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Carlson CK, Loveless TB, Milisavljevic M, Kelly PI, Mills JH, Tyo KEJ, Liu CC. A massively parallel in vivo assay of TdT mutants yields variants with altered nucleotide insertion biases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598561. [PMID: 38915690 PMCID: PMC11195295 DOI: 10.1101/2024.06.11.598561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA with random nucleotides. TdT's de novo DNA synthesis ability has found utility in DNA recording, DNA data storage, oligonucleotide synthesis, and nucleic acid labeling, but TdT's intrinsic nucleotide biases limit its versatility in such applications. Here, we describe a multiplexed assay for profiling and engineering the bias and overall activity of TdT variants in high throughput. In our assay, a library of TdTs is encoded next to a CRISPR-Cas9 target site in HEK293T cells. Upon transfection of Cas9 and sgRNA, the target site is cut, allowing TdT to intercept the double strand break and add nucleotides. Each resulting insertion is sequenced alongside the identity of the TdT variant that generated it. Using this assay, 25,623 unique TdT variants, constructed by site-saturation mutagenesis at strategic positions, were profiled. This resulted in the isolation of several altered-bias TdTs that expanded the capabilities of our TdT-based DNA recording system, Cell History Recording by Ordered Insertion (CHYRON), by increasing the information density of recording through an unbiased TdT and achieving dual-channel recording of two distinct inducers (hypoxia and Wnt) through two differently biased TdTs. Select TdT variants were also tested in vitro , revealing concordance between each variant's in vitro bias and the in vivo bias determined from the multiplexed high throughput assay. Overall, our work, and the multiplex assay it features, should support the continued development of TdT-based DNA recorders, in vitro applications of TdT, and further study of the biology of TdT.
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2
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Loparo JJ. Holding it together: DNA end synapsis during non-homologous end joining. DNA Repair (Amst) 2023; 130:103553. [PMID: 37572577 PMCID: PMC10530278 DOI: 10.1016/j.dnarep.2023.103553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/14/2023]
Abstract
DNA double strand breaks (DSBs) are common lesions whose misrepair are drivers of oncogenic transformations. The non-homologous end joining (NHEJ) pathway repairs the majority of these breaks in vertebrates by directly ligating DNA ends back together. Upon formation of a DSB, a multiprotein complex is assembled on DNA ends which tethers them together within a synaptic complex. Synapsis is a critical step of the NHEJ pathway as loss of synapsis can result in mispairing of DNA ends and chromosome translocations. As DNA ends are commonly incompatible for ligation, the NHEJ machinery must also process ends to enable rejoining. This review describes how recent progress in single-molecule approaches and cryo-EM have advanced our molecular understanding of DNA end synapsis during NHEJ and how synapsis is coordinated with end processing to determine the fidelity of repair.
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Affiliation(s)
- Joseph J Loparo
- Dept. of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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3
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Du G, Yang R, Qiu J, Xia J. Multifaceted Influence of Histone Deacetylases on DNA Damage Repair: Implications for Hepatocellular Carcinoma. J Clin Transl Hepatol 2023; 11:231-243. [PMID: 36406320 PMCID: PMC9647118 DOI: 10.14218/jcth.2022.00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers and a leading cause of cancer-related mortality worldwide, but its pathogenesis remains largely unknown. Nevertheless, genomic instability has been recognized as one of the facilitating characteristics of cancer hallmarks that expedites the acquisition of genetic diversity. Genomic instability is associated with a greater tendency to accumulate DNA damage and tumor-specific DNA repair defects, which gives rise to gene mutations and chromosomal damage and causes oncogenic transformation and tumor progression. Histone deacetylases (HDACs) have been shown to impair a variety of cellular processes of genome stability, including the regulation of DNA damage and repair, reactive oxygen species generation and elimination, and progression to mitosis. In this review, we provide an overview of the role of HDAC in the different aspects of DNA repair and genome instability in HCC as well as the current progress on the development of HDAC-specific inhibitors as new cancer therapies.
