1
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Cao Y, Wu C, Ma L. Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance. J Biochem Mol Toxicol 2024; 38:e23587. [PMID: 38014925 DOI: 10.1002/jbt.23587] [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: 07/25/2023] [Revised: 10/17/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
Chemoresistance, a roadblock in the chemotherapy process, has been impeding its effective treatment. KDM5B, a member of the histone demethylase family, has been crucial in the emergence and growth of malignancies. More significantly, KDM5B has recently been linked closely to cancer's resistance to chemotherapy. In this review, we explain the biological properties of KDM5B, its function in the emergence and evolution of cancer treatment resistance, and our hopes for future drug resistance-busting combinations involving KDM5B and related targets or medications.
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Affiliation(s)
- Yaquan Cao
- College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
| | - Chunli Wu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory of Cardio-Cerebrovascular Drug, China Meheco Topfond Pharmaceutical Company, Zhumadian, China
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2
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Sallmyr A, Bhandari SK, Naila T, Tomkinson AE. Mammalian DNA ligases; roles in maintaining genome integrity. J Mol Biol 2024; 436:168276. [PMID: 37714297 PMCID: PMC10843057 DOI: 10.1016/j.jmb.2023.168276] [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: 06/18/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The joining of breaks in the DNA phosphodiester backbone is essential for genome integrity. Breaks are generated during normal processes such as DNA replication, cytosine demethylation during differentiation, gene rearrangement in the immune system and germ cell development. In addition, they are generated either directly by a DNA damaging agent or indirectly due to damage excision during repair. Breaks are joined by a DNA ligase that catalyzes phosphodiester bond formation at DNA nicks with 3' hydroxyl and 5' phosphate termini. Three human genes encode ATP-dependent DNA ligases. These enzymes have a conserved catalytic core consisting of three subdomains that encircle nicked duplex DNA during ligation. The DNA ligases are targeted to different nuclear DNA transactions by specific protein-protein interactions. Both DNA ligase IIIα and DNA ligase IV form stable complexes with DNA repair proteins, XRCC1 and XRCC4, respectively. There is functional redundancy between DNA ligase I and DNA ligase IIIα in DNA replication, excision repair and single-strand break repair. Although DNA ligase IV is a core component of the major double-strand break repair pathway, non-homologous end joining, the other enzymes participate in minor, alternative double-strand break repair pathways. In contrast to the nucleus, only DNA ligase IIIα is present in mitochondria and is essential for maintaining the mitochondrial genome. Human immunodeficiency syndromes caused by mutations in either LIG1 or LIG4 have been described. Preclinical studies with DNA ligase inhibitors have identified potentially targetable abnormalities in cancer cells and evidence that DNA ligases are potential targets for cancer therapy.
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Affiliation(s)
- Annahita Sallmyr
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Seema Khattri Bhandari
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Tasmin Naila
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Alan E Tomkinson
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States.
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3
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Krasikova YS, Lavrik OI, Rechkunova NI. The XPA Protein-Life under Precise Control. Cells 2022; 11:cells11233723. [PMID: 36496984 PMCID: PMC9739396 DOI: 10.3390/cells11233723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Nucleotide excision repair (NER) is a central DNA repair pathway responsible for removing a wide variety of DNA-distorting lesions from the genome. The highly choreographed cascade of core NER reactions requires more than 30 polypeptides. The xeroderma pigmentosum group A (XPA) protein plays an essential role in the NER process. XPA interacts with almost all NER participants and organizes the correct NER repair complex. In the absence of XPA's scaffolding function, no repair process occurs. In this review, we briefly summarize our current knowledge about the XPA protein structure and analyze the formation of contact with its protein partners during NER complex assembling. We focus on different ways of regulation of the XPA protein's activity and expression and pay special attention to the network of post-translational modifications. We also discuss the data that is not in line with the currently accepted hypothesis about the functioning of the XPA protein.
