101
|
Marrack P, Krovi SH, Silberman D, White J, Kushnir E, Nakayama M, Crooks J, Danhorn T, Leach S, Anselment R, Scott-Browne J, Gapin L, Kappler J. The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor. eLife 2017; 6:30918. [PMID: 29148973 PMCID: PMC5701794 DOI: 10.7554/elife.30918] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/16/2017] [Indexed: 01/24/2023] Open
Abstract
Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of two different T cell receptor β chains and various MHC alleles, we show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor α and β chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 of the T cell receptor α chain. Thus, in addition to determining specificity for antigen, the non germline encoded elements of T cell receptors may help the proteins cope with the extremely polymorphic nature of major histocompatibility complex products within the species.
Collapse
Affiliation(s)
- Philippa Marrack
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Sai Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Daniel Silberman
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Janice White
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Eleanor Kushnir
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States.,Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, United States
| | - James Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Thomas Danhorn
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Sonia Leach
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Randy Anselment
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | | | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - John Kappler
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| |
Collapse
|
102
|
Han J, Ruan C, Huen MSY, Wang J, Xie A, Fu C, Liu T, Huang J. BRCA2 antagonizes classical and alternative nonhomologous end-joining to prevent gross genomic instability. Nat Commun 2017; 8:1470. [PMID: 29133916 PMCID: PMC5684403 DOI: 10.1038/s41467-017-01759-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/13/2017] [Indexed: 12/27/2022] Open
Abstract
BRCA2-deficient cells exhibit gross genomic instability, but the underlying mechanisms are not fully understood. Here we report that inactivation of BRCA2 but not RAD51 destabilizes RPA-coated single-stranded DNA (ssDNA) structures at resected DNA double-strand breaks (DSBs) and greatly enhances the frequency of nuclear fragmentation following cell exposure to DNA damage. Importantly, these BRCA2-associated deficits are fueled by the aberrant activation of classical (c)- and alternative (alt)- nonhomologous end-joining (NHEJ), and rely on the well-defined DNA damage signaling pathway involving the pro-c-NHEJ factor 53BP1 and its downstream effector RIF1. We further show that the 53BP1–RIF1 axis promotes toxic end-joining events via the retention of Artemis at DNA damage sites. Accordingly, loss of 53BP1, RIF1, or Artemis prolongs the stability of RPA-coated DSB intermediates in BRCA2-deficient cells and restores nuclear integrity. We propose that BRCA2 antagonizes 53BP1, RIF1, and Artemis-dependent c-NHEJ and alt-NHEJ to prevent gross genomic instability in a RAD51-independent manner. The genomic instability phenotype characteristic of BRCA2-deficient cells is not fully mechanistically understood. Here the authors show BRCA2 inactivation destabilizes RPA-coated single-stranded DNA and leads to toxic non homologous end-joining events.
Collapse
Affiliation(s)
- Jinhua Han
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chunyan Ruan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Michael S Y Huen
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Anyong Xie
- Institute of Translational Medicine, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chun Fu
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Ting Liu
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
103
|
Affiliation(s)
- Guido Keijzers
- From the Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen
| | - Daniela Bakula
- From the Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen
| | - Morten Scheibye-Knudsen
- From the Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen
| |
Collapse
|
104
|
Yazdani R, Abolhassani H, Tafaroji J, Azizi G, Hamidieh AA, Chou J, Geha RS, Aghamohammadi A. Cernunnos deficiency associated with BCG adenitis and autoimmunity: First case from the national Iranian registry and review of the literature. Clin Immunol 2017; 183:201-206. [DOI: 10.1016/j.clim.2017.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/15/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
|
105
|
Efficient repair of DNA double strand breaks in individuals from high level natural radiation areas of Kerala coast, south-west India. Mutat Res 2017; 806:39-50. [PMID: 28963924 DOI: 10.1016/j.mrfmmm.2017.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 08/14/2017] [Accepted: 09/11/2017] [Indexed: 11/21/2022]
Abstract
High level natural radiation areas (HLNRA) of Kerala coastal strip (55km long and 0.5km wide) in southwest India exhibit wide variations in the level of background dose (< 1.0-45.0mGy/year) due to thorium deposits in the beach sand. The areas with ≤1.5mGy/year are considered as normal level natural radiation area (NLNRA), whereas areas with >1.5mGy/year are HLNRA. Individuals belonging to HLNRA were stratified into two groups, Low dose group (LDG: 1.51-5.0mGy/year) and high dose group (HDG: >5.0mGy/year). The mean annual dose received by the individuals from NLNRA, LDG and HDG was 1.3±0.1, 2.7±0.9 and 9.4±2.3mGy/year, respectively. Induction and repair of DNA double strand breaks (DSBs) in terms of gamma-H2AX positive cells were analysed in peripheral blood mononuclear cells (PBMCs) using flow cytometry. Induction of DSBs was studied at low (0.25Gy) and high challenge doses (1.0 and 2.0Gy) of gamma radiation in 78 individuals {NLNRA, N=23; HLNRA (LDG, N=21 and HDG, N=34)}. Repair kinetics of DSBs were evaluated in PBMCs of 30 individuals belonging to NLNRA (N=8), LDG (N=7) and HDG (N=15) at low (0.25Gy) and high doses (2.0Gy) of gamma radiation. Transcription profile of DNA damage response (DDR) and DSB repair genes involved in non-homologous end joining (NHEJ) and homologous recombination repair (HRR) pathways was analysed after a challenge dose of 2.0Gy in PBMCs of NLNRA (N=10) and HDG, HLNRA (N=10) group. Our results revealed significantly lower induction and efficient repair of DSBs in HLNRA groups as compared to NLNRA. Transcription profile of DCLRE1C, XRCC4, NBS1 and CDK2 showed significant up-regulation (p≤0.05) in HDG at a challenge dose of 2.0Gy indicating active involvement of DDR and DSB repair pathways. In conclusion, lower induction and efficient repair of DNA DSBs in HLNRA groups is suggestive of an in vivo radio-adaptive response due to priming effect of chronic low dose radiation prevailing in this area.
Collapse
|
106
|
Charlier C, Bouvignies G, Pelupessy P, Walrant A, Marquant R, Kozlov M, De Ioannes P, Bolik-Coulon N, Sagan S, Cortes P, Aggarwal AK, Carlier L, Ferrage F. Structure and Dynamics of an Intrinsically Disordered Protein Region That Partially Folds upon Binding by Chemical-Exchange NMR. J Am Chem Soc 2017; 139:12219-12227. [PMID: 28780862 DOI: 10.1021/jacs.7b05823] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, yet specific, interactions with a variety of protein partners. Often, if not always, interactions with a protein partner lead to partial folding of the IDR. Characterizing the conformational space of such complexes is challenging: in solution-state NMR, signals of the IDR in the interacting region become broad, weak, and often invisible, while X-ray crystallography only provides information on fully ordered regions. There is thus a need for a simple method to characterize both fully and partially ordered regions in the bound state of IDPs. Here, we introduce an approach based on monitoring chemical exchange by NMR to investigate the state of an IDR that folds upon binding through the observation of the free state of the protein. Structural constraints for the bound state are obtained from chemical shifts, and site-specific dynamics of the bound state are characterized by relaxation rates. The conformation of the interacting part of the IDR was determined and subsequently docked onto the structure of the folded partner. We apply the method to investigate the interaction between the disordered C-terminal region of Artemis and the DNA binding domain of Ligase IV. We show that we can accurately reproduce the structure of the core of the complex determined by X-ray crystallography and identify a broader interface. The method is widely applicable to the biophysical investigation of complexes of disordered proteins and folded proteins.
Collapse
Affiliation(s)
- Cyril Charlier
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Astrid Walrant
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Rodrigue Marquant
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Mikhail Kozlov
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Pablo De Ioannes
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Sandrine Sagan
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Patricia Cortes
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States.,Department of Molecular, Cellular and Biomedical Science, CUNY School of Medicine, City College of New York , 160 Convent Avenue, New York, New York 10031, United States
| | - Aneel K Aggarwal
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Ludovic Carlier
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, Département de chimie, École normale supérieure, UPMC Université Paris 06, CNRS, PSL Research University , 24 rue Lhomond, Paris 75005, France.,Sorbonne Universités, UPMC Université Paris 06, École normale supérieure, CNRS, Laboratoire des Biomolécules (LBM) , Paris 75005, France
| |
Collapse
|
107
|
Cryo-EM structure of human DNA-PK holoenzyme. Cell Res 2017; 27:1341-1350. [PMID: 28840859 DOI: 10.1038/cr.2017.110] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/22/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023] Open
Abstract
DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the major DNA repair pathway. Here, we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6 Å resolution. In the complex structure, DNA-PKcs, KU70, KU80 and DNA duplex form a 650-kDa heterotetramer with 1:1:1:1 stoichiometry. The N-terminal α-solenoid (∼2 800 residues) of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/80-DNA. DNA-PKcs and KU70/80 together form a DNA-binding tunnel, which cradles ∼30-bp DNA and prevents sliding inward of DNA-PKcs along with DNA duplex, suggesting a mechanism by which the broken DNA end is protected from unnecessary processing. Structural and biochemical analyses indicate that KU70/80 and DNA coordinately induce conformational changes of DNA-PKcs and allosterically stimulate its kinase activity. We propose a model for activation of DNA-PKcs in which allosteric signals are generated upon DNA-PK holoenzyme formation and transmitted to the kinase domain through N-terminal HEAT repeats and FAT domain of DNA-PKcs. Our studies suggest a mechanism for recognition and protection of broken DNA ends and provide a structural basis for understanding the activation of DNA-PKcs and DNA-PK-mediated NHEJ pathway.
