1
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Kratz K, Artola-Borán M, Kobayashi-Era S, Koh G, Oliveira G, Kobayashi S, Oliveira A, Zou X, Richter J, Tsuda M, Sasanuma H, Takeda S, Loizou JI, Sartori AA, Nik-Zainal S, Jiricny J. FANCD2-Associated Nuclease 1 Partially Compensates for the Lack of Exonuclease 1 in Mismatch Repair. Mol Cell Biol 2021; 41:e0030321. [PMID: 34228493 PMCID: PMC8384067 DOI: 10.1128/mcb.00303-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 11/20/2022] Open
Abstract
Germline mutations in the mismatch repair (MMR) genes MSH2, MSH6, MLH1, and PMS2 are linked to cancer of the colon and other organs, characterized by microsatellite instability and a large increase in mutation frequency. Unexpectedly, mutations in EXO1, encoding the only exonuclease genetically implicated in MMR, are not linked to familial cancer and cause a substantially weaker mutator phenotype. This difference could be explained if eukaryotic cells possessed additional exonucleases redundant with EXO1. Analysis of the MLH1 interactome identified FANCD2-associated nuclease 1 (FAN1), a novel enzyme with biochemical properties resembling EXO1. We now show that FAN1 efficiently substitutes for EXO1 in MMR assays and that this functional complementation is modulated by its interaction with MLH1. FAN1 also contributes to MMR in vivo; cells lacking both EXO1 and FAN1 have an MMR defect and display resistance to N-methyl-N-nitrosourea (MNU) and 6-thioguanine (TG). Moreover, FAN1 loss amplifies the mutational profile of EXO1-deficient cells, suggesting that the two nucleases act redundantly in the same antimutagenic pathway. However, the increased drug resistance and mutator phenotype of FAN1/EXO1-deficient cells are less prominent than those seen in cells lacking MSH6 or MLH1. Eukaryotic cells thus apparently possess additional mechanisms that compensate for the loss of EXO1.
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Affiliation(s)
- Katja Kratz
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mariela Artola-Borán
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Saho Kobayashi-Era
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Gene Koh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, United Kingdom
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, United Kingdom
| | - Goncalo Oliveira
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Shunsuke Kobayashi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Andreia Oliveira
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Xueqing Zou
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, United Kingdom
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, United Kingdom
| | - Julia Richter
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Joanna I. Loizou
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | | | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, United Kingdom
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, United Kingdom
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
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2
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Porro A, Mohiuddin M, Zurfluh C, Spegg V, Dai J, Iehl F, Ropars V, Collotta G, Fishwick KM, Mozaffari NL, Guérois R, Jiricny J, Altmeyer M, Charbonnier JB, Pearson CE, Sartori AA. FAN1-MLH1 interaction affects repair of DNA interstrand cross-links and slipped-CAG/CTG repeats. Sci Adv 2021; 7:7/31/eabf7906. [PMID: 34330701 PMCID: PMC8324060 DOI: 10.1126/sciadv.abf7906] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/15/2021] [Indexed: 05/05/2023]
Abstract
FAN1, a DNA structure-specific nuclease, interacts with MLH1, but the repair pathways in which this complex acts are unknown. FAN1 processes DNA interstrand crosslinks (ICLs) and FAN1 variants are modifiers of the neurodegenerative Huntington's disease (HD), presumably by regulating HD-causing CAG repeat expansions. Here, we identify specific amino acid residues in two adjacent FAN1 motifs that are critical for MLH1 binding. Disruption of the FAN1-MLH1 interaction confers cellular hypersensitivity to ICL damage and defective repair of CAG/CTG slip-outs, intermediates of repeat expansion mutations. FAN1-S126 phosphorylation, which hinders FAN1-MLH1 association, is cell cycle-regulated by cyclin-dependent kinase activity and attenuated upon ICL induction. Our data highlight the FAN1-MLH1 complex as a phosphorylation-regulated determinant of ICL response and repeat stability, opening novel paths to modify cancer and neurodegeneration.
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Affiliation(s)
- Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Christina Zurfluh
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Jingqi Dai
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Florence Iehl
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Virginie Ropars
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Giulio Collotta
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Keri M Fishwick
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Raphaël Guérois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Jean-Baptiste Charbonnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
- Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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3
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Zou X, Koh GCC, Nanda AS, Degasperi A, Urgo K, Roumeliotis TI, Agu CA, Badja C, Momen S, Young J, Amarante TD, Side L, Brice G, Perez-Alonso V, Rueda D, Gomez C, Bushell W, Harris R, Choudhary JS, Jiricny J, Skarnes WC, Nik-Zainal S. A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. Nat Cancer 2021; 2:643-657. [PMID: 34164627 PMCID: PMC7611045 DOI: 10.1038/s43018-021-00200-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023]
Abstract
Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. We generated isogenic CRISPR-Cas9 knockouts (Δ) of 43 genes in human induced pluripotent stem cells, cultured them in the absence of added DNA damage, and performed whole-genome sequencing of 173 subclones. ΔOGG1, ΔUNG, ΔEXO1, ΔRNF168, ΔMLH1, ΔMSH2, ΔMSH6, ΔPMS1, and ΔPMS2 produced marked mutational signatures indicative of being critical mitigators of endogenous DNA modifications. Detailed analyses revealed mutational mechanistic insights, including how 8-oxo-dG elimination is sequence-context-specific while uracil clearance is sequence-context-independent. Mismatch repair (MMR) deficiency signatures are engendered by oxidative damage (C>A transversions), differential misincorporation by replicative polymerases (T>C and C>T transitions), and we propose a 'reverse template slippage' model for T>A transversions. ΔMLH1, ΔMSH6, and ΔMSH2 signatures were similar to each other but distinct from ΔPMS2. Finally, we developed a classifier, MMRDetect, where application to 7,695 WGS cancers showed enhanced detection of MMR-deficient tumors, with implications for responsiveness to immunotherapies.
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Affiliation(s)
- Xueqing Zou
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Gene Ching Chiek Koh
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Arjun Scott Nanda
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Cherif Badja
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Sophie Momen
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Jamie Young
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Tauanne Dias Amarante
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Lucy Side
- UCL Institute for Women's Health, Great Ormond Street Hospital, London, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Glen Brice
- Southwest Thames Regional Genetics Service, St George's University of London, London, UK
| | - Vanesa Perez-Alonso
- Pediatrics Department, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | - Daniel Rueda
- Hereditary Cancer Laboratory, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | | | | | - Rebecca Harris
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Jyoti S Choudhary
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Josef Jiricny
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - William C Skarnes
- Wellcome Sanger Institute, Hinxton, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
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4
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Zou X, Koh G, Nanda S, Degasperi A, Urgo K, Bushell W, Agu C, Perez-Alonso V, Rueda D, Foreman J, Harris R, Jiricny J, Skarnes B, Nik-Zainal S. Abstract 4887: Direct mutational consequences of CRISPR-cas9 gene-edited DNA repair genes. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-4887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer whole-genome sequencing has revealed characteristic mutational signatures associated with defective DNA repair that underpin human genetic diseases. To define the direct mutagenic effects of DNA repair deficiency at the genome-wide level, we investigate mutational signatures generated by CRISPR-Cas9-based knockouts of 42 genes involved in DNA repair/replication using a human-induced pluripotent stem cell line. Knockouts (Δ) of nine DNA repair genes reveal substitution/indel mutational signatures. Notably, dissection of signatures of defective mismatch repair (MMR) uncovers gene-specific characteristics including distinguishing features of ΔMLH1, ΔMSH2, and ΔMSH6 from ΔPMS2. This gene-specificity is also exhibited by hIPSCs derived from patients with autosomal recessive Constitutional Mismatch Repair Deficiency (CMMRD) that carry biallelic germline mutations of MMR genes. Furthermore, gene-specificity manifests in whole genome sequenced primary human cancers. Additionally, detailed analyses reveal putative sources of endogenous DNA damage that contribute to MMR signatures, including guanine oxidation, errors of DNA polymerases and reversed template slippage or double slippage. Finally, we find that using all mutational signatures of MMR-deficiency as identified in this study results in improved sensitivity and specificity in classifying MMR-deficient tumors, critical for accurate patient stratification for therapeutic intervention.
Citation Format: Xueqing Zou, Gene Koh, Scott Nanda, Andrea Degasperi, Katie Urgo, Wendy Bushell, Chukwuma Agu, Vanesa Perez-Alonso, Daniel Rueda, Julia Foreman, Rebecca Harris, Josef Jiricny, Bill Skarnes, Serena Nik-Zainal. Direct mutational consequences of CRISPR-cas9 gene-edited DNA repair genes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4887.
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Affiliation(s)
- Xueqing Zou
- 1University of Cambridge, Cambridge, United Kingdom
| | - Gene Koh
- 1University of Cambridge, Cambridge, United Kingdom
| | - Scott Nanda
- 1University of Cambridge, Cambridge, United Kingdom
| | | | - Katie Urgo
- 2Sanger Institute, Cambridge, United Kingdom
| | | | | | | | - Daniel Rueda
- 3Doce de Octubre University Hospital, Madrid, Spain
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5
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Giovannini S, Weller MC, Hanzlíková H, Shiota T, Takeda S, Jiricny J. ATAD5 deficiency alters DNA damage metabolism and sensitizes cells to PARP inhibition. Nucleic Acids Res 2020; 48:4928-4939. [PMID: 32297953 PMCID: PMC7229844 DOI: 10.1093/nar/gkaa255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 01/05/2023] Open
Abstract
Replication factor C (RFC), a heteropentamer of RFC1-5, loads PCNA onto DNA during replication and repair. Once DNA synthesis has ceased, PCNA must be unloaded. Recent findings assign the uloader role primarily to an RFC-like (RLC) complex, in which the largest RFC subunit, RFC1, has been replaced with ATAD5 (ELG1 in Saccharomyces cerevisiae). ATAD5-RLC appears to be indispensable, given that Atad5 knock-out leads to embryonic lethality. In order to learn how the retention of PCNA on DNA might interfere with normal DNA metabolism, we studied the response of ATAD5-depleted cells to several genotoxic agents. We show that ATAD5 deficiency leads to hypersensitivity to methyl methanesulphonate (MMS), camptothecin (CPT) and mitomycin C (MMC), agents that hinder the progression of replication forks. We further show that ATAD5-depleted cells are sensitive to poly(ADP)ribose polymerase (PARP) inhibitors and that the processing of spontaneous oxidative DNA damage contributes towards this sensitivity. We posit that PCNA molecules trapped on DNA interfere with the correct metabolism of arrested replication forks, phenotype reminiscent of defective homologous recombination (HR). As Atad5 heterozygous mice are cancer-prone and as ATAD5 mutations have been identified in breast and endometrial cancers, our finding may open a path towards the therapy of these tumours.