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Affiliation(s)
- Gan Du
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- The First Clinical College, Chongqing Medical University, Chongqing, China
| | - Ruizhe Yang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- The First Clinical College, Chongqing Medical University, Chongqing, China
| | - Jianguo Qiu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Correspondence to: Jie Xia, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, No. 1 Yi Xue Yuan Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel/Fax: +86-23-68486780, E-mail: ; Jianguo Qiu, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1 You Yi Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel: +86-23-68486780, Fax: +86-23-89011016, E-mail:
| | - Jie Xia
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
- Correspondence to: Jie Xia, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, No. 1 Yi Xue Yuan Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel/Fax: +86-23-68486780, E-mail: ; Jianguo Qiu, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No.1 You Yi Road, Yuzhong District, Chongqing 400016, China. ORCID: https://orcid.org/0000-0003-4574-9376. Tel: +86-23-68486780, Fax: +86-23-89011016, E-mail:
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4
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Serrano-Benítez A, Cortés-Ledesma F, Ruiz JF. "An End to a Means": How DNA-End Structure Shapes the Double-Strand Break Repair Process. Front Mol Biosci 2020; 6:153. [PMID: 31998749 PMCID: PMC6965357 DOI: 10.3389/fmolb.2019.00153] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022] Open
Abstract
Endogenously-arising DNA double-strand breaks (DSBs) rarely harbor canonical 5′-phosphate, 3′-hydroxyl moieties at the ends, which are, regardless of the pathway used, ultimately required for their repair. Cells are therefore endowed with a wide variety of enzymes that can deal with these chemical and structural variations and guarantee the formation of ligatable termini. An important distinction is whether the ends are directly “unblocked” by specific enzymatic activities without affecting the integrity of the DNA molecule and its sequence, or whether they are “processed” by unspecific nucleases that remove nucleotides from the termini. DNA end structure and configuration, therefore, shape the repair process, its requirements, and, importantly, its final outcome. Thus, the molecular mechanisms that coordinate and integrate the cellular response to blocked DSBs, although still largely unexplored, can be particularly relevant for maintaining genome integrity and avoiding malignant transformation and cancer.
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Affiliation(s)
- Almudena Serrano-Benítez
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER-CSIC-University of Seville-Pablo de Olavide University), Seville, Spain
| | - Felipe Cortés-Ledesma
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER-CSIC-University of Seville-Pablo de Olavide University), Seville, Spain.,Topology and DNA breaks Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Jose F Ruiz
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER-CSIC-University of Seville-Pablo de Olavide University), Seville, Spain.,Department of Plant Biochemistry and Molecular Biology, University of Seville, Seville, Spain
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5
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Trimidal SG, Benjamin R, Bae JE, Han MV, Kong E, Singer A, Williams TS, Yang B, Schiller MR. Can Designer Indels Be Tailored by Gene Editing?: Can Indels Be Customized? Bioessays 2019; 41:e1900126. [PMID: 31693213 PMCID: PMC7202862 DOI: 10.1002/bies.201900126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/01/2019] [Indexed: 12/23/2022]
Abstract
Genome editing with engineered nucleases (GEENs) introduce site-specific DNA double-strand breaks (DSBs) and repairs DSBs via nonhomologous end-joining (NHEJ) pathways that eventually create indels (insertions/deletions) in a genome. Whether the features of indels resulting from gene editing could be customized is asked. A review of the literature reveals how gene editing technologies via NHEJ pathways impact gene editing. The survey consolidates a body of literature that suggests that the type (insertion, deletion, and complex) and the approximate length of indel edits can be somewhat customized with different GEENs and by manipulating the expression of key NHEJ genes. Structural data suggest that binding of GEENs to DNA may interfere with binding of key components of DNA repair complexes, favoring either classical- or alternative-NHEJ. The hypotheses have some limitations, but if validated, will enable scientists to better control indel makeup, holding promise for basic science and clinical applications of gene editing. Also see the video abstract here https://youtu.be/vTkJtUsLi3w.