Collapse
|
108
|
Abstract
Transfer of gene-corrected autologous hematopoietic stem cells in patients with primary immunodeficiencies has emerged as a new therapeutic approach. Patients with various conditions lacking a suitable donor have been treated with retroviral vectors and a gene-addition strategy. Initial promising results were shadowed by the occurrence of malignancies in some of these patients. Current trials, developed in the last decade, use safer viral vectors to overcome the risk of genotoxicity and have led to improved clinical outcomes. This review reflects the progresses made in specific disorders, including adenosine deaminase deficiency, X-linked severe combined immunodeficiency, chronic granulomatous disease, and Wiskott-Aldrich syndrome.
Collapse
|
109
|
Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Mol Cell 2017; 66:801-817. [PMID: 28622525 DOI: 10.1016/j.molcel.2017.05.015] [Citation(s) in RCA: 1138] [Impact Index Per Article: 162.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/09/2023]
Abstract
In vertebrate cells, the DNA damage response is controlled by three related kinases: ATM, ATR, and DNA-PK. It has been 20 years since the cloning of ATR, the last of the three to be identified. During this time, our understanding of how these kinases regulate DNA repair and associated events has grown profoundly, although major questions remain unanswered. Here, we provide a historical perspective of their discovery and discuss their established functions in sensing and responding to genotoxic stress. We also highlight what is known regarding their structural similarities and common mechanisms of regulation, as well as emerging non-canonical roles and how our knowledge of ATM, ATR, and DNA-PK is being translated to benefit human health.
Collapse
Affiliation(s)
- Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
| |
Collapse
|
110
|
Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 2017; 18:495-506. [PMID: 28512351 DOI: 10.1038/nrm.2017.48] [Citation(s) in RCA: 963] [Impact Index Per Article: 137.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks (DSBs) are the most dangerous type of DNA damage because they can result in the loss of large chromosomal regions. In all mammalian cells, DSBs that occur throughout the cell cycle are repaired predominantly by the non-homologous DNA end joining (NHEJ) pathway. Defects in NHEJ result in sensitivity to ionizing radiation and the ablation of lymphocytes. The NHEJ pathway utilizes proteins that recognize, resect, polymerize and ligate the DNA ends in a flexible manner. This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations. In this Review, we discuss the most recent findings regarding the relative involvement of the different NHEJ proteins in the repair of various DNA-end configurations. We also discuss the shunting of DNA-end repair to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA) and the relevance of these different pathways to human disease.
Collapse
|
111
|
Mosse I, Kilchevsky A, Nikolova N, Zhelev N. Some problems and errors in cytogenetic biodosimetry. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2016.1259018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Irma Mosse
- National Academy of Sciences, Institute of Genetics and Cytology, Minsk, Belarus
| | - Alexander Kilchevsky
- National Academy of Sciences, Institute of Genetics and Cytology, Minsk, Belarus
| | - Nevena Nikolova
- Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Nikolai Zhelev
- Centre for Molecular Cellular Biosensor Research (CMCBR), School of Science, Engineering and Technology, Abertay University, Dundee, Scotland, UK
| |
Collapse
|
112
|
Chirgadze DY, Ascher DB, Blundell TL, Sibanda BL. DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage. Methods Enzymol 2017; 592:145-157. [PMID: 28668119 DOI: 10.1016/bs.mie.2017.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is central to the regulation of the DNA damage response and repair through nonhomologous end joining. The structure has proved challenging due to its large size and multiple HEAT repeats. We have recently reported crystals of selenomethionine-labeled DNA-PKcs complexed with native KU80ct194 (KU80 residues 539-732) diffracting to 4.3Å resolution. The novel use of crystals of selenomethionine-labeled protein expressed in HeLa cells has facilitated the use of single anomalous X-ray scattering of this 4128 amino acid, multiple HEAT-repeat structure. The monitoring of the selenomethionines in the anomalous-difference density map has allowed the checking of the amino acid residue registration in the electron density, and the labeling of the Ku-C-terminal moiety with selenomethionine has further allowed its identification in the structure of the complex with DNA-PKcs. The crystal structure defines a stage on which many of the components assemble and regulate the kinase activity through modulating the conformation and allosteric regulation of kinase activity.
Collapse
|
113
|
Outcome of hematopoietic cell transplantation for DNA double-strand break repair disorders. J Allergy Clin Immunol 2017; 141:322-328.e10. [PMID: 28392333 DOI: 10.1016/j.jaci.2017.02.036] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/25/2017] [Accepted: 02/06/2017] [Indexed: 01/19/2023]
Abstract
BACKGROUND Rare DNA breakage repair disorders predispose to infection and lymphoreticular malignancies. Hematopoietic cell transplantation (HCT) is curative, but coadministered chemotherapy or radiotherapy is damaging because of systemic radiosensitivity. We collected HCT outcome data for Nijmegen breakage syndrome, DNA ligase IV deficiency, Cernunnos-XRCC4-like factor (Cernunnos-XLF) deficiency, and ataxia-telangiectasia (AT). METHODS fludarabine or less and 40 mg/kg cyclophosphamide or less were used. RESULTS Fifty-five new, 14 updated, and 18 previously published patients were analyzed. Median age at HCT was 48 months (range, 1.5-552 months). Twenty-nine patients underwent transplantation for infection, 21 had malignancy, 13 had bone marrow failure, 13 received pre-emptive transplantation, 5 had multiple indications, and 6 had no information. Twenty-two received MAC, 59 received RIC, and 4 were infused; information was unavailable for 2 patients. Seventy-three of 77 patients with DNA ligase IV deficiency, Cernunnos-XLF deficiency, or Nijmegen breakage syndrome received conditioning. Survival was 53 (69%) of 77 and was worse for those receiving MAC than for those receiving RIC (P = .006). Most deaths occurred early after transplantation, suggesting poor tolerance of conditioning. Survival in patients with AT was 25%. Forty-one (49%) of 83 patients experienced acute GvHD, which was less frequent in those receiving RIC compared with those receiving MAC (26/56 [46%] vs 12/21 [57%], P = .45). Median follow-up was 35 months (range, 2-168 months). No secondary malignancies were reported during 15 years of follow-up. Growth and developmental delay remained after HCT; immune-mediated complications resolved. CONCLUSION RIC HCT resolves DNA repair disorder-associated immunodeficiency. Long-term follow-up is required for secondary malignancy surveillance. Routine HCT for AT is not recommended.
Collapse
|
114
|
Fisher MR, Rivera-Reyes A, Bloch NB, Schatz DG, Bassing CH. Immature Lymphocytes Inhibit Rag1 and Rag2 Transcription and V(D)J Recombination in Response to DNA Double-Strand Breaks. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 198:2943-2956. [PMID: 28213501 PMCID: PMC5360515 DOI: 10.4049/jimmunol.1601639] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/16/2017] [Indexed: 12/26/2022]
Abstract
Mammalian cells have evolved a common DNA damage response (DDR) that sustains cellular function, maintains genomic integrity, and suppresses malignant transformation. In pre-B cells, DNA double-strand breaks (DSBs) induced at Igκ loci by the Rag1/Rag2 (RAG) endonuclease engage this DDR to modulate transcription of genes that regulate lymphocyte-specific processes. We previously reported that RAG DSBs induced at one Igκ allele signal through the ataxia telangiectasia mutated (ATM) kinase to feedback-inhibit RAG expression and RAG cleavage of the other Igκ allele. In this article, we show that DSBs induced by ionizing radiation, etoposide, or bleomycin suppress Rag1 and Rag2 mRNA levels in primary pre-B cells, pro-B cells, and pro-T cells, indicating that inhibition of Rag1 and Rag2 expression is a prevalent DSB response among immature lymphocytes. DSBs induced in pre-B cells signal rapid transcriptional repression of Rag1 and Rag2, causing downregulation of both Rag1 and Rag2 mRNA, but only Rag1 protein. This transcriptional inhibition requires the ATM kinase and the NF-κB essential modulator protein, implicating a role for ATM-mediated activation of canonical NF-κB transcription factors. Finally, we demonstrate that DSBs induced in pre-B cells by etoposide or bleomycin inhibit recombination of Igκ loci and a chromosomally integrated substrate. Our data indicate that immature lymphocytes exploit a common DDR signaling pathway to limit DSBs at multiple genomic locations within developmental stages wherein monoallelic Ag receptor locus recombination is enforced. We discuss the implications of our findings for mechanisms that orchestrate the differentiation of monospecific lymphocytes while suppressing oncogenic Ag receptor locus translocations.
Collapse
Affiliation(s)
- Megan R Fisher
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Adrian Rivera-Reyes
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
- Cancer Biology Program of the Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104; and
| | - Noah B Bloch
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, Howard Hughes Medical Institute, New Haven, CT 06520
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104;
- Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
- Cancer Biology Program of the Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104; and
| |
Collapse
|
115
|
Carrillo J, Calvete O, Pintado-Berninches L, Manguan-García C, Sevilla Navarro J, Arias-Salgado EG, Sastre L, Guenechea G, López Granados E, de Villartay JP, Revy P, Benitez J, Perona R. Mutations in XLF/NHEJ1/Cernunnos gene results in downregulation of telomerase genes expression and telomere shortening. Hum Mol Genet 2017; 26:1900-1914. [DOI: 10.1093/hmg/ddx098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/08/2017] [Indexed: 01/08/2023] Open
|
116
|
The development of T cells from stem cells in mice and humans. Future Sci OA 2017; 3:FSO186. [PMID: 28883990 PMCID: PMC5583695 DOI: 10.4155/fsoa-2016-0095] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/20/2017] [Indexed: 12/19/2022] Open
Abstract
T cells develop from hematopoietic stem cells in the specialized microenvironment of the thymus. The main transcriptional players of T-cell differentiation such as Notch, Tcf-1, Gata3 and Bcl11b have been identified, but their role and regulation are not yet completely understood. In humans, functional experiments on T-cell development have traditionally been rather difficult to perform, but novel in vitro culture systems and in vivo xenograft models have allowed detailed studies on human T-cell development. Recent work has allowed the use of human severe combined immunodeficiency stem cells to unravel developmental checkpoints for human thymocyte development.