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Affiliation(s)
- Sara Giovannini
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Marie-Christine Weller
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Hana Hanzlíková
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142-20 Prague 4, Czech Republic
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Tetsuya Shiota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, 606-8501 Kyoto, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, 606-8501 Kyoto, Japan
| | - Josef Jiricny
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
- To whom correspondence should be addressed. Tel: +41 44 633 6260;
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6
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Georgakopoulos-Soares I, Koh G, Momen SE, Jiricny J, Hemberg M, Nik-Zainal S. Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts. Nat Commun 2020; 11:1980. [PMID: 32332764 PMCID: PMC7181645 DOI: 10.1038/s41467-020-15901-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 03/27/2020] [Indexed: 01/07/2023] Open
Abstract
The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. Here, we introduce a method to evaluate indels, orientating them relative to gene transcription. In so doing, we reveal a number of surprising findings: First, there is a transcriptional strand asymmetry in the distribution of mononucleotide repeat tracts in the reference human genome. Second, there is a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers. We suggest that this is due to the activity of transcription-coupled nucleotide excision repair (TC-NER). Furthermore, TC-NER interacts with mismatch repair (MMR) under physiological conditions to produce strand bias. Finally, we show how insertions and deletions differ in their dependencies on these repair pathways. Our analytical approach reveals insights into the contribution of DNA repair towards indel mutagenesis in human cells.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Gene Koh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Sophie E Momen
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Josef Jiricny
- Institute of Molecular Life Sciences, University of Zurich and Institute of Biochemistry, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK.
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, CB2 0XZ, UK.
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7
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Giovannini S, Weller MC, Repmann S, Moch H, Jiricny J. Synthetic lethality between BRCA1 deficiency and poly(ADP-ribose) polymerase inhibition is modulated by processing of endogenous oxidative DNA damage. Nucleic Acids Res 2019; 47:9132-9143. [PMID: 31329989 PMCID: PMC6753488 DOI: 10.1093/nar/gkz624] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/11/2019] [Accepted: 07/12/2019] [Indexed: 01/06/2023] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) facilitate the repair of DNA single-strand breaks (SSBs). When PARPs are inhibited, unrepaired SSBs colliding with replication forks give rise to cytotoxic double-strand breaks. These are normally rescued by homologous recombination (HR), but, in cells with suboptimal HR, PARP inhibition leads to genomic instability and cell death, a phenomenon currently exploited in the therapy of ovarian cancers in BRCA1/2 mutation carriers. In spite of their promise, resistance to PARP inhibitors (PARPis) has already emerged. In order to identify the possible underlying causes of the resistance, we set out to identify the endogenous source of DNA damage that activates PARPs. We argued that if the toxicity of PARPis is indeed caused by unrepaired SSBs, these breaks must arise spontaneously, because PARPis are used as single agents. We now show that a significant contributor to PARPi toxicity is oxygen metabolism. While BRCA1-depleted or -mutated cells were hypersensitive to the clinically approved PARPi olaparib, its toxicity was significantly attenuated by depletion of OGG1 or MYH DNA glycosylases, as well as by treatment with reactive oxygen species scavengers, growth under hypoxic conditions or chemical OGG1 inhibition. Thus, clinical resistance to PARPi therapy may emerge simply through reduced efficiency of oxidative damage repair.
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Affiliation(s)
- Sara Giovannini
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Marie-Christine Weller
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Simone Repmann
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Holger Moch
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, CH-8091 Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
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8
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Porro A, Berti M, Pizzolato J, Bologna S, Kaden S, Saxer A, Ma Y, Nagasawa K, Sartori AA, Jiricny J. Author Correction: FAN1 interaction with ubiquitylated PCNA alleviates replication stress and preserves genomic integrity independently of BRCA2. Nat Commun 2017; 8:2285. [PMID: 29263317 PMCID: PMC5738404 DOI: 10.1038/s41467-017-02130-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Antonio Porro
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Matteo Berti
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Julia Pizzolato
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Serena Bologna
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.,Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Svenja Kaden
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Anja Saxer
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Josef Jiricny
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland. .,Institute of Molecular Life Sciences of the University of Zurich and Institute of Biochemistry of the ETH Zurich, Otto-Stern-Weg 3, Zurich, 8093, Switzerland.
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9
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Jiricny J. An appreciation of Sir Adrian Peter Bird: winner of the Charles Rodolphe Brupbacher Prize for Cancer Research 2017. Swiss Med Wkly 2017; 147:w14541. [PMID: 29039626 DOI: 10.4414/smw.2017.14541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Josef Jiricny
- Institute of Molecular Life Sciences, University of Zurich, Switzerland, and Institute of Biochemistry, ETH, Zurich, Switzerland
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10
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Peña-Diaz J, Bregenhorn S, Ghodgaonkar M, Follonier C, Artola-Borán M, Castor D, Lopes M, Sartori AA, Jiricny J. Noncanonical Mismatch Repair as a Source of Genomic Instability in Human Cells. Mol Cell 2017; 67:162. [PMID: 28686873 DOI: 10.1016/j.molcel.2017.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Hermans N, Laffeber C, Cristovão M, Artola-Borán M, Mardenborough Y, Ikpa P, Jaddoe A, Winterwerp HHK, Wyman C, Jiricny J, Kanaar R, Friedhoff P, Lebbink JHG. Dual daughter strand incision is processive and increases the efficiency of DNA mismatch repair. Nucleic Acids Res 2016; 44:6770-86. [PMID: 27174933 PMCID: PMC5001592 DOI: 10.1093/nar/gkw411] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 05/03/2016] [Indexed: 12/27/2022] Open
Abstract
DNA mismatch repair (MMR) is an evolutionarily-conserved process responsible for the repair of replication errors. In Escherichia coli, MMR is initiated by MutS and MutL, which activate MutH to incise transiently-hemimethylated GATC sites. MMR efficiency depends on the distribution of these GATC sites. To understand which molecular events determine repair efficiency, we quantitatively studied the effect of strand incision on unwinding and excision activity. The distance between mismatch and GATC site did not influence the strand incision rate, and an increase in the number of sites enhanced incision only to a minor extent. Two GATC sites were incised by the same activated MMR complex in a processive manner, with MutS, the closed form of MutL and MutH displaying different roles. Unwinding and strand excision were more efficient on a substrate with two nicks flanking the mismatch, as compared to substrates containing a single nick or two nicks on the same side of the mismatch. Introduction of multiple nicks by the human MutLα endonuclease also contributed to increased repair efficiency. Our data support a general model of prokaryotic and eukaryotic MMR in which, despite mechanistic differences, mismatch-activated complexes facilitate efficient repair by creating multiple daughter strand nicks.
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Affiliation(s)
- Nicolaas Hermans
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands
| | - Charlie Laffeber
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands
| | - Michele Cristovão
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands
| | - Mariela Artola-Borán
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - Yannicka Mardenborough
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands
| | - Pauline Ikpa
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands
| | - Aruna Jaddoe
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands
| | - Herrie H K Winterwerp
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, 1006 BE Amsterdam, The Netherlands
| | - Claire Wyman
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands Department of Radiation Oncology, Erasmus Medical Center Rotterdam, 3015 CE Rotterdam, The Netherlands
| | - Josef Jiricny
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
| | - Roland Kanaar
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands Department of Radiation Oncology, Erasmus Medical Center Rotterdam, 3015 CE Rotterdam, The Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus Medical Center Rotterdam, 3015 AA Rotterdam,The Netherlands Department of Radiation Oncology, Erasmus Medical Center Rotterdam, 3015 CE Rotterdam, The Netherlands
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12
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Bregenhorn S, Kallenberger L, Artola-Borán M, Peña-Diaz J, Jiricny J. Non-canonical uracil processing in DNA gives rise to double-strand breaks and deletions: relevance to class switch recombination. Nucleic Acids Res 2016; 44:2691-705. [PMID: 26743004 PMCID: PMC4824095 DOI: 10.1093/nar/gkv1535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/23/2015] [Indexed: 12/24/2022] Open
Abstract
During class switch recombination (CSR), antigen-stimulated B-cells rearrange their immunoglobulin constant heavy chain (CH) loci to generate antibodies with different effector functions. CSR is initiated by activation-induced deaminase (AID), which converts cytosines in switch (S) regions, repetitive sequences flanking the CH loci, to uracils. Although U/G mispairs arising in this way are generally efficiently repaired to C/Gs by uracil DNA glycosylase (UNG)-initiated base excision repair (BER), uracil processing in S-regions of activated B-cells occasionally gives rise to double strand breaks (DSBs), which trigger CSR. Surprisingly, genetic experiments revealed that CSR is dependent not only on AID and UNG, but also on mismatch repair (MMR). To elucidate the role of MMR in CSR, we studied the processing of uracil-containing DNA substrates in extracts of MMR-proficient and –deficient human cells, as well as in a system reconstituted from recombinant BER and MMR proteins. Here, we show that the interplay of these repair systems gives rise to DSBs in vitro and to genomic deletions and mutations in vivo, particularly in an S-region sequence. Our findings further suggest that MMR affects pathway choice in DSB repair. Given its amenability to manipulation, our system represents a powerful tool for the molecular dissection of CSR.