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Affiliation(s)
- Yuliya S. Krasikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nadejda I. Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Correspondence:
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4
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Curreli S, Benedetti F, Yuan W, Munawwar A, Cocchi F, Gallo RC, Sherman NE, Zella D. Characterization of the interactome profiling of Mycoplasma fermentans DnaK in cancer cells reveals interference with key cellular pathways. Front Microbiol 2022; 13:1022704. [PMID: 36386669 PMCID: PMC9651203 DOI: 10.3389/fmicb.2022.1022704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/03/2022] [Indexed: 06/10/2024] Open
Abstract
Chaperone proteins are redundant in nature and, to achieve their function, they bind a large repertoire of client proteins. DnaK is a bacterial chaperone protein that recognizes misfolded and aggregated proteins and drives their folding and intracellular trafficking. Some Mycoplasmas are associated with cancers, and we demonstrated that infection with a strain of Mycoplasma fermentans isolated in our lab promoted lymphoma in a mouse model. Its DnaK is expressed intracellularly in infected cells, it interacts with key proteins to hamper essential pathways related to DNA repair and p53 functions and uninfected cells can take-up extracellular DnaK. We profile here for the first time the eukaryotic proteins interacting with DnaK transiently expressed in five cancer cell lines. A total of 520 eukaryotic proteins were isolated by immunoprecipitation and identified by Liquid Chromatography Mass Spectrometry (LC-MS) analysis. Among the cellular DnaK-binding partners, 49 were shared between the five analyzed cell lines, corroborating the specificity of the interaction of DnaK with these proteins. Enrichment analysis revealed multiple RNA biological processes, DNA repair, chromatin remodeling, DNA conformational changes, protein-DNA complex subunit organization, telomere organization and cell cycle as the most significant ontology terms. This is the first study to show that a bacterial chaperone protein interacts with key eukaryotic components thus suggesting DnaK could become a perturbing hub for the functions of important cellular pathways. Given the close interactions between bacteria and host cells in the local microenvironment, these results provide a foundation for future mechanistic studies on how bacteria interfere with essential cellular processes.
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Affiliation(s)
- Sabrina Curreli
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Francesca Benedetti
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Weirong Yuan
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Arshi Munawwar
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Fiorenza Cocchi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Robert C. Gallo
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nicholas E. Sherman
- Biomolecular Analysis Facility Core, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Davide Zella
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
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5
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Kim SH, Kim GH, Kemp MG, Choi JH. TREX1 degrades the 3' end of the small DNA oligonucleotide products of nucleotide excision repair in human cells. Nucleic Acids Res 2022; 50:3974-3984. [PMID: 35357486 PMCID: PMC9023299 DOI: 10.1093/nar/gkac214] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 01/01/2023] Open
Abstract
The nucleotide excision repair (NER) machinery removes UV photoproducts from DNA in the form of small, excised damage-containing DNA oligonucleotides (sedDNAs) ∼30 nt in length. How cells process and degrade these byproducts of DNA repair is not known. Using a small scale RNA interference screen in UV-irradiated human cells, we identified TREX1 as a major regulator of sedDNA abundance. Knockdown of TREX1 increased the level of sedDNAs containing the two major UV photoproducts and their association with the NER proteins TFIIH and RPA. Overexpression of wild-type but not nuclease-inactive TREX1 significantly diminished sedDNA levels, and studies with purified recombinant TREX1 showed that the enzyme efficiently degrades DNA located 3′ of the UV photoproduct in the sedDNA. Knockdown or overexpression of TREX1 did not impact the overall rate of UV photoproduct removal from genomic DNA or cell survival, which indicates that TREX1 function in sedDNA degradation does not impact NER efficiency. Taken together, these results indicate a previously unknown role for TREX1 in promoting the degradation of the sedDNA products of the repair reaction. Because TREX1 mutations and inefficient DNA degradation impact inflammatory and immune signaling pathways, the regulation of sedDNA degradation by TREX1 may contribute to photosensitive skin disorders.