Collapse
|
117
|
Tabatabaeifar S, Thomassen M, Larsen MJ, Larsen SR, Kruse TA, Sørensen JA. The subclonal structure and genomic evolution of oral squamous cell carcinoma revealed by ultra-deep sequencing. Oncotarget 2017; 8:16571-16580. [PMID: 28157713 PMCID: PMC5369985 DOI: 10.18632/oncotarget.15014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/24/2017] [Indexed: 01/15/2023] Open
Abstract
Recent studies suggest that head and neck squamous cell carcinomas are very heterogeneous between patients; however the subclonal structure remains unexplored mainly due to studies using only a single biopsy per patient. To deconvolute the clonal structure and describe the genomic cancer evolution, we applied whole-exome sequencing combined with ultra-deep targeted sequencing on oral squamous cell carcinomas (OSCC). From each patient, a set of biopsies was sampled from distinct geographical sites in primary tumor and lymph node metastasis.We demonstrate that the included OSCCs show a high degree of inter-patient heterogeneity but a low degree of intra-tumor heterogeneity. However, some OSCC cancers contain complex subclonal architectures comprising distinct subclones only found in geographically distinct regions of the primary tumors. In several cases we find mutations in the primary tumor that are not present in the lymph node metastasis. We conclude that metastatic potential in our population is acquired early in tumor evolution as evident by the ongoing parallel evolution in several primary tumors.
Collapse
Affiliation(s)
- Siavosh Tabatabaeifar
- Department of Plastic Surgery, Odense University Hospital, Odense, Denmark
- Department of University of Southern Denmark, Institute of Clinical Research, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of University of Southern Denmark, Institute of Clinical Research, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of University of Southern Denmark, Institute of Clinical Research, Odense, Denmark
| | - Stine R Larsen
- Department of Clinical Pathology, Odense University Hospital, Odense, Denmark
- Department of University of Southern Denmark, Institute of Clinical Research, Odense, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of University of Southern Denmark, Institute of Clinical Research, Odense, Denmark
| | - Jens A Sørensen
- Department of Plastic Surgery, Odense University Hospital, Odense, Denmark
- Department of University of Southern Denmark, Institute of Clinical Research, Odense, Denmark
| |
Collapse
|
118
|
Rulten SL, Grundy GJ. Non-homologous end joining: Common interaction sites and exchange of multiple factors in the DNA repair process. Bioessays 2017; 39. [PMID: 28133776 DOI: 10.1002/bies.201600209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-homologous end-joining (NHEJ) is the dominant means of repairing chromosomal DNA double strand breaks (DSBs), and is essential in human cells. Fifteen or more proteins can be involved in the detection, signalling, synapsis, end-processing and ligation events required to repair a DSB, and must be assembled in the confined space around the DNA ends. We review here a number of interaction points between the core NHEJ components (Ku70, Ku80, DNA-PKcs, XRCC4 and Ligase IV) and accessory factors such as kinases, phosphatases, polymerases and structural proteins. Conserved protein-protein interaction sites such as Ku-binding motifs (KBMs), XLF-like motifs (XLMs), FHA and BRCT domains illustrate that different proteins compete for the same binding sites on the core machinery, and must be spatially and temporally regulated. We discuss how post-translational modifications such as phosphorylation, ADP-ribosylation and ubiquitinylation may regulate sequential steps in the NHEJ pathway or control repair at different types of DNA breaks.
Collapse
Affiliation(s)
- Stuart L Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Gabrielle J Grundy
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| |
Collapse
|
119
|
Niewolik D, Peter I, Butscher C, Schwarz K. Autoinhibition of the Nuclease ARTEMIS Is Mediated by a Physical Interaction between Its Catalytic and C-terminal Domains. J Biol Chem 2017; 292:3351-3365. [PMID: 28082683 DOI: 10.1074/jbc.m116.770461] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/12/2017] [Indexed: 12/13/2022] Open
Abstract
The nuclease ARTEMIS is essential for the development of B and T lymphocytes. It is required for opening DNA hairpins generated during antigen receptor gene assembly from variable (V), diversity (D), and joining (J) subgenic elements (V(D)J recombination). As a member of the non-homologous end-joining pathway, it is also involved in repairing a subset of pathological DNA double strand breaks. Loss of ARTEMIS function therefore results in radiosensitive severe combined immunodeficiency (RS-SCID). The hairpin opening activity is dependent on the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), which can bind to and phosphorylate ARTEMIS. The ARTEMIS C terminus is dispensable for cellular V(D)J recombination and in vitro nuclease assays with C-terminally truncated ARTEMIS showing DNA-PKcs-independent hairpin opening activity. Therefore, it has been postulated that ARTEMIS is regulated via autoinhibition by its C terminus. To obtain evidence for the autoinhibition model, we performed co-immunoprecipitation experiments with combinations of ARTEMIS mutants. We show that an N-terminal fragment comprising the catalytic domain can interact both with itself and with a C-terminal fragment. Amino acid exchanges N456A+S457A+E458Q in the C terminus of full-length ARTEMIS resulted in unmasking of the N terminus and in increased ARTEMIS activity in cellular V(D)J recombination assays. Mutations in ARTEMIS-deficient patients impaired the interaction with the C terminus and also affected protein stability. The interaction between the N- and C-terminal domains was not DNA-PKcs-dependent, and phosphomimetic mutations in the C-terminal domain did not result in unmasking of the catalytic domain. Our experiments provide strong evidence that a physical interaction between the C-terminal and catalytic domains mediates ARTEMIS autoinhibition.
Collapse
Affiliation(s)
| | - Ingrid Peter
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm, Germany 89081
| | - Carmen Butscher
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm, Germany 89081
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm; Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm, Germany 89081
| |
Collapse
|
120
|
Hewitt G, Korolchuk VI. Repair, Reuse, Recycle: The Expanding Role of Autophagy in Genome Maintenance. Trends Cell Biol 2016; 27:340-351. [PMID: 28011061 DOI: 10.1016/j.tcb.2016.11.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/25/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
(Macro)Autophagy is a catabolic pathway that delivers excess, aggregated, or damaged proteins and organelles to lysosomes for degradation. Autophagy is activated in response to numerous cellular stressors such as increased levels of reactive oxygen species (ROS) and low levels of cellular nutrients as well as DNA damage. Although autophagy occurs in the cytoplasm, its inhibition leads to accumulation of DNA damage and genomic instability. In the past few years, our understanding of the interplay between autophagy and genomic stability has greatly increased. In this review we summarize these recent advances in understanding the molecular mechanisms linking autophagy to DNA repair.
Collapse
Affiliation(s)
- Graeme Hewitt
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Viktor I Korolchuk
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK.
| |
Collapse
|
121
|
Rajao DS, Loving CL, Waide EH, Gauger PC, Dekkers JCM, Tuggle CK, Vincent AL. Pigs with Severe Combined Immunodeficiency Are Impaired in Controlling Influenza A Virus Infection. J Innate Immun 2016; 9:193-202. [PMID: 27988511 DOI: 10.1159/000451007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/24/2016] [Indexed: 11/19/2022] Open
Abstract
Influenza A viruses (IAV) infect many host species, including humans and pigs. Severe combined immunodeficiency (SCID) is a condition characterized by a deficiency of T, B, and/or natural killer (NK) cells. Animal models of SCID have great value for biomedical research. Here, we evaluated the pathogenesis and the innate immune response to the 2009 H1N1 pandemic IAV (H1N1pdm09) using a recently identified line of naturally occurring SCID pigs deficient in T and B lymphocytes that still have functional NK cells. SCID pigs challenged with H1N1pdm09 showed milder lung pathology compared to the non-SCID heterozygous carrier pigs. Viral titers in the lungs and nasal swabs of challenged SCID pigs were significantly higher than in carrier pigs 7 days postinfection, despite higher levels of IL-1β and IFN-α in the lungs of SCID pigs. The lower levels of pulmonary pathology were associated with the T and B cell absence in response to infection. The higher viral titers, prolonged shedding, and delayed viral clearance indicated that innate immunity was insufficient for controlling IAV in pigs. This recently identified line of SCID pigs provides a valuable model to understand the immune mechanisms associated with influenza protection and recovery in a natural host.
