1
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Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E, Wang AA, Keegan S, Laverty DJ, Piett CG, Pongor LS, Xu ML, Andrade J, Thomas A, Sicinski P, Askenazi M, Ueberheide B, Fenyö D, Nagel ZD, Pagano M. CDK-independent role of D-type cyclins in regulating DNA mismatch repair. Mol Cell 2024; 84:1224-1242.e13. [PMID: 38458201 PMCID: PMC10997477 DOI: 10.1016/j.molcel.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 01/04/2024] [Accepted: 02/09/2024] [Indexed: 03/10/2024]
Abstract
Although mismatch repair (MMR) is essential for correcting DNA replication errors, it can also recognize other lesions, such as oxidized bases. In G0 and G1, MMR is kept in check through unknown mechanisms as it is error-prone during these cell cycle phases. We show that in mammalian cells, D-type cyclins are recruited to sites of oxidative DNA damage in a PCNA- and p21-dependent manner. D-type cyclins inhibit the proteasomal degradation of p21, which competes with MMR proteins for binding to PCNA, thereby inhibiting MMR. The ability of D-type cyclins to limit MMR is CDK4- and CDK6-independent and is conserved in G0 and G1. At the G1/S transition, the timely, cullin-RING ubiquitin ligase (CRL)-dependent degradation of D-type cyclins and p21 enables MMR activity to efficiently repair DNA replication errors. Persistent expression of D-type cyclins during S-phase inhibits the binding of MMR proteins to PCNA, increases the mutational burden, and promotes microsatellite instability.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bearach Miwatani-Minter
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hailey V Goldberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marc A Kerzhnerman
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jesse B Howard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ethan Lane
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John W Hobbs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew A Wang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel J Laverty
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cortt G Piett
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lorinc S Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged 6728, Hungary
| | - Miranda Li Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Andrade
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Histology and Embryology, Center for Biostructure Research, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zachary D Nagel
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA.
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2
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Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E, Wang AA, Keegan S, Laverty DJ, Piett CG, Pongor LS, Xu ML, Andrade J, Thomas A, Sicinski P, Askenazi M, Ueberheide B, Fenyö D, Nagel ZD, Pagano M. D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575420. [PMID: 38260436 PMCID: PMC10802603 DOI: 10.1101/2024.01.12.575420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The large majority of oxidative DNA lesions occurring in the G1 phase of the cell cycle are repaired by base excision repair (BER) rather than mismatch repair (MMR) to avoid long resections that can lead to genomic instability and cell death. However, the molecular mechanisms dictating pathway choice between MMR and BER have remained unknown. Here, we show that, during G1, D-type cyclins are recruited to sites of oxidative DNA damage in a PCNA- and p21-dependent manner. D-type cyclins shield p21 from its two ubiquitin ligases CRL1SKP2 and CRL4CDT2 in a CDK4/6-independent manner. In turn, p21 competes through its PCNA-interacting protein degron with MMR components for their binding to PCNA. This inhibits MMR while not affecting BER. At the G1/S transition, the CRL4AMBRA1-dependent degradation of D-type cyclins renders p21 susceptible to proteolysis. These timely degradation events allow the proper binding of MMR proteins to PCNA, enabling the repair of DNA replication errors. Persistent expression of cyclin D1 during S-phase increases the mutational burden and promotes microsatellite instability. Thus, the expression of D-type cyclins inhibits MMR in G1, whereas their degradation is necessary for proper MMR function in S.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bearach Miwatani-Minter
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hailey V. Goldberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marc A. Kerzhnerman
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jesse B. Howard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ethan Lane
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John W. Hobbs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew A. Wang
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sarah Keegan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Cortt G. Piett
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lorinc S. Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Hungarian Centre of Excellence for Molecular Medicine, University of Szeged, Szeged, H-6728, Hungary
| | - Miranda Li Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Andrade
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
- Department of Histology and Embryology, Center for Biostructure Research, Medical University of Warsaw, Chalubinskiego 5, 02-004 Warsaw, Poland
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zachary D. Nagel
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
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3
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Khatib JB, Nicolae CM, Moldovan GL. Role of Translesion DNA Synthesis in the Metabolism of Replication-associated Nascent Strand Gaps. J Mol Biol 2024; 436:168275. [PMID: 37714300 PMCID: PMC10842951 DOI: 10.1016/j.jmb.2023.168275] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Translesion DNA synthesis (TLS) is a DNA damage tolerance pathway utilized by cells to overcome lesions encountered throughout DNA replication. During replication stress, cancer cells show increased dependency on TLS proteins for cellular survival and chemoresistance. TLS proteins have been described to be involved in various DNA repair pathways. One of the major emerging roles of TLS is single-stranded DNA (ssDNA) gap-filling, primarily after the repriming activity of PrimPol upon encountering a lesion. Conversely, suppression of ssDNA gap accumulation by TLS is considered to represent a mechanism for cancer cells to evade the toxicity of chemotherapeutic agents, specifically in BRCA-deficient cells. Thus, TLS inhibition is emerging as a potential treatment regimen for DNA repair-deficient tumors.
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Affiliation(s)
- Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA. https://twitter.com/JudeBKhatib
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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4
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Venkadakrishnan J, Lahane G, Dhar A, Xiao W, Bhat KM, Pandita TK, Bhat A. Implications of Translesion DNA Synthesis Polymerases on Genomic Stability and Human Health. Mol Cell Biol 2023; 43:401-425. [PMID: 37439479 PMCID: PMC10448981 DOI: 10.1080/10985549.2023.2224199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 07/14/2023] Open
Abstract
Replication fork arrest-induced DNA double strand breaks (DSBs) caused by lesions are effectively suppressed in cells due to the presence of a specialized mechanism, commonly referred to as DNA damage tolerance (DDT). In eukaryotic cells, DDT is facilitated through translesion DNA synthesis (TLS) carried out by a set of DNA polymerases known as TLS polymerases. Another parallel mechanism, referred to as homology-directed DDT, is error-free and involves either template switching or fork reversal. The significance of the DDT pathway is well established. Several diseases have been attributed to defects in the TLS pathway, caused either by mutations in the TLS polymerase genes or dysregulation. In the event of a replication fork encountering a DNA lesion, cells switch from high-fidelity replicative polymerases to low-fidelity TLS polymerases, which are associated with genomic instability linked with several human diseases including, cancer. The role of TLS polymerases in chemoresistance has been recognized in recent years. In addition to their roles in the DDT pathway, understanding noncanonical functions of TLS polymerases is also a key to unraveling their importance in maintaining genomic stability. Here we summarize the current understanding of TLS pathway in DDT and its implication for human health.
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Affiliation(s)
| | - Ganesh Lahane
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Arti Dhar
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Wei Xiao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Krishna Moorthi Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Tej K. Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Audesh Bhat
- Center for Molecular Biology, Central University of Jammu, UT Jammu and Kashmir, India
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5
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Egger T, Aze A, Maiorano D. Detection of endogenous translesion DNA synthesis in single mammalian cells. CELL REPORTS METHODS 2023; 3:100501. [PMID: 37426760 PMCID: PMC10326377 DOI: 10.1016/j.crmeth.2023.100501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/07/2023] [Accepted: 05/18/2023] [Indexed: 07/11/2023]
Abstract
Translesion DNA synthesis (TLS) is an evolutionarily conserved process that cells activate to tolerate DNA damage. TLS facilitates proliferation under DNA damage conditions and is exploited by cancer cells to gain therapy resistance. It has been so far challenging to analyze endogenous TLS factors such as PCNAmUb and TLS DNA polymerases in single mammalian cells due to a lack of suitable detection tools. We have adapted a flow cytometry-based quantitative method allowing detection of endogenous, chromatin-bound TLS factors in single mammalian cells, either untreated or exposed to DNA-damaging agents. This high-throughput procedure is quantitative, accurate, and allows unbiased analysis of TLS factors' recruitment to chromatin, as well as occurrence of DNA lesions with respect to the cell cycle. We also demonstrate detection of endogenous TLS factors by immunofluorescence microscopy and provide insights into TLS dynamics upon DNA replication forks stalled by UV-C-induced DNA damage.
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Affiliation(s)
- Tom Egger
- Institut de Génétique Humaine (IGH) CNRS UMR9002, Université de Montpellier, Molecular Bases of Human Pathologies Department, “Genome Surveillance and Stability” Laboratory, 34396 Cedex 5 Montpellier, France
| | - Antoine Aze
- Institut de Génétique Humaine (IGH) CNRS UMR9002, Université de Montpellier, Molecular Bases of Human Pathologies Department, “Genome Surveillance and Stability” Laboratory, 34396 Cedex 5 Montpellier, France
| | - Domenico Maiorano
- Institut de Génétique Humaine (IGH) CNRS UMR9002, Université de Montpellier, Molecular Bases of Human Pathologies Department, “Genome Surveillance and Stability” Laboratory, 34396 Cedex 5 Montpellier, France
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6
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Schrader CE, Williams T, Pechhold K, Linehan EK, Tsuchimoto D, Nakabeppu Y. APE2 Promotes AID-Dependent Somatic Hypermutation in Primary B Cell Cultures That Is Suppressed by APE1. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1804-1814. [PMID: 37074207 PMCID: PMC10234595 DOI: 10.4049/jimmunol.2100946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/29/2023] [Indexed: 04/20/2023]
Abstract
Somatic hypermutation (SHM) is necessary for Ab diversification and involves error-prone DNA repair of activation-induced cytidine deaminase-induced lesions in germinal center (GC) B cells but can also cause genomic instability. GC B cells express low levels of the DNA repair protein apurinic/apyrimidinic (AP) endonuclease (APE)1 and high levels of its homolog APE2. Reduced SHM in APE2-deficient mice suggests that APE2 promotes SHM, but these GC B cells also exhibit reduced proliferation that could impact mutation frequency. In this study, we test the hypothesis that APE2 promotes and APE1 suppresses SHM. We show how APE1/APE2 expression changes in primary murine spleen B cells during activation, impacting both SHM and class-switch recombination (CSR). High levels of both APE1 and APE2 early after activation promote CSR. However, after 2 d, APE1 levels decrease steadily with each cell division, even with repeated stimulation, whereas APE2 levels increase with each stimulation. When GC-level APE1/APE2 expression was engineered by reducing APE1 genetically (apex1+/-) and overexpressing APE2, bona fide activation-induced cytidine deaminase-dependent VDJH4 intron SHM became detectable in primary B cell cultures. The C terminus of APE2 that interacts with proliferating cell nuclear Ag promotes SHM and CSR, although its ATR-Chk1-interacting Zf-GRF domain is not required. However, APE2 does not increase mutations unless APE1 is reduced. Although APE1 promotes CSR, it suppresses SHM, suggesting that downregulation of APE1 in the GC is required for SHM. Genome-wide expression data compare GC and cultured B cells and new models depict how APE1 and APE2 expression and protein interactions change during B cell activation and affect the balance between accurate and error-prone repair during CSR and SHM.