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Affiliation(s)
- Seon Hee Kim
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-340, Republic of Korea
| | - Geun Hoe Kim
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-340, Republic of Korea
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH 45435, USA.,Dayton Veterans Administration Medical Center, Dayton, OH 45428, USA
| | - Jun-Hyuk Choi
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-340, Republic of Korea
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6
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Zhao S, Xu B, Ma W, Chen H, Jiang C, Cai J, Meng X. DNA Damage Repair in Brain Tumor Immunotherapy. Front Immunol 2022; 12:829268. [PMID: 35095931 PMCID: PMC8792754 DOI: 10.3389/fimmu.2021.829268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/22/2021] [Indexed: 12/01/2022] Open
Abstract
With the gradual understanding of tumor development, many tumor therapies have been invented and applied in clinical work, and immunotherapy has been widely concerned as an emerging hot topic in the last decade. It is worth noting that immunotherapy is nowadays applied under too harsh conditions, and many tumors are defined as “cold tumors” that are not sensitive to immunotherapy, and brain tumors are typical of them. However, there is much evidence that suggests a link between DNA damage repair mechanisms and immunotherapy. This may be a breakthrough for the application of immunotherapy in brain tumors. Therefore, in this review, first, we will describe the common pathways of DNA damage repair. Second, we will focus on immunotherapy and analyze the mechanisms of DNA damage repair involved in the immune process. Third, we will review biomarkers that have been or may be used to evaluate immunotherapy for brain tumors, such as TAMs, RPA, and other molecules that may provide a precursor assessment for the rational implementation of immunotherapy for brain tumors. Finally, we will discuss the rational combination of immunotherapy with other therapeutic approaches that have an impact on the DNA damage repair process in order to open new pathways for the application of immunotherapy in brain tumors, to maximize the effect of immunotherapy on DNA damage repair mechanisms, and to provide ideas and guidance for immunotherapy in brain tumors.
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Affiliation(s)
- Shihong Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Boya Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wenbin Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chuanlu Jiang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jinquan Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangqi Meng
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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7
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Kim JY, Bahar E, Lee JY, Chang S, Kim SH, Park EY, Do SI, Yoon H, Kim HS. ARL6IP5 reduces cisplatin-resistance by suppressing DNA repair and promoting apoptosis pathways in ovarian carcinoma. Cell Death Dis 2022; 13:239. [PMID: 35293383 PMCID: PMC8924236 DOI: 10.1038/s41419-022-04568-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 12/31/2021] [Accepted: 01/20/2022] [Indexed: 11/18/2022]
Abstract
Ovarian carcinoma (OC) is the most lethal gynecological malignancy due to frequent recurrence resulting from cisplatin-resistance. ARL6IP5 is a novel gene implicated to suppress cisplatin-resistance by activating apoptosis and inhibiting DNA repair through XRCC1 and PARP1. We investigated the clinicopathological and prognostic significance of the immunohistochemical ARL6IP5 expression on 79 post-chemotherapy OC patient tissue samples; in vitro, the effect of ARL6IP5 overexpression (OE) and knockdown (KD) on cancer hallmark functions and the effect of ARL6IP5 on the expression of DNA repair and apoptosis-related proteins were observed in OC cells and their cisplatin-resistant (CisR) counterparts. ARL6IP5 expression was significantly associated with chemotherapeutic response and was an independent prognosticator of progression-free and overall survival of high-grade serous OC patients. ARL6IP5-OE decreased cellular proliferation, invasion, migration, adhesion, and increased apoptosis (p < 0.05); the opposite was observed for ARL6IP5-KD. Notably, ARL6IP5-OE reduced cisplatin-resistance of both OC and CisR OC cells, while ARL6IP5-KD increased cisplatin-resistance (p < 0.05). ARL6IP5-OE suppressed the expressions of DNA repair proteins and increased those of pro-apoptotic proteins; the opposite was observed for ARL6IP5-KD. The recombinant ARL6IP5 protein (rARL6IP5) had the greatest apoptotic effect among cisplatin and olaparib, in both OC and CisR OC cells; moreover, rARL6IP5 was the only single agent in CisR OC cells to retain higher apoptotic efficacy compared with control (p < 0.05), indicating that the apoptotic pathway influenced by rARL6IP5 remained effective in CisR OC cells compared to cisplatin and olaparib. In conclusion, we demonstrated that ARL6IP5 is an independent prognosticator of OC patients with cellular functions of a tumor-suppressor, possibly influencing the development of cisplatin-resistance and progression of OC cells through regulation of DNA repair and apoptosis. rARL6IP5 had significantly greater apoptotic efficacy compared to conventional chemotherapeutic agents in both OC and CisR OC cells, suggesting that ARL6IP5 may be a valuable novel chemotherapeutic against CisR OC.