Collapse
Affiliation(s)
- Daniela S Rajao
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA, ARS, Ames, IA, USA
| | | | | | | | | | | | | |
Collapse
|
122
|
Chang HHY, Watanabe G, Gerodimos CA, Ochi T, Blundell TL, Jackson SP, Lieber MR. Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency. J Biol Chem 2016; 291:24377-24389. [PMID: 27703001 PMCID: PMC5114395 DOI: 10.1074/jbc.m116.752329] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/26/2016] [Indexed: 02/02/2023] Open
Abstract
The nonhomologous DNA end-joining (NHEJ) pathway is a key mechanism for repairing dsDNA breaks that occur often in eukaryotic cells. In the simplest model, these breaks are first recognized by Ku, which then interacts with other NHEJ proteins to improve their affinity at DNA ends. These include DNA-PKcs and Artemis for trimming the DNA ends; DNA polymerase μ and λ to add nucleotides; and the DNA ligase IV complex to ligate the ends with the additional factors, XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor/Cernunos), and PAXX (paralog of XRCC4 and XLF). In vivo studies have demonstrated the degrees of importance of these NHEJ proteins in the mechanism of repair of dsDNA breaks, but interpretations can be confounded by other cellular processes. In vitro studies with NHEJ proteins have been performed to evaluate the nucleolytic resection, polymerization, and ligation steps, but a complete system has been elusive. Here we have developed a NHEJ reconstitution system that includes the nuclease, polymerase, and ligase components to evaluate relative NHEJ efficiency and analyze ligated junctional sequences for various types of DNA ends, including blunt, 5' overhangs, and 3' overhangs. We find that different dsDNA end structures have differential dependence on these enzymatic components. The dependence of some end joining on only Ku and XRCC4·DNA ligase IV allows us to formulate a physical model that incorporates nuclease and polymerase components as needed.
Collapse
Affiliation(s)
- Howard H Y Chang
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Go Watanabe
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Christina A Gerodimos
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Takashi Ochi
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Tom L Blundell
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Stephen P Jackson
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Michael R Lieber
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and.
| |
Collapse
|
123
|
Shabani M, Nichols KE, Rezaei N. Primary immunodeficiencies associated with EBV-Induced lymphoproliferative disorders. Crit Rev Oncol Hematol 2016; 108:109-127. [PMID: 27931829 DOI: 10.1016/j.critrevonc.2016.10.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/10/2016] [Accepted: 10/27/2016] [Indexed: 12/27/2022] Open
Abstract
Primary immunodeficiency diseases (PIDs) are a subgroup of inherited immunological disorders that increase susceptibility to viral infections. Among the range of viral pathogens involved, EBV remains a major threat because of its high prevalence of infection among the adult population and its tendency to progress to life-threatening lymphoproliferative disorders (LPDs) and/or malignancy. The high mortality in immunodeficient patients with EBV-driven LPDs, despite institution of diverse and often intensive treatments, prompts the need to better study these PIDs to identify and understand the affected molecular pathways that increase susceptibility to EBV infection and progression. In this article, we have provided a detailed literature review of the reported cases of EBV-driven LPDs in patients with PID. We discuss the PIDs associated with development of EBV-LPDs. Then, we review the nature and the therapeutic outcome of common EBV- driven LPDs in the PID patients and review the mechanisms common to the major PIDs. Deep study of these common pathways and gaining a better insight into the disease nature and outcomes, may lead to earlier diagnosis of the disease, choosing the best treatment modalities available and development of novel therapeutic strategies to decrease morbidity and mortality brought about by EBV infection.
Collapse
Affiliation(s)
- Mahsima Shabani
- Research Center for Immunodeficiencies, Children's Medical School, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; International Hematology/Oncology Of Pediatrics Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical School, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Systematic Review and Meta-Analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Boston, MA, USA.
| |
Collapse
|
124
|
Cavazzana M, Ribeil JA, Lagresle-Peyrou C, André-Schmutz I. Gene Therapy with Hematopoietic Stem Cells: The Diseased Bone Marrow's Point of View. Stem Cells Dev 2016; 26:71-76. [PMID: 27750026 DOI: 10.1089/scd.2016.0230] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
When considering inherited diseases that can be treated by gene transfer into hematopoietic stem cells (HSCs), there are only two in which the HSC and progenitor cell distribution inside the bone marrow and its microenvironment are exactly the same as in a healthy subject: metachromatic leukodystrophy (MLD) and adrenoleukodystrophy (ALD). In all other settings [X-linked severe combined immunodeficiency (X-SCID), adenosine deaminase deficiency, Wiskott-Aldrich syndrome, and β-hemoglobinopathies], the bone marrow content of the different stem and precursor cells and the cells' relationship with the stroma have very specific characteristics. These peculiarities can influence the cells' harvesting and behavior in culture, and the postgraft uptake and further behavior of the gene-modified hematopoietic/precursor cells. In the present mini-review, we shall briefly summarize these characteristics and outline the possible consequences and challenges.
Collapse
Affiliation(s)
- Marina Cavazzana
- 1 Biotherapy Department, Necker Children's Hospital , Assistance Publique-Hôpitaux de Paris, Paris, France .,2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM , Paris, France .,3 Paris Descartes-Sorbonne Paris Cité University , Imagine Institute, Paris, France .,4 Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163 , Paris, France
| | - Jean-Antoine Ribeil
- 1 Biotherapy Department, Necker Children's Hospital , Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Chantal Lagresle-Peyrou
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM , Paris, France .,3 Paris Descartes-Sorbonne Paris Cité University , Imagine Institute, Paris, France .,4 Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163 , Paris, France
| | - Isabelle André-Schmutz
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM , Paris, France .,3 Paris Descartes-Sorbonne Paris Cité University , Imagine Institute, Paris, France .,4 Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163 , Paris, France
| |
Collapse
|
125
|
Liang S, Esswein SR, Ochi T, Wu Q, Ascher DB, Chirgadze D, Sibanda BL, Blundell TL. Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached. Struct Chem 2016. [DOI: 10.1007/s11224-016-0841-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
126
|
Punwani D, Kawahara M, Yu J, Sanford U, Roy S, Patel K, Carbonaro DA, Karlen AD, Khan S, Cornetta K, Rothe M, Schambach A, Kohn DB, Malech HL, McIvor RS, Puck JM, Cowan MJ. Lentivirus Mediated Correction of Artemis-Deficient Severe Combined Immunodeficiency. Hum Gene Ther 2016; 28:112-124. [PMID: 27611239 DOI: 10.1089/hum.2016.064] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
During B and T lymphocyte maturation, V(D)J recombination is initiated by creation of DNA double-strand breaks. Artemis is an exonuclease essential for their subsequent repair by nonhomologous end-joining. Mutations in DCLRE1C, the gene encoding Artemis, cause T-B-NK+ severe combined immunodeficiency (ART-SCID) and also confer heightened sensitivity to ionizing radiation and alkylating chemotherapy. Although allogeneic hematopoietic cell transplantation can treat ART-SCID, conditioning regimens are poorly tolerated, leading to early mortality and/or late complications, including short stature, endocrinopathies, and dental aplasia. However, without alkylating chemotherapy as preconditioning, patients usually have graft rejection or limited T cell and no B cell recovery. Thus, addition of normal DCLRE1C cDNA to autologous hematopoietic stem cells is an attractive strategy to treat ART-SCID. We designed a self-inactivating lentivirus vector containing human Artemis cDNA under transcriptional regulation of the human endogenous Artemis promoter (AProArt). Fibroblasts from ART-SCID patients transduced with AProArt lentivirus showed correction of radiosensitivity. Mobilized peripheral blood CD34+ cells from an ART-SCID patient as well as hematopoietic stem cells from Artemis-deficient mice demonstrated restored T and B cell development following AProArt transduction. Murine hematopoietic cells transduced with AProArt exhibited no increase in replating potential in an in vitro immortalization assay, and analysis of AProArt lentivirus insertions showed no predilection for sites that could activate oncogenes. These efficacy and safety findings support institution of a clinical trial of gene addition therapy for ART-SCID.
Collapse
Affiliation(s)
- Divya Punwani
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Misako Kawahara
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Jason Yu
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Ukina Sanford
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Sushmita Roy
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Kiran Patel
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Denise A Carbonaro
- 2 Departments of Microbiology, Immunology and Molecular Genetics and Pediatrics, University of California Los Angeles , Los Angeles, California
| | - Andrea D Karlen
- 3 Department of Genetics, Cell Biology and Development, University of Minnesota , Minneapolis, Minnesota
| | - Sara Khan
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Kenneth Cornetta
- 4 Department of Medical and Molecular Genetics, Indiana University, and the Indiana University Viral Production Facility, Indianapolis, Indiana
| | - Michael Rothe
- 5 Institute for Experimental Hematology, Hannover Medical School , Hannover, Germany
| | - Axel Schambach
- 5 Institute for Experimental Hematology, Hannover Medical School , Hannover, Germany
| | - Donald B Kohn
- 2 Departments of Microbiology, Immunology and Molecular Genetics and Pediatrics, University of California Los Angeles , Los Angeles, California
| | - Harry L Malech
- 6 Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, Division of Intramural Research, National Institutes of Health , Bethesda, Maryland
| | - R Scott McIvor
- 3 Department of Genetics, Cell Biology and Development, University of Minnesota , Minneapolis, Minnesota
| | - Jennifer M Puck
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| | - Morton J Cowan
- 1 Department of Pediatrics, University of California School of Medicine and University of California San Francisco Benioff Children's Hospital , San Francisco, San Francisco, California
| |
Collapse
|
127
|
Tahiat A, Badran YR, Chou J, Cangemi B, Lefranc G, Labgaa ZM, Oussalam S, Kaddouri-Slimani A, Belarbi A, Bendissari-Bouzid K, Gharnaout M, Geha RS, Djidjik R, Massaad MJ. Epidermodysplasia verruciformis as a manifestation of ARTEMIS deficiency in a young adult. J Allergy Clin Immunol 2016; 139:372-375.e4. [PMID: 27568080 DOI: 10.1016/j.jaci.2016.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/08/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Azzedine Tahiat
- Algiers Faculty of Medicine, Department of Immunology, Beni Messous University Hospital, University of Algiers 1, Algiers, Algeria
| | - Yousef R Badran
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Brittney Cangemi
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Gerard Lefranc
- Institute of Human Genetics, CNRS UPR 1142, and Montpellier University, Montpellier, France
| | - Zakaria-Merouane Labgaa
- Algiers Faculty of Medicine, Department of Immunology, Beni Messous University Hospital, University of Algiers 1, Algiers, Algeria
| | - Salma Oussalam
- Department of Pathology, Beni Messous University Hospital, Algiers, Algeria
| | | | - Ayad Belarbi
- Department of Pathology, Douera Hospital, Algiers, Algeria
| | | | - Merzak Gharnaout
- Department of Pneumology, Phthisiology and Allergy, Rouiba Hospital, Algiers, Algeria
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Réda Djidjik
- Algiers Faculty of Medicine, Department of Immunology, Beni Messous University Hospital, University of Algiers 1, Algiers, Algeria
| | - Michel J Massaad
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass.
| |
Collapse
|
128
|
Abstract
Severe combined immunodeficiency disorders represent pediatric emergencies due to absence of adaptive immune responses to infections. The conditions result from either intrinsic defects in T-cell development (ie, severe combined immunodeficiency disease [SCID]) or congenital athymia (eg, complete DiGeorge anomaly). Hematopoietic stem cell transplant provides the only clinically approved cure for SCID, although gene therapy research trials are showing significant promise. For greatest survival, patients should undergo transplant before 3.5 months of age and before the onset of infections. Newborn screening programs have yielded successful early identification and treatment of infants with SCID and congenital athymia in the United States.
