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CCR PEDIATRIC ONCOLOGY SERIES CCR Pediatric Oncology Series Recommendations for Childhood Cancer Screening and Surveillance in DNA Repair Disorders Michael F. Walsh1, Vivian Y. Chang2, Wendy K. Kohlmann3, Hamish S. Scott4, Christopher Cunniff5, Franck Bourdeaut6, Jan J. Molenaar7, Christopher C. Porter8, John T. Sandlund9, Sharon E. Plon10, Lisa L. Wang10, and Sharon A. Savage11 Abstract DNA repair syndromes are heterogeneous disorders caused by around the world to discuss and develop cancer surveillance pathogenic variants in genes encoding proteins key in DNA guidelines for children with cancer-prone disorders. Herein, replication and/or the cellular response to DNA damage. The we focus on the more common of the rare DNA repair dis- majority of these syndromes are inherited in an autosomal- orders: ataxia telangiectasia, Bloom syndrome, Fanconi ane- recessive manner, but autosomal-dominant and X-linked reces- mia, dyskeratosis congenita, Nijmegen breakage syndrome, sive disorders also exist. The clinical features of patients with DNA Rothmund–Thomson syndrome, and Xeroderma pigmento- repair syndromes are highly varied and dependent on the under- sum. Dedicated syndrome registries and a combination of lying genetic cause. Notably, all patients have elevated risks of basic science and clinical research have led to important in- syndrome-associated cancers, and many of these cancers present sights into the underlying biology of these disorders. Given the in childhood. Although it is clear that the risk of cancer is rarity of these disorders, it is recommended that centralized increased, there are limited data defining the true incidence of centers of excellence be involved directly or through consulta- cancer and almost no evidence-based approaches to cancer tion in caring for patients with heritable DNA repair syn- surveillance in patients with DNA repair disorders. -
"Protein Quaternary Structure: Subunit&Ndash;Subunit
Protein Quaternary Secondary article Structure: Subunit–Subunit Article Contents . Introduction Interactions . Quaternary Structure Assembly . Folding and Function Susan Jones, University College, London, England . Protein–Protein Recognition Sites . Concluding Remarks Janet M Thornton, University College, London, England The quaternary structure of proteins is the highest level of structural organization observed in these macromolecules. The multimeric proteins that result from quaternary structure formation involve the association of protein subunits through hydrophobic and electrostatic interactions. Protein quaternary structure has important implications for protein folding and function. Introduction from, other components. Using these definitions, the Proteins are organized into a structural hierarchy. The haemoglobin tetramer (comprised of two a and two b polypeptide chain at the primary structural level comprises polypeptide chains) is defined as an oligomer consisting of a linear, noncovalently linked amino acid residue se- two protomers, each consisting of two monomers, i.e. one a quence. Secondary structure is the level at which the linear and one b polypeptide chain. The definition of a subunit sequences aggregate to form structural motifs such as allows the term to be used for either the a-orb-monomer, helices and sheets. The tertiary structure is formed by or for the ab-protomer. The term multimer is also widely packing of the secondary structural elements into one or used in the literature and is defined here as a protein with a more compact globular domains. In many cases proteins finite number of subunits that need not be identical. are composed of only a single polypeptide chain that has The quaternary nature of some proteins was first tertiary structure as its highest level of organization, e.g. -
Understanding the Role of Rad52 in Homologous Recombination for Therapeutic Advancement