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Affiliation(s)
- Carol E. Schrader
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Travis Williams
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Klaus Pechhold
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Erin K. Linehan
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Daisuke Tsuchimoto
- Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusaku Nakabeppu
- Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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7
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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8
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Capanni C, Schena E, Di Giampietro ML, Montecucco A, Mattioli E, Lattanzi G. The role of prelamin A post-translational maturation in stress response and 53BP1 recruitment. Front Cell Dev Biol 2022; 10:1018102. [PMID: 36467410 PMCID: PMC9709412 DOI: 10.3389/fcell.2022.1018102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/24/2022] [Indexed: 11/25/2023] Open
Abstract
Lamin A is a main constituent of the nuclear lamina and contributes to nuclear shaping, mechano-signaling transduction and gene regulation, thus affecting major cellular processes such as cell cycle progression and entry into senescence, cellular differentiation and stress response. The role of lamin A in stress response is particularly intriguing, yet not fully elucidated, and involves prelamin A post-translational processing. Here, we propose prelamin A as the tool that allows lamin A plasticity during oxidative stress response and permits timely 53BP1 recruitment to DNA damage foci. We show that while PCNA ubiquitination, p21 decrease and H2AX phosphorylation occur soon after stress induction in the absence of prelamin A, accumulation of non-farnesylated prelamin A follows and triggers recruitment of 53BP1 to lamin A/C complexes. Then, the following prelamin A processing steps causing transient accumulation of farnesylated prelamin A and maturation to lamin A reduce lamin A affinity for 53BP1 and favor its release and localization to DNA damage sites. Consistent with these observations, accumulation of prelamin A forms in cells under basal conditions impairs histone H2AX phosphorylation, PCNA ubiquitination and p21 degradation, thus affecting the early stages of stress response. As a whole, our results are consistent with a physiological function of prelamin A modulation during stress response aimed at timely recruitment/release of 53BP1 and other molecules required for DNA damage repair. In this context, it becomes more obvious how farnesylated prelamin A accumulation to toxic levels alters timing of DNA damage signaling and 53BP1 recruitment, thus contributing to cellular senescence and accelerated organismal aging as observed in progeroid laminopathies.
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Affiliation(s)
- Cristina Capanni
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, Bologna, Italy
- IRCCS Rizzoli Orthopedic Institute, Bologna, Italy
| | - Elisa Schena
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, Bologna, Italy
- IRCCS Rizzoli Orthopedic Institute, Bologna, Italy
| | | | | | - Elisabetta Mattioli
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, Bologna, Italy
- IRCCS Rizzoli Orthopedic Institute, Bologna, Italy
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, Bologna, Italy
- IRCCS Rizzoli Orthopedic Institute, Bologna, Italy
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9
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Benureau Y, Pouvelle C, Dupaigne P, Baconnais S, Moreira Tavares E, Mazón G, Despras E, Le Cam E, Kannouche P. Changes in the architecture and abundance of replication intermediates delineate the chronology of DNA damage tolerance pathways at UV-stalled replication forks in human cells. Nucleic Acids Res 2022; 50:9909-9929. [PMID: 36107774 PMCID: PMC9508826 DOI: 10.1093/nar/gkac746] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022] Open
Abstract
DNA lesions in S phase threaten genome stability. The DNA damage tolerance (DDT) pathways overcome these obstacles and allow completion of DNA synthesis by the use of specialised translesion (TLS) DNA polymerases or through recombination-related processes. However, how these mechanisms coordinate with each other and with bulk replication remains elusive. To address these issues, we monitored the variation of replication intermediate architecture in response to ultraviolet irradiation using transmission electron microscopy. We show that the TLS polymerase η, able to accurately bypass the major UV lesion and mutated in the skin cancer-prone xeroderma pigmentosum variant (XPV) syndrome, acts at the replication fork to resolve uncoupling and prevent post-replicative gap accumulation. Repriming occurs as a compensatory mechanism when this on-the-fly mechanism cannot operate, and is therefore predominant in XPV cells. Interestingly, our data support a recombination-independent function of RAD51 at the replication fork to sustain repriming. Finally, we provide evidence for the post-replicative commitment of recombination in gap repair and for pioneering observations of in vivo recombination intermediates. Altogether, we propose a chronology of UV damage tolerance in human cells that highlights the key role of polη in shaping this response and ensuring the continuity of DNA synthesis.
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Affiliation(s)
- Yann Benureau
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Caroline Pouvelle
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
| | - Pauline Dupaigne
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Sonia Baconnais
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Eliana Moreira Tavares
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Gerard Mazón
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Emmanuelle Despras
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
| | - Eric Le Cam
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Patricia L Kannouche
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
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10
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Tang F, Wang Y, Gao Z, Guo S, Wang Y. Polymerase η Recruits DHX9 Helicase to Promote Replication across Guanine Quadruplex Structures. J Am Chem Soc 2022; 144:14016-14020. [PMID: 35905379 PMCID: PMC9378570 DOI: 10.1021/jacs.2c05312] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA polymerase η (Pol η) catalyzes accurate bypass of ultraviolet light-induced cyclobutane pyrimidine dimers, and it also functions in several other related processes, including bypassing DNA with unusual structures. Here, we performed unbiased proteome-wide profiling of Pol η-interacting proteins by using two independent approaches, i.e., proximity labeling and affinity pull-down followed by LC-MS/MS analysis. We identified several helicases, including DHX9, as novel Pol η-interacting proteins. Additionally, ChIP-Seq analysis showed that Pol η is enriched at guanine quadruplex (G4) structure sites in chromatin. Moreover, Pol η promotes the recruitment of DHX9 to G4 structure loci in chromatin and facilitates DHX9-mediated unwinding of G4 structures. Deficiency in Pol η or DHX9 leads to attenuated replication across G4 regions in genomic DNA. Together, we unveiled the interaction between Pol η and DHX9 and demonstrated that the interaction promotes the replicative bypass of G4 structures in chromatin.
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Affiliation(s)
- Feng Tang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinan Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Zi Gao
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Shiyuan Guo
- Genetics, Genomics and Bioinformatics Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
- Genetics, Genomics and Bioinformatics Graduate Program, University of California, Riverside, California 92521-0403, United States
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11
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Meng Y, Zhou M, Wang T, Zhang G, Tu Y, Gong S, Zhang Y, Christiani DC, Au W, Liu Y, Xia ZL. Occupational lead exposure on genome-wide DNA methylation and DNA damage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119252. [PMID: 35385786 DOI: 10.1016/j.envpol.2022.119252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023]
Abstract
Lead (Pb) exposure can induce DNA damage and alter DNA methylation but their inter-relationships have not been adequately determined. Our overall aims were to explore such relationships and to evaluate underlying epigenetic mechanisms of Pb-induced genotoxicity in Chinese workers. Blood Pb levels (BLLs) were determined and used as individual's Pb-exposure dose and the Comet assay (i.e., % tail DNA) was conducted to evaluate DNA damage. In the screening assay, 850 K BeadChip sequencing was performed on peripheral blood from 10 controls (BLLs ≤100 μg/L) and 20 exposed workers (i.e., 10 DNA-damaged and 10 DNA-undamaged workers). Using the technique, differentially methylated positions (DMPs) between the controls and the exposed workers were identified. In addition, DMPs were identified between the DNA-undamaged and DNA-damaged workers (% tail DNA >2.14%). In our validation assay, methylation levels of four candidate genes were measured by pyrosequencing in an independent sample set (n = 305), including RRAGC (Ras related GTP binding C), USP1 (Ubiquitin specific protease 1), COPS7B (COP9 signalosome subunit 7 B) and CHEK1 (Checkpoint kinase 1). The result of comparisons between the controls and the Pb-exposed workers show that DMPs were significantly enriched in genes related to nerve conduction and cell cycle. Between DNA-damaged group and DNA-undamaged group, differentially methylated genes were enriched in the pathways related to cell cycle and DNA integrity checkpoints. Additionally, methylation levels of RRAGC and USP1 were negatively associated with BLLs (P < 0.05), and the former mediated 19.40% of the effect of Pb on the % tail DNA. These findings collectively indicated that Pb-induced DNA damage was closely related to methylation of genes in cell cycle regulation, and methylation levels of RRAGC were involved in Pb-induced genotoxicity.
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Affiliation(s)
- Yu Meng
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Mengyu Zhou
- The MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tuanwei Wang
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Guanghui Zhang
- Department of Environmental Health, College of Preventive Medicine, Army Medical University, Chongqing, China; Department of Occupational & Environmental Health, School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Yuting Tu
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Shiyang Gong
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - Yunxia Zhang
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China
| | - David C Christiani
- Environmental Medicine and Epidemiology Program, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - William Au
- University of Medicine, Pharmacy, Science and Technology, Targu Mures, Romania, and Shantou University Medical College, Shantou, China
| | - Yun Liu
- The MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhao-Lin Xia
- Department of Occupational Health & Toxicology, School of Public Health, Fudan University, Shanghai, China; School of Public Health, Xinjiang Medical University, Urumqi, China.
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12
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Lerner LK, Bonte D, Le Guillou M, Mohammad MM, Kasraian Z, Sarasin A, Despras E, Aoufouchi S. Expression of Constitutive Fusion of Ubiquitin to PCNA Restores the Level of Immunoglobulin A/T Mutations During Somatic Hypermutation in the Ramos Cell Line. Front Immunol 2022; 13:871766. [PMID: 35432321 PMCID: PMC9010874 DOI: 10.3389/fimmu.2022.871766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/11/2022] [Indexed: 12/05/2022] Open
Abstract
Somatic hypermutation (SHM) of immunoglobulin (Ig) genes is a B cell specific process required for the generation of specific and high affinity antibodies during the maturation of the immune response against foreign antigens. This process depends on the activity of both activation-induced cytidine deaminase (AID) and several DNA repair factors. AID-dependent SHM creates the full spectrum of mutations in Ig variable (V) regions equally distributed at G/C and A/T bases. In most mammalian cells, deamination of deoxycytidine into uracil during S phase induces targeted G/C mutagenesis using either direct replication of uracils or TLS mediated bypass, however only the machinery of activated B lymphocytes can generate A/T mutagenesis around AID-created uracils. The molecular mechanism behind the latter remains incompletely understood to date. However, the lack of a cellular model that reproduces both G/C and A/T mutation spectra constitutes the major hurdle to elucidating it. The few available B cell lines used thus far to study Ig SHM indeed undergo mainly G/C mutations, that make them inappropriate or of limited use. In this report, we show that in the Ramos cell line that undergoes constitutive G/C-biased SHM in culture, the low rate of A/T mutations is due to an imbalance in the ubiquitination/deubiquitination reaction of PCNA, with the deubiquitination reaction being predominant. The inhibition of the deubiquitinase complex USP1-UAF1 or the expression of constitutive fusion of ubiquitin to PCNA provides the missing clue required for DNA polymerase η recruitment and thereafter the introduction of A/T base pair (bp) mutations during the process of IgV gene diversification. This study reports the establishment of the first modified human B cell line that recapitulates the mechanism of SHM of Ig genes in vitro.
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Affiliation(s)
- Leticia K. Lerner
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dorine Bonte
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Morwenna Le Guillou
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Mahwish Mian Mohammad
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
- Sorbonne Université, Paris, France
| | - Zeinab Kasraian
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Alain Sarasin
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Emmanuelle Despras
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
| | - Said Aoufouchi
- Centre National de la Recherche Scientifique UMR 9019, B Cell and Genome Plasticity Team, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris-Saclay, Orsay, France
- Sorbonne Université, Paris, France
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13
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Caldecott KW, Ward ME, Nussenzweig A. The threat of programmed DNA damage to neuronal genome integrity and plasticity. Nat Genet 2022; 54:115-120. [PMID: 35145299 DOI: 10.1038/s41588-021-01001-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023]
Abstract
The neuronal genome is particularly sensitive to loss or attenuation of DNA repair, and many neurological diseases ensue when DNA repair is impaired. It is well-established that the neuronal genome is subjected to stochastic DNA damage, most likely because of extensive oxidative stress in the brain. However, recent studies have identified unexpected high levels of 'programmed' DNA breakage in neurons, which we propose arise during physiological DNA metabolic processes intrinsic to neuronal development, differentiation and maintenance. The role of programmed DNA breaks in normal neuronal physiology and disease remains relatively unexplored thus far. However, bulk and single-cell sequencing analyses of neurodegenerative diseases have revealed age-related somatic mutational signatures that are enriched in regulatory regions of the genome. Here, we explore a paradigm of DNA repair in neurons, in which the genome is safeguarded from erroneous impacts of programmed genome breakage intrinsic to normal neuronal function.