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Affiliation(s)
- Sara G Trimidal
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Ronald Benjamin
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Ji Eun Bae
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Mira V Han
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Elizabeth Kong
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Aaron Singer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Tyler S Williams
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Bing Yang
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Martin R Schiller
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
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6
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Plugged into the Ku-DNA hub: The NHEJ network. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:62-76. [PMID: 30851288 DOI: 10.1016/j.pbiomolbio.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To shed light on these dynamic interplays, we review here current knowledge on proteins directly interacting with Ku and on the contact points involved, with a particular accent on the different classes of Ku-binding motifs identified in several Ku partners. An integrated structural model of the core NHEJ network at the synapsis step is proposed.
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7
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Loc'h J, Delarue M. Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands. Curr Opin Struct Biol 2018; 53:22-31. [PMID: 29656238 DOI: 10.1016/j.sbi.2018.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 01/08/2023]
Abstract
Terminal deoxynucleotidyltransferase (TdT) is a member of the polX family which is involved in DNA repair. It has been known for years as an untemplated DNA polymerase used during V(D)J recombination to generate diversity at the CDR3 region of immunoglobulins and T-cell receptors. Recently, however, TdT was crystallized in the presence of a complete DNA synapsis made of two double-stranded DNA (dsDNA), each with a 3' protruding end, and overlapping with only one micro-homology base-pair, thus giving structural insight for the first time into DNA synthesis across strands. It was subsequently shown that TdT indeed has an in trans template-dependent activity in the presence of an excess of the downstream DNA duplex. A possible biological role of this dual activity is discussed.
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Affiliation(s)
- Jérôme Loc'h
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
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8
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Gholami S, Mohammadi SM, Movasaghpour Akbari A, Abedelahi A, Alihemmati A, Fallahi S, Nozad Charoudeh H. Terminal Deoxynucleotidyl Transferase (TdT) Inhibiti on of Cord Blood Derived B and T Cells Expansion. Adv Pharm Bull 2017; 7:215-220. [PMID: 28761823 PMCID: PMC5527235 DOI: 10.15171/apb.2017.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/30/2017] [Accepted: 05/01/2017] [Indexed: 01/01/2023] Open
Abstract
Purpose: Terminal deoxynucleotidyl transferase(TdT) is a DNA polymerase that is present in immature pre-B and pre-T cells. TdT inserts N-nucleotides to the V (D) J gene segment during rearrangements of genes, therefore, it plays a vital role in the development and variation of the immune system in vertebrates. Here we evaluated the relationship between cytokines like interleukin-2 (IL-2), interleukin-7 (IL-7), and interleukin-15 (IL-15) and TdT expression in cord blood mononuclear cells and also effect of inhibition in the expansion of B and T cells derived from cord blood. Methodes: The cord blood mononuclear cells were cultured with different combination of cytokines for 21days, which they were harvested in definite days (7, 14 and 21) and evaluated by flow cytometry. Results: Our data indicated that TdT expression increased in cord blood mononuclear cells using immune cell key cytokines without being dependent on the type of cytokines. TdT inhibition reduced both the expansion of B and T cells derived from cord blood and also declined the apoptosis and proliferation. Considered together, TdT played an important role in the control of the expansion of B and T cells derived from cord blood. Conclusion: considered together, it was observed that TdT expression was increased by cytokines and TdT inhibition not only reduced B and Tcells derived from cord blood, but it also affected the rate of apoptosis and proliferation.