Collapse
|
129
|
XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination. Blood 2016; 128:650-9. [PMID: 27281794 DOI: 10.1182/blood-2016-02-701029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/31/2016] [Indexed: 12/12/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining pathway (NHEJ) is important not only for repair of spontaneous breaks but also for breaks induced in developing lymphocytes during V(D)J (variable [V], diversity [D], and joining [J] genes) recombination of their antigen receptor loci to create a diverse repertoire. Mutations in the NHEJ factor XLF result in extreme sensitivity for ionizing radiation, microcephaly, and growth retardation comparable to mutations in LIG4 and XRCC4, which together form the NHEJ ligation complex. However, the effect on the immune system is variable (mild to severe immunodeficiency) and less prominent than that seen in deficiencies of NHEJ factors ARTEMIS and DNA-dependent protein kinase catalytic subunit, with defects in the hairpin opening step, which is crucial and unique for V(D)J recombination. Therefore, we aimed to study the role of XLF during V(D)J recombination. We obtained clinical data from 9 XLF-deficient patients and performed immune phenotyping and antigen receptor repertoire analysis of immunoglobulin (Ig) and T-cell receptor (TR) rearrangements, using next-generation sequencing in 6 patients. The results were compared with XRCC4 and LIG4 deficiency. Both Ig and TR rearrangements showed a significant decrease in the number of nontemplated (N) nucleotides inserted by terminal deoxynucleotidyl transferase, which resulted in a decrease of 2 to 3 amino acids in the CDR3. Such a reduction in the number of N-nucleotides has a great effect on the junctional diversity, and thereby on the total diversity of the Ig and TR repertoire. This shows that XLF has an important role during V(D)J recombination in creating diversity of the repertoire by stimulating N-nucleotide insertion.
Collapse
|
130
|
DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: Cell cycle and proliferation-dependent regulation. Semin Cancer Biol 2016; 37-38:51-64. [DOI: 10.1016/j.semcancer.2016.03.003] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 12/18/2022]
|
131
|
End-processing nucleases and phosphodiesterases: An elite supporting cast for the non-homologous end joining pathway of DNA double-strand break repair. DNA Repair (Amst) 2016; 43:57-68. [PMID: 27262532 DOI: 10.1016/j.dnarep.2016.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Nonhomologous end joining (NHEJ) is an error-prone DNA double-strand break repair pathway that is active throughout the cell cycle. A substantial fraction of NHEJ repair events show deletions and, less often, insertions in the repair joints, suggesting an end-processing step comprising the removal of mismatched or damaged nucleotides by nucleases and other phosphodiesterases, as well as subsequent strand extension by polymerases. A wide range of nucleases, including Artemis, Metnase, APLF, Mre11, CtIP, APE1, APE2 and WRN, are biochemically competent to carry out such double-strand break end processing, and have been implicated in NHEJ by at least circumstantial evidence. Several additional DNA end-specific phosphodiesterases, including TDP1, TDP2 and aprataxin are available to resolve various non-nucleotide moieties at DSB ends. This review summarizes the biochemical specificities of these enzymes and the evidence for their participation in the NHEJ pathway.
Collapse
|
132
|
Mutations in XRCC4 cause primordial dwarfism without causing immunodeficiency. J Hum Genet 2016; 61:679-85. [PMID: 27169690 DOI: 10.1038/jhg.2016.46] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/10/2016] [Accepted: 04/06/2016] [Indexed: 12/13/2022]
Abstract
In successive reports from 2014 to 2015, X-ray repair cross-complementing protein 4 (XRCC4) has been identified as a novel causative gene of primordial dwarfism. XRCC4 is indispensable for non-homologous end joining (NHEJ), the major pathway for repairing DNA double-strand breaks. As NHEJ is essential for V(D)J recombination during lymphocyte development, it is generally believed that abnormalities in XRCC4 cause severe combined immunodeficiency. Contrary to expectations, however, no overt immunodeficiency has been observed in patients with primordial dwarfism harboring XRCC4 mutations. Here, we describe the various XRCC4 mutations that lead to disease and discuss their impact on NHEJ and V(D)J recombination.
Collapse
|
133
|
Assessment of Radiation Induced Therapeutic Effect and Cytotoxicity in Cancer Patients Based on Transcriptomic Profiling. Int J Mol Sci 2016; 17:250. [PMID: 26907258 PMCID: PMC4783980 DOI: 10.3390/ijms17020250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 01/31/2016] [Accepted: 02/03/2016] [Indexed: 12/11/2022] Open
Abstract
Toxicity induced by radiation therapy is a curse for cancer patients undergoing treatment. It is imperative to understand and define an ideal condition where the positive effects notably outweigh the negative. We used a microarray meta-analysis approach to measure global gene-expression before and after radiation exposure. Bioinformatic tools were used for pathways, network, gene ontology and toxicity related studies. We found 429 differentially expressed genes at fold change >2 and p-value <0.05. The most significantly upregulated genes were synuclein alpha (SNCA), carbonic anhydrase I (CA1), X-linked Kx blood group (XK), glycophorin A and B (GYPA and GYPB), and hemogen (HEMGN), while downregulated ones were membrane-spanning 4-domains, subfamily A member 1 (MS4A1), immunoglobulin heavy constant mu (IGHM), chemokine (C-C motif) receptor 7 (CCR7), BTB and CNC homology 1 transcription factor 2 (BACH2), and B-cell CLL/lymphoma 11B (BCL11B). Pathway analysis revealed calcium-induced T lymphocyte apoptosis and the role of nuclear factor of activated T-cells (NFAT) in regulation of the immune response as the most inhibited pathways, while apoptosis signaling was significantly activated. Most of the normal biofunctions were significantly decreased while cell death and survival process were activated. Gene ontology enrichment analysis revealed the immune system process as the most overrepresented group under the biological process category. Toxicity function analysis identified liver, kidney and heart to be the most affected organs during and after radiation therapy. The identified biomarkers and alterations in molecular pathways induced by radiation therapy should be further investigated to reduce the cytotoxicity and development of fatigue.
Collapse
|
134
|
Abstract
The balance between DNA damage, especially double strand breaks, and DNA damage repair is a critical determinant of chromosomal translocation frequency. The non-homologous end-joining repair (NHEJ) pathways seem to play the major role in the generation of chromosomal translocations. The "landscape" of chromosomal translocation identified in malignancies is largely due to selection processes which operate on the growth advantages conveyed to the cells by the functional consequences of chromosomal translocations (i.e., oncogenic fusion proteins and overexpression of oncogenes, both compromising tumor suppressor gene functions). Newer studies have shown that there is an abundance of local rearrangements in many tumors, like small deletions and inversions. A better understanding of the interplay between DNA repair mechanisms and the generation of tumorigenic translocations will, among many other things, depend on an improved understanding of DNA repair mechanisms and their interplay with chromatin and the 3D organization of the interphase nucleus.
Collapse
|
135
|
Prochazkova J, Loizou JI. Programmed DNA breaks in lymphoid cells: repair mechanisms and consequences in human disease. Immunology 2016; 147:11-20. [PMID: 26455503 PMCID: PMC4988471 DOI: 10.1111/imm.12547] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 01/08/2023] Open
Abstract
In recent years, several novel congenital human disorders have been described with defects in lymphoid B-cell and T-cell functions that arise due to mutations in known and/or novel components of DNA repair and damage response pathways. Examples include impaired DNA double-strand break repair, as well as compromised DNA damage-induced signal transduction, including phosphorylation and ubiquitination. These disorders reinforce the importance of genome stability pathways in the development of lymphoid cells in humans. Furthermore, these conditions inform our knowledge of the biology of the mechanisms of genome stability and in some cases may provide potential routes to help exploit these pathways therapeutically. Here we review the mechanisms that repair programmed DNA lesions that occur during B-cell and T-cell development, as well as human diseases that arise through defects in these pathways.
Collapse
Affiliation(s)
- Jana Prochazkova
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Joanna I. Loizou
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| |
Collapse
|
136
|
Allerston CK, Lee SY, Newman JA, Schofield CJ, McHugh PJ, Gileadi O. The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities. Nucleic Acids Res 2015; 43:11047-60. [PMID: 26582912 PMCID: PMC4678830 DOI: 10.1093/nar/gkv1256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/30/2015] [Indexed: 11/30/2022] Open
Abstract
The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions.