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8
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Yoshioka KI, Kusumoto-Matsuo R, Matsuno Y, Ishiai M. Genomic Instability and Cancer Risk Associated with Erroneous DNA Repair. Int J Mol Sci 2021; 22:12254. [PMID: 34830134 PMCID: PMC8625880 DOI: 10.3390/ijms222212254] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022] Open
Abstract
Many cancers develop as a consequence of genomic instability, which induces genomic rearrangements and nucleotide mutations. Failure to correct DNA damage in DNA repair defective cells, such as in BRCA1 and BRCA2 mutated backgrounds, is directly associated with increased cancer risk. Genomic rearrangement is generally a consequence of erroneous repair of DNA double-strand breaks (DSBs), though paradoxically, many cancers develop in the absence of DNA repair defects. DNA repair systems are essential for cell survival, and in cancers deficient in one repair pathway, other pathways can become upregulated. In this review, we examine the current literature on genomic alterations in cancer cells and the association between these alterations and DNA repair pathway inactivation and upregulation.
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Affiliation(s)
- Ken-ichi Yoshioka
- Laboratory of Genome Stability Maintenance, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (R.K.-M.); (Y.M.)
| | - Rika Kusumoto-Matsuo
- Laboratory of Genome Stability Maintenance, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (R.K.-M.); (Y.M.)
| | - Yusuke Matsuno
- Laboratory of Genome Stability Maintenance, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (R.K.-M.); (Y.M.)
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Masamichi Ishiai
- Central Radioisotope Division, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
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9
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Gaul L, Svejstrup JQ. Transcription-coupled repair and the transcriptional response to UV-Irradiation. DNA Repair (Amst) 2021; 107:103208. [PMID: 34416541 DOI: 10.1016/j.dnarep.2021.103208] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 02/07/2023]
Abstract
Lesions in genes that result in RNA polymerase II (RNAPII) stalling or arrest are particularly toxic as they are a focal point of genome instability and potently block further transcription of the affected gene. Thus, cells have evolved the transcription-coupled nucleotide excision repair (TC-NER) pathway to identify damage-stalled RNAPIIs, so that the lesion can be rapidly repaired and transcription can continue. However, despite the identification of several factors required for TC-NER, how RNAPII is remodelled, modified, removed, or whether this is even necessary for repair remains enigmatic, and theories are intensely contested. Recent studies have further detailed the cellular response to UV-induced ubiquitylation and degradation of RNAPII and its consequences for transcription and repair. These advances make it pertinent to revisit the TC-NER process in general and with specific discussion of the fate of RNAPII stalled at DNA lesions.
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Affiliation(s)
- Liam Gaul
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark.
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10
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Frock RL, Sadeghi C, Meng J, Wang JL. DNA End Joining: G0-ing to the Core. Biomolecules 2021; 11:biom11101487. [PMID: 34680120 PMCID: PMC8533500 DOI: 10.3390/biom11101487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/28/2022] Open
Abstract
Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.