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Affiliation(s)
- Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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14
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Tyagi A, Haq S, Ramakrishna S. Redox regulation of DUBs and its therapeutic implications in cancer. Redox Biol 2021; 48:102194. [PMID: 34814083 PMCID: PMC8608616 DOI: 10.1016/j.redox.2021.102194] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reactive oxygen species (ROS) act as a double-edged sword in cancer, where low levels of ROS are beneficial but excessive accumulation leads to cancer progression. Elevated levels of ROS in cancer are counteracted by the antioxidant defense system. An imbalance between ROS generation and the antioxidant system alters gene expression and cellular signaling, leading to cancer progression or death. Post-translational modifications, such as ubiquitination, phosphorylation, and SUMOylation, play a critical role in the maintenance of ROS homeostasis by controlling ROS production and clearance. Recent evidence suggests that deubiquitinating enzymes (DUBs)-mediated ubiquitin removal from substrates is regulated by ROS. ROS-mediated oxidation of the catalytic cysteine (Cys) of DUBs, leading to their reversible inactivation, has emerged as a key mechanism regulating DUB-controlled cellular events. A better understanding of the mechanism by which DUBs are susceptible to ROS and exploring the ways to utilize ROS to pharmacologically modulate DUB-mediated signaling pathways might provide new insight for anticancer therapeutics. This review assesses the recent findings regarding ROS-mediated signaling in cancers, emphasizes DUB regulation by oxidation, highlights the relevant recent findings, and proposes directions of future research based on the ROS-induced modifications of DUB activity.
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Affiliation(s)
- Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea; College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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15
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Park SH, Kim Y, Ra JS, Wie MW, Kang MS, Kang S, Myung K, Lee KY. Timely termination of repair DNA synthesis by ATAD5 is important in oxidative DNA damage-induced single-strand break repair. Nucleic Acids Res 2021; 49:11746-11764. [PMID: 34718749 PMCID: PMC8599757 DOI: 10.1093/nar/gkab999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) generate oxidized bases and single-strand breaks (SSBs), which are fixed by base excision repair (BER) and SSB repair (SSBR), respectively. Although excision and repair of damaged bases have been extensively studied, the function of the sliding clamp, proliferating cell nuclear antigen (PCNA), including loading/unloading, remains unclear. We report that, in addition to PCNA loading by replication factor complex C (RFC), timely PCNA unloading by the ATPase family AAA domain-containing protein 5 (ATAD5)-RFC-like complex is important for the repair of ROS-induced SSBs. We found that PCNA was loaded at hydrogen peroxide (H2O2)-generated direct SSBs after the 3'-terminus was converted to the hydroxyl moiety by end-processing enzymes. However, PCNA loading rarely occurred during BER of oxidized or alkylated bases. ATAD5-depleted cells were sensitive to acute H2O2 treatment but not methyl methanesulfonate treatment. Unexpectedly, when PCNA remained on DNA as a result of ATAD5 depletion, H2O2-induced repair DNA synthesis increased in cancerous and normal cells. Based on higher H2O2-induced DNA breakage and SSBR protein enrichment by ATAD5 depletion, we propose that extended repair DNA synthesis increases the likelihood of DNA polymerase stalling, shown by increased PCNA monoubiquitination, and consequently, harmful nick structures are more frequent.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Youyoung Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Min Woo Wie
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
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16
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Fang H, Zhu X, Yang H, Oh J, Barbour JA, Wong JWH. Deficiency of replication-independent DNA mismatch repair drives a 5-methylcytosine deamination mutational signature in cancer. SCIENCE ADVANCES 2021; 7:eabg4398. [PMID: 34730999 PMCID: PMC8565909 DOI: 10.1126/sciadv.abg4398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Multiple mutational signatures have been associated with DNA mismatch repair (MMR)–deficient cancers, but the mechanisms underlying their origin remain unclear. Here, using mutation data from cancer genomes, we identify a previously unknown function of MMR that is able to protect genomes from 5-methylcytosine (5mC) deamination–induced somatic mutations in a replication-independent manner. Cancers with deficiency of MMR proteins MSH2/MSH6 (MutSα) exhibit mutational signature contributions distinct from those that are deficient in MLH1/PMS2 (MutLα). This disparity arises from unrepaired 5mC deamination–induced mismatches rather than replicative DNA polymerase errors. In cancers with biallelic loss of MBD4 DNA glycosylase, repair of 5mC deamination damage is strongly associated with H3K36me3 chromatin, implicating MutSα as the essential factor in its repair. We thus uncover a noncanonical role of MMR in the protection against 5mC deamination–induced mutation in human cancers.
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17
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Fuchs RP, Isogawa A, Paulo JA, Onizuka K, Takahashi T, Amunugama R, Duxin JP, Fujii S. Crosstalk between repair pathways elicits double-strand breaks in alkylated DNA and implications for the action of temozolomide. eLife 2021; 10:e69544. [PMID: 34236314 PMCID: PMC8289412 DOI: 10.7554/elife.69544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Temozolomide (TMZ), a DNA methylating agent, is the primary chemotherapeutic drug used in glioblastoma treatment. TMZ induces mostly N-alkylation adducts (N7-methylguanine and N3-methyladenine) and some O6-methylguanine (O6mG) adducts. Current models propose that during DNA replication, thymine is incorporated across from O6mG, promoting a futile cycle of mismatch repair (MMR) that leads to DNA double-strand breaks (DSBs). To revisit the mechanism of O6mG processing, we reacted plasmid DNA with N-methyl-N-nitrosourea (MNU), a temozolomide mimic, and incubated it in Xenopus egg-derived extracts. We have shown that in this system, MMR proteins are enriched on MNU-treated DNA and we observed robust, MMR-dependent, repair synthesis. Our evidence also suggests that MMR, initiated at O6mG:C sites, is strongly stimulated in cis by repair processing of other lesions, such as N-alkylation adducts. Importantly, MNU-treated plasmids display DSBs in extracts, the frequency of which increases linearly with the square of alkylation dose. We suggest that DSBs result from two independent repair processes, one involving MMR at O6mG:C sites and the other involving base excision repair acting at a nearby N-alkylation adduct. We propose a new, replication-independent mechanism of action of TMZ, which operates in addition to the well-studied cell cycle-dependent mode of action.
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Affiliation(s)
- Robert P Fuchs
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Asako Isogawa
- Cancer Research Center of Marseille, UMR7258, CNRSMarseilleFrance
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku UniversitySendaiJapan
| | | | - Ravindra Amunugama
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Julien P Duxin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Shingo Fujii
- Cancer Research Center of Marseille, UMR7258, CNRSMarseilleFrance
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18
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Gu S, Bodai Z, Cowan QT, Komor AC. Base Editors: Expanding the Types of DNA Damage Products Harnessed for Genome Editing. ACTA ACUST UNITED AC 2021; 1. [PMID: 34368792 DOI: 10.1016/j.ggedit.2021.100005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Base editors are an innovative addition to the genome editing toolbox that introduced a new genome editing strategy to the field. Instead of using double-stranded DNA breaks, base editors use nucleobase modification chemistry to efficiently and precisely incorporate single nucleotide variants (SNVs) into the genome of living cells. Two classes of DNA base editors currently exist: deoxycytidine deamination-derived editors (CBEs, which facilitate C•G to T•A mutations) and deoxyadenosine deamination-derived base editors (ABEs, which facilitate A•T to G•C mutations). More recently, the development of mitochondrial base editors allowed the introduction of C•G to T•A mutations into mitochondrial DNA as well. Base editors show great potential as therapeutic agents and research tools, and extensive studies have been carried out to improve upon the original base editor constructs to aid researchers in a variety of disciplines. Despite their widespread use, there are few publications that focus on elucidating the biological pathways involved during the processing of base editor intermediates. Because base editors introduce unique types of DNA damage products (a U•G mismatch with a DNA backbone nick for CBEs, and an I•T mismatch with a DNA backbone nick for ABEs) to facilitate genome editing, a deep understanding of the DNA damage repair pathways that facilitate or impede base editing represents an important aspect for the further expansion and improvement of the technologies. Here, we first review canonical deoxyuridine, deoxyinosine, and single-stranded break repair. Then, we discuss how interactions among these different repair processes can lead to different base editing outcomes. Through this review, we hope to promote thoughtful discussions on the DNA repair mechanisms of base editing, as well as help researchers in the improvement of the current base editors and the development of new base editors.
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Affiliation(s)
- Sifeng Gu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
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Neri S, Guidotti S, Bini C, Pelotti S, D'Adamo S, Minguzzi M, Platano D, Santi S, Mariani E, Cattini L, Borzì RM. Oxidative stress-induced DNA damage and repair in primary human osteoarthritis chondrocytes: focus on IKKα and the DNA Mismatch Repair System. Free Radic Biol Med 2021; 166:212-225. [PMID: 33636333 DOI: 10.1016/j.freeradbiomed.2021.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/15/2022]
Abstract
During osteoarthritis development, chondrocytes are subjected to a functional derangement. This increases their susceptibility to stressful conditions such as oxidative stress, a characteristic of the aging tissue, which can further provoke extrinsic senescence by DNA damage responses. It was previously observed that IκB kinase α knockdown increases the replicative potential of primary human OA chondrocytes cultured in monolayer and the survival of the same cells undergoing hypertrophic-like differentiation in 3-D. In this paper we investigated whether IKKα knockdown could modulate oxidative stress-induced senescence of OA chondrocytes undergoing a DDR and particularly the involvement in this process of the DNA mismatch repair system, the principal mechanism for repair of replicative and recombinational errors, devoted to genomic stability maintenance in actively replicating cells. This repair system is also implicated in oxidative stress-mediated DNA damage repair. We analyzed microsatellite instability and expression of the mismatch repair components in human osteoarthritis chondrocytes after IKKα knockdown and H2O2 exposure. Only low MSI levels and incidence were detected and exclusively in IKKα proficient cells. Moreover, we found that IKKα proficient and deficient chondrocytes differently regulated MMR proteins after oxidative stress, both at mRNA and protein level, suggesting a reduced susceptibility of IKKα deficient cells. Our data suggest an involvement of the MMR system in the response to oxidative stress that tends to be more efficient in IKKαKD cells. This argues for a partial contribution of the MMR system to the better ability to recover DNA damage already observed in these cells.
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Affiliation(s)
- Simona Neri
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Serena Guidotti
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Carla Bini
- Department of Medical and Surgical Sciences, (DIMEC), Unit of Legal Medicine, University of Bologna, Via Irnerio, 49, 40126, Bologna, Italy.