Author Manuscript Published OnlineFirst on October 15, 2012; DOI: 10.1158/1078-0432.CCR-11-3150 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. The Role of Rad52 in Homologous Recombination MOLECULAR PATHWAYS: Understanding the role of Rad52 in homologous recombination for therapeutic advancement Benjamin H. Lok 1,2 and Simon N. Powell 1 1 Memorial Sloan-Kettering Cancer Center, New York, NY 2 New York University School of Medicine, New York, NY Corresponding author: Simon N. Powell, MD PhD Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY Mailing address: 1250 1st Avenue, Box 33, New York, NY 10065 Telephone: 212-639-6072 Facsimile: 212-794-3188 E-mail: [email protected] Conflicts of interest. The authors have no potential conflict of interest to report. 1 Downloaded from clincancerres.aacrjournals.org on September 26, 2021. © 2012 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 15, 2012; DOI: 10.1158/1078-0432.CCR-11-3150 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. The Role of Rad52 in Homologous Recombination Table of Contents Abstract ......................................................................................................................................................... 2 Background .................................................................................................................................................. -
Use of the XRCC2 Promoter for in Vivo Cancer Diagnosis and Therapy
Chen et al. Cell Death and Disease (2018) 9:420 DOI 10.1038/s41419-018-0453-9 Cell Death & Disease ARTICLE Open Access Use of the XRCC2 promoter for in vivo cancer diagnosis and therapy Yu Chen1,ZhenLi1,ZhuXu1, Huanyin Tang1,WenxuanGuo1, Xiaoxiang Sun1,WenjunZhang1, Jian Zhang2, Xiaoping Wan1, Ying Jiang1 and Zhiyong Mao 1 Abstract The homologous recombination (HR) pathway is a promising target for cancer therapy as it is frequently upregulated in tumors. One such strategy is to target tumors with cancer-specific, hyperactive promoters of HR genes including RAD51 and RAD51C. However, the promoter size and the delivery method have limited its potential clinical applications. Here we identified the ~2.1 kb promoter of XRCC2, similar to ~6.5 kb RAD51 promoter, as also hyperactivated in cancer cells. We found that XRCC2 expression is upregulated in nearly all types of cancers, to a degree comparable to RAD51 while much higher than RAD51C. Further study demonstrated that XRCC2 promoter is hyperactivated in cancer cell lines, and diphtheria toxin A (DTA) gene driven by XRCC2 promoter specifically eliminates cancer cells. Moreover, lentiviral vectors containing XRCC2 promoter driving firefly luciferase or DTA were created and applied to subcutaneous HeLa xenograft mice. We demonstrated that the pXRCC2-luciferase lentivirus is an effective tool for in vivo cancer visualization. Most importantly, pXRCC2-DTA lentivirus significantly inhibited the growth of HeLa xenografts in comparison to the control group. In summary, our results strongly indicate that virus-mediated delivery of constructs built upon the XRCC2 promoter holds great potential for tumor diagnosis and therapy. -
Biochemistry of Recombinational DNA Repair
BiochemistryBiochemistry ofof RecombinationalRecombinational DNADNA Repair:Repair: CommonCommon ThemesThemes StephenStephen KowalczykowskiKowalczykowski UniversityUniversity ofof California,California, DavisDavis •Overview of genetic recombination and its function. •Biochemical mechanism of recombination in Eukaryotes. •Universal features: steps common to all organisms. HomologousHomologous RecombinationRecombination AB ab+ Ab aB+ Genesis:Genesis: ScienceScience andand thethe BeginningBeginning ofof TimeTime How does recombination occur? And why? DNADNA ReplicationReplication CanCan ProduceProduce dsDNAdsDNA BreaksBreaks andand ssDNAssDNA GapsGaps RepairRepair ofof DNADNA BreaksBreaks Non-Homologous Homologous End-Joining (NHEJ) Recombination (HR) (error-prone) (error-free) dsDNA Break-Repair Synthesis-Dependent ssDNA Annealing (DSBR) Strand-Annealing (SSA) (SDSA) DoubleDouble--StrandStrand DNADNA BreakBreak RepairRepair 5' 3' 3' 5' + 3' 5' 5' 3' Initiation 1 5' 3' Helicase and/or 3' 5' nuclease 2 5' 3' 3' 3' 3' 5' Homologous Pairing & DNA Strand 3 Exchange 3' 5' 5' 3' RecA-like protein 5' 3' Accessory proteins 3' 3' 5' 4 3' 5' 5' 3' 5' 3' 3' 5' DNA Heteroduplex 5 Branch migration Extension proteins 3' 5' 5' 3' 5' 3' 3' 5' Resolution 6 Resolvase Spliced Patched ProteinsProteins InvolvedInvolved inin RecombinationalRecombinational DNADNA RepairRepair E. coli Archaea S. cerevisiae Human Initiation RecBCD -- -- -- SbcCD Mre11/Rad50 Mre11/Rad50/Xrs2 Mre11/Rad50/Nbs1 RecQ Sgs1(?) Sgs1(?) RecQ1/4/5 LM/WRN(?) RecJ -- ExoI ExoI UvrD -- Srs2 -- Homologous Pairing RecA RadA Rad51 Rad51 & DNA Strand SSB SSB/RPA RPA RPA Exchange RecF(R) RadB/B2/B3(?) Rad55/57 Rad51B/C/D/Xrcc2/3 RecO -- Rad52 Rad52 -- -- Rad59 -- -- Rad54 Rad54/Rdh54 Rad54/54B Brca2 DNA Heteroduplex RuvAB Rad54 Rad54 Rad54 Extension RecG -- -- RecQ Sgs1(?) RecQL/4/5 LM/WRN(?) Resolution RuvC Hjc/Hje -- -- -- -- Mus81/Mms4 Mus81/Mms4 ProteinsProteins InvolvedInvolved inin RecombinationalRecombinational DNADNA RepairRepair 5' 3' E. -