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Affiliation(s)
- Sanaz Gholami
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Anatomical Sciences Department, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Ali Abedelahi
- Anatomical Sciences Department, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Alihemmati
- Anatomical Sciences Department, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shirin Fallahi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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9
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Rother MB, Jensen K, van der Burg M, van de Bovenkamp FS, Kroek R, van IJcken WFJ, van der Velden VHJ, Cupedo T, Olstad OK, van Dongen JJM, van Zelm MC. Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin. Sci Rep 2016; 6:33924. [PMID: 27658954 PMCID: PMC5034271 DOI: 10.1038/srep33924] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/31/2016] [Indexed: 11/25/2022] Open
Abstract
Newborns are unable to mount antibody responses towards certain antigens. This has been related to the restricted repertoire of immunoglobulin (Ig) genes of their B cells. The mechanisms underlying the restricted fetal Ig gene repertoire are currently unresolved. We here addressed this with detailed molecular and cellular analysis of human precursor-B cells from fetal liver, fetal bone marrow (BM), and pediatric BM. In the absence of selection processes, fetal B-cell progenitors more frequently used proximal V, D and J genes in complete IGH gene rearrangements, despite normal Ig locus contraction. Fewer N-nucleotides were added in IGH gene rearrangements in the context of low TdT and XRCC4 expression. Moreover, fetal progenitor-B cells expressed lower levels of IL7Rα than their pediatric counterparts. Analysis of progenitor-B cells from IL7Rα-deficient patients revealed that TdT expression and N-nucleotides additions in Dh-Jh junctions were dependent on functional IL7Rα. Thus, IL7Rα affects TdT expression, and decreased expression of this receptor underlies at least in part the skewed Ig repertoire formation in fetal B-cell precursors. These new insights provide a better understanding of the formation of adaptive immunity in the developing fetus.
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Affiliation(s)
- Magdalena B. Rother
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Kristin Jensen
- Department of Medical Biochemistry, Oslo University Hospital, Norway
- Volvat Medical Center, Oslo, Norway
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | | | - Roel Kroek
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | | | | | - Tom Cupedo
- Department of Hematology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Ole K. Olstad
- Department of Medical Biochemistry, Oslo University Hospital, Norway
- Volvat Medical Center, Oslo, Norway
| | | | - Menno C. van Zelm
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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10
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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]
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11
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Troshchynsky A, Dzneladze I, Chen L, Sheng Y, Saridakis V, Wu GE. Functional analyses of polymorphic variants of human terminal deoxynucleotidyl transferase. Genes Immun 2015; 16:388-98. [PMID: 26043173 DOI: 10.1038/gene.2015.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/11/2022]
Abstract
Human terminal deoxynucleotidyl transferase (hTdT) is a DNA polymerase that functions to generate diversity in the adaptive immune system. Here, we focus on the function of naturally occurring single-nucleotide polymorphisms (SNPs) of hTdT to evaluate their role in genetic-generated immune variation. The data demonstrate that the genetic variations generated by the hTdT SNPs will vary the human immune repertoire and thus its responses. Human TdT catalyzes template-independent addition of nucleotides (N-additions) during coding joint formation in V(D)J recombination. Its activity is crucial to the diversity of the antigen receptors of B and T lymphocytes. We used in vitro polymerase assays and in vivo human cell V(D)J recombination assays to evaluate the activity and the N-addition levels of six natural (SNP) variants of hTdT. In vitro, the variants differed from wild-type hTdT in polymerization ability with four having significantly lower activity. In vivo, the presence of TdT varied both the efficiency of recombination and N-addition, with two variants generating coding joints with significantly fewer N-additions. Although likely heterozygous, individuals possessing these genetic changes may have less diverse B- and T-cell receptors that would particularly effect individuals prone to adaptive immune disorders, including autoimmunity.