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, (DIMEC), Unit of Legal Medicine, University of Bologna, Via Irnerio, 49, 40126, Bologna, Italy.
| | - Stefania D'Adamo
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Manuela Minguzzi
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum-Università di Bologna, Bologna, Italy.
| | - Daniela Platano
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum-Università di Bologna, Bologna, Italy.
| | - Spartaco Santi
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna at IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Erminia Mariani
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum-Università di Bologna, Bologna, Italy.
| | - Luca Cattini
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
| | - Rosa Maria Borzì
- IRCCS Istituto Ortopedico Rizzoli, Laboratory of Immunorheumatology and Tissue Regeneration, Via di Barbiano 1/10, 40136, Bologna, Italy.
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20
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Zhuo M, Gorgun FM, Tyler DS, Englander EW. Transient activation of tumoral DNA damage tolerance pathway coupled with immune checkpoint blockade exerts durable tumor regression in mouse melanoma. Pigment Cell Melanoma Res 2020; 34:605-617. [PMID: 33124186 DOI: 10.1111/pcmr.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/02/2020] [Accepted: 10/21/2020] [Indexed: 12/21/2022]
Abstract
Major advances in cancer therapy rely on engagement of the patient's immune system and suppression of mechanisms that impede the antitumor immune response. Among the most notable is immune checkpoint blockade (ICB) therapy that releases immune cells from suppression. Although ICB has had significant success particularly in melanoma, it eradicates tumors in subsets of patients and sequencing data across different cancers suggest that tumors with high mutational loads are more likely to respond to ICB. This is consistent with the premise that greater tumoral mutational loads contribute to formation of neoantigens that spur the body's antitumor immune response. Prompted by strong evidence supporting the therapeutic benefits of neoantigens in the context of ICB, we have developed a mouse melanoma combination treatment, where intratumoral administration of DNA-damaging drug transiently activates intrinsic mutagenic DNA damage tolerance pathway and improves success rates of ICB. Using the YUMM1.7 cells melanoma model, we demonstrate that intratumoral delivery of cisplatin activates translesion synthesis DNA polymerases-catalyzed DNA synthesis on damaged DNA, which when coupled with ICB regimen, elicits durable tumor regression. We expect that this new combination protocol affords insights with clinical relevance that will help expand the range of patients who benefit from ICB therapy.
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Affiliation(s)
- Ming Zhuo
- Department of Surgery, University of Texas Medical Branch, Galveston, TX, USA
| | - Falih M Gorgun
- Department of Surgery, University of Texas Medical Branch, Galveston, TX, USA
| | - Douglas S Tyler
- Department of Surgery, University of Texas Medical Branch, Galveston, TX, USA
| | - Ella W Englander
- Department of Surgery, University of Texas Medical Branch, Galveston, TX, USA
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21
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Ijsselsteijn R, Jansen JG, de Wind N. DNA mismatch repair-dependent DNA damage responses and cancer. DNA Repair (Amst) 2020; 93:102923. [DOI: 10.1016/j.dnarep.2020.102923] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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22
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Mas-Ponte D, Supek F. DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers. Nat Genet 2020; 52:958-968. [PMID: 32747826 PMCID: PMC7610516 DOI: 10.1038/s41588-020-0674-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 06/30/2020] [Indexed: 01/12/2023]
Abstract
Certain mutagens, including the APOBEC3 (A3) cytosine deaminase enzymes, can create multiple genetic changes in a single event. Activity of A3s results in striking 'mutation showers' occurring near DNA breakpoints; however, less is known about the mechanisms underlying the majority of A3 mutations. We classified the diverse patterns of clustered mutagenesis in tumor genomes, which identified a new A3 pattern: nonrecurrent, diffuse hypermutation (omikli). This mechanism occurs independently of the known focal hypermutation (kataegis), and is associated with activity of the DNA mismatch-repair pathway, which can provide the single-stranded DNA substrate needed by A3, and contributes to a substantial proportion of A3 mutations genome wide. Because mismatch repair is directed towards early-replicating, gene-rich chromosomal domains, A3 mutagenesis has a high propensity to generate impactful mutations, which exceeds that of other common carcinogens such as tobacco smoke and ultraviolet exposure. Cells direct their DNA repair capacity towards more important genomic regions; thus, carcinogens that subvert DNA repair can be remarkably potent.
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Affiliation(s)
- David Mas-Ponte
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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23
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Ma X, Tang TS, Guo C. Regulation of translesion DNA synthesis in mammalian cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:680-692. [PMID: 31983077 DOI: 10.1002/em.22359] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/29/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
The genomes of all living cells are under endogenous and exogenous attacks every day, causing diverse genomic lesions. Most of the lesions can be timely repaired by multiple DNA repair pathways. However, some may persist during S-phase, block DNA replication, and challenge genome integrity. Eukaryotic cells have evolved DNA damage tolerance (DDT) to mitigate the lethal effects of arrested DNA replication without prior removal of the offending DNA damage. As one important mode of DDT, translesion DNA synthesis (TLS) utilizes multiple low-fidelity DNA polymerases to incorporate nucleotides opposite DNA lesions to maintain genome integrity. Three different mechanisms have been proposed to regulate the polymerase switching between high-fidelity DNA polymerases in the replicative machinery and one or more specialized enzymes. Additionally, it is known that proliferating cell nuclear antigen (PCNA) mono-ubiquitination is essential for optimal TLS. Given its error-prone property, TLS is closely associated with spontaneous and drug-induced mutations in cells, which can potentially lead to tumorigenesis and chemotherapy resistance. Therefore, TLS process must be tightly modulated to avoid unwanted mutagenesis. In this review, we will focus on polymerase switching and PCNA mono-ubiquitination, the two key events in TLS pathway in mammalian cells, and summarize current understandings of regulation of TLS process at the levels of protein-protein interactions, post-translational modifications as well as transcription and noncoding RNAs. Environ. Mol. Mutagen. 61:680-692, 2020. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiaolu Ma
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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24
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Sharma M, Narayanan N, Nair DT. The proofreading activity of Pfprex from Plasmodium falciparum can prevent mutagenesis of the apicoplast genome by oxidized nucleotides. Sci Rep 2020; 10:11157. [PMID: 32636411 PMCID: PMC7341739 DOI: 10.1038/s41598-020-67853-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/11/2020] [Indexed: 01/28/2023] Open
Abstract
The DNA polymerase module of the Pfprex enzyme (PfpPol) is responsible for duplication of the genome of the apicoplast organelle in the malaria parasite. We show that PfpPol can misincorporate oxidized nucleotides such as 8oxodGTP opposite dA. This event gives rise to transversion mutations that are known to lead to adverse physiological outcomes. The apicoplast genome is particularly vulnerable to the harmful effects of 8oxodGTP due to very high AT content (~ 87%). We show that the proofreading activity of PfpPol has the unique ability to remove the oxidized nucleotide from the primer terminus. Due to this property, the proofreading domain of PfpPol is able to prevent mutagenesis of the AT-rich apicoplast genome and neutralize the deleterious genotoxic effects of ROS generated in the apicoplast due to normal metabolic processes. The proofreading activity of the Pfprex enzyme may, therefore, represent an attractive target for therapeutic intervention. Also, a survey of DNA repair pathways shows that the observed property of Pfprex constitutes a novel form of dynamic error correction wherein the repair of promutagenic damaged nucleotides is concomitant with DNA replication.
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Affiliation(s)
- Minakshi Sharma
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Kalinga Institute of Industrial Technology, Patia, Bhubaneshwar, Odisha, 751024, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
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25
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Cenni V, Squarzoni S, Loi M, Mattioli E, Lattanzi G, Capanni C. Emerin Phosphorylation during the Early Phase of the Oxidative Stress Response Influences Emerin-BAF Interaction and BAF Nuclear Localization. Cells 2020; 9:cells9061415. [PMID: 32517247 PMCID: PMC7349582 DOI: 10.3390/cells9061415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Reactive Oxygen Species (ROS) are reactive molecules required for the maintenance of physiological functions. Oxidative stress arises when ROS production exceeds the cellular ability to eliminate such molecules. In this study, we showed that oxidative stress induces post-translational modification of the inner nuclear membrane protein emerin. In particular, emerin is phosphorylated at the early stages of the oxidative stress response, while protein phosphorylation is abolished upon recovery from stress. A finely tuned balance between emerin phosphorylation and O-GlcNAcylation seems to govern this dynamic and modulates emerin–BAF interaction and BAF nucleoplasmic localization during the oxidative stress response. Interestingly, emerin post-translational modifications, similar to those observed during the stress response, are detected in cells bearing LMNA gene mutations and are characterized by a free radical generating environment. On the other hand, under oxidative stress conditions, a delay in DNA damage repair and cell cycle progression is found in cells from Emery–Dreifuss Muscular Dystrophy type 1, which do not express emerin. These results suggest a role of the emerin–BAF protein platform in the DNA damage response aimed at counteracting the detrimental effects of elevated levels of ROS.
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Affiliation(s)
- Vittoria Cenni
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Stefano Squarzoni
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Manuela Loi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40127 Bologna, Italy
| | - Elisabetta Mattioli
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Cristina Capanni
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, 40136 Bologna, Italy; (V.C.); (S.S.); (M.L.); (E.M.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Correspondence: ; Tel.: +39-051-6366856; Fax: +39-051-4689922
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26
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Basbous J, Aze A, Chaloin L, Lebdy R, Hodroj D, Ribeyre C, Larroque M, Shepard C, Kim B, Pruvost A, Moreaux J, Maiorano D, Mechali M, Constantinou A. Dihydropyrimidinase protects from DNA replication stress caused by cytotoxic metabolites. Nucleic Acids Res 2020; 48:1886-1904. [PMID: 31853544 PMCID: PMC7038975 DOI: 10.1093/nar/gkz1162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/28/2023] Open
Abstract
Imbalance in the level of the pyrimidine degradation products dihydrouracil and dihydrothymine is associated with cellular transformation and cancer progression. Dihydropyrimidines are degraded by dihydropyrimidinase (DHP), a zinc metalloenzyme that is upregulated in solid tumors but not in the corresponding normal tissues. How dihydropyrimidine metabolites affect cellular phenotypes remains elusive. Here we show that the accumulation of dihydropyrimidines induces the formation of DNA-protein crosslinks (DPCs) and causes DNA replication and transcriptional stress. We used Xenopus egg extracts to recapitulate DNA replication invitro. We found that dihydropyrimidines interfere directly with the replication of both plasmid and chromosomal DNA. Furthermore, we show that the plant flavonoid dihydromyricetin inhibits human DHP activity. Cellular exposure to dihydromyricetin triggered DPCs-dependent DNA replication stress in cancer cells. This study defines dihydropyrimidines as potentially cytotoxic metabolites that may offer an opportunity for therapeutic-targeting of DHP activity in solid tumors.