Collapse
Affiliation(s)
- Charles K Allerston
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
| | - Sook Y Lee
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Joseph A Newman
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Opher Gileadi
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
| |
Collapse
|
137
|
Fischer A, Notarangelo LD, Neven B, Cavazzana M, Puck JM. Severe combined immunodeficiencies and related disorders. Nat Rev Dis Primers 2015; 1:15061. [PMID: 27189259 DOI: 10.1038/nrdp.2015.61] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Severe combined immunodeficiencies (SCIDs) comprise a group of rare, monogenic diseases that are characterized by an early onset and a profound block in the development of T lymphocytes. Given that adaptive immunity is abrogated, patients with SCID are prone to recurrent infections caused by both non-opportunistic and opportunistic pathogens, leading to early death unless immunity can be restored. Several molecular defects causing SCIDs have been identified, along with many other defects causing profound, albeit incomplete, T cell immunodeficiencies; the latter are referred to as atypical SCIDs or combined immunodeficiencies. The pathophysiology of many of these conditions has now been characterized. Early, accurate and precise diagnosis combined with the ongoing implementation of newborn screening have enabled major advances in the care of infants with SCID, including better outcomes of allogeneic haematopoietic stem cell transplantation. Gene therapy is also becoming an effective option. Further advances and a progressive extension of the indications for gene therapy can be expected in the future. The assessment of long-term outcomes of patients with SCID is now a major challenge, with a view to evaluating the quality and sustainability of immune restoration, the risks of sequelae and the ability to relieve the non-haematopoietic syndromic manifestations that accompany some of these conditions.
Collapse
Affiliation(s)
- Alain Fischer
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,Immunology and Pediatric Hematology Department, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR 1163, Paris, France.,Collège de France, Paris, France
| | - Luigi D Notarangelo
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bénédicte Neven
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,Immunology and Pediatric Hematology Department, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR 1163, Paris, France
| | - Marina Cavazzana
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,INSERM UMR 1163, Paris, France.,Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, Paris, France
| | - Jennifer M Puck
- Division of Allergy, Immunology and Blood and Marrow Transplantation, Department of Pediatrics, University of California at San Francisco, San Francisco, California, USA
| |
Collapse
|
138
|
Volk T, Pannicke U, Reisli I, Bulashevska A, Ritter J, Björkman A, Schäffer AA, Fliegauf M, Sayar EH, Salzer U, Fisch P, Pfeifer D, Di Virgilio M, Cao H, Yang F, Zimmermann K, Keles S, Caliskaner Z, Güner SÜ, Schindler D, Hammarström L, Rizzi M, Hummel M, Pan-Hammarström Q, Schwarz K, Grimbacher B. DCLRE1C (ARTEMIS) mutations causing phenotypes ranging from atypical severe combined immunodeficiency to mere antibody deficiency. Hum Mol Genet 2015; 24:7361-72. [PMID: 26476407 DOI: 10.1093/hmg/ddv437] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/12/2015] [Indexed: 11/14/2022] Open
Abstract
Null mutations in genes involved in V(D)J recombination cause a block in B- and T-cell development, clinically presenting as severe combined immunodeficiency (SCID). Hypomorphic mutations in the non-homologous end-joining gene DCLRE1C (encoding ARTEMIS) have been described to cause atypical SCID, Omenn syndrome, Hyper IgM syndrome and inflammatory bowel disease-all with severely impaired T-cell immunity. By whole-exome sequencing, we investigated the molecular defect in a consanguineous family with three children clinically diagnosed with antibody deficiency. We identified perfectly segregating homozygous variants in DCLRE1C in three index patients with recurrent respiratory tract infections, very low B-cell numbers and serum IgA levels. In patients, decreased colony survival after irradiation, impaired proliferative response and reduced counts of naïve T cells were observed in addition to a restricted T-cell receptor repertoire, increased palindromic nucleotides in the complementarity determining regions 3 and long stretches of microhomology at switch junctions. Defective V(D)J recombination was complemented by wild-type ARTEMIS protein in vitro. Subsequently, homozygous or compound heterozygous DCLRE1C mutations were identified in nine patients from the same geographic region. We demonstrate that DCLRE1C mutations can cause a phenotype presenting as only antibody deficiency. This novel association broadens the clinical spectrum associated with ARTEMIS mutations. Clinicians should consider the possibility that an immunodeficiency with a clinically mild initial presentation could be a combined immunodeficiency, so as to provide appropriate care for affected patients.
Collapse
Affiliation(s)
- Timo Volk
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany
| | | | - Alla Bulashevska
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Julia Ritter
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Andrea Björkman
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Alejandro A Schäffer
- Department of Health and Human Services, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Manfred Fliegauf
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | | | - Ulrich Salzer
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Paul Fisch
- Center for Pathology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, Freiburg, Germany
| | | | - Hongzhi Cao
- Science and Technology Department, BGI-Shenzhen, Shenzhen, China
| | - Fang Yang
- Science and Technology Department, BGI-Shenzhen, Shenzhen, China
| | - Karin Zimmermann
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Sevgi Keles
- Department of Pediatric Immunology and Allergy
| | - Zafer Caliskaner
- Department of Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | | | - Detlev Schindler
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Lennart Hammarström
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Marta Rizzi
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Michael Hummel
- Institute of Pathology, Campus Benjamin Franklin, Charité - University Medicine Berlin, Berlin, Germany
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University Ulm, Ulm, Germany, Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg, Hessen, Germany and
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany, Institute of Immunity and Transplantation, University College London, Royal Free Campus, London, UK
| |
Collapse
|
139
|
Rivera-Munoz P, Abramowski V, Jacquot S, André P, Charrier S, Lipson-Ruffert K, Fischer A, Galy A, Cavazzana M, de Villartay JP. Lymphopoiesis in transgenic mice over-expressing Artemis. Gene Ther 2015; 23:176-86. [PMID: 26361272 DOI: 10.1038/gt.2015.95] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 12/27/2022]
Abstract
Artemis is a factor of the non-homologous end joining pathway involved in DNA double-strand break repair that has a critical role in V(D)J recombination. Mutations in DCLRE1C/ARTEMIS gene result in radiosensitive severe combined immunodeficiency in humans owing to a lack of mature T and B cells. Given the known drawbacks of allogeneic hematopoietic stem cell transplantation (HSCT), gene therapy appears as a promising alternative for these patients. However, the safety of an unregulated expression of Artemis has to be established. We developed a transgenic mouse model expressing human Artemis under the control of the strong CMV early enhancer/chicken beta actin promoter through knock-in at the ROSA26 locus to analyze this issue. Transgenic mice present a normal development, maturation and function of T and B cells with no signs of lymphopoietic malignancies for up to 15 months. These results suggest that the over-expression of Artemis in mice (up to 40 times) has no deleterious effects in early and mature lymphoid cells and support the safety of gene therapy as a possible curative treatment for Artemis-deficient patients.
Collapse
Affiliation(s)
- P Rivera-Munoz
- Laboratory of Genome Dynamics in the Immune System (DGSI), INSERM UMR1163, Paris, France.,Paris-Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - V Abramowski
- Laboratory of Genome Dynamics in the Immune System (DGSI), INSERM UMR1163, Paris, France.,Paris-Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - S Jacquot
- Institut Clinique de la Souris, PHENOMIN, CNRS, INSERM, Université de Strasbourg, Illkirch, France
| | - P André
- Institut Clinique de la Souris, PHENOMIN, CNRS, INSERM, Université de Strasbourg, Illkirch, France
| | | | - K Lipson-Ruffert
- Service des Animaux Transgéaniques, UPS44, CNRS, Villejuif, France
| | - A Fischer
- Paris-Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Unité d'Immunologie et Hématologie Pédiatrique, AP/HP, Hôpital Necker-Enfants Malades, Paris, France.,Collège de France, Paris, France
| | | | - M Cavazzana
- Paris-Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Unité d'Immunologie et Hématologie Pédiatrique, AP/HP, Hôpital Necker-Enfants Malades, Paris, France
| | - J-P de Villartay
- Laboratory of Genome Dynamics in the Immune System (DGSI), INSERM UMR1163, Paris, France.,Paris-Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
| |
Collapse
|
140
|
Houghton BC, Booth C, Thrasher AJ. Lentivirus technologies for modulation of the immune system. Curr Opin Pharmacol 2015; 24:119-27. [PMID: 26363252 DOI: 10.1016/j.coph.2015.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 01/21/2023]
Abstract
Lentiviral vectors (LVV) are important tools for the treatment of immune system disorders. Integration of therapeutic genetic material into the haematopoietic stem cell compartment using LVV can mediate long-term correction of haematopoietic lineages, thereby correcting disease phenotypes. Twenty years of vector development have successfully brought LVV to the clinic, with follow up studies of clinical trials treating primary immunodeficiencies now being reported. Results have demonstrated clear improvements in the quality of life for patients with a number of conditions in the absence of the severe adverse events observed in earlier retroviral gene therapy trials. Growing interest in gene modified adoptive T cell transfer as an alternative strategy has driven further technology innovation, including characterisation of novel viral envelopes. We will also discuss the progression of gene editing technology to preclinical investigations in models of immune deficiency.