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Affiliation(s)
- A Troshchynsky
- Department of Biology, York University, Toronto, Ontario, Canada
| | - I Dzneladze
- Department of Biology, York University, Toronto, Ontario, Canada
| | - L Chen
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Y Sheng
- Department of Biology, York University, Toronto, Ontario, Canada
| | - V Saridakis
- Department of Biology, York University, Toronto, Ontario, Canada
| | - G E Wu
- Department of Biology, York University, Toronto, Ontario, Canada.,School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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12
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Mutations in the NHEJ component XRCC4 cause primordial dwarfism. Am J Hum Genet 2015; 96:412-24. [PMID: 25728776 DOI: 10.1016/j.ajhg.2015.01.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/16/2015] [Indexed: 11/20/2022] Open
Abstract
Non-homologous end joining (NHEJ) is a key cellular process ensuring genome integrity. Mutations in several components of the NHEJ pathway have been identified, often associated with severe combined immunodeficiency (SCID), consistent with the requirement for NHEJ during V(D)J recombination to ensure diversity of the adaptive immune system. In contrast, we have recently found that biallelic mutations in LIG4 are a common cause of microcephalic primordial dwarfism (MPD), a phenotype characterized by prenatal-onset extreme global growth failure. Here we provide definitive molecular genetic evidence supported by biochemical, cellular, and immunological data for mutations in XRCC4, encoding the obligate binding partner of LIG4, causing MPD. We report the identification of biallelic mutations in XRCC4 in five families. Biochemical and cellular studies demonstrate that these alterations substantially decrease XRCC4 protein levels leading to reduced cellular ligase IV activity. Consequently, NHEJ-dependent repair of ionizing-radiation-induced DNA double-strand breaks is compromised in XRCC4 cells. Similarly, immunoglobulin junctional diversification is impaired in cells. However, immunoglobulin levels are normal, and individuals lack overt signs of immunodeficiency. Additionally, in contrast to individuals with LIG4 mutations, pancytopenia leading to bone marrow failure has not been observed. Hence, alterations that alter different NHEJ proteins give rise to a phenotypic spectrum, from SCID to extreme growth failure, with deficiencies in certain key components of this repair pathway predominantly exhibiting growth deficits, reflecting differential developmental requirements for NHEJ proteins to support growth and immune maturation.
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13
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Le Guen T, Ragu S, Guirouilh-Barbat J, Lopez BS. Role of the double-strand break repair pathway in the maintenance of genomic stability. Mol Cell Oncol 2014; 2:e968020. [PMID: 27308383 PMCID: PMC4905226 DOI: 10.4161/23723548.2014.968020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/18/2014] [Indexed: 11/19/2022]
Abstract
DNA double-strand breaks (DSBs) are highly lethal lesions that jeopardize genome integrity. However, DSBs are also used to generate diversity during the physiological processes of meiosis or establishment of the immune repertoire. Therefore, DSB repair must be tightly controlled. Two main strategies are used to repair DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). HR is generally considered to be error-free, whereas NHEJ is considered to be error-prone. However, recent data challenge these assertions. Here, we present the molecular mechanisms involved in HR and NHEJ and the recently described alternative end-joining mechanism, which is exclusively mutagenic. Whereas NHEJ is not intrinsically error-prone but adaptable, HR has the intrinsic ability to modify the DNA sequence. Importantly, in both cases the initial structure of the DNA impacts the outcome. Finally, the consequences and applications of these repair mechanisms are discussed. Both HR and NHEJ are double-edged swords, essential for maintenance of genome stability and diversity but also able to generate genome instability.
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Affiliation(s)
- Tangui Le Guen
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
| | - Sandrine Ragu
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
| | - Josée Guirouilh-Barbat
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
| | - Bernard S Lopez
- Université Paris Sud; CNRS UMR 8200; Institut de Cancérologie Gustave-Roussy; Team labeled "Ligue 2014" ; Villejuif, France
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14
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Chromosomal translocations in human cells are generated by canonical nonhomologous end-joining. Mol Cell 2014; 55:829-842. [PMID: 25201414 DOI: 10.1016/j.molcel.2014.08.002] [Citation(s) in RCA: 259] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/14/2014] [Accepted: 07/29/2014] [Indexed: 01/28/2023]
Abstract
Breakpoint junctions of the chromosomal translocations that occur in human cancers display hallmarks of nonhomologous end-joining (NHEJ). In mouse cells, translocations are suppressed by canonical NHEJ (c-NHEJ) components, which include DNA ligase IV (LIG4), and instead arise from alternative NHEJ (alt-NHEJ). Here we used designer nucleases (ZFNs, TALENs, and CRISPR/Cas9) to introduce DSBs on two chromosomes to study translocation joining mechanisms in human cells. Remarkably, translocations were altered in cells deficient for LIG4 or its interacting protein XRCC4. Translocation junctions had significantly longer deletions and more microhomology, indicative of alt-NHEJ. Thus, unlike mouse cells, translocations in human cells are generated by c-NHEJ. Human cancer translocations induced by paired Cas9 nicks also showed a dependence on c-NHEJ, despite having distinct joining characteristics. These results demonstrate an unexpected and striking species-specific difference for common genomic rearrangements associated with tumorigenesis.