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Affiliation(s)
- Jihane Basbous
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Antoine Aze
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, 34293 Montpellier Cedex 5, France
| | - Rana Lebdy
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Dana Hodroj
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France.,Cancer Research Center of Toulouse (CRCT), 31037 Toulouse Cedex 1, France
| | - Cyril Ribeyre
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Marion Larroque
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France.,Institut du Cancer de Montpellier (ICM),34298 Montpellier Cedex 5, France
| | - Caitlin Shepard
- School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Baek Kim
- School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Alain Pruvost
- Service de Pharmacologie et Immunoanalyse (SPI), Plateforme SMArt-MS, CEA, INRA, Université Paris-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Jérôme Moreaux
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Domenico Maiorano
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Marcel Mechali
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
| | - Angelos Constantinou
- Institute of Human Genetics (IGH), CNRS, Université de Montpellier, 34396 Montpellier Cedex 5, France
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Németh E, Lovrics A, Gervai JZ, Seki M, Rospo G, Bardelli A, Szüts D. Two main mutational processes operate in the absence of DNA mismatch repair. DNA Repair (Amst) 2020; 89:102827. [PMID: 32126497 DOI: 10.1016/j.dnarep.2020.102827] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of tumour genome sequences has demonstrated high rates of base substitution mutagenesis upon the inactivation of DNA mismatch repair (MMR), and the resulting somatic mutations in MMR deficient tumours appear to significantly enhance the response to immune therapy. A handful of different algorithmically derived base substitution mutation signatures have been attributed to MMR deficiency in tumour somatic mutation datasets. In contrast, mutation data obtained from whole genome sequences of isogenic wild type and MMR deficient cell lines in this study, as well as from published sources, show a more uniform experimental mutation spectrum of MMR deficiency. In order to resolve this discrepancy, we reanalysed mutation data from MMR deficient tumour whole exome and whole genome sequences. We derived two base substitution signatures using non-negative matrix factorisation, which together adequately describe mutagenesis in all tumour and cell line samples. The two new signatures broadly resemble COSMIC signatures 6 and 20, but perform better than existing COSMIC signatures at identifying MMR deficient tumours in mutation signature deconstruction. We show that the contribution of the two identified signatures, one of which is dominated by C to T mutations at CpG sites, is biased by the different sequence composition of the exome and the whole genome. We further show that the identity of the inactivated MMR gene, the tissue type, the mutational burden or the patient's age does not influence the mutation spectrum, but that a tendency for a greater contribution by the CpG mutational process is observed in tumours as compared to cultured cells. Our analysis suggest that two separable mutational processes operate in the genomes of MMR deficient cells.
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Affiliation(s)
- Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Anna Lovrics
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Masayuki Seki
- Department of Biochemistry, Tohoku Medical & Pharmaceutical University, Miyagi 981-8558, Japan
| | - Giuseppe Rospo
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo TO, Italy; Department of Oncology, University of Turin, 10060, Candiolo TO, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo TO, Italy; Department of Oncology, University of Turin, 10060, Candiolo TO, Italy
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary.
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28
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Poetsch AR. The genomics of oxidative DNA damage, repair, and resulting mutagenesis. Comput Struct Biotechnol J 2020; 18:207-219. [PMID: 31993111 PMCID: PMC6974700 DOI: 10.1016/j.csbj.2019.12.013] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/13/2019] [Accepted: 12/21/2019] [Indexed: 12/22/2022] Open
Abstract
Reactive oxygen species are a constant threat to DNA as they modify bases with the risk of disrupting genome function, inducing genome instability and mutation. Such risks are due to primary oxidative DNA damage and also mediated by the repair process. This leads to a delicate decision process for the cell as to whether to repair a damaged base at a specific genomic location or better leave it unrepaired. Persistent DNA damage can disrupt genome function, but on the other hand it can also contribute to gene regulation by serving as an epigenetic mark. When such processes are out of balance, pathophysiological conditions could get accelerated, because oxidative DNA damage and resulting mutagenic processes are tightly linked to ageing, inflammation, and the development of multiple age-related diseases, such as cancer and neurodegenerative disorders. Recent technological advancements and novel data analysis strategies have revealed that oxidative DNA damage, its repair, and related mutations distribute heterogeneously over the genome at multiple levels of resolution. The involved mechanisms act in the context of genome sequence, in interaction with genome function and chromatin. This review addresses what we currently know about the genome distribution of oxidative DNA damage, repair intermediates, and mutations. It will specifically focus on the various methodologies to measure oxidative DNA damage distribution and discuss the mechanistic conclusions derived from the different approaches. It will also address the consequences of oxidative DNA damage, specifically how it gives rise to mutations, genome instability, and how it can act as an epigenetic mark.
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29
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Masuda Y, Masutani C. Spatiotemporal regulation of PCNA ubiquitination in damage tolerance pathways. Crit Rev Biochem Mol Biol 2019; 54:418-442. [PMID: 31736364 DOI: 10.1080/10409238.2019.1687420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA is constantly exposed to a wide variety of exogenous and endogenous agents, and most DNA lesions inhibit DNA synthesis. To cope with such problems during replication, cells have molecular mechanisms to resume DNA synthesis in the presence of DNA lesions, which are known as DNA damage tolerance (DDT) pathways. The concept of ubiquitination-mediated regulation of DDT pathways in eukaryotes was established via genetic studies in the yeast Saccharomyces cerevisiae, in which two branches of the DDT pathway are regulated via ubiquitination of proliferating cell nuclear antigen (PCNA): translesion DNA synthesis (TLS) and homology-dependent repair (HDR), which are stimulated by mono- and polyubiquitination of PCNA, respectively. Over the subsequent nearly two decades, significant progress has been made in understanding the mechanisms that regulate DDT pathways in other eukaryotes. Importantly, TLS is intrinsically error-prone because of the miscoding nature of most damaged nucleotides and inaccurate replication of undamaged templates by TLS polymerases (pols), whereas HDR is theoretically error-free because the DNA synthesis is thought to be predominantly performed by pol δ, an accurate replicative DNA pol, using the undamaged sister chromatid as its template. Thus, the regulation of the choice between the TLS and HDR pathways is critical to determine the appropriate biological outcomes caused by DNA damage. In this review, we summarize our current understanding of the species-specific regulatory mechanisms of PCNA ubiquitination and how cells choose between TLS and HDR. We then provide a hypothetical model for the spatiotemporal regulation of DDT pathways in human cells.
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Affiliation(s)
- Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
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IJspeert H, van Schouwenburg PA, Pico-Knijnenburg I, Loeffen J, Brugieres L, Driessen GJ, Blattmann C, Suerink M, Januszkiewicz-Lewandowska D, Azizi AA, Seidel MG, Jacobs H, van der Burg M. Repertoire Sequencing of B Cells Elucidates the Role of UNG and Mismatch Repair Proteins in Somatic Hypermutation in Humans. Front Immunol 2019; 10:1913. [PMID: 31507588 PMCID: PMC6718458 DOI: 10.3389/fimmu.2019.01913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/29/2019] [Indexed: 01/12/2023] Open
Abstract
The generation of high-affinity antibodies depends on somatic hypermutation (SHM). SHM is initiated by the activation-induced cytidine deaminase (AID), which generates uracil (U) lesions in the B-cell receptor (BCR) encoding genes. Error-prone processing of U lesions creates a typical spectrum of point mutations during SHM. The aim of this study was to determine the molecular mechanism of SHM in humans; currently available knowledge is limited by the number of mutations analyzed per patient. We collected a unique cohort of 10 well-defined patients with bi-allelic mutations in genes involved in base excision repair (BER) (UNG) or mismatch repair (MMR) (MSH2, MSH6, or PMS2) and are the first to present next-generation sequencing (NGS) data of the BCR, allowing us to study SHM extensively in humans. Analysis using ARGalaxy revealed selective skewing of SHM mutation patterns specific for each genetic defect, which are in line with the five-pathway model of SHM that was recently proposed based on mice data. However, trans-species comparison revealed differences in the role of PMS2 and MSH2 in strand targeting between mice and man. In conclusion, our results indicate a role for UNG, MSH2, MSH6, and PMS2 in the generation of SHM in humans comparable to their function in mice. However, we observed differences in strand targeting between humans and mice, emphasizing the importance of studying molecular mechanisms in a human setting. The here developed method combining NGS and ARGalaxy analysis of BCR mutation data forms the basis for efficient SHM analyses of other immune deficiencies.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, Netherlands.,Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Pauline A van Schouwenburg
- Department of Immunology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ingrid Pico-Knijnenburg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Jan Loeffen
- Department of Pediatric Oncology and Hematology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Laurence Brugieres
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Gertjan J Driessen
- Department of Paediatrics, Juliana Children's Hospital, Haga Teaching Hospital, The Hague, Netherlands
| | - Claudia Blattmann
- Department of Pediatric Hematology and Oncology, Palliative Care, Olgahospital Klinikum Stuttgart, Stuttgart, Germany
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria
| | - Marcus G Seidel
- Research Unit Pediatric Hematology and Immunology, Division of Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Graz, Austria
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
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31
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Supek F, Lehner B. Scales and mechanisms of somatic mutation rate variation across the human genome. DNA Repair (Amst) 2019; 81:102647. [PMID: 31307927 DOI: 10.1016/j.dnarep.2019.102647] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cancer genome sequencing has revealed that somatic mutation rates vary substantially across the human genome and at scales from megabase-sized domains to individual nucleotides. Here we review recent work that has both revealed the major mutation biases that operate across the genome and the molecular mechanisms that cause them. The default mutation rate landscape in mammalian genomes results in active genes having low mutation rates because of a combination of factors that increase DNA repair: early DNA replication, transcription, active chromatin modifications and accessible chromatin. Therefore, either an increase in the global mutation rate or a redistribution of mutations from inactive to active DNA can increase the rate at which consequential mutations are acquired in active genes. Several environmental carcinogens and intrinsic mechanisms operating in tumor cells likely cause cancer by this second mechanism: by specifically increasing the mutation rate in active regions of the genome.
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Affiliation(s)
- Fran Supek
- Genome Data Science, Institut de Recerca Biomedica (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain; Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
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32
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Ding N, Miller SA, Savant SS, O’Hagan HM. JAK2 regulates mismatch repair protein-mediated epigenetic alterations in response to oxidative damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:308-319. [PMID: 30548332 PMCID: PMC8504556 DOI: 10.1002/em.22269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/25/2018] [Accepted: 11/30/2018] [Indexed: 05/09/2023]
Abstract
At sites of chronic inflammation epithelial cells undergo aberrant DNA methylation that contributes to tumorigenesis. Inflammation is associated with an increase in reactive oxygen species (ROS) that cause oxidative DNA damage, which has also been linked to epigenetic alterations. We previously demonstrated that in response to ROS, mismatch repair proteins MSH2 and MSH6 recruit epigenetic silencing proteins DNA methyltransferase 1 (DNMT1) and polycomb repressive complex 2 (PRC2) members to sites of DNA damage, resulting in transcriptional repression of tumor suppressor genes (TSGs). However, it was unclear what signal is unique to ROS that results in the chromatin binding of MSH2 and MSH6. Herein, we demonstrate that in response to hydrogen peroxide (H2 O2 ), JAK2 localizes to the nucleus and interacts with MSH2 and MSH6. Inhibition or knockdown of JAK2 reduces the H2 O2 -induced chromatin interaction of MSH2, MSH6, DNMT1, and PRC2 members, reduces H2 O2 -induced global increase in trimethylation of lysine 27 of histone H3 (H3K27me3), and abrogates oxidative damage-induced transcriptional repression of candidate TSGs. Moreover, JAK2 mRNA expression is associated with CpG island methylator phenotype (CIMP) status in human colorectal cancer. Our findings provide novel insight into the connection between kinase activation and epigenetic alterations during oxidative damage and inflammation. Environ. Mol. Mutagen. 60:308-319, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Ning Ding
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America. 47405
| | - Sam A. Miller
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America. 47405
- Genome, Cell, and Developmental Biology, Department of Biology, Indiana University Bloomington, Indiana, United States of America. 47405
| | - Sudha S. Savant
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America. 47405
| | - Heather M. O’Hagan
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, United States of America. 47405
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America. 46202
- Corresponding author: 1001 East 3rd Street, Jordan Hall Room 108, Bloomington, IN 47405, USA, Tel: +1-812-855-3035. Fax: +1-812-855-4436,
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33
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Gupta D, Heinen CD. The mismatch repair-dependent DNA damage response: Mechanisms and implications. DNA Repair (Amst) 2019; 78:60-69. [PMID: 30959407 DOI: 10.1016/j.dnarep.2019.03.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/25/2019] [Accepted: 03/16/2019] [Indexed: 12/22/2022]
Abstract
An important role for the DNA mismatch repair (MMR) pathway in maintaining genomic stability is embodied in its conservation through evolution and the link between loss of MMR function and tumorigenesis. The latter is evident as inheritance of mutations within the major MMR genes give rise to the cancer predisposition condition, Lynch syndrome. Nonetheless, how MMR loss contributes to tumorigenesis is not completely understood. In addition to preventing the accumulation of mutations, MMR also directs cellular responses, such as cell cycle checkpoint or apoptosis activation, to different forms of DNA damage. Understanding this MMR-dependent DNA damage response may provide insight into the full tumor suppressing capabilities of the MMR pathway. Here, we delve into the proposed mechanisms for the MMR-dependent response to DNA damaging agents. We discuss how these pre-clinical findings extend to the clinical treatment of cancers, emphasizing MMR status as a crucial variable in selection of chemotherapeutic regimens. Also, we discuss how loss of the MMR-dependent damage response could promote tumorigenesis via the establishment of a survival advantage to endogenous levels of stress in MMR-deficient cells.