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Affiliation(s)
- Stephanie Bregenhorn
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Department of Biology, Swiss Federal Institute of Technology (ETH) Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lia Kallenberger
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Mariela Artola-Borán
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Javier Peña-Diaz
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland University of Copenhagen, Faculty of Health Sciences Center for Healthy Aging, Department of Neuroscience and Pharmacology, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Department of Biology, Swiss Federal Institute of Technology (ETH) Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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13
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Pizzolato J, Mukherjee S, Schärer OD, Jiricny J. FANCD2-associated nuclease 1, but not exonuclease 1 or flap endonuclease 1, is able to unhook DNA interstrand cross-links in vitro. J Biol Chem 2015. [PMID: 26221031 DOI: 10.1074/jbc.m115.663666] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cisplatin and its derivatives, nitrogen mustards and mitomycin C, are used widely in cancer chemotherapy. Their efficacy is linked primarily to their ability to generate DNA interstrand cross-links (ICLs), which effectively block the progression of transcription and replication machineries. Release of this block, referred to as unhooking, has been postulated to require endonucleases that incise one strand of the duplex on either side of the ICL. Here we investigated how the 5' flap nucleases FANCD2-associated nuclease 1 (FAN1), exonuclease 1 (EXO1), and flap endonuclease 1 (FEN1) process a substrate reminiscent of a replication fork arrested at an ICL. We now show that EXO1 and FEN1 cleaved the substrate at the boundary between the single-stranded 5' flap and the duplex, whereas FAN1 incised it three to four nucleotides in the double-stranded region. This affected the outcome of processing of a substrate containing a nitrogen mustard-like ICL two nucleotides in the duplex region because FAN1, unlike EXO1 and FEN1, incised the substrate predominantly beyond the ICL and, therefore, failed to release the 5' flap. We also show that FAN1 was able to degrade a linear ICL substrate. This ability of FAN1 to traverse ICLs in DNA could help to elucidate its biological function, which is currently unknown.
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Affiliation(s)
- Julia Pizzolato
- From the Institute of Molecular Cancer Research, University of Zurich and
| | | | - Orlando D Schärer
- the Departments of Chemistry and Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-3400
| | - Josef Jiricny
- From the Institute of Molecular Cancer Research, University of Zurich and the Department of Biology, Swiss Institute of Technology (ETH) Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland, and
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14
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Gentili C, Castor D, Kaden S, Lauterbach D, Gysi M, Steigemann P, Gerlich DW, Jiricny J, Ferrari S. Chromosome Missegregation Associated with RUVBL1 Deficiency. PLoS One 2015; 10:e0133576. [PMID: 26201077 PMCID: PMC4511761 DOI: 10.1371/journal.pone.0133576] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/30/2015] [Indexed: 12/31/2022] Open
Abstract
RUVBL1 (RuvB-like1) and RUVBL2 (RuvB-like 2) are integral components of multisubunit protein complexes involved in processes ranging from cellular metabolism, transcription and chromatin remodeling to DNA repair. Here, we show that although RUVBL1 and RUVBL2 are known to form heterodimeric complexes in which they stabilize each other, the subunits separate during cytokinesis. In anaphase-to-telophase transition, RUVBL1 localizes to structures of the mitotic spindle apparatus, where it partially co-localizes with polo-like kinase 1 (PLK1). The ability of PLK1 to phosphorylate RUVBL1-but not RUVBL2-in vitro and their physical association in vivo suggest that this kinase differentially regulates the function of the RuvB-like proteins during mitosis. We further show that siRNA-mediated knock-down of RuvB-like proteins causes severe defects in chromosome alignment and segregation. In addition, we show that the ATPase activity of RUVBL1 is indispensable for cell proliferation. Our data thus demonstrate that RUVBL1 is essential for efficient mitosis and proliferation.
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Affiliation(s)
- Christian Gentili
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Dennis Castor
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Svenja Kaden
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - David Lauterbach
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Mario Gysi
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Patrick Steigemann
- Institute of Biochemistry, Schafmattstrasse 18, HPM E17.2, Swiss Institute of Technology Zurich (ETHZ), CH-8093, Zurich, Switzerland
| | - Daniel W. Gerlich
- Institute of Biochemistry, Schafmattstrasse 18, HPM E17.2, Swiss Institute of Technology Zurich (ETHZ), CH-8093, Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Stefano Ferrari
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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15
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Repmann S, Olivera-Harris M, Jiricny J. Influence of oxidized purine processing on strand directionality of mismatch repair. J Biol Chem 2015; 290:9986-99. [PMID: 25694431 DOI: 10.1074/jbc.m114.629907] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/23/2022] Open
Abstract
Replicative DNA polymerases are high fidelity enzymes that misincorporate nucleotides into nascent DNA with a frequency lower than [1/10(5)], and this precision is improved to about [1/10(7)] by their proofreading activity. Because this fidelity is insufficient to replicate most genomes without error, nature evolved postreplicative mismatch repair (MMR), which improves the fidelity of DNA replication by up to 3 orders of magnitude through correcting biosynthetic errors that escaped proofreading. MMR must be able to recognize non-Watson-Crick base pairs and excise the misincorporated nucleotides from the nascent DNA strand, which carries by definition the erroneous genetic information. In eukaryotes, MMR is believed to be directed to the nascent strand by preexisting discontinuities such as gaps between Okazaki fragments in the lagging strand or breaks in the leading strand generated by the mismatch-activated endonuclease of the MutL homologs PMS1 in yeast and PMS2 in vertebrates. We recently demonstrated that the eukaryotic MMR machinery can make use also of strand breaks arising during excision of uracils or ribonucleotides from DNA. We now show that intermediates of MutY homolog-dependent excision of adenines mispaired with 8-oxoguanine (G(O)) also act as MMR initiation sites in extracts of human cells or Xenopus laevis eggs. Unexpectedly, G(O)/C pairs were not processed in these extracts and failed to affect MMR directionality, but extracts supplemented with exogenous 8-oxoguanine DNA glycosylase (OGG1) did so. Because OGG1-mediated excision of G(O) might misdirect MMR to the template strand, our findings suggest that OGG1 activity might be inhibited during MMR.
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Affiliation(s)
- Simone Repmann
- From the Institute of Molecular Cancer Research of the University of Zurich and the Swiss Institutes of Technology Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Maite Olivera-Harris
- From the Institute of Molecular Cancer Research of the University of Zurich and the Swiss Institutes of Technology Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Josef Jiricny
- From the Institute of Molecular Cancer Research of the University of Zurich and the Swiss Institutes of Technology Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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16
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Olivera Harris M, Kallenberger L, Artola Borán M, Enoiu M, Costanzo V, Jiricny J. Mismatch repair-dependent metabolism of O6-methylguanine-containing DNA in Xenopus laevis egg extracts. DNA Repair (Amst) 2015; 28:1-7. [PMID: 25697728 DOI: 10.1016/j.dnarep.2015.01.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 11/27/2022]
Abstract
The cytotoxicity of SN1-type alkylating agents such as N-methyl-N'-nitrosourea (MNU), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), or the cancer chemotherapeutics temozolomide, dacarbazine and streptozotocin has been ascribed to the persistence of O(6)-methylguanine ((me)G) in genomic DNA. One hypothesis posits that (me)G toxicity is caused by futile attempts of the mismatch repair (MMR) system to process (me)G/C or (me)G/T mispairs arising during replication, while an alternative proposal suggests that the latter lesions activate DNA damage signaling, cell cycle arrest and apoptosis directly. Attempts to elucidate the molecular mechanism of (me)G-induced cell killing in vivo have been hampered by the fact that the above reagents induce several types of modifications in genomic DNA, which are processed by different repair pathways. In contrast, defined substrates studied in vitro did not undergo replication. We set out to re-examine this phenomenon in replication-competent Xenopus laevis egg extracts, using either phagemid substrates containing a single (me)G residue, or methylated sperm chromatin. Our findings provide further support for the futile cycling hypothesis.
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Affiliation(s)
- Maite Olivera Harris
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Department of Biology, Swiss Federal Institute of Technology (ETH), Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lia Kallenberger
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Mariela Artola Borán
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Milica Enoiu
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Vincenzo Costanzo
- IFOM-European Institute of Oncology Campus, Via Adamello 16, 20139 Milano, Italy
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Department of Biology, Swiss Federal Institute of Technology (ETH), Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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Abstract
The emergence of resistance to cisplatin is a serious drawback of cancer therapy. To help elucidate the molecular basis of this resistance, we examined matched ovarian cancer cell lines that differ in their DNA mismatch repair (MMR) status and the response to cisplatin. Checkpoint activation by cisplatin was identical in both lines. However, sensitive cells delayed S-phase transition, arrested at G(2)/M and died by apoptosis. The G(2)/M block was characterized by selective disappearance of homologous recombination (HR) proteins, which likely resulted in incomplete repair of the cisplatin adducts. In contrast, resistant cells transiently arrested at G(2)/M, maintained constant levels of HR proteins and ultimately resumed cell cycle progression. The net contribution of MMR to the cisplatin response was examined using matched semi-isogenic (HCT116+/-chr3) or strictly isogenic (293T-Lalpha(-/+)) cell lines. Delayed transition through S-phase in response to cisplatin was also observed in the MMR-proficient HCT116+chr3 cells. Unlike in the ovarian cell lines, however, both HCT116+chr3 and HCT116 permanently arrested at G(2)/M with an intact complement of HR proteins and died by apoptosis. A similar G(2)/M arrest was observed in the strictly isogenic 293T-Lalpha(-/+) cells. This confirmed that although MMR undoubtedly contributes towards the cytotoxicity of cisplatin, it is only one of several pathways that modulate the cellular response to this drug. However, our data highlighted the importance of HR to cisplatin cytotoxicity and suggested that HR status might represent a novel prognostic marker and possibly also a therapeutic target, the inhibition of which would substantially sensitize cells to cisplatin chemotherapy.