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15
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Gigi V, Lewis S, Shestova O, Mijušković M, Deriano L, Meng W, Luning Prak ET, Roth DB. RAG2 mutants alter DSB repair pathway choice in vivo and illuminate the nature of 'alternative NHEJ'. Nucleic Acids Res 2014; 42:6352-64. [PMID: 24753404 PMCID: PMC4041462 DOI: 10.1093/nar/gku295] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA double-stranded breaks (DSBs) can be repaired by several mechanisms, including classical NHEJ (c-NHEJ) and a poorly defined, error-prone process termed alternative NHEJ (a-NHEJ). How cells choose between these alternatives to join physiologic DSBs remains unknown. Here, we show that deletion of RAG2's C-terminus allows a-NHEJ to repair RAG-mediated DSBs in developing lymphocytes from both c-NHEJ-proficient and c-NHEJ-deficient mice, demonstrating that the V(D)J recombinase influences repair pathway choice in vivo. Analysis of V(D)J junctions revealed that, contrary to expectation, junctional characteristics alone do not reliably distinguish between a-NHEJ and c-NHEJ. These data suggest that a-NHEJ is not necessarily mutagenic, and may be more prevalent than previously appreciated. Whole genome sequencing of a lymphoma arising in a p53−/− mouse bearing a C-terminal RAG2 truncation reveals evidence of a-NHEJ and also of aberrant recognition of DNA sequences resembling RAG recognition sites.
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Affiliation(s)
- Vered Gigi
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susanna Lewis
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Olga Shestova
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martina Mijušković
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ludovic Deriano
- Departments of Immunology and Genomes & Genetics, Institut Pasteur, CNRS-URA 1961, 75015 Paris, France
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David B Roth
- Department of Pathology and Laboratory Medicine and Abramson Family Cancer Research Institute, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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16
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Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, Tubio J, Alexandrov LB, Van Loo P, Cooke SL, Marshall J, Martincorena I, Hinton J, Gundem G, van Delft FW, Nik-Zainal S, Jones DR, Ramakrishna M, Titley I, Stebbings L, Leroy C, Menzies A, Gamble J, Robinson B, Mudie L, Raine K, O’Meara S, Teague JW, Butler AP, Cazzaniga G, Biondi A, Zuna J, Kempski H, Muschen M, Ford AM, Stratton MR, Greaves M, Campbell PJ. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nat Genet 2014; 46:116-25. [PMID: 24413735 PMCID: PMC3960636 DOI: 10.1038/ng.2874] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 12/13/2013] [Indexed: 12/16/2022]
Abstract
The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of non-templated sequence at junctions, ∼30-fold enrichment at promoters and enhancers of genes actively transcribed in B cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single-cell tracking shows that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions. Integration of data on point mutations and rearrangements identifies ATF7IP and MGA as two new tumor-suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1-positive lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B cell differentiation.