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Affiliation(s)
- Dipika Gupta
- Center for Molecular Oncology, UConn Health, Farmington, CT 06030, USA
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34
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Ding N, Maiuri AR, O'Hagan HM. The emerging role of epigenetic modifiers in repair of DNA damage associated with chronic inflammatory diseases. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2019; 780:69-81. [PMID: 31395351 PMCID: PMC6690501 DOI: 10.1016/j.mrrev.2017.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022]
Abstract
At sites of chronic inflammation epithelial cells are exposed to high levels of reactive oxygen species (ROS), which can contribute to the initiation and development of many different human cancers. Aberrant epigenetic alterations that cause transcriptional silencing of tumor suppressor genes are also implicated in many diseases associated with inflammation, including cancer. However, it is not clear how altered epigenetic gene silencing is initiated during chronic inflammation. The high level of ROS at sites of inflammation is known to induce oxidative DNA damage in surrounding epithelial cells. Furthermore, DNA damage is known to trigger several responses, including recruitment of DNA repair proteins, transcriptional repression, chromatin modifications and other cell signaling events. Recruitment of epigenetic modifiers to chromatin in response to DNA damage results in transient covalent modifications to chromatin such as histone ubiquitination, acetylation and methylation and DNA methylation. DNA damage also alters non-coding RNA expression. All of these alterations have the potential to alter gene expression at sites of damage. Typically, these modifications and gene transcription are restored back to normal once the repair of the DNA damage is completed. However, chronic inflammation may induce sustained DNA damage and DNA damage responses that result in these transient covalent chromatin modifications becoming mitotically stable epigenetic alterations. Understanding how epigenetic alterations are initiated during chronic inflammation will allow us to develop pharmaceutical strategies to prevent or treat chronic inflammation-induced cancer. This review will focus on types of DNA damage and epigenetic alterations associated with chronic inflammatory diseases, the types of DNA damage and transient covalent chromatin modifications induced by inflammation and oxidative DNA damage and how these modifications may result in epigenetic alterations.
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Affiliation(s)
- Ning Ding
- Medical Sciences Program, School of Medicine, Indiana University, Bloomington, IN 47405, USA
| | - Ashley R Maiuri
- Medical Sciences Program, School of Medicine, Indiana University, Bloomington, IN 47405, USA
| | - Heather M O'Hagan
- Medical Sciences Program, School of Medicine, Indiana University, Bloomington, IN 47405, USA; Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA.
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35
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Pilzecker B, Jacobs H. Mutating for Good: DNA Damage Responses During Somatic Hypermutation. Front Immunol 2019; 10:438. [PMID: 30915081 PMCID: PMC6423074 DOI: 10.3389/fimmu.2019.00438] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Somatic hypermutation (SHM) of immunoglobulin (Ig) genes plays a key role in antibody mediated immunity. SHM in B cells provides the molecular basis for affinity maturation of antibodies. In this way SHM is key in optimizing antibody dependent immune responses. SHM is initiated by targeting the Activation-Induced Cytidine Deaminase (AID) to rearranged V(D)J and switch regions of Ig genes. The mutation rate of this programmed mutagenesis is ~10-3 base pairs per generation, a million-fold higher than the non-AID targeted genome of B cells. AID is a processive enzyme that binds single-stranded DNA and deaminates cytosines in DNA. Cytosine deamination generates highly mutagenic deoxy-uracil (U) in the DNA of both strands of the Ig loci. Mutagenic processing of the U by the DNA damage response generates the entire spectrum of base substitutions characterizing SHM at and around the initial U lesion. Starting from the U as a primary lesion, currently five mutagenic DNA damage response pathways have been identified in generating a well-defined SHM spectrum of C/G transitions, C/G transversions, and A/T mutations around this initial lesion. These pathways include (1) replication opposite template U generates transitions at C/G, (2) UNG2-dependent translesion synthesis (TLS) generates transversions at C/G, (3) a hybrid pathway comprising non-canonical mismatch repair (ncMMR) and UNG2-dependent TLS generates transversions at C/G, (4) ncMMR generates mutations at A/T, and (5) UNG2- and PCNA Ubiquitination (PCNA-Ub)-dependent mutations at A/T. Furthermore, specific strand-biases of SHM spectra arise as a consequence of a biased AID targeting, ncMMR, and anti-mutagenic repriming. Here, we review mammalian SHM with special focus on the mutagenic DNA damage response pathways involved in processing AID induced Us, the origin of characteristic strand biases, and relevance of the cell cycle.
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Affiliation(s)
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
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36
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Ameziane El Hassani R, Buffet C, Leboulleux S, Dupuy C. Oxidative stress in thyroid carcinomas: biological and clinical significance. Endocr Relat Cancer 2019; 26:R131-R143. [PMID: 30615595 DOI: 10.1530/erc-18-0476] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
At physiological concentrations, reactive oxygen species (ROS), including superoxide anions and H2O2, are considered as second messengers that play key roles in cellular functions, such as proliferation, gene expression, host defence and hormone synthesis. However, when they are at supraphysiological levels, ROS are considered potent DNA-damaging agents. Their increase induces oxidative stress, which can initiate and maintain genomic instability. The thyroid gland represents a good model for studying the impact of oxidative stress on genomic instability. Indeed, one particularity of this organ is that follicular thyroid cells synthesise thyroid hormones through a complex mechanism that requires H2O2. Because of their detection in thyroid adenomas and in early cell transformation, both oxidative stress and DNA damage are believed to be neoplasia-preceding events in thyroid cells. Oxidative DNA damage is, in addition, detected in the advanced stages of thyroid cancer, suggesting that oxidative lesions of DNA also contribute to the maintenance of genomic instability during the subsequent phases of tumourigenesis. Finally, ionizing radiation and the mutation of oncogenes, such as RAS and BRAF, play a key role in thyroid carcinogenesis through separate and unique mechanisms: they upregulate the expression of two distinct 'professional' ROS-generating systems, the NADPH oxidases DUOX1 and NOX4, which cause DNA damage that may promote chromosomal instability, tumourigenesis and dedifferentiation.
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Affiliation(s)
- Rabii Ameziane El Hassani
- Laboratory of Biology of Human Pathologies 'BioPatH', Faculty of Sciences, Mohammed V University of Rabat, Rabat, Morocco
| | - Camille Buffet
- UMR 8200 CNRS, Gustave Roussy and Paris Sud University, Villejuif, France
| | - Sophie Leboulleux
- Department of Nuclear Medicine and Endocrine Oncology, Gustave Roussy and Paris Sud University, Villejuif, France
| | - Corinne Dupuy
- UMR 8200 CNRS, Gustave Roussy and Paris Sud University, Villejuif, France
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37
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Lsm12 Mediates Deubiquitination of DNA Polymerase η To Help Saccharomyces cerevisiae Resist Oxidative Stress. Appl Environ Microbiol 2019; 85:AEM.01988-18. [PMID: 30366994 DOI: 10.1128/aem.01988-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/13/2018] [Indexed: 12/20/2022] Open
Abstract
In Saccharomyces cerevisiae, the Y family DNA polymerase η (Polη) regulates genome stability in response to different forms of environmental stress by translesion DNA synthesis. To elucidate the role of Polη in oxidative stress-induced DNA damage, we deleted or overexpressed the corresponding gene RAD30 and used transcriptome analysis to screen the potential genes associated with RAD30 to respond to DNA damage. Under 2 mM H2O2 treatment, the deletion of RAD30 resulted in a 2.2-fold decrease in survival and a 2.8-fold increase in DNA damage, whereas overexpression of RAD30 increased survival and decreased DNA damage by 1.2- and 1.4-fold, respectively, compared with the wild-type strain. Transcriptome and phenotypic analyses identified Lsm12 as a main factor involved in oxidative stress-induced DNA damage. Deleting LSM12 caused growth defects, while its overexpression enhanced cell growth under 2 mM H2O2 treatment. This effect was due to the physical interaction of Lsm12 with the UBZ domain of Polη to enhance Polη deubiquitination through Ubp3 and consequently promote Polη recruitment. Overall, these findings demonstrate that Lsm12 is a novel regulator mediating Polη deubiquitination to promote its recruitment under oxidative stress. Furthermore, this study provides a potential strategy to maintain the genome stability of industrial strains during fermentation.IMPORTANCE Polη was shown to be critical for cell growth in the yeast Saccharomyces cerevisiae, and deletion of its corresponding gene RAD30 caused a severe growth defect under exposure to oxidative stress with 2 mM H2O2 Furthermore, we found that Lsm12 physically interacts with Polη and promotes Polη deubiquitination and recruitment. Overall, these findings indicate Lsm12 is a novel regulator mediating Polη deubiquitination that regulates its recruitment in response to DNA damage induced by oxidative stress.
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38
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Maneuvers on PCNA Rings during DNA Replication and Repair. Genes (Basel) 2018; 9:genes9080416. [PMID: 30126151 PMCID: PMC6116012 DOI: 10.3390/genes9080416] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
DNA replication and repair are essential cellular processes that ensure genome duplication and safeguard the genome from deleterious mutations. Both processes utilize an abundance of enzymatic functions that need to be tightly regulated to ensure dynamic exchange of DNA replication and repair factors. Proliferating cell nuclear antigen (PCNA) is the major coordinator of faithful and processive replication and DNA repair at replication forks. Post-translational modifications of PCNA, ubiquitination and acetylation in particular, regulate the dynamics of PCNA-protein interactions. Proliferating cell nuclear antigen (PCNA) monoubiquitination elicits ‘polymerase switching’, whereby stalled replicative polymerase is replaced with a specialized polymerase, while PCNA acetylation may reduce the processivity of replicative polymerases to promote homologous recombination-dependent repair. While regulatory functions of PCNA ubiquitination and acetylation have been well established, the regulation of PCNA-binding proteins remains underexplored. Considering the vast number of PCNA-binding proteins, many of which have similar PCNA binding affinities, the question arises as to the regulation of the strength and sequence of their binding to PCNA. Here I provide an overview of post-translational modifications on both PCNA and PCNA-interacting proteins and discuss their relevance for the regulation of the dynamic processes of DNA replication and repair.