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Affiliation(s)
- Elisabetta Pani
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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18
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Ghodgaonkar MM, Kehl P, Ventura I, Hu L, Bignami M, Jiricny J. Phenotypic characterization of missense polymerase-δ mutations using an inducible protein-replacement system. Nat Commun 2014; 5:4990. [PMID: 25241845 DOI: 10.1038/ncomms5990] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/14/2014] [Indexed: 01/12/2023] Open
Abstract
Next-generation sequencing has revolutionized the search for disease-causing genetic alterations. Unfortunately, the task of distinguishing the handful of causative mutations from rare variants remains daunting. We now describe an assay that permits the analysis of all types of mutations in any gene of choice through the generation of stable human cell lines, in which the endogenous protein has been inducibly replaced with its genetic variant. Here we studied the phenotype of variants of the essential replicative polymerase-δ carrying missense mutations in its active site, similar to those recently identified in familial colon cancer patients. We show that expression of the mutants but not the wild-type protein endows the engineered cells with a mutator phenotype and that the mutations affect the fidelity and/or the exonuclease activity of the isolated enzyme in vitro. This proof-of-principle study demonstrates the general applicability of this experimental approach in the study of genotype-phenotype correlations.
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Affiliation(s)
- Medini Manohar Ghodgaonkar
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Patrick Kehl
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Ilenia Ventura
- 1] Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland [2] Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 11061, Italy
| | - Liyan Hu
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Margherita Bignami
- 1] Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland [2] Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 11061, Italy
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
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Alvino E, Passarelli F, Cannavò E, Fortes C, Mastroeni S, Caporali S, Jiricny J, Cappellini GCA, Scoppola A, Marchetti P, Modesti A, D’Atri S. High expression of the mismatch repair protein MSH6 is associated with poor patient survival in melanoma. Am J Clin Pathol 2014; 142:121-32. [PMID: 24926095 DOI: 10.1309/ajcpcx2d9yulbblg] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES The outcome of patients with primary melanoma (PM) cannot be completely explained based on currently adopted clinical-histopathologic criteria. In this study, we evaluated the potential prognostic value of mismatch repair protein expression in PMs. METHODS We examined the immunohistochemical staining of mismatch repair proteins in 18 benign nevi and 101 stage I to III PMs and investigated their association with tumor clinicopathologic variables and melanoma mortality. RESULTS Expression of MSH2, MLH1, and PMS2 was high in benign nevi and reduced in a subset of PMs. Conversely, MSH6 expression was absent or extremely low in benign nevi and increased in a subset of PMs. In the multivariate analysis, including sex, age, Breslow thickness, and ulceration, high MSH6 expression in PMs (ie, immunostaining in >20% of tumor cells) was significantly associated with an increased risk of melanoma mortality (relative risk, 3.76; 95% confidence interval, 1.12-12.70). CONCLUSIONS MSH6 protein expression can be a valuable marker to improve prognosis assessment in PMs.
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Affiliation(s)
- Ester Alvino
- Institute of Translational Pharmacology, National Council of Research, Rome, Italy
| | | | - Elda Cannavò
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Cristina Fortes
- Epidemiology Unit, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Simona Mastroeni
- Epidemiology Unit, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Simona Caporali
- Laboratory of Molecular Oncology, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Alessandro Scoppola
- Department of Oncology and Dermatological Oncology, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Paolo Marchetti
- Department of Oncology, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Andrea Modesti
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata,” Rome, Italy
| | - Stefania D’Atri
- Laboratory of Molecular Oncology, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
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Abstract
Mutations in the mismatch repair (MMR) genes MSH2, MSH6, MLH1 and PMS2 are associated with Lynch Syndrome (LS), a familial predisposition to early-onset cancer of the colon and other organs. Because not all LS families carry mutations in these four genes, the search for cancer-associated mutations was extended to genes encoding other members of the mismatch repairosome. This effort identified mutations in EXO1, which encodes the sole exonuclease implicated in MMR. One of these mutations, E109K, was reported to abrogate the catalytic activity of the enzyme, yet, in the crystal structure of the EXO1/DNA complex, this glutamate is far away from both DNA and the catalytic site of the enzyme. In an attempt to elucidate the reason underlying the putative loss of function of this variant, we expressed it in Escherichia coli, and tested its activity in a series of biochemical assays. We now report that, contrary to earlier reports, and unlike the catalytic site mutant D173A, the EXO1 E109K variant resembled the wild-type (wt) enzyme on all tested substrates. In the light of our findings, we attempt here to reinterpret the results of the phenotypic characterization of a knock-in mouse carrying the E109K mutation and cells derived from it.
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Affiliation(s)
- Stephanie Bregenhorn
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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21
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Vonlanthen J, Okoniewski MJ, Menigatti M, Cattaneo E, Pellegrini-Ochsner D, Haider R, Jiricny J, Staiano T, Buffoli F, Marra G. A comprehensive look at transcription factor gene expression changes in colorectal adenomas. BMC Cancer 2014; 14:46. [PMID: 24472434 PMCID: PMC4078005 DOI: 10.1186/1471-2407-14-46] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological processes are controlled by transcription networks. Expression changes of transcription factor (TF) genes in precancerous lesions are therefore crucial events in tumorigenesis. Our aim was to obtain a comprehensive picture of these changes in colorectal adenomas. METHODS Using a 3-pronged selection procedure, we analyzed transcriptomic data on 34 human tissue samples (17 adenomas and paired samples of normal mucosa, all collected with ethics committee approval and written, informed patient consent) to identify TFs with highly significant tumor-associated gene expression changes whose potential roles in colorectal tumorigenesis have been under-researched. Microarray data were subjected to stringent statistical analysis of TF expression in tumor vs. normal tissues, MetaCore-mediated identification of TF networks displaying enrichment for genes that were differentially expressed in tumors, and a novel quantitative analysis of the publications examining the TF genes' roles in colorectal tumorigenesis. RESULTS The 261 TF genes identified with this procedure included DACH1, which plays essential roles in the proper proliferation and differentiation of retinal and leg precursor cell populations in Drosophila melanogaster. Its possible roles in colorectal tumorigenesis are completely unknown, but it was found to be markedly overexpressed (mRNA and protein) in all colorectal adenomas and in most colorectal carcinomas. However, DACH1 expression was absent in some carcinomas, most of which were DNA mismatch-repair deficient. When networks were built using the set of TF genes identified by all three selection procedures, as well as the entire set of transcriptomic changes in adenomas, five hub genes (TGFB1, BIRC5, MYB, NR3C1, and TERT) where identified as putatively crucial components of the adenomatous transformation process. CONCLUSION The transcription-regulating network of colorectal adenomas (compared with that of normal colorectal mucosa) is characterized by significantly altered expression of over 250 TF genes, many of which have never been investigated in relation to colorectal tumorigenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, Zurich 8051, Switzerland.
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Tiwari A, Schneider M, Fiorino A, Haider R, Okoniewski MJ, Roschitzki B, Uzozie A, Menigatti M, Jiricny J, Marra G. Early insights into the function of KIAA1199, a markedly overexpressed protein in human colorectal tumors. PLoS One 2013; 8:e69473. [PMID: 23936024 PMCID: PMC3720655 DOI: 10.1371/journal.pone.0069473] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 06/10/2013] [Indexed: 12/28/2022] Open
Abstract
We previously reported that the expression of KIAA1199 in human colorectal tumors (benign and malignant) is markedly higher than that in the normal colonic mucosa. In this study, we investigated the functions of the protein encoded by this gene, which are thus far unknown. Immunostaining studies were used to reveal its subcellular localization, and proteomic and gene expression experiments were conducted to identify proteins that might interact with KIAA1199 and molecular pathways in which it might play roles. Using colon cancer cell lines, we showed that both endogenous and ectopically expressed KIAA1199 is secreted into the extracellular environment. In the cells, it was found mainly in the perinuclear space (probably the ER) and cell membrane. Both cellular compartments were also over-represented in lists of proteins identified by mass spectrometry as putative KIAA1199 interactors and/or proteins encoded by genes whose transcription was significantly changed by KIAA1199 expression. These proteomic and transcriptomic datasets concordantly link KIAA1199 to several genes/proteins and molecular pathways, including ER processes like protein binding, transport, and folding; and Ca2+, G-protein, ephrin, and Wnt signaling. Immunoprecipitation experiments confirmed KIAA1199’s interaction with the cell-membrane receptor ephrin A2 and with the ER receptor ITPR3, a key player in Ca2+ signaling. By modulating Ca2+ signaling, KIAA1199 could affect different branches of the Wnt network. Our findings suggest it may negatively regulate the Wnt/CTNNB1 signaling, and its expression is associated with decreased cell proliferation and invasiveness.
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Affiliation(s)
- Amit Tiwari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mirjam Schneider
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Antonio Fiorino
- Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Ritva Haider
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Michal J. Okoniewski
- Functional Genomics Center of the ETH and University of Zurich, Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center of the ETH and University of Zurich, Zurich, Switzerland
| | - Anuli Uzozie
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- * E-mail:
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Menigatti M, Staiano T, Manser CN, Bauerfeind P, Komljenovic A, Robinson M, Jiricny J, Buffoli F, Marra G. Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions. Oncogenesis 2013; 2:e56. [PMID: 23857251 PMCID: PMC3740287 DOI: 10.1038/oncsis.2013.21] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/10/2013] [Accepted: 05/15/2013] [Indexed: 12/15/2022] Open
Abstract
Epigenetic silencing of protein-encoding genes is common in early-stage colorectal tumorigenesis. Less is known about the methylation-mediated silencing of genes encoding microRNAs (miRNAs), which are also important epigenetic modulators of gene expression. Using quantitative PCR, we identified 56 miRNAs that were expressed in normal colorectal mucosa and in HT29 colorectal cancer cells treated with demethylating agents but not in untreated HT29 cells, suggesting that they probably undergo methylation-induced silencing during colorectal tumorigenesis. One of these, miR-195, had recently been reported to be underexpressed in colorectal cancers and to exert tumor-suppressor effects in colorectal cancer cells. We identified the transcription start site (TSS) for primary miRNA (pri-miR)-497/195, the primary precursor that yields miR-195 and another candidate on our list, miR-497, and a single CpG island upstream to the TSS, which controls expression of both miRNAs. Combined bisulfite restriction analysis and bisulfite genomic sequencing studies revealed monoallelic methylation of this island in normal colorectal mucosa (50/50 samples) and full methylation in most colorectal adenomas (38/50; 76%). The hypermethylated precancerous lesions displayed significantly downregulated expression of both miRNAs. Similar methylation patterns were observed at two known imprinted genes, MEG3 and GNAS-AS1, which encode several of the 56 miRNAs on our list. Imprinting at these loci was lost in over half the adenomas (62% at MEG3 and 52% at GNAS-AS1). Copy-number alterations at MEG3, GNAS-AS1 and pri-miR-497/195, which are frequent in colorectal cancers, were less common in adenomas and confined to tumors displaying differential methylation at the involved locus. Our data show that somatically acquired, epigenetic changes at monoallelically methylated regions encoding miRNAs are relatively frequent in sporadic colorectal adenomas and might contribute to the onset and progression of these tumors.