Collapse
Affiliation(s)
- Benjamin C Houghton
- Molecular and Cellular Immunology, Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Claire Booth
- Molecular and Cellular Immunology, Institute of Child Health, University College London, London WC1N 1EH, UK; Department of Paediatric Immunology, Great Ormond Street Hospital NHS Foundation Trust, London WC1N 3JH, UK.
| | - Adrian J Thrasher
- Molecular and Cellular Immunology, Institute of Child Health, University College London, London WC1N 1EH, UK; Department of Paediatric Immunology, Great Ormond Street Hospital NHS Foundation Trust, London WC1N 3JH, UK
| |
Collapse
|
141
|
Glial Expression of the Caenorhabditis elegans Gene swip-10 Supports Glutamate Dependent Control of Extrasynaptic Dopamine Signaling. J Neurosci 2015; 35:9409-23. [PMID: 26109664 DOI: 10.1523/jneurosci.0800-15.2015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Glial cells play a critical role in shaping neuronal development, structure, and function. In a screen for Caenorhabditis elegans mutants that display dopamine (DA)-dependent, Swimming-Induced Paralysis (Swip), we identified a novel gene, swip-10, the expression of which in glia is required to support normal swimming behavior. swip-10 mutants display reduced locomotion rates on plates, consistent with our findings of elevated rates of presynaptic DA vesicle fusion using fluorescence recovery after photobleaching. In addition, swip-10 mutants exhibit elevated DA neuron excitability upon contact with food, as detected by in vivo Ca(2+) monitoring, that can be rescued by glial expression of swip-10. Mammalian glia exert powerful control of neuronal excitability via transporter-dependent buffering of extracellular glutamate (Glu). Consistent with this idea, swip-10 paralysis was blunted in mutants deficient in either vesicular Glu release or Glu receptor expression and could be phenocopied by mutations that disrupt the function of plasma membrane Glu transporters, most noticeably glt-1, the ortholog of mammalian astrocytic GLT1 (EAAT2). swip-10 encodes a protein containing a highly conserved metallo-β-lactamase domain, within which our swip-10 mutations are located and where engineered mutations disrupt Swip rescue. Sequence alignments identify the CNS-expressed gene MBLAC1 as a putative mammalian ortholog. Together, our studies provide evidence of a novel pathway in glial cells regulated by swip-10 that limits DA neuron excitability, DA secretion, and DA-dependent behaviors through modulation of Glu signaling.
Collapse
|
142
|
Waide EH, Dekkers JCM, Ross JW, Rowland RRR, Wyatt CR, Ewen CL, Evans AB, Thekkoot DM, Boddicker NJ, Serão NVL, Ellinwood NM, Tuggle CK. Not All SCID Pigs Are Created Equally: Two Independent Mutations in the Artemis Gene Cause SCID in Pigs. THE JOURNAL OF IMMUNOLOGY 2015; 195:3171-9. [PMID: 26320255 DOI: 10.4049/jimmunol.1501132] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/28/2015] [Indexed: 01/07/2023]
Abstract
Mutations in >30 genes are known to result in impairment of the adaptive immune system, causing a group of disorders collectively known as SCID. SCID disorders are split into groups based on their presence and/or functionality of B, T, and NK cells. Piglets from a line of Yorkshire pigs at Iowa State University were shown to be affected by T(-)B(-)NK(+) SCID, representing, to our knowledge, the first example of naturally occurring SCID in pigs. In this study, we present evidence for two spontaneous mutations as the molecular basis for this SCID phenotype. Flow cytometry analysis of thymocytes showed an increased frequency of immature T cells in SCID pigs. Fibroblasts from these pigs were more sensitive to ionizing radiation than non-SCID piglets, eliminating the RAG1 and RAG2 genes. Genetic and molecular analyses showed that two mutations were present in the Artemis gene, which in the homozygous or compound heterozygous state cause the immunodeficient phenotype. Rescue of SCID fibroblast radiosensitivity by human Artemis protein demonstrated that the identified Artemis mutations are the direct cause of this cellular phenotype. The work presented in the present study reveals two mutations in the Artemis gene that cause T(-)B(-)NK(+) SCID in pigs. The SCID pig can be an important biomedical model, but these mutations would be undesirable in commercial pig populations. The identified mutations and associated genetic tests can be used to address both of these issues.
Collapse
Affiliation(s)
- Emily H Waide
- Department of Animal Sciences, Iowa State University, Ames, IA 50011
| | - Jack C M Dekkers
- Department of Animal Sciences, Iowa State University, Ames, IA 50011
| | - Jason W Ross
- Department of Animal Sciences, Iowa State University, Ames, IA 50011
| | - Raymond R R Rowland
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502; and
| | - Carol R Wyatt
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502; and
| | - Catherine L Ewen
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502; and
| | - Alyssa B Evans
- Department of Animal Sciences, Iowa State University, Ames, IA 50011
| | - Dinesh M Thekkoot
- Department of Animal Sciences, Iowa State University, Ames, IA 50011
| | | | - Nick V L Serão
- Department of Animal Sciences, Iowa State University, Ames, IA 50011
| | | | | |
Collapse
|
143
|
Chang HHY, Watanabe G, Lieber MR. Unifying the DNA end-processing roles of the artemis nuclease: Ku-dependent artemis resection at blunt DNA ends. J Biol Chem 2015; 290:24036-50. [PMID: 26276388 DOI: 10.1074/jbc.m115.680900] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 11/06/2022] Open
Abstract
Artemis is a member of the metallo-β-lactamase protein family of nucleases. It is essential in vertebrates because, during V(D)J recombination, the RAG complex generates hairpins when it creates the double strand breaks at V, D, and J segments, and Artemis is required to open the hairpins so that they can be joined. Artemis is a diverse endo- and exonuclease, and creating a unified model for its wide range of nuclease properties has been challenging. Here we show that Artemis resects iteratively into blunt DNA ends with an efficiency that reflects the AT-richness of the DNA end. GC-rich ends are not cut by Artemis alone because of a requirement for DNA end breathing (and confirmed using fixed pseudo-Y structures). All DNA ends are cut when both the DNA-dependent protein kinase catalytic subunit and Ku accompany Artemis but not when Ku is omitted. These are the first biochemical data demonstrating a Ku dependence of Artemis action on DNA ends of any configuration. The action of Artemis at blunt DNA ends is slower than at overhangs, consistent with a requirement for a slow DNA end breathing step preceding the cut. The AT sequence dependence, the order of strand cutting, the length of the cuts, and the Ku-dependence of Artemis action at blunt ends can be reconciled with the other nucleolytic properties of both Artemis and Artemis·DNA-PKcs in a model incorporating DNA end breathing of blunt ends to form transient single to double strand boundaries that have structural similarities to hairpins and fixed 5' and 3' overhangs.
Collapse
Affiliation(s)
- Howard H Y Chang
- From the Departments of Pathology, Biochemistry and Molecular Biology, Biological Sciences, and Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Go Watanabe
- From the Departments of Pathology, Biochemistry and Molecular Biology, Biological Sciences, and Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Michael R Lieber
- From the Departments of Pathology, Biochemistry and Molecular Biology, Biological Sciences, and Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California
| |
Collapse
|
144
|
Lobachevsky P, Woodbine L, Hsiao KC, Choo S, Fraser C, Gray P, Smith J, Best N, Munforte L, Korneeva E, Martin RF, Jeggo PA, Martin OA. Evaluation of Severe Combined Immunodeficiency and Combined Immunodeficiency Pediatric Patients on the Basis of Cellular Radiosensitivity. J Mol Diagn 2015; 17:560-75. [PMID: 26151233 DOI: 10.1016/j.jmoldx.2015.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/12/2015] [Accepted: 05/06/2015] [Indexed: 01/12/2023] Open
Abstract
Pediatric patients with severe or nonsevere combined immunodeficiency have increased susceptibility to severe, life-threatening infections and, without hematopoietic stem cell transplantation, may fail to thrive. A subset of these patients have the radiosensitive (RS) phenotype, which may necessitate conditioning before hematopoietic stem cell transplantation, and this conditioning includes radiomimetic drugs, which may significantly affect treatment response. To provide statistical criteria for classifying cellular response to ionizing radiation as the measure of functional RS screening, we analyzed the repair capacity and survival of ex vivo irradiated primary skin fibroblasts from five dysmorphic and/or developmentally delayed pediatric patients with severe combined immunodeficiency and combined immunodeficiency. We developed a mathematical framework for the analysis of γ histone 2A isoform X foci kinetics to quantitate DNA-repair capacity, thus establishing crucial criteria for identifying RS. The results, presented in a diagram showing each patient as a point in a 2D RS map, were in agreement with findings from the assessment of cellular RS by clonogenic survival and from the genetic analysis of factors involved in the nonhomologous end-joining repair pathway. We provide recommendations for incorporating into clinical practice the functional assays and genetic analysis used for establishing RS status before conditioning. This knowledge would enable the selection of the most appropriate treatment regimen, reducing the risk for severe therapy-related adverse effects.