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39
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Yang Y, Gao Y, Zlatanou A, Tateishi S, Yurchenko V, Rogozin IB, Vaziri C. Diverse roles of RAD18 and Y-family DNA polymerases in tumorigenesis. Cell Cycle 2018; 17:833-843. [PMID: 29683380 PMCID: PMC6056224 DOI: 10.1080/15384101.2018.1456296] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Mutagenesis is a hallmark and enabling characteristic of cancer cells. The E3 ubiquitin ligase RAD18 and its downstream effectors, the ‘Y-family’ Trans-Lesion Synthesis (TLS) DNA polymerases, confer DNA damage tolerance at the expense of DNA replication fidelity. Thus, RAD18 and TLS polymerases are attractive candidate mediators of mutagenesis and carcinogenesis. The skin cancer-propensity disorder xeroderma pigmentosum-variant (XPV) is caused by defects in the Y-family DNA polymerase Pol eta (Polη). However it is unknown whether TLS dysfunction contributes more generally to other human cancers. Recent analyses of cancer genomes suggest that TLS polymerases generate many of the mutational signatures present in diverse cancers. Moreover biochemical studies suggest that the TLS pathway is often reprogrammed in cancer cells and that TLS facilitates tolerance of oncogene-induced DNA damage. Here we review recent evidence supporting widespread participation of RAD18 and the Y-family DNA polymerases in the different phases of multi-step carcinogenesis.
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Affiliation(s)
- Yang Yang
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
| | - Yanzhe Gao
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
| | - Anastasia Zlatanou
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
| | - Satoshi Tateishi
- b Division of Cell Maintenance , Institute of Molecular Embryology and Genetics (IMEG) , Kumamoto University , Kumamoto , Japan
| | - Vyacheslav Yurchenko
- c Life Science Research Center , University of Ostrava , Ostrava , Czech Republic
| | - Igor B Rogozin
- d National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Cyrus Vaziri
- a Department of Pathology and Laboratory Medicine , University of North Carolina at Chapel Hill Chapel Hill , NC , USA
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40
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Koi M, Okita Y, Carethers JM. Fusobacterium nucleatum Infection in Colorectal Cancer: Linking Inflammation, DNA Mismatch Repair and Genetic and Epigenetic Alterations. J Anus Rectum Colon 2018; 2:37-46. [PMID: 30116794 PMCID: PMC6090547 DOI: 10.23922/jarc.2017-055] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 01/30/2018] [Indexed: 12/13/2022] Open
Abstract
It has been recently reported that the population of Fusobacterium, particularly Fusobacterium nucleatum (Fn), is overrepresented in colorectal cancers and adenomas. The promoting effects of Fn infection on adenoma and/or carcinoma formation have been shown in ApcMin/+mice. Characteristics of Fn-associated CRC were identified through studies using human CRC cohorts, and include right-sided colon location, CpG island methylation phenotype-high (CIMP-H), high level of microsatellite instability (MSI-H), and poor patient prognosis. A subset of Fn-associated CRC exhibits a low level of microsatellite instability (MSI-L) and elevated microsatellite alterations in selected tetra-nucleotide repeats (EMAST) induced by translocation of MSH3 from the nucleus to the cytoplasm in response to oxidative DNA damage or inflammatory signals. The association between CIMP/MSI-H and Fn-infection can be explained by the role of the mismatch repair (MMR) protein complex formed between MSH2 and MSH6 (MutSα) to repair aberrant bases generated by ROS to form 7,8-dihydro-8-oxo-guanine (8-oxoG). Clustered 8-oxoGs formed at CpG-rich regions including promoters by ROS is refractory to base excision repair (BER). Under these conditions, MutSα initiates repair in cooperation with DNA methyltransferases (DNMTs) and the polycomb repressive complex 4 (PRC4). DNMTs at damaged sites methylate CpG islands to repress transcription of target genes and promote repair reactions. Thus, continuous generation of ROS through chronic Fn infection may initiate 1) CIMP-positive adenoma and carcinoma in an MSH2/MSH6-dependent manner, and/or 2) MSI-L/EMAST CRC in an MSH3-dependent manner. The poor prognosis of Fn-associated CRC can be explained by Fn-induced immune-evasion and/or chemo-resistance.
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Affiliation(s)
- Minoru Koi
- Division of Gastroenterology, Department of Internal Medicine, and Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yoshiki Okita
- Division of Gastroenterology, Department of Internal Medicine, and Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John M Carethers
- Division of Gastroenterology, Department of Internal Medicine, and Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
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Zhu X, Ma X, Tu Y, Huang M, Liu H, Wang F, Gong J, Wang J, Li X, Chen Q, Shen H, Zhu S, Wang Y, Liu Y, Guo C, Tang TS. Parkin regulates translesion DNA synthesis in response to UV radiation. Oncotarget 2018; 8:36423-36437. [PMID: 28430587 PMCID: PMC5482665 DOI: 10.18632/oncotarget.16855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/27/2017] [Indexed: 01/12/2023] Open
Abstract
Deficiency of Parkin is a major cause of early-onset Parkinson's disease (PD). Notably, PD patients also exhibit a significantly higher risk in melanoma and other skin tumors, while the mechanism remains largely unknown. In this study, we show that depletion of Parkin causes compromised cell viability and genome stability after ultraviolet (UV) radiation. We demonstrate that Parkin promotes efficient Rad18-dependent proliferating cell nuclear antigen (PCNA) monoubiquitination by facilitating the formation of Replication protein A (RPA)-coated ssDNA upon UV radiation. Furthermore, Parkin is found to physically interact with NBS1 (Nijmegen breakage syndrome 1), and to be required for optimal recruitment of NBS1 and DNA polymerase eta (Polη) to UV-induced damage sites. Consequently, depletion of Parkin leads to increased UV-induced mutagenesis. These findings unveil an important role of Parkin in protecting genome stability through positively regulating translesion DNA synthesis (TLS) upon UV damage, providing a novel mechanistic link between Parkin deficiency and predisposition to skin cancers in PD patients.
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Affiliation(s)
- Xuefei Zhu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolu Ma
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingfeng Tu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Huang
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Fengli Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Juanjuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiuqiang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoling Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Chen
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongyan Shen
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu Zhu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Liu
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
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42
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Quinet A, Lerner LK, Martins DJ, Menck CFM. Filling gaps in translesion DNA synthesis in human cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:127-142. [PMID: 30442338 DOI: 10.1016/j.mrgentox.2018.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/21/2018] [Indexed: 01/06/2023]
Abstract
During DNA replication, forks may encounter unrepaired lesions that hamper DNA synthesis. Cells have universal strategies to promote damage bypass allowing cells to survive. DNA damage tolerance can be performed upon template switch or by specialized DNA polymerases, known as translesion (TLS) polymerases. Human cells count on more than eleven TLS polymerases and this work reviews the functions of some of these enzymes: Rev1, Pol η, Pol ι, Pol κ, Pol θ and Pol ζ. The mechanisms of damage bypass vary according to the lesion, as well as to the TLS polymerases available, and may occur directly at the fork during replication. Alternatively, the lesion may be skipped, leaving a single-stranded DNA gap that will be replicated later. Details of the participation of these enzymes are revised for the replication of damaged template. TLS polymerases also have functions in other cellular processes. These include involvement in somatic hypermutation in immunoglobulin genes, direct participation in recombination and repair processes, and contributing to replicating noncanonical DNA structures. The importance of DNA damage replication to cell survival is supported by recent discoveries that certain genes encoding TLS polymerases are induced in response to DNA damaging agents, protecting cells from a subsequent challenge to DNA replication. We retrace the findings on these genotoxic (adaptive) responses of human cells and show the common aspects with the SOS responses in bacteria. Paradoxically, although TLS of DNA damage is normally an error prone mechanism, in general it protects from carcinogenesis, as evidenced by increased tumorigenesis in xeroderma pigmentosum variant patients, who are deficient in Pol η. As these TLS polymerases also promote cell survival, they constitute an important mechanism by which cancer cells acquire resistance to genotoxic chemotherapy. Therefore, the TLS polymerases are new potential targets for improving therapy against tumors.
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Affiliation(s)
- Annabel Quinet
- Saint Louis University School of Medicine, St. Louis, MO, United States.
| | - Leticia K Lerner
- MRC Laboratory of Molecular Biology,Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Davi J Martins
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carlos F M Menck
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Akagi J, Yokoi M, Cho YM, Toyoda T, Ohmori H, Hanaoka F, Ogawa K. Hypersensitivity of mouse embryonic fibroblast cells defective for DNA polymerases η, ι and κ to various genotoxic compounds: Its potential for application in chemical genotoxic screening. DNA Repair (Amst) 2017; 61:76-85. [PMID: 29247828 DOI: 10.1016/j.dnarep.2017.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/19/2017] [Accepted: 11/23/2017] [Indexed: 12/11/2022]
Abstract
Genotoxic agents cause modifications of genomic DNA, such as alkylation, oxidation, bulky adduct formation, and strand breaks, which potentially induce mutations and changes to the structure or number of genes. Majority of point mutations are generated during error-prone bypass of modified nucleotides (translesion DNA synthesis, TLS); however, when TLS fails, replication forks stalled at lesions eventually result in more lethal effects, formation of double-stranded breaks (DSBs). Here we compared sensitivities to various compounds among mouse embryonic fibroblasts derived from wild-type and knock-out mice lacking one of the three Y-family TLS DNA polymerases (Polη, Polι, and Polκ) or all of them (TKO). The compounds tested in this study include genotoxins such as methyl methanesulfonate (MMS) and nongenotoxins such as ammonium chloride. We found that TKO cells exhibited the highest sensitivities to most of the tested genotoxins, but not to the non-genotoxins. In order to quantitatively evaluate the hypersensitivity of TKO cells to different chemicals, we calculated ratios of half-maximal inhibitory concentration for WT and TKO cells. The ratios for 9 out of 10 genotoxins ranged from 2.29 to 5.73, while those for 5 nongenotoxins ranged from 0.81 to 1.63. Additionally, the two markers for DNA damage, ubiquitylated proliferating cell nuclear antigen and γ-H2AX after MMS treatment, were accumulated in TKO cells more greatly than in WT cells. Furthermore, following MMS treatment, TKO cells exhibited increased frequency of sister chromatid exchange compared with WT cells. These results indicated that the hypersensitivity of TKO cells to genotoxins resulted from replication fork stalling and subsequent DNA double-strand breaks, thus demonstrating that TKO cells should be useful for evaluating chemical genotoxicity.
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Affiliation(s)
- Junichi Akagi
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan.
| | - Masayuki Yokoi
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan; Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo Prefecture 657-8501, Japan
| | - Young-Man Cho
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Takeshi Toyoda
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Haruo Ohmori
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Fumio Hanaoka
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan; Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki Prefecture 305-8577, Japan
| | - Kumiko Ogawa
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
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Garcia-Exposito L, Bournique E, Bergoglio V, Bose A, Barroso-Gonzalez J, Zhang S, Roncaioli JL, Lee M, Wallace CT, Watkins SC, Opresko PL, Hoffmann JS, O'Sullivan RJ. Proteomic Profiling Reveals a Specific Role for Translesion DNA Polymerase η in the Alternative Lengthening of Telomeres. Cell Rep 2017; 17:1858-1871. [PMID: 27829156 PMCID: PMC5406014 DOI: 10.1016/j.celrep.2016.10.048] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/18/2016] [Accepted: 10/14/2016] [Indexed: 11/22/2022] Open
Abstract
Cancer cells rely on the activation of telomerase or the alternative lengthening of telomeres (ALT) pathways for telomere maintenance and survival. ALT involves homologous recombination (HR)-dependent exchange and/or HR-associated synthesis of telomeric DNA. Utilizing proximity-dependent biotinylation (BioID), we sought to determine the proteome of telomeres in cancer cells that employ these distinct telomere elongation mechanisms. Our analysis reveals that multiple DNA repair networks converge at ALT telomeres. These include the specialized translesion DNA synthesis (TLS) proteins FANCJ-RAD18-PCNA and, most notably, DNA polymerase eta (Polη). We observe that the depletion of Polη leads to increased ALT activity and late DNA polymerase δ (Polδ)-dependent synthesis of telomeric DNA in mitosis. We propose that Polη fulfills an important role in managing replicative stress at ALT telomeres, maintaining telomere recombination at tolerable levels and stimulating DNA synthesis by Polδ.