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Affiliation(s)
- M Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - T Staiano
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - C N Manser
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - P Bauerfeind
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - A Komljenovic
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - M Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - J Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - F Buffoli
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - G Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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Ghodgaonkar MM, Lazzaro F, Olivera-Pimentel M, Artola-Borán M, Cejka P, Reijns MA, Jackson AP, Plevani P, Muzi-Falconi M, Jiricny J. Ribonucleotides misincorporated into DNA act as strand-discrimination signals in eukaryotic mismatch repair. Mol Cell 2013; 50:323-32. [PMID: 23603115 PMCID: PMC3653069 DOI: 10.1016/j.molcel.2013.03.019] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/30/2013] [Accepted: 03/14/2013] [Indexed: 11/28/2022]
Abstract
To improve replication fidelity, mismatch repair (MMR) must detect non-Watson-Crick base pairs and direct their repair to the nascent DNA strand. Eukaryotic MMR in vitro requires pre-existing strand discontinuities for initiation; consequently, it has been postulated that MMR in vivo initiates at Okazaki fragment termini in the lagging strand and at nicks generated in the leading strand by the mismatch-activated MLH1/PMS2 endonuclease. We now show that a single ribonucleotide in the vicinity of a mismatch can act as an initiation site for MMR in human cell extracts and that MMR activation in this system is dependent on RNase H2. As loss of RNase H2 in S.cerevisiae results in a mild MMR defect that is reflected in increased mutagenesis, MMR in vivo might also initiate at RNase H2-generated nicks. We therefore propose that ribonucleotides misincoporated during DNA replication serve as physiological markers of the nascent DNA strand.
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Affiliation(s)
- Medini Manohar Ghodgaonkar
- Institute of Molecular Cancer Research of the University of Zurich and ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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25
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Abstract
The mismatch repair (MMR) system detects non-Watson-Crick base pairs and strand misalignments arising during DNA replication and mediates their removal by catalyzing excision of the mispair-containing tract of nascent DNA and its error-free resynthesis. In this way, MMR improves the fidelity of replication by several orders of magnitude. It also addresses mispairs and strand misalignments arising during recombination and prevents synapses between nonidentical DNA sequences. Unsurprisingly, MMR malfunction brings about genomic instability that leads to cancer in mammals. But MMR proteins have recently been implicated also in other processes of DNA metabolism, such as DNA damage signaling, antibody diversification, and repair of interstrand cross-links and oxidative DNA damage, in which their functions remain to be elucidated. This article reviews the progress in our understanding of the mechanism of replication error repair made during the past decade.
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Affiliation(s)
- Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland.
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26
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Campo VA, Patenaude AM, Kaden S, Horb L, Firka D, Jiricny J, Di Noia JM. MSH6- or PMS2-deficiency causes re-replication in DT40 B cells, but it has little effect on immunoglobulin gene conversion or on repair of AID-generated uracils. Nucleic Acids Res 2013; 41:3032-46. [PMID: 23314153 PMCID: PMC3597665 DOI: 10.1093/nar/gks1470] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mammalian antibody repertoire is shaped by somatic hypermutation (SHM) and class switch recombination (CSR) of the immunoglobulin (Ig) loci of B lymphocytes. SHM and CSR are triggered by non-canonical, error-prone processing of G/U mismatches generated by activation-induced deaminase (AID). In birds, AID does not trigger SHM, but it triggers Ig gene conversion (GC), a ‘homeologous’ recombination process involving the Ig variable region and proximal pseudogenes. Because recombination fidelity is controlled by the mismatch repair (MMR) system, we investigated whether MMR affects GC in the chicken B cell line DT40. We show here that Msh6−/− and Pms2−/− DT40 cells display cell cycle defects, including genomic re-replication. However, although IgVλ GC tracts in MMR-deficient cells were slightly longer than in normal cells, Ig GC frequency, donor choice or the number of mutations per sequence remained unaltered. The finding that the avian MMR system, unlike that of mammals, does not seem to contribute towards the processing of G/U mismatches in vitro could explain why MMR is unable to initiate Ig GC in this species, despite initiating SHM and CSR in mammalian cells. Moreover, as MMR does not counteract or govern Ig GC, we report a rare example of ‘homeologous’ recombination insensitive to MMR.
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Affiliation(s)
- Vanina A Campo
- Institut de Recherches Cliniques de Montréal, Division of Immunity and Viral Infections, Montréal, H2W 1R7 Québec, Canada
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27
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Peña-Diaz J, Bregenhorn S, Ghodgaonkar M, Follonier C, Artola-Borán M, Castor D, Lopes M, Sartori AA, Jiricny J. Noncanonical mismatch repair as a source of genomic instability in human cells. Mol Cell 2012; 47:669-80. [PMID: 22864113 DOI: 10.1016/j.molcel.2012.07.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/19/2012] [Accepted: 06/29/2012] [Indexed: 11/24/2022]
Abstract
Mismatch repair (MMR) is a key antimutagenic process that increases the fidelity of DNA replication and recombination. Yet genetic experiments showed that MMR is required for antibody maturation, a process during which the immunoglobulin loci of antigen-stimulated B cells undergo extensive mutagenesis and rearrangements. In an attempt to elucidate the mechanism underlying the latter events, we set out to search for conditions that compromise MMR fidelity. Here, we describe noncanonical MMR (ncMMR), a process in which the MMR pathway is activated by various DNA lesions rather than by mispairs. ncMMR is largely independent of DNA replication, lacks strand directionality, triggers PCNA monoubiquitylation, and promotes recruitment of the error-prone polymerase-η to chromatin. Importantly, ncMMR is not limited to B cells but occurs also in other cell types. Moreover, it contributes to mutagenesis induced by alkylating agents. Activation of ncMMR may therefore play a role in genomic instability and cancer.
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Affiliation(s)
- Javier Peña-Diaz
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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28
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Enoiu M, Jiricny J, Schärer OD. Repair of cisplatin-induced DNA interstrand crosslinks by a replication-independent pathway involving transcription-coupled repair and translesion synthesis. Nucleic Acids Res 2012; 40:8953-64. [PMID: 22810206 PMCID: PMC3467066 DOI: 10.1093/nar/gks670] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) formed by antitumor agents, such as cisplatin or mitomycin C, are highly cytotoxic DNA lesions. Their repair is believed to be triggered primarily by the stalling of replication forks at ICLs in S-phase. There is, however, increasing evidence that ICL repair can also occur independently of replication. Using a reporter assay, we describe a pathway for the repair of cisplatin ICLs that depends on transcription-coupled nucleotide excision repair protein CSB, the general nucleotide excision repair factors XPA, XPF and XPG, but not the global genome nucleotide excision repair factor XPC. In this pathway, Rev1 and Polζ are involved in the error-free bypass of cisplatin ICLs. The requirement for CSB, Rev1 or Polζ is specific for the repair of ICLs, as the repair of cisplatin intrastrand crosslinks does not require these genes under identical conditions. We directly show that this pathway contributes to the removal of ICLs outside of S-phase. Finally, our studies reveal that defects in replication- and transcription-dependent pathways are additive in terms of cellular sensitivity to treatment with cisplatin or mitomycin C. We conclude that transcription- and replication-dependent pathways contribute to cellular survival following treatment with crosslinking agents.
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Affiliation(s)
- Milica Enoiu
- Institute of Molecular Cancer Research, University of Zürich, 8057 Zürich, Switzerland
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Vasovcak P, Krepelova A, Menigatti M, Puchmajerova A, Skapa P, Augustinakova A, Amann G, Wernstedt A, Jiricny J, Marra G, Wimmer K. Unique mutational profile associated with a loss of TDG expression in the rectal cancer of a patient with a constitutional PMS2 deficiency. DNA Repair (Amst) 2012; 11:616-23. [PMID: 22608206 PMCID: PMC3387372 DOI: 10.1016/j.dnarep.2012.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/21/2012] [Accepted: 04/24/2012] [Indexed: 12/14/2022]
Abstract
Cells with DNA repair defects have increased genomic instability and are more likely to acquire secondary mutations that bring about cellular transformation. We describe the frequency and spectrum of somatic mutations involving several tumor suppressor genes in the rectal carcinoma of a 13-year-old girl harboring biallelic, germline mutations in the DNA mismatch repair gene PMS2. Apart from microsatellite instability, the tumor DNA contained a number of C:G → T:A or G:C → A:T transitions in CpG dinucleotides, which often result through spontaneous deamination of cytosine or 5-methylcytosine. Four DNA glycosylases, UNG2, SMUG1, MBD4 and TDG, are involved in the repair of these deamination events. We identified a heterozygous missense mutation in TDG, which was associated with TDG protein loss in the tumor. The CpGs mutated in this patient's tumor are generally methylated in normal colonic mucosa. Thus, it is highly likely that loss of TDG contributed to the supermutator phenotype and that most of the point mutations were caused by deamination of 5-methylcytosine to thymine, which remained uncorrected owing to the TDG deficiency. This case provides the first in vivo evidence of the key role of TDG in protecting the human genome against the deleterious effects of 5-methylcytosine deamination.