Biochemistry-2018-Hartman.Pdf
Article Cite This: Biochemistry 2019, 58, 1527−1538 pubs.acs.org/biochemistry Experimental Evaluation of Coevolution in a Self-Assembling Particle Emily C. Hartman,† Marco J. Lobba,† Andrew H. Favor,† Stephanie A. Robinson,† Matthew B. Francis,*,†,‡ and Danielle Tullman-Ercek*,§ † Department of Chemistry, University of California, Berkeley, California 94720-1460, United States ‡ Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States § Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208-3120, United States *S Supporting Information ABSTRACT: Protein evolution occurs via restricted evolutionary paths that are influenced by both previous and subsequent mutations. This effect, termed epistasis, is critical in population genetics, drug resistance, and immune escape; however, the effect of epistasis on the level of protein fitness is less well characterized. We generated and characterized a 6615-member library of all two-amino acid combinations in a highly mutable loop of a virus-like particle. This particle is a model of protein self- assembly and a promising vehicle for drug delivery and imaging. In addition to characterizing the effect of all double mutants on assembly, thermostability, and acid stability, we observed many instances of epistasis, in which combinations of mutations are either more deleterious or more beneficial than expected. These results were used to generate rules governing the effects of multiple mutations on the self-assembly of the virus-like particle. rotein evolution occurs through complex pathways, often have a significant impact on biotechnology in the coming involving nonintuitive leaps between functional var- decades.23,24 To maximize this potential, it is important to P − iants.1 3 These paths include local minima and maxima, in understand how non-native functions can be hindered by which the effect of a given mutation depends entirely on the unanticipated epistatic effects. -
Distinct Pathways of Homologous Recombination Controlled by the SWS1–SWSAP1–SPIDR Complex ✉ Rohit Prakash 1 , Thomas Sandoval1, Florian Morati 2, Jennifer A
ARTICLE https://doi.org/10.1038/s41467-021-24205-6 OPEN Distinct pathways of homologous recombination controlled by the SWS1–SWSAP1–SPIDR complex ✉ Rohit Prakash 1 , Thomas Sandoval1, Florian Morati 2, Jennifer A. Zagelbaum3, Pei-Xin Lim 1, Travis White1, Brett Taylor 1, Raymond Wang1, Emilie C. B. Desclos4, Meghan R. Sullivan5, Hayley L. Rein5, Kara A. Bernstein 5, Przemek M. Krawczyk4, Jean Gautier3, Mauro Modesti 2, Fabio Vanoli 1 & ✉ Maria Jasin 1 1234567890():,; Homology-directed repair (HDR), a critical DNA repair pathway in mammalian cells, is complex, leading to multiple outcomes with different impacts on genomic integrity. However, the factors that control these different outcomes are often not well understood. Here we show that SWS1–SWSAP1-SPIDR controls distinct types of HDR. Despite their requirement for stable assembly of RAD51 recombinase at DNA damage sites, these proteins are not essential for intra-chromosomal HDR, providing insight into why patients and mice with mutations are viable. However, SWS1–SWSAP1-SPIDR is critical for inter-homolog HDR, the first mitotic factor identified specifically for this function. Furthermore, SWS1–SWSAP1-SPIDR drives the high level of sister-chromatid exchange, promotes long-range loss of hetero- zygosity often involved with cancer initiation, and impels the poor growth of BLM helicase- deficient cells. The relevance of these genetic interactions is evident as SWSAP1 loss prolongs Blm-mutant embryo survival, suggesting a possible druggable target for the treat- ment of Bloom syndrome. 1 Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. 2 Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France. -
Role of Transglutaminase 2 in Cell Death, Survival, and Fibrosis