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Affiliation(s)
- Laura Garcia-Exposito
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Elodie Bournique
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan Barroso-Gonzalez
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Callen T Wallace
- Department of Cell Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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45
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Choe KN, Moldovan GL. Forging Ahead through Darkness: PCNA, Still the Principal Conductor at the Replication Fork. Mol Cell 2017; 65:380-392. [PMID: 28157503 DOI: 10.1016/j.molcel.2016.12.020] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/28/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) lies at the center of the faithful duplication of eukaryotic genomes. With its distinctive doughnut-shaped molecular structure, PCNA was originally studied for its role in stimulating DNA polymerases. However, we now know that PCNA does much more than promote processive DNA synthesis. Because of the complexity of the events involved, cellular DNA replication poses major threats to genomic integrity. Whatever predicament lies ahead for the replication fork, PCNA is there to orchestrate the events necessary to handle it. Through its many protein interactions and various post-translational modifications, PCNA has far-reaching impacts on a myriad of cellular functions.
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Affiliation(s)
- Katherine N Choe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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46
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Yang Y, Gao Y, Mutter-Rottmayer L, Zlatanou A, Durando M, Ding W, Wyatt D, Ramsden D, Tanoue Y, Tateishi S, Vaziri C. DNA repair factor RAD18 and DNA polymerase Polκ confer tolerance of oncogenic DNA replication stress. J Cell Biol 2017; 216:3097-3115. [PMID: 28835467 PMCID: PMC5626543 DOI: 10.1083/jcb.201702006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/27/2017] [Accepted: 07/21/2017] [Indexed: 12/30/2022] Open
Abstract
The elevated CDK2 activity of oncogene-expressing cells induces DNA replication stress. Yang et al. show that the DNA repair protein RAD18 facilitates damage-tolerant DNA synthesis via the DNA polymerase κ in cells with aberrantly high CDK2 activity, suggesting an important new role for RAD18 in sustaining neoplastic cell survival. The mechanisms by which neoplastic cells tolerate oncogene-induced DNA replication stress are poorly understood. Cyclin-dependent kinase 2 (CDK2) is a major mediator of oncogenic DNA replication stress. In this study, we show that CDK2-inducing stimuli (including Cyclin E overexpression, oncogenic RAS, and WEE1 inhibition) activate the DNA repair protein RAD18. CDK2-induced RAD18 activation required initiation of DNA synthesis and was repressed by p53. RAD18 and its effector, DNA polymerase κ (Polκ), sustained ongoing DNA synthesis in cells harboring elevated CDK2 activity. RAD18-deficient cells aberrantly accumulated single-stranded DNA (ssDNA) after CDK2 activation. In RAD18-depleted cells, the G2/M checkpoint was necessary to prevent mitotic entry with persistent ssDNA. Rad18−/− and Polκ−/− cells were highly sensitive to the WEE1 inhibitor MK-1775 (which simultaneously activates CDK2 and abrogates the G2/M checkpoint). Collectively, our results show that the RAD18–Polκ signaling axis allows tolerance of CDK2-mediated oncogenic stress and may allow neoplastic cells to breach tumorigenic barriers.
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Affiliation(s)
- Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liz Mutter-Rottmayer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anastasia Zlatanou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael Durando
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Weimin Ding
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - David Wyatt
- Lineberger Comprehensive Cancer Center, Curriculumin Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Dale Ramsden
- Lineberger Comprehensive Cancer Center, Curriculumin Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yuki Tanoue
- Division of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Satoshi Tateishi
- Division of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC .,Lineberger Comprehensive Cancer Center, Curriculumin Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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47
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Guan J, Yu S, Zheng X. NEDDylation antagonizes ubiquitination of proliferating cell nuclear antigen and regulates the recruitment of polymerase η in response to oxidative DNA damage. Protein Cell 2017; 9:365-379. [PMID: 28831681 PMCID: PMC5876183 DOI: 10.1007/s13238-017-0455-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/21/2017] [Indexed: 01/27/2023] Open
Abstract
NEDDylation has been shown to participate in the DNA damage pathway, but the substrates of neural precursor cell expressed developmentally downregulated 8 (NEDD8) and the roles of NEDDylation involved in the DNA damage response (DDR) are largely unknown. Translesion synthesis (TLS) is a damage-tolerance mechanism, in which RAD18/RAD6-mediated monoubiquitinated proliferating cell nuclear antigen (PCNA) promotes recruitment of polymerase η (polη) to bypass lesions. Here we identify PCNA as a substrate of NEDD8, and show that E3 ligase RAD18-catalyzed PCNA NEDDylation antagonizes its ubiquitination. In addition, NEDP1 acts as the deNEDDylase of PCNA, and NEDP1 deletion enhances PCNA NEDDylation but reduces its ubiquitination. In response to H2O2 stimulation, NEDP1 disassociates from PCNA and RAD18-dependent PCNA NEDDylation increases markedly after its ubiquitination. Impairment of NEDDylation by Ubc12 knockout enhances PCNA ubiquitination and promotes PCNA-polη interaction, while up-regulation of NEDDylation by NEDD8 overexpression or NEDP1 deletion reduces the excessive accumulation of ubiquitinated PCNA, thus inhibits PCNA-polη interaction and blocks polη foci formation. Moreover, Ubc12 knockout decreases cell sensitivity to H2O2-induced oxidative stress, but NEDP1 deletion aggravates this sensitivity. Collectively, our study elucidates the important role of NEDDylation in the DDR as a modulator of PCNA monoubiquitination and polη recruitment.
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Affiliation(s)
- Junhong Guan
- State Key Lab of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shuyu Yu
- State Key Lab of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaofeng Zheng
- State Key Lab of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, 100871, China.
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48
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Thientosapol ES, Sharbeen G, Lau KKE, Bosnjak D, Durack T, Stevanovski I, Weninger W, Jolly CJ. Proximity to AGCT sequences dictates MMR-independent versus MMR-dependent mechanisms for AID-induced mutation via UNG2. Nucleic Acids Res 2017; 45:3146-3157. [PMID: 28039326 PMCID: PMC5389528 DOI: 10.1093/nar/gkw1300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022] Open
Abstract
AID deaminates C to U in either strand of Ig genes, exclusively producing C:G/G:C to T:A/A:T transition mutations if U is left unrepaired. Error-prone processing by UNG2 or mismatch repair diversifies mutation, predominantly at C:G or A:T base pairs, respectively. Here, we show that transversions at C:G base pairs occur by two distinct processing pathways that are dictated by sequence context. Within and near AGCT mutation hotspots, transversion mutation at C:G was driven by UNG2 without requirement for mismatch repair. Deaminations in AGCT were refractive both to processing by UNG2 and to high-fidelity base excision repair (BER) downstream of UNG2, regardless of mismatch repair activity. We propose that AGCT sequences resist faithful BER because they bind BER-inhibitory protein(s) and/or because hemi-deaminated AGCT motifs innately form a BER-resistant DNA structure. Distal to AGCT sequences, transversions at G were largely co-dependent on UNG2 and mismatch repair. We propose that AGCT-distal transversions are produced when apyrimidinic sites are exposed in mismatch excision patches, because completion of mismatch repair would require bypass of these sites.
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Affiliation(s)
- Eddy Sanchai Thientosapol
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - George Sharbeen
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - K K Edwin Lau
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Daniel Bosnjak
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Timothy Durack
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Igor Stevanovski
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Wolfgang Weninger
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Christopher J Jolly
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
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49
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Supek F, Lehner B. Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes. Cell 2017; 170:534-547.e23. [PMID: 28753428 DOI: 10.1016/j.cell.2017.07.003] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/17/2017] [Accepted: 07/05/2017] [Indexed: 02/07/2023]
Abstract
Many processes can cause the same nucleotide change in a genome, making the identification of the mechanisms causing mutations a difficult challenge. Here, we show that clustered mutations provide a more precise fingerprint of mutagenic processes. Of nine clustered mutation signatures identified from >1,000 tumor genomes, three relate to variable APOBEC activity and three are associated with tobacco smoking. An additional signature matches the spectrum of translesion DNA polymerase eta (POLH). In lymphoid cells, these mutations target promoters, consistent with AID-initiated somatic hypermutation. In solid tumors, however, they are associated with UV exposure and alcohol consumption and target the H3K36me3 chromatin of active genes in a mismatch repair (MMR)-dependent manner. These regions normally have a low mutation rate because error-free MMR also targets H3K36me3 chromatin. Carcinogens and error-prone repair therefore redistribute mutations to the more important regions of the genome, contributing a substantial mutation load in many tumors, including driver mutations.
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Affiliation(s)
- Fran Supek
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Division of Electronics, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
| | - Ben Lehner
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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50
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Kanao R, Masutani C. Regulation of DNA damage tolerance in mammalian cells by post-translational modifications of PCNA. Mutat Res 2017; 803-805:82-88. [PMID: 28666590 DOI: 10.1016/j.mrfmmm.2017.06.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/25/2017] [Accepted: 06/19/2017] [Indexed: 11/29/2022]
Abstract
DNA damage tolerance pathways, which include translesion DNA synthesis (TLS) and template switching, are crucial for prevention of DNA replication arrest and maintenance of genomic stability. However, these pathways utilize error-prone DNA polymerases or template exchange between sister DNA strands, and consequently have the potential to induce mutations or chromosomal rearrangements. Post-translational modifications of proliferating cell nuclear antigen (PCNA) play important roles in controlling these pathways. For example, TLS is mediated by mono-ubiquitination of PCNA at lysine 164, for which RAD6-RAD18 is the primary E2-E3 complex. Elaborate protein-protein interactions between mono-ubiquitinated PCNA and Y-family DNA polymerases constitute the core of the TLS regulatory system, and enhancers of PCNA mono-ubiquitination and de-ubiquitinating enzymes finely regulate TLS and suppress TLS-mediated mutagenesis. The template switching pathway is promoted by K63-linked poly-ubiquitination of PCNA at lysine 164. Poly-ubiquitination is achieved by a coupled reaction mediated by two sets of E2-E3 complexes, RAD6-RAD18 and MMS2-UBC13-HTLF/SHPRH. In addition to these mono- and poly-ubiquitinations, simultaneous mono-ubiquitinations on multiple units of the PCNA homotrimeric ring promote an unidentified damage tolerance mechanism that remains to be fully characterized. Furthermore, SUMOylation of PCNA in mammalian cells can negatively regulate recombination. Other modifications, including ISGylation, acetylation, methylation, or phosphorylation, may also play roles in DNA damage tolerance and control of genomic stability.
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Affiliation(s)
- Rie Kanao
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.
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