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Affiliation(s)
| | | | - Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jose Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Human Genetics, VIB and University of Leuven, Leuven, Belgium
| | - Susanna L Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - John Marshall
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Jonathan Hinton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Frederik W van Delft
- Institute for Cancer Research, Sutton, London, UK
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne, UK
| | | | - David R Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Ian Titley
- Institute for Cancer Research, Sutton, London, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Catherine Leroy
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - John Gamble
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ben Robinson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Laura Mudie
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sarah O’Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon W Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam P Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Hospital San Gerardo, Via Pergolesi, 33, 20052 Monza (Mi), Italy
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Hospital San Gerardo, Via Pergolesi, 33, 20052 Monza (Mi), Italy
| | - Jan Zuna
- CLIP, Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic
| | - Helena Kempski
- Paediatric Malignancy Unit, CBL Level 2, Molecular Haematology & Cancer Biology Unit, Camelia Botnar Laboratories, Level 2, Great Ormond Street Hospital for Children & UCL Institute of Child Health, Great Ormond Street, London WC1N 3JH
| | - Markus Muschen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA
| | | | | | - Mel Greaves
- Institute for Cancer Research, Sutton, London, UK
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Addenbrooke’s NHS Foundation Trust, Cambridge, UK
- University of Cambridge, Cambridge, UK
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17
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Bétermier M, Bertrand P, Lopez BS. Is non-homologous end-joining really an inherently error-prone process? PLoS Genet 2014; 10:e1004086. [PMID: 24453986 PMCID: PMC3894167 DOI: 10.1371/journal.pgen.1004086] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA double-strand breaks (DSBs) are harmful lesions leading to genomic instability or diversity. Non-homologous end-joining (NHEJ) is a prominent DSB repair pathway, which has long been considered to be error-prone. However, recent data have pointed to the intrinsic precision of NHEJ. Three reasons can account for the apparent fallibility of NHEJ: 1) the existence of a highly error-prone alternative end-joining process; 2) the adaptability of canonical C-NHEJ (Ku- and Xrcc4/ligase IV-dependent) to imperfect complementary ends; and 3) the requirement to first process chemically incompatible DNA ends that cannot be ligated directly. Thus, C-NHEJ is conservative but adaptable, and the accuracy of the repair is dictated by the structure of the DNA ends rather than by the C-NHEJ machinery. We present data from different organisms that describe the conservative/versatile properties of C-NHEJ. The advantages of the adaptability/versatility of C-NHEJ are discussed for the development of the immune repertoire and the resistance to ionizing radiation, especially at low doses, and for targeted genome manipulation.
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Affiliation(s)
- Mireille Bétermier
- CNRS, Centre de Génétique Moléculaire, UPR3404, Gif-sur-Yvette, France
- CNRS, Centre de Recherches de Gif-sur-Yvette, FRC3115, Gif-sur-Yvette, France
- Université Paris-Sud, Département de Biologie, Orsay, France
| | - Pascale Bertrand
- CEA, DSV, Institut de Radiobiologie Moléculaire et Cellulaire, Laboratoire Réparation et Vieillissement, Fontenay-aux-Roses, France
- UMR 8200 CNRS, Villejuif, France
| | - Bernard S. Lopez
- Université Paris-Sud, Département de Biologie, Orsay, France
- UMR 8200 CNRS, Villejuif, France
- Institut de Cancérologie, Gustave Roussy, Villejuif, France
- * E-mail:
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18
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Abstract
Deregulated activation of β-catenin in cancer has been correlated with genomic instability. During thymocyte development, β-catenin activates transcription in partnership with T-cell-specific transcription factor 1 (Tcf-1). We previously reported that targeted activation of β-catenin in thymocytes (CAT mice) induces lymphomas that depend on recombination activating gene (RAG) and myelocytomatosis oncogene (Myc) activities. Here we show that these lymphomas have recurring Tcra/Myc translocations that resulted from illegitimate RAG recombination events and resembled oncogenic translocations previously described in human T-ALL. We therefore used the CAT animal model to obtain mechanistic insights into the transformation process. ChIP-seq analysis uncovered a link between Tcf-1 and RAG2 showing that the two proteins shared binding sites marked by trimethylated histone-3 lysine-4 (H3K4me3) throughout the genome, including near the translocation sites. Pretransformed CAT thymocytes had increased DNA damage at the translocating loci and showed altered repair of RAG-induced DNA double strand breaks. These cells were able to survive despite DNA damage because activated β-catenin promoted an antiapoptosis gene expression profile. Thus, activated β-catenin promotes genomic instability that leads to T-cell lymphomas as a consequence of altered double strand break repair and increased survival of thymocytes with damaged DNA.
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