Cyrille Cuenin 3, Roel Vermeulen 8, Deborah Jarvis 9, André F. S. Amaral 9, Florian Kronenberg 10, Paolo Vineis 11,12 and Nicole Probst-Hensch 1,2,* 1 Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; [email protected] (A.J.); [email protected] (M.I.); [email protected] (C.S.) 2 Department of Public Health, University of Basel, 4001 Basel, Switzerland 3 International Agency for Research on Cancer, 69372 Lyon, France; [email protected] (A.G.); [email protected] (A.N.); [email protected] (Z.H.); [email protected] (C.C.) 4 ISGlobal, Barcelona Institute for Global Health, 08003 Barcelona, Spain; [email protected] (A.-E.C.); [email protected] (M.K.) 5 Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain 6 CIBER Epidemiología y Salud Pública (CIBERESP), 08005 Barcelona, Spain 7 Department of Economics, Business and Statistics, University of Palermo, 90128 Palermo, Italy; [email protected] 8 Environmental Epidemiology Division, Utrecht University, Institute for Risk Assessment Sciences, 3584CM Utrecht, Netherlands; [email protected] 9 Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College, SW3 6LR London, UK; [email protected] (D.J.); [email protected] (A.F.S.A.) 10 Division of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; [email protected] 11 MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG London, UK; [email protected] 12 Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy * Correspondence: [email protected]; Tel.: +41-61-284-8378 Int.
    [Show full text]
  • Methods for Detection of Point Mutations: Performance and Quality
    Clinical Chemistry 43:7 1114–1128 (1997) Review Methods for detection of point mutations: performance and quality assessment Downloaded from https://academic.oup.com/clinchem/article/43/7/1114/5640834 by guest on 29 September 2021 Peter Nollau and Christoph Wagener*, on behalf of the IFCC Scientific Division, Committee on Molecular Biology Techniques We give an overview of current methods for the detec- 10) What kind of quality assessment can be achieved? tion of point mutations as well as small insertions and Here, different methods for the detection of point muta- deletions in clinical diagnostics. For each method, the tions and small deletions or insertions will be discussed following characteristics are specified: (a) principle, (b) on the basis of the above criteria (for simplification, we major modifications, (c) maximum fragment size that shall refer to point mutations only in the text, though in can be analyzed, (d) ratio and type of mutations that can general, small deletions or insertions are detected equally be detected, (e) minimum ratio of mutant to wild-type well by the methods described). In general, PCR is either alleles at which mutations can be detected, and (f) used for the generation of DNA fragments, or is part of detection methods. Special attention is paid to the the detection method. Screening methods for unknown possibilities of quality assessment and the potential for mutations as well as methods for the detection of known standardization and automation. mutations are included. Though DNA sequencing tech- niques will not be covered, we stress that DNA sequenc- INDEXING TERMS: alleles • electrophoresis • gene insertions ing is considered the gold standard and remains the • gene deletions • polymerase chain reaction definitive procedure for the detection of mutations so far.
    [Show full text]
  • And IRAK1 Knock-In Mice Production Defined by the Study of IRAK2 Two
    Two Phases of Inflammatory Mediator Production Defined by the Study of IRAK2 and IRAK1 Knock-in Mice This information is current as Eduardo Pauls, Sambit K. Nanda, Hilary Smith, Rachel of September 29, 2021. Toth, J. Simon C. Arthur and Philip Cohen J Immunol 2013; 191:2717-2730; Prepublished online 5 August 2013; doi: 10.4049/jimmunol.1203268 http://www.jimmunol.org/content/191/5/2717 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2013/08/06/jimmunol.120326 Material 8.DC1 http://www.jimmunol.org/ References This article cites 55 articles, 33 of which you can access for free at: http://www.jimmunol.org/content/191/5/2717.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 29, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *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 Errata An erratum has been published regarding this article. Please see next page or: /content/191/10/5317.full.pdf 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 © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606.
    [Show full text]
  • Activity Across Human Cell Types Different Requirements for IRAK1/4
    Immune Complex-Mediated Cell Activation from Systemic Lupus Erythematosus and Rheumatoid Arthritis Patients Elaborate Different Requirements for IRAK1/4 Kinase This information is current as Activity across Human Cell Types of October 7, 2021. Eugene Y. Chiang, Xin Yu and Jane L. Grogan J Immunol 2011; 186:1279-1288; Prepublished online 15 December 2010; doi: 10.4049/jimmunol.1002821 Downloaded from http://www.jimmunol.org/content/186/2/1279 Supplementary http://www.jimmunol.org/content/suppl/2010/12/15/jimmunol.100282 Material 1.DC1 http://www.jimmunol.org/ References This article cites 53 articles, 23 of which you can access for free at: http://www.jimmunol.org/content/186/2/1279.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on October 7, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *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 All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Immune Complex-Mediated Cell Activation from Systemic Lupus Erythematosus and Rheumatoid Arthritis Patients Elaborate Different Requirements for IRAK1/4 Kinase Activity across Human Cell Types Eugene Y.
    [Show full text]
  • Snapshot: Pathways of Antiviral Innate Immunity Lijun Sun, Siqi Liu, and Zhijian J
    SnapShot: Pathways of Antiviral Innate Immunity Lijun Sun, Siqi Liu, and Zhijian J. Chen Department of Molecular Biology, HHMI, UT Southwestern Medical Center, Dallas, TX 75390-9148, USA 436 Cell 140, February 5, 2010 ©2010 Elsevier Inc. DOI 10.1016/j.cell.2010.01.041 See online version for legend and references. SnapShot: Pathways of Antiviral Innate Immunity Lijun Sun, Siqi Liu, and Zhijian J. Chen Department of Molecular Biology, HHMI, UT Southwestern Medical Center, Dallas, TX 75390-9148, USA Viral diseases remain a challenging global health issue. Innate immunity is the first line of defense against viral infection. A hallmark of antiviral innate immune responses is the production of type 1 interferons and inflammatory cytokines. These molecules not only rapidly contain viral infection by inhibiting viral replication and assembly but also play a crucial role in activating the adaptive immune system to eradicate the virus. Recent research has unveiled multiple signaling pathways that detect viral infection, with several pathways detecting the presence of viral nucleic acids. This SnapShot focuses on innate signaling pathways triggered by viral nucleic acids that are delivered to the cytosol and endosomes of mammalian host cells. Cytosolic Pathways Many viral infections, especially those of RNA viruses, result in the delivery and replication of viral RNA in the cytosol of infected host cells. These viral RNAs often contain 5′-triphosphate (5′-ppp) and panhandle-like secondary structures composed of double-stranded segments. These features are recognized by members of the RIG-I-like Recep- tor (RLR) family, which includes RIG-I, MDA5, and LGP2 (Fujita, 2009; Yoneyama et al., 2004).
    [Show full text]