cells Review Role of Transglutaminase 2 in Cell Death, Survival, and Fibrosis Hideki Tatsukawa * and Kiyotaka Hitomi Cellular Biochemistry Laboratory, Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Nagoya 464-8601, Aichi, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-52-747-6808 Abstract: Transglutaminase 2 (TG2) is a ubiquitously expressed enzyme catalyzing the crosslink- ing between Gln and Lys residues and involved in various pathophysiological events. Besides this crosslinking activity, TG2 functions as a deamidase, GTPase, isopeptidase, adapter/scaffold, protein disulfide isomerase, and kinase. It also plays a role in the regulation of hypusination and serotonylation. Through these activities, TG2 is involved in cell growth, differentiation, cell death, inflammation, tissue repair, and fibrosis. Depending on the cell type and stimulus, TG2 changes its subcellular localization and biological activity, leading to cell death or survival. In normal unstressed cells, intracellular TG2 exhibits a GTP-bound closed conformation, exerting prosurvival functions. However, upon cell stimulation with Ca2+ or other factors, TG2 adopts a Ca2+-bound open confor- mation, demonstrating a transamidase activity involved in cell death or survival. These functional discrepancies of TG2 open form might be caused by its multifunctional nature, the existence of splicing variants, the cell type and stimulus, and the genetic backgrounds and variations of the mouse models used. TG2 is also involved in the phagocytosis of dead cells by macrophages and in fibrosis during tissue repair. Here, we summarize and discuss the multifunctional and controversial Citation: Tatsukawa, H.; Hitomi, K. roles of TG2, focusing on cell death/survival and fibrosis. -
Dimerization and Domain Swapping in G-Protein-Coupled Receptors: a Computational Study Paul R
Dimerization and Domain Swapping in G-Protein-Coupled Receptors: A Computational Study Paul R. Gouldson, Ph.D., Christopher Higgs, Ph.D., Richard E. Smith, B.Sc., Mark K. Dean, B.Sc., George V. Gkoutos, M.Sc., and Christopher A. Reynolds, Ph.D. In recent years there has been an increasing number of swapped dimers and contact dimers as the models used were reports describing G protein-coupled receptor (GPCR) restricted to the helical part of the receptor. However, it is dimerization and heterodimerization. However, the evidence proposed that for the purpose of signalling, the domain on the nature of the dimers and their role in GPCR swapped dimer and the corresponding contact dimer are activation is inconclusive. Consequently, we present here a equivalent. The evolutionary trace analysis suggests that review of our computational studies on G protein-coupled every GPCR family and subfamily (for which sufficient receptor dimerization and domain swapping. The studies sequence data is available) has the potential to dimerize described include molecular dynamics simulations on through this common functional site on helices 5 and 6. The receptor monomers and dimers in the absence of ligand, in evolutionary trace results on the G protein are briefly the presence of an agonist, and in the presence of an described and these are consistent with GPCR dimerization. antagonist (or more precisely an inverse agonist). Two In addition to the functional site on helices 5 and 6, the distinct sequence-based approaches to studying protein evolutionary trace analysis identified a second functional interfaces are also described, namely correlated mutation site on helices 2 and 3. -
Genetic Polymorphism of DNA Repair Genes (XRCC1, XRCC2 & XRCC3)
International Journal of Health Sciences and Research www.ijhsr.org ISSN: 2249-9571 Original Research Article Genetic Polymorphism of DNA Repair Genes (XRCC1, XRCC2 & XRCC3) in Breast Cancer Patients from Rural Maharashtra Kailas D. Datkhile1, Suresh J. Bhosale2, Madhavi N. Patil1, Tejasvi S. Khamkar1, Pratik P. Durgawale1, Satish V. Kakade3 1Molecular & Genetic Laboratory, 2Department of Surgery, 3Department of Preventive and Social Medicine, Krishna Institute of Medical Sciences University, Taluka-Karad, Dist-Satara, Pin-415 110 Maharashtra, India Corresponding Author: Kailas D. Datkhile Received: 17/01/2017 Revised: 28/01/2017 Accepted: 30/01/2017 ABSTRACT Background & Objectives: Breast cancer is a major concern of health risk, moreover the leading cause of cancer causing deaths in women of rural parts of India. In this study, we focused to determine the frequency of polymorphisms in DNA repair genes, XRCC1 at codon (cd) 194, cd 280, cd 399, XRCC 2 at cd 188 and XRCC3 at cd 241 to evaluate their role in breast cancer risk. Methods: We used polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to analyze XRCC genes polymorphisms in 150 breast cancer women and 200 age matched disease-free controls. Results: The result from our study showed that allele frequencies of selected genes were not statistically different between the groups for XRCC1 Trp194, Gln399, XRCC2 His188 and XRCC3 Met241. XRCC1 His280 (OR= 4.14; 95% CI= (2.63-6.53); p= <0.0001) genotype significantly increased the risk of breast cancer. Interpretation & conclusions: This study indicates that polymorphisms in cd280 of XRCC1 gene could play a role in modifying genetic susceptibility of individuals towards breast cancer among women from rural Maharashtra. -