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Affiliation(s)
- P Vasovcak
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, V Uvalu 84, 15006 Prague 5, Czech Republic.
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Peña-Diaz J, Jiricny J. Mammalian mismatch repair: error-free or error-prone? Trends Biochem Sci 2012; 37:206-14. [PMID: 22475811 DOI: 10.1016/j.tibs.2012.03.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 02/15/2012] [Accepted: 03/01/2012] [Indexed: 01/13/2023]
Abstract
A considerable surge of interest in the mismatch repair (MMR) system has been brought about by the discovery of a link between Lynch syndrome, an inherited predisposition to cancer of the colon and other organs, and malfunction of this key DNA metabolic pathway. This review focuses on recent advances in our understanding of the molecular mechanisms of canonical MMR, which improves replication fidelity by removing misincorporated nucleotides from the nascent DNA strand. We also discuss the involvement of MMR proteins in two other processes: trinucleotide repeat expansion and antibody maturation, in which MMR proteins are required for mutagenesis rather than for its prevention.
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Affiliation(s)
- Javier Peña-Diaz
- Institute of Molecular Cancer Research of the University of Zurich, Switzerland
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Dittrich CM, Kratz K, Sendoel A, Gruenbaum Y, Jiricny J, Hengartner MO. LEM-3 - A LEM domain containing nuclease involved in the DNA damage response in C. elegans. PLoS One 2012; 7:e24555. [PMID: 22383942 PMCID: PMC3285610 DOI: 10.1371/journal.pone.0024555] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 08/12/2011] [Indexed: 11/20/2022] Open
Abstract
The small nematode Caenorhabditis elegans displays a spectrum of DNA damage responses similar to humans. In order to identify new DNA damage response genes, we isolated in a forward genetic screen 14 new mutations conferring hypersensitivity to ionizing radiation. We present here our characterization of lem-3, one of the genes identified in this screen. LEM-3 contains a LEM domain and a GIY nuclease domain. We confirm that LEM-3 has DNase activity in vitro. lem-3(lf) mutants are hypersensitive to various types of DNA damage, including ionizing radiation, UV-C light and crosslinking agents. Embryos from irradiated lem-3 hermaphrodites displayed severe defects during cell division, including chromosome mis-segregation and anaphase bridges. The mitotic defects observed in irradiated lem-3 mutant embryos are similar to those found in baf-1 (barrier-to-autointegration factor) mutants. The baf-1 gene codes for an essential and highly conserved protein known to interact with the other two C. elegans LEM domain proteins, LEM-2 and EMR-1. We show that baf-1, lem-2, and emr-1 mutants are also hypersensitive to DNA damage and that loss of lem-3 sensitizes baf-1 mutants even in the absence of DNA damage. Our data suggest that BAF-1, together with the LEM domain proteins, plays an important role following DNA damage – possibly by promoting the reorganization of damaged chromatin.
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Affiliation(s)
- Christina M. Dittrich
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Molecular Life Sciences PhD program, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Katja Kratz
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Ataman Sendoel
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Yosef Gruenbaum
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Michael O. Hengartner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- * E-mail:
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Brachner A, Braun J, Ghodgaonkar M, Castor D, Zlopaša L, Ehrlich V, Jiricny J, Gotzmann J, Knasmüller S, Foisner R. The endonuclease Ankle1 requires its LEM and GIY-YIG motifs for DNA cleavage in vivo. J Cell Sci 2012; 125:1048-57. [PMID: 22399800 PMCID: PMC4335191 DOI: 10.1242/jcs.098392] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The LEM domain (for lamina-associated polypeptide, emerin, MAN1 domain) defines a group of nuclear proteins that bind chromatin through interaction of the LEM motif with the conserved DNA crosslinking protein, barrier-to-autointegration factor (BAF). Here, we describe a LEM protein annotated in databases as 'Ankyrin repeat and LEM domain-containing protein 1' (Ankle1). We show that Ankle1 is conserved in metazoans and contains a unique C-terminal GIY-YIG motif that confers endonuclease activity in vitro and in vivo. In mammals, Ankle1 is predominantly expressed in hematopoietic tissues. Although most characterized LEM proteins are components of the inner nuclear membrane, ectopic Ankle1 shuttles between cytoplasm and nucleus. Ankle1 enriched in the nucleoplasm induces DNA cleavage and DNA damage response. This activity requires both the catalytic C-terminal GIY-YIG domain and the LEM motif, which binds chromatin via BAF. Hence, Ankle1 is an unusual LEM protein with a GIY-YIG-type endonuclease activity in higher eukaryotes.
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Affiliation(s)
- Andreas Brachner
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Juliane Braun
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Medini Ghodgaonkar
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | - Dennis Castor
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | - Livija Zlopaša
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Veronika Ehrlich
- Institute of Cancer Research, Inner Medicine I, Medical University of Vienna, Austria
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | - Josef Gotzmann
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Siegfried Knasmüller
- Institute of Cancer Research, Inner Medicine I, Medical University of Vienna, Austria
| | - Roland Foisner
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
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Kovac M, Laczko E, Haider R, Jiricny J, Mueller H, Heinimann K, Marra G. Familial colorectal cancer: eleven years of data from a registry program in Switzerland. Fam Cancer 2012; 10:605-16. [PMID: 21671081 DOI: 10.1007/s10689-011-9458-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Deleterious germ-line variants involving the DNA mismatch repair (MMR) genes have been identified as the cause of the hereditary nonpolyposis colorectal cancer syndrome known as the Lynch syndrome, but in numerous familial clusters of colon cancer, the cause remains obscure. We analyzed data for 235 German-speaking Swiss families with nonpolyposis forms of colorectal cancer (one of the largest and most ethnically homogeneous cohorts of its kind) to identify the phenotypic features of forms that cannot be explained by MMR deficiency. Based on the results of microsatellite instability analysis and immunostaining of proband tumor samples, the kindreds were classified as MMR-proficient (n = 134, 57%) or MMR-deficient (n = 101, 43%). In 81 of the latter kindreds, deleterious germ-line MMR-gene variants have already been found (62 different variants, including 13 that have not been previously reported), confirming the diagnosis of Lynch syndrome. Compared with MMR-deficient kindreds, the 134 who were MMR proficient were less likely to meet the Amsterdam Criteria II regarding autosomal dominant transmission. They also had primary cancers with later onset and colon-segment distribution patterns resembling those of sporadic colorectal cancers, and they had lower frequencies of metachronous colorectal cancers and extracolonic cancers in general. Although the predisposition to colorectal cancer in these kindreds is probably etiologically heterogeneous, we were unable to identify distinct phenotypic subgroups solely on the basis of the clinical data collected in this study. Further insight, however, is expected to emerge from the molecular characterization of their tumors.
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Affiliation(s)
- Michal Kovac
- Research Group Human Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
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Cattaneo E, Laczko E, Buffoli F, Zorzi F, Bianco MA, Menigatti M, Bartosova Z, Haider R, Helmchen B, Sabates-Bellver J, Tiwari A, Jiricny J, Marra G. Preinvasive colorectal lesion transcriptomes correlate with endoscopic morphology (polypoid vs. nonpolypoid). EMBO Mol Med 2011; 3:334-47. [PMID: 21538994 PMCID: PMC3377079 DOI: 10.1002/emmm.201100141] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 03/22/2011] [Accepted: 03/22/2011] [Indexed: 01/10/2023] Open
Abstract
Improved colonoscopy is revealing precancerous lesions that were frequently missed in the past, and ∼30% of those detected today have nonpolypoid morphologies ranging from slightly raised to depressed. To characterize these lesions molecularly, we assessed transcription of 23,768 genes in 42 precancerous lesions (25 slightly elevated nonpolypoid and 17 pedunculated polypoid), each with corresponding samples of normal mucosa. Nonpolypoid versus polypoid morphology explained most gene expression variance among samples; histology, size, and degree of dysplasia were also linked to specific patterns. Expression changes in polypoid lesions frequently affected cell-cycling pathways, whereas cell-survival dysregulation predominated in nonpolypoid lesions. The latter also displayed fewer and less dramatic expression changes than polypoid lesions. Paradigmatic of this trend was progressive loss through the normal > nonpolypoid > polypoid > cancer sequence of TMIGD1 mRNA and protein. This finding, along with TMIGD1 protein expression patterns in tissues and cell lines, suggests that TMIGD1 might be associated with intestinal-cell differentiation. We conclude that molecular dysregulation in slightly elevated, nonpolypoid, precancerous colorectal lesions may be somewhat less severe than that observed in classic adenomatous polyps.
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Affiliation(s)
- Elisa Cattaneo
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
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Veljkovic E, Jiricny J, Menigatti M, Rehrauer H, Han W. Chronic exposure to cigarette smoke condensate in vitro induces epithelial to mesenchymal transition-like changes in human bronchial epithelial cells, BEAS-2B. Toxicol In Vitro 2011; 25:446-53. [PMID: 21095227 DOI: 10.1016/j.tiv.2010.11.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 11/08/2010] [Accepted: 11/16/2010] [Indexed: 12/11/2022]
Abstract
Cigarette smoke causes lung tumorigenesis; however, the mechanisms underlying transformation are unknown. We investigated if tobacco compounds induce DNA promoter hypermethylation in BEAS-2B cells treated with low doses of cigarette smoke condensate (CSC) for one month. Transcriptional profiles and anchorage-independent growth were explored using Affymetrix microarray and soft agar assay, respectively. To investigate if tobacco compounds induce hypermethylation, CSC/dimethyl sulfoxide (DMSO)-treated cells were further treated with 5-Aza-2'-deoxycytidine (5AzaC) and trychostatin A (TSA). This treatment was followed by transcriptional profiling. CSC-exposed cells acquired a fibroblast-like shape with enhanced anchorage-independent growth. Silencing of epithelial cadherin, the hallmark of epithelial to mesenchymal transition (EMT), was observed upon exposure to CSC. Changes in the expression of genes involved in epidermal development, intercellular junction formation, and cytoskeleton formation were identified. Gene expression profiles from 5AzaC- and TSA-treated cells revealed 130 genes possibly methylated due to chronic CSC exposure. Our results suggest that E-cadherin may also be silenced by hypermethylation in an in vitro model of chronic exposure to low doses of CSC. This study demonstrates evidence for a tobacco compound induced EMT-like process in vitro and provides insight into possible mechanisms of gene silencing occurring during this treatment.