Collapse
Affiliation(s)
- Pavel Lobachevsky
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lisa Woodbine
- Sussex Centre for Genome Damage and Stability, University of Sussex-Falmer, Brighton, United Kingdom
| | - Kuang-Chih Hsiao
- Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Sharon Choo
- Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Chris Fraser
- Oncology Unit, Children's Health Services, Queensland Health, Herston, Queensland, Australia
| | - Paul Gray
- Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Jai Smith
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nickala Best
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Laura Munforte
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Elena Korneeva
- Sussex Centre for Genome Damage and Stability, University of Sussex-Falmer, Brighton, United Kingdom
| | - Roger F Martin
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Penny A Jeggo
- Sussex Centre for Genome Damage and Stability, University of Sussex-Falmer, Brighton, United Kingdom
| | - Olga A Martin
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia; The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia; Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
| |
Collapse
|
145
|
Cowan MJ, Gennery AR. Radiation-sensitive severe combined immunodeficiency: The arguments for and against conditioning before hematopoietic cell transplantation--what to do? J Allergy Clin Immunol 2015; 136:1178-85. [PMID: 26055221 DOI: 10.1016/j.jaci.2015.04.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 02/01/2015] [Accepted: 04/06/2015] [Indexed: 10/23/2022]
Abstract
Defects in DNA cross-link repair 1C (DCLRE1C), protein kinase DNA activated catalytic polypeptide (PRKDC), ligase 4 (LIG4), NHEJ1, and NBS1 involving the nonhomologous end-joining (NHEJ) DNA repair pathway result in radiation-sensitive severe combined immunodeficiency (SCID). Results of hematopoietic cell transplantation for radiation-sensitive SCID suggest that minimizing exposure to alkylating agents and ionizing radiation is important for optimizing survival and minimizing late effects. However, use of preconditioning with alkylating agents is associated with a greater likelihood of full T- and B-cell reconstitution compared with no conditioning or immunosuppression alone. A reduced-intensity regimen using fludarabine and low-dose cyclophosphamide might be effective for patients with LIG4, NHEJ1, and NBS1 defects, although more data are needed to confirm these findings and characterize late effects. For patients with mutations in DCLRE1C (Artemis-deficient SCID), there is no optimal approach that uses standard dose-alkylating agents without significant late effects. Until nonchemotherapy agents, such as anti-CD45 or anti-CD117, become available, options include minimizing exposure to alkylators, such as single-agent low-dose targeted busulfan, or achieving T-cell reconstitution, followed several years later with a conditioning regimen to restore B-cell immunity. Gene therapy for these disorders will eventually remove the issues of rejection and graft-versus-host disease. Prospective multicenter studies are needed to evaluate these approaches in this rare but highly vulnerable patient population.
Collapse
Affiliation(s)
- Morton J Cowan
- Allergy Immunology and Blood and Marrow Transplant Division, University of California San Francisco Benioff Children's Hospital, San Francisco, Calif.
| | - Andrew R Gennery
- Paediatric Immunology Department, Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
146
|
Ghosh S, Thrasher AJ, Gaspar HB. Gene therapy for monogenic disorders of the bone marrow. Br J Haematol 2015; 171:155-170. [DOI: 10.1111/bjh.13520] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sujal Ghosh
- Infection, Immunity, Inflammation and Physiological Medicine; Molecular and Cellular Immunology Section; University College London - Institute of Child Health; London UK
- Department of Paediatric Oncology, Haematology and Clinical Immunology; Medical Faculty; Centre of Child and Adolescent Health; Heinrich-Heine-University; Düsseldorf Germany
| | - Adrian J. Thrasher
- Infection, Immunity, Inflammation and Physiological Medicine; Molecular and Cellular Immunology Section; University College London - Institute of Child Health; London UK
| | - H. Bobby Gaspar
- Infection, Immunity, Inflammation and Physiological Medicine; Molecular and Cellular Immunology Section; University College London - Institute of Child Health; London UK
| |
Collapse
|
147
|
Abstract
INTRODUCTION OR BACKGROUND The V(D)J recombination is a DNA rearrangement process that generates the diversity of T and B lymphocyte immune repertoire. It proceeds through the generation of a DNA double-strand break (DNA-DSB) by the Rag1/2 lymphoid-specific factors, which is repaired by the non-homologous end joining (NHEJ) DNA repair pathway. V(D)J recombination also constitutes a checkpoint in the lymphoid development. SOURCES OF DATA V(D)J recombination defect results in severe combined immune deficiency (SCID) with a lack of T and B lymphocytes. AREAS OF AGREEMENT The V(D)J recombination represents one of the few programmed molecular events leading to DNA-DSBs that strictly relies on NHEJ. Two NHEJ factors, Artemis and XLF/Cernunnos, were identified through the molecular studies of SCID patients. Mutations in PRKDC and DNA Ligase IV genes also result in SCID. GROWING POINTS Studies in mice have demonstrated that XLF/Cernunnos is dispensable for V(D)J recombination in lymphoid cells but not for the repair of genotoxic-induced DNA-DSBs, which raises the question of the implication of Rag1/2 factors in the DNA repair phase of V(D)J recombination. AREAS TIMELY FOR DEVELOPING RESEARCH New factors of NHEJ, such as PAXX, are being identified. Patients with NHEJ deficiency (XRCC4) without immune deficiency were recently reported. We, therefore, may not have yet the complete picture of DNA-DSB repair in the context of V(D)J recombination.
Collapse
Affiliation(s)
- Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris, France
| |
Collapse
|
148
|
Rahman SH, Kuehle J, Reimann C, Mlambo T, Alzubi J, Maeder ML, Riedel H, Fisch P, Cantz T, Rudolph C, Mussolino C, Joung JK, Schambach A, Cathomen T. Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model. PLoS Genet 2015; 11:e1005239. [PMID: 26000857 PMCID: PMC4441453 DOI: 10.1371/journal.pgen.1005239] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/26/2015] [Indexed: 12/22/2022] Open
Abstract
In vitro disease modeling based on induced pluripotent stem cells (iPSCs) provides a powerful system to study cellular pathophysiology, especially in combination with targeted genome editing and protocols to differentiate iPSCs into affected cell types. In this study, we established zinc-finger nuclease-mediated genome editing in primary fibroblasts and iPSCs generated from a mouse model for radiosensitive severe combined immunodeficiency (RS-SCID), a rare disorder characterized by cellular sensitivity to radiation and the absence of lymphocytes due to impaired DNA-dependent protein kinase (DNA-PK) activity. Our results demonstrate that gene editing in RS-SCID fibroblasts rescued DNA-PK dependent signaling to overcome radiosensitivity. Furthermore, in vitro T-cell differentiation from iPSCs was employed to model the stage-specific T-cell maturation block induced by the disease causing mutation. Genetic correction of the RS-SCID iPSCs restored T-lymphocyte maturation, polyclonal V(D)J recombination of the T-cell receptor followed by successful beta-selection. In conclusion, we provide proof that iPSC-based in vitro T-cell differentiation is a valuable paradigm for SCID disease modeling, which can be utilized to investigate disorders of T-cell development and to validate gene therapy strategies for T-cell deficiencies. Moreover, this study emphasizes the significance of designer nucleases as a tool for generating isogenic disease models and their future role in producing autologous, genetically corrected transplants for various clinical applications. Due to the limited availability and lifespan of some primary cells, in vitro disease modeling with induced pluripotent stem cells (iPSCs) offers a valuable complementation to in vivo studies. The goal of our study was to establish an in vitro disease model for severe combined immunodeficiency (SCID), a group of inherited disorders of the immune system characterized by the lack of T-lymphocytes. To this end, we generated iPSCs from fibroblasts of a radiosensitive SCID (RS-SCID) mouse model and established a protocol to recapitulate T-lymphopoiesis from iPSCs in vitro. We used designer nucleases to edit the underlying mutation in prkdc, the gene encoding DNA-PKcs, and demonstrated that genetic correction of the disease locus rescued DNA-PK dependent signaling, restored normal radiosensitivity, and enabled T-cell maturation and polyclonal T-cell receptor recombination. We hence provide proof that the combination of two promising technology platforms, iPSCs and designer nucleases, with a protocol to generate T-cells in vitro, represents a powerful paradigm for SCID disease modeling and the evaluation of therapeutic gene editing strategies. Furthermore, our system provides a basis for further development of iPSC-derived cell products with the potential for various clinical applications, including infusions of in vitro derived autologous T-cells to stabilize patients after hematopoietic stem cell transplantation.
Collapse
Affiliation(s)
- Shamim H. Rahman
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Johannes Kuehle
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Christian Reimann
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Tafadzwa Mlambo
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Jamal Alzubi
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Morgan L. Maeder
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Heimo Riedel
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Department of Biochemistry and Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Paul Fisch
- Institute of Pathology, University Medical Center Freiburg, Freiburg, Germany
| | - Tobias Cantz
- Translational Hepatology and Stem Cell Biology, REBIRTH cluster of excellence, Hannover Medical School, Hannover, Germany
| | - Cornelia Rudolph
- Institute for Cellular and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | - Claudio Mussolino
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - J. Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- * E-mail: (AS); (TC)
| | - Toni Cathomen
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- * E-mail: (AS); (TC)
| |
Collapse
|
149
|
Mousallem T, Urban TJ, McSweeney KM, Kleinstein SE, Zhu M, Adeli M, Parrott RE, Roberts JL, Krueger B, Buckley RH, Goldstein DB. Clinical application of whole-genome sequencing in patients with primary immunodeficiency. J Allergy Clin Immunol 2015; 136:476-9.e6. [PMID: 25981738 DOI: 10.1016/j.jaci.2015.02.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 12/19/2014] [Accepted: 02/03/2015] [Indexed: 11/17/2022]
Affiliation(s)
- Talal Mousallem
- Departments of Internal Medicine and Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC; Department of Pediatrics, Duke University Medical Center, Durham, NC.
| | - Thomas J Urban
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - K Melodi McSweeney
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Sarah E Kleinstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Mingfu Zhu
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC
| | | | - Roberta E Parrott
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Joseph L Roberts
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Brian Krueger
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Rebecca H Buckley
- Department of Pediatrics, Duke University Medical Center, Durham, NC; Department of Immunology, Duke University School of Medicine, Durham, NC.
| | - David B Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| |
Collapse
|
150
|
Feuerhahn S, Chen LY, Luke B, Porro A. No DDRama at chromosome ends: TRF2 takes centre stage. Trends Biochem Sci 2015; 40:275-85. [DOI: 10.1016/j.tibs.2015.03.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 12/13/2022]
|