Systematic Characterization of Pan-Cancer Mutation Clusters
Research Collection Journal Article Systematic characterization of pan-cancer mutation clusters Author(s): Buljan, Marija; Blattmann, Peter; Aebersold, Ruedi; Boutros, Michael Publication Date: 2018-03-01 Permanent Link: https://doi.org/10.3929/ethz-b-000256182 Originally published in: Molecular Systems Biology 14(3), http://doi.org/10.15252/msb.20177974 Rights / License: Creative Commons Attribution 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Published online: March 23, 2018 Article Systematic characterization of pan-cancer mutation clusters Marija Buljan1,2 , Peter Blattmann1 , Ruedi Aebersold1,3,* & Michael Boutros2,4,5,** Abstract or single point mutations. Eventually, they all lead to changes in the expression levels or to altered functions of cancer driver genes and Cancer genome sequencing has shown that driver genes can often their products. Analysis of different cancer genomics datasets has be distinguished not only by the elevated mutation frequency but further underscored a high degree of heterogeneity in the mutation also by specific nucleotide positions that accumulate changes at a frequency and spectrum among different cancer types (Garraway & high rate. However, properties associated with a residue’s poten- Lander, 2013; Lawrence et al, 2013) and uncovered a long tail of tial to drive tumorigenesis when mutated have not yet been low-frequency driver mutations (Garraway & Lander, 2013). As a systematically investigated. Here, using a novel methodological corollary, in spite of the great progress in charting mutational events approach, we identify and characterize a compendium of 180 that define different cancer types, the task to distinguish driver and hotspot residues within 160 human proteins which occur with a passenger mutations in an individual genome remains a formidable significant frequency and are likely to have functionally relevant challenge. -
FANCG Promotes Formation of a Newly Identified Protein Complex
Oncogene (2008) 27, 3641–3652 & 2008 Nature Publishing Group All rights reserved 0950-9232/08 $30.00 www.nature.com/onc ORIGINAL ARTICLE FANCG promotes formation of a newly identified protein complex containing BRCA2, FANCD2 and XRCC3 JB Wilson1, K Yamamoto2,9, AS Marriott1, S Hussain3, P Sung4, ME Hoatlin5, CG Mathew6, M Takata2,10, LH Thompson7, GM Kupfer8 and NJ Jones1 1Molecular Oncology and Stem Cell Research Group, School of Biological Sciences, University of Liverpool, Liverpool, UK; 2Department of Immunology and Medical Genetics, Kawasaki Medical School, Kurashiki, Okayama, Japan; 3Department of Biochemistry, University of Cambridge, Cambridge, UK; 4Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; 5Division of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland, OR, USA; 6Department of Medical and Molecular Genetics, King’s College London School of Medicine, Guy’s Hospital, London, UK; 7Biosciences and Biotechnology Division, L441, Lawrence Livermore National Laboratory, Livermore, CA, USA and 8Department of Pediatrics, Division of Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA Fanconi anemia (FA) is a human disorder characterized intricate interface between FANC and HRR proteins in by cancer susceptibility and cellular sensitivity to DNA maintaining chromosome stability. crosslinks and other damages. Thirteen complementation Oncogene (2008) 27, 3641–3652; doi:10.1038/sj.onc.1211034; groups and genes are identified, including BRCA2, which published online 21 January 2008 is defective in the FA-D1 group. Eight of the FA proteins, including FANCG, participate in a nuclear core complex Keywords: Fanconi anemia; ATR; interstrand cross- that is required for the monoubiquitylation of FANCD2 links; DNA repair; RAD51 paralog; replication restart; and FANCI.