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Affiliation(s)
- Emilija Veljkovic
- Philip Morris International R&D, Philip Morris Products SA, Neuchâtel, Switzerland.
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36
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Cortázar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, Steinacher R, Jiricny J, Bird A, Schär P. Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Nature 2011; 470:419-23. [PMID: 21278727 DOI: 10.1038/nature09672] [Citation(s) in RCA: 286] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 11/17/2010] [Indexed: 12/18/2022]
Abstract
Thymine DNA glycosylase (TDG) is a member of the uracil DNA glycosylase (UDG) superfamily of DNA repair enzymes. Owing to its ability to excise thymine when mispaired with guanine, it was proposed to act against the mutability of 5-methylcytosine (5-mC) deamination in mammalian DNA. However, TDG was also found to interact with transcription factors, histone acetyltransferases and de novo DNA methyltransferases, and it has been associated with DNA demethylation in gene promoters following activation of transcription, altogether implicating an engagement in gene regulation rather than DNA repair. Here we use a mouse genetic approach to determine the biological function of this multifaceted DNA repair enzyme. We find that, unlike other DNA glycosylases, TDG is essential for embryonic development, and that this phenotype is associated with epigenetic aberrations affecting the expression of developmental genes. Fibroblasts derived from Tdg null embryos (mouse embryonic fibroblasts, MEFs) show impaired gene regulation, coincident with imbalanced histone modification and CpG methylation at promoters of affected genes. TDG associates with the promoters of such genes both in fibroblasts and in embryonic stem cells (ESCs), but epigenetic aberrations only appear upon cell lineage commitment. We show that TDG contributes to the maintenance of active and bivalent chromatin throughout cell differentiation, facilitating a proper assembly of chromatin-modifying complexes and initiating base excision repair to counter aberrant de novo methylation. We thus conclude that TDG-dependent DNA repair has evolved to provide epigenetic stability in lineage committed cells.
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Affiliation(s)
- Daniel Cortázar
- Department of Biomedicine, Institute of Biochemistry and Genetics, University of Basel, 4048 Basel, Switzerland
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Kratz K, Schöpf B, Kaden S, Sendoel A, Eberhard R, Lademann C, Cannavó E, Sartori AA, Hengartner MO, Jiricny J. Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensitizes cells to interstrand crosslinking agents. Cell 2010; 142:77-88. [PMID: 20603016 DOI: 10.1016/j.cell.2010.06.022] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/29/2010] [Accepted: 06/15/2010] [Indexed: 11/28/2022]
Abstract
Cytotoxicity of cisplatin and mitomycin C (MMC) is ascribed largely to their ability to generate interstrand crosslinks (ICLs) in DNA, which block the progression of replication forks. The processing of ICLs requires the Fanconi anemia (FA) pathway, excision repair, and translesion DNA synthesis (TLS). It also requires homologous recombination (HR), which repairs double-strand breaks (DSBs) generated by cleavage of the blocked replication forks. Here we describe KIAA1018, an evolutionarily conserved protein that has an N-terminal ubiquitin-binding zinc finger (UBZ) and a C-terminal nuclease domain. KIAA1018 is a 5'-->3' exonuclease and a structure-specific endonuclease that preferentially incises 5' flaps. Like cells from FA patients, human cells depleted of KIAA1018 are sensitized to ICL-inducing agents and display chromosomal instability. The link of KIAA1018 to the FA pathway is further strengthened by its recruitment to DNA damage through interaction of its UBZ domain with monoubiquitylated FANCD2. We therefore propose to name KIAA1018 FANCD2-associated nuclease, FAN1.
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Affiliation(s)
- Katja Kratz
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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38
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Abstract
High-resolution crystal structures of DNA complexes with the bacterial MutM protein show how the enzyme feels its way around the double helix in search of an oxidized guanine before flipping it out into its active site and excising it.
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Affiliation(s)
- Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich and ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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Menigatti M, Cattaneo E, Sabates-Bellver J, Ilinsky VV, Went P, Buffoli F, Marquez VE, Jiricny J, Marra G. The protein tyrosine phosphatase receptor type R gene is an early and frequent target of silencing in human colorectal tumorigenesis. Mol Cancer 2009; 8:124. [PMID: 20015382 PMCID: PMC2801661 DOI: 10.1186/1476-4598-8-124] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 12/16/2009] [Indexed: 12/19/2022] Open
Abstract
Background Tumor development in the human colon is commonly accompanied by epigenetic changes, such as DNA methylation and chromatin modifications. These alterations result in significant, inheritable changes in gene expression that contribute to the selection of tumor cells with enhanced survival potential. Results A recent high-throughput gene expression analysis conducted by our group identified numerous genes whose transcription was markedly diminished in colorectal tumors. One of these, the protein-tyrosine phosphatase receptor type R (PTPRR) gene, was dramatically downregulated from the earliest stages of cellular transformation. Here, we show that levels of both major PTPRR transcript variants are markedly decreased (compared with normal mucosal levels) in precancerous and cancerous colorectal tumors, as well in colorectal cancer cell lines. The expression of the PTPRR-1 isoform was inactivated in colorectal cancer cells as a result of de novo CpG island methylation and enrichment of transcription-repressive histone-tail marks, mainly H3K27me3. De novo methylation of the PTPRR-1 transcription start site was demonstrated in 29/36 (80%) colorectal adenomas, 42/44 (95%) colorectal adenocarcinomas, and 8/8 (100%) liver metastases associated with the latter tumors. Conclusions Epigenetic downregulation of PTPRR seems to be an early alteration in colorectal cell transformation, which is maintained during the clonal selection associated with tumor progression. It may represent a preliminary step in the constitutive activation of the RAS/RAF/MAPK/ERK signalling, an effect that will later be consolidated by mutations in genes encoding key components of this pathway.
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Affiliation(s)
- Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Switzerland.
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Abstract
Whether 5-methylcytosine (meC) can be enzymatically removed from vertebrate DNA has been the subject of extensive study and also some controversy. Rai et al. (2008) now report that cytosine demethylation can be accomplished in a one-cell zebrafish embryo by the combined action of a cytidine deaminase and a thymine DNA glycosylase.
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Affiliation(s)
- Josef Jiricny
- Department of Biology, Swiss Federal Institutes of Technology (ETH), 8057 Zurich, Switzerland.
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Abstract
The human mismatch repair (MMR) gene MSH2 is the second most frequently mutated hereditary nonpolyposis colorectal cancer (HNPCC) susceptibility locus. Given that missense mutations account for 17% of all identified alterations in this gene, the study of their pathogenicity is of increasing importance. Previously, we showed that pathogenic MSH2 missense mutations typically impaired the repair activity of the protein. In this study, we took advantage of its crystal structure and attempted to correlate the mismatch binding and ATP-catalyzed mismatch release activities with the location of 18 nontruncating MSH2 mutations. We observed that the MMR-deficient mutations situated in the amino-terminal connector and lever domains of MSH2 (V161D, G162R, G164R, L173P, L187P, C333Y, and D603N) affected protein stability, whereas mutations in the ATPase domain (A636P, G674A, C697F, I745_I746del, and E749 K) mainly caused defects in mismatch binding or release. Of the MMR-proficient variants, four (T33P, A272 V, G322D, and V923E) showed slightly reduced mismatch binding and/or release efficiencies compared to wild-type (WT) protein, while two variants (N127S and A834 T) showed no defects in the assays. Similar to our biochemical data, the mutations that affected protein stability were associated with an absence of the protein in tumors in immunohistochemical (IHC) analyses. In contrast, the protein with the mutation E749 K, which abrogates MMR but not protein stability, is well expressed in tumors. In conclusion, pathogenic missense mutations in MSH2 may interfere with different mechanisms that tend to cluster in separate protein domains with varying effects on protein stability, which could be taken into account when interpreting IHC data.
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Affiliation(s)
- Saara Ollila
- Department of Biological and Environmental Sciences, Genetics, University of Helsinki, Helsinki, Finland
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Bujalkova M, Zavodna K, Krivulcik T, Ilencikova D, Wolf B, Kovac M, Karner-Hanusch J, Heinimann K, Marra G, Jiricny J, Bartosova Z. Multiplex SNaPshot genotyping for detecting loss of heterozygosity in the mismatch-repair genes MLH1 and MSH2 in microsatellite-unstable tumors. Clin Chem 2008; 54:1844-54. [PMID: 18772310 DOI: 10.1373/clinchem.2008.108902] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND In the workup of patients with suspected hereditary nonpolyposis colorectal cancer (HNPCC), detection of loss of heterozygosity (LOH) could help pinpoint the mismatch-repair (MMR) gene carrying the germline mutation, but analysis of microsatellite markers has proved unreliable for this purpose. We developed a simple, low-cost method based on single-nucleotide polymorphism (SNP) genotyping and capillary electrophoresis for the assessment of LOH at 2 MMR loci simultaneously. METHODS We used the Applied Biosystems SNaPshot Multiplex Kit with meticulously selected primers to assess 14 common SNPs in MLH1 [mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)] and MSH2 [mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)] and optimized the protocol for DNA isolated from peripheral blood and fresh/frozen or archival microsatellite-unstable tumors from patients with confirmed (n = 42) or suspected (n = 25) HNPCC. The 42 tumors from patients with confirmed MLH1 or MSH2 germline mutations were used to validate the method's diagnostic accuracy against results obtained with DNA sequencing or multiplex ligation-dependent probe amplification. RESULTS The SNaPshot assay provided better detection of certain SNPs than DNA sequencing. The MLH1 and MSH2 SNP marker sets were informative in 82% and 76% of the 67 cases analyzed, respectively. The new assay displayed 100% specificity for detecting LOH and predicted the location of the germline mutation in 40% of the cases (54% of those involving MLH1, 22% in MSH2). CONCLUSIONS Our SNP-based method for detecting LOH in MLH1 and MSH2 is simple to perform with instruments available in most clinical genetics laboratories. It can be a valuable addition to protocols now used to guide mutational screening of patients with suspected HNPCC.
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Affiliation(s)
- Maria Bujalkova
- Laboratory of Cancer Genetics, Cancer Research Institute of Slovak Academy of Sciences, Bratislava, Slovakia
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Mojas N, Lopes M, Jiricny J. Mismatch repair-dependent processing of methylation damage gives rise to persistent single-stranded gaps in newly replicated DNA. Genes Dev 2008; 21:3342-55. [PMID: 18079180 DOI: 10.1101/gad.455407] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
O(6)-Methylguanine ((Me)G) is a highly cytotoxic DNA modification generated by S(N)1-type methylating agents. Despite numerous studies implicating DNA replication, mismatch repair (MMR), and homologous recombination (HR) in (Me)G toxicity, its mode of action has remained elusive. We studied the molecular transactions in the DNA of yeast and mammalian cells treated with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Although replication fork progression was unaffected in the first cell cycle after treatment, electron microscopic analysis revealed an accumulation of (Me)G- and MMR-dependent single-stranded DNA (ssDNA) gaps in newly replicated DNA. Progression into the second cell cycle required HR, while the following G(2) arrest required the continued presence of (Me)G. Yeast cells overcame this block, while mammalian cells generally failed to recover, and those that did contained multiple sister chromatid exchanges. Notably, the arrest could be abolished by removal of (Me)G after the first S phase. These new data provide compelling support for the hypothesis that MMR attempts to correct (Me)G/C or (Me)G/T mispairs arising during replication. Due to the persistence of (Me)G in the exposed template strand, repair synthesis cannot take place, which leaves single-stranded gaps behind the replication fork. During the subsequent S phase, these gaps cause replication fork collapse and elicit recombination and cell cycle arrest.
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Affiliation(s)
- Nina Mojas
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
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Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G. Transcriptome profile of human colorectal adenomas. Mol Cancer Res 2008; 5:1263-75. [PMID: 18171984 DOI: 10.1158/1541-7786.mcr-07-0267] [Citation(s) in RCA: 370] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected to extensive clinical, pathologic, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. To characterize the molecular processes underlying the transformation of normal colonic epithelium, we compared the transcriptomes of 32 prospectively collected adenomas with those of normal mucosa from the same individuals. Important differences emerged not only between the expression profiles of normal and adenomatous tissues but also between those of small and large adenomas. A key feature of the transformation process was the remodeling of the Wnt pathway reflected in patent overexpression and underexpression of 78 known components of this signaling cascade. The expression of 19 Wnt targets was closely correlated with clear up-regulation of KIAA1199, whose function is currently unknown. In normal mucosa, KIAA1199 expression was confined to cells in the lower portion of intestinal crypts, where Wnt signaling is physiologically active, but it was markedly increased in all adenomas, where it was expressed in most of the epithelial cells, and in colon cancer cell lines, it was markedly reduced by inactivation of the beta-catenin/T-cell factor(s) transcription complex, the pivotal mediator of Wnt signaling. Our transcriptomic profiles of normal colonic mucosa and colorectal adenomas shed new light on the early stages of colorectal tumorigenesis and identified KIAA1199 as a novel target of the Wnt signaling pathway and a putative marker of colorectal adenomatous transformation.
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Affiliation(s)
- Jacob Sabates-Bellver
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Fischer F, Baerenfaller K, Jiricny J. 5-Fluorouracil is efficiently removed from DNA by the base excision and mismatch repair systems. Gastroenterology 2007; 133:1858-68. [PMID: 18054558 DOI: 10.1053/j.gastro.2007.09.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 08/23/2007] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS 5-Fluorouracil (FU) is one of the mainstays of colon cancer chemotherapy. Although developed as an inhibitor of thymidylate synthase, its cytotoxicity has been linked also to its incorporation into RNA. Surprisingly, although FU is incorporated also into DNA, little is known about its metabolism in this nucleic acid. METHODS Using extracts of human cells and circular DNA substrates containing a single FU residue either paired with adenine or mispaired with guanine, we studied the enzymology of FU processing. RESULTS In nicked circular substrates, FU/G mispairs were efficiently repaired by mismatch repair (MMR). In covalently closed circular DNA, which is refractory to MMR, FU/G repair was initiated by either thymine-DNA glycosylase or uracil-DNA glycosylase, whereas FU/A pairs were processed by UNG. Methylated CpG binding domain 4 protein and single-strand selective monofunctional uracil-DNA glycosylase 1 did not detectably contribute to FU removal; however, because these recombinant enzymes process FU/G and FU/A in oligonucleotide substrates, respectively, they too may be involved in FU metabolism in vivo. CONCLUSIONS The functional redundancy of MMR and DNA glycosylases in FU processing should ensure that the drug is efficiently removed from DNA before it can interfere with essential DNA metabolic processes, such as transcription. However, in FU-treated cells, the nucleotide pools are depleted of thymine. The repair synthesis might thus be inhibited and leave cytotoxic gaps or breaks in DNA. Moreover, FU and/or 5-fluorouracil-2'-deoxyuridine-5'-triphosphate removed from DNA will increase the intracellular concentration of the drug and thus exacerbate its cytotoxicity.
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Affiliation(s)
- Franziska Fischer
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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Sammalkorpi H, Alhopuro P, Lehtonen R, Tuimala J, Mecklin JP, Järvinen HJ, Jiricny J, Karhu A, Aaltonen LA. Background mutation frequency in microsatellite-unstable colorectal cancer. Cancer Res 2007; 67:5691-8. [PMID: 17575135 DOI: 10.1158/0008-5472.can-06-4314] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microsatellite instability (MSI) is observed in approximately 12% of colorectal cancers. Genes containing a mononucleotide microsatellite in the coding sequence are particularly prone to inactivation in MSI tumorigenesis, and much work has been conducted to identify genes with high repetitive tract mutation rates in these tumors. Much less attention has been paid to background mutation frequencies, and no work has focused on nontranscribed regions. Here, we studied 114 nontranscribed intergenic A/T and C/G repeats 6 to 10 bp in length, located distant from known genes, to examine background mutation frequencies in MSI colorectal cancers. A strong correlation with tract length was observed, and mutation frequencies of up to 87% were observed in 8 to 10 bp tracts. Subsequently, to compare the background mutation rate in transcribed and nontranscribed noncoding repeats, we screened nine randomly selected intronic C/G8 repeats. In addition, the coding repeats of seven suggested MSI target genes, and nine previously published intronic A8 and G8 repeats were analyzed. Intronic repeats seemed to mutate less frequently than nontranscribed intergenic repeats. Our results show that strand slippage mutations in mismatch repair-deficient cells are as abundant in short intergenic repeats as in many proposed MSI target genes. However, under mismatch repair deficiency, strand slippage mutations in transcribed sequences seem to be repaired more efficiently than in intergenic nontranscribed sequences. The mechanisms causing these differences are not yet understood and should be a subject for further studies. For MSI target gene identification, repeats in transcribed sequences seem to be the most appropriate reference group for coding region repeat mutations.
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Affiliation(s)
- Heli Sammalkorpi
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Finland
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Cannavo E, Gerrits B, Marra G, Schlapbach R, Jiricny J. Characterization of the Interactome of the Human MutL Homologues MLH1, PMS1, and PMS2. J Biol Chem 2007; 282:2976-86. [PMID: 17148452 DOI: 10.1074/jbc.m609989200] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Postreplicative mismatch repair (MMR) involves the concerted action of at least 20 polypeptides. Although the minimal human MMR system has recently been reconstituted in vitro, genetic evidence from different eukaryotic organisms suggests that some steps of the MMR process may be carried out by more than one protein. Moreover, MMR proteins are involved also in other pathways of DNA metabolism, but their exact role in these processes is unknown. In an attempt to gain novel insights into the function of MMR proteins in human cells, we searched for interacting partners of the MutL homologues MLH1 and PMS2 by tandem affinity purification and of PMS1 by large scale immunoprecipitation. In addition to proteins known to interact with the MutL homologues during MMR, mass spectrometric analyses identified a number of other polypeptides, some of which bound to the above proteins with very high affinity. Whereas some of these interactors may represent novel members of the mismatch repairosome, others appear to implicate the MutL homologues in biological processes ranging from intracellular transport through cell signaling to cell morphology, recombination, and ubiquitylation.
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Affiliation(s)
- Elda Cannavo
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
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49
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Abstract
The mismatch repair process corrects errors in newly synthesized DNA. In this issue, Modrich and colleagues (Kadyrov et al., 2006) show that a component of the human mismatch repair machinery, MutLalpha, has endonuclease activity. MutLalpha introduces single-strand breaks near the mismatch and thus generates new entry points for the exonuclease EXOI to degrade the strand containing the mismatch.
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Affiliation(s)
- Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, CH-8006 Zurich, Switzerland.
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50
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Abstract
By removing biosynthetic errors from newly synthesized DNA, mismatch repair (MMR) improves the fidelity of DNA replication by several orders of magnitude. Loss of MMR brings about a mutator phenotype, which causes a predisposition to cancer. But MMR status also affects meiotic and mitotic recombination, DNA-damage signalling, apoptosis and cell-type-specific processes such as class-switch recombination, somatic hypermutation and triplet-repeat expansion. This article reviews our current understanding of this multifaceted DNA-repair system in human cells.
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Affiliation(s)
- Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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