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11
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Krasikova Y, Rechkunova N, Lavrik O. Nucleotide Excision Repair: From Molecular Defects to Neurological Abnormalities. Int J Mol Sci 2021; 22:ijms22126220. [PMID: 34207557 PMCID: PMC8228863 DOI: 10.3390/ijms22126220] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/14/2023] Open
Abstract
Nucleotide excision repair (NER) is the most versatile DNA repair pathway, which can remove diverse bulky DNA lesions destabilizing a DNA duplex. NER defects cause several autosomal recessive genetic disorders. Xeroderma pigmentosum (XP) is one of the NER-associated syndromes characterized by low efficiency of the removal of bulky DNA adducts generated by ultraviolet radiation. XP patients have extremely high ultraviolet-light sensitivity of sun-exposed tissues, often resulting in multiple skin and eye cancers. Some XP patients develop characteristic neurodegeneration that is believed to derive from their inability to repair neuronal DNA damaged by endogenous metabolites. A specific class of oxidatively induced DNA lesions, 8,5′-cyclopurine-2′-deoxynucleosides, is considered endogenous DNA lesions mainly responsible for neurological problems in XP. Growing evidence suggests that XP is accompanied by defective mitophagy, as in primary mitochondrial disorders. Moreover, NER pathway is absent in mitochondria, implying that the mitochondrial dysfunction is secondary to nuclear NER defects. In this review, we discuss the current understanding of the NER molecular mechanism and focuses on the NER linkage with the neurological degeneration in patients with XP. We also present recent research advances regarding NER involvement in oxidative DNA lesion repair. Finally, we highlight how mitochondrial dysfunction may be associated with XP.
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Affiliation(s)
- Yuliya Krasikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Y.K.); (N.R.)
| | - Nadejda Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Y.K.); (N.R.)
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Y.K.); (N.R.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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12
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Identification of differentially abundant mRNA transcripts and autocrine/paracrine factors in oocytes and follicle cells of mud crabs. Anim Reprod Sci 2021; 230:106784. [PMID: 34090094 DOI: 10.1016/j.anireprosci.2021.106784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 11/20/2022]
Abstract
The late vitellogenic stage of the mud crab is characterized by large and obvious follicle cells as well as an enlarged oocyte nucleus and a prominent germinal vesicle (GV). The aim of this study was evaluation of functions of oocytes and follicle cells during meiosis as well as at identifying associated ovarian autocrine/paracrine factors using comparative transcriptomics. The results from the KEGG pathway analysis indicated DNA replication, nucleotide excision repair, spliceosome and the ribosome pathways were highly associated with oocyte maturation across both transcriptomes. In addition, there was a larger abundance of mRNA transcripts for cell cycle-related genes in the oocyte, as well as cyclin A, cyclin B and CKS1B in the GV than at the time of germinal vesicle breakdown (GVBD). These findings indicate these cell cycle-related genes might be involved in GVBD induction. Results when there was localization of ligands and the respective receptors of VEGF, TGFβ propeptide and BMP9/10 indicated these proteins might be autocrine/paracrine factors. Results from functional analysis of VEGF, TGFβ propeptide and BMP9/10 in oocyte maturation using RNA interference revealed that these proteins might be involved in oocyte maturation by regulating cyclin abundance. This is the first study on the functions of VEGF in oocyte maturation in invertebrates.
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13
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Wright G, Sonavane M, Gassman NR. Activated STAT3 Is a Novel Regulator of the XRCC1 Promoter and Selectively Increases XRCC1 Protein Levels in Triple Negative Breast Cancer. Int J Mol Sci 2021; 22:ijms22115475. [PMID: 34067421 PMCID: PMC8196947 DOI: 10.3390/ijms22115475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Base Excision Repair (BER) addresses base lesions and abasic sites induced by exogenous and endogenous stressors. X-ray cross complementing group 1 (XRCC1) functions as a scaffold protein in BER and single-strand break repair (SSBR), facilitating and coordinating repair through its interaction with a host of critical repair proteins. Alterations of XRCC1 protein and gene expression levels are observed in many cancers, including colorectal, ovarian, and breast cancer. While increases in the expression level of XRCC1 are reported, the transcription factors responsible for this up-regulation are not known. In this study, we identify the signal transducer and activator of transcription 3 (STAT3) as a novel regulator of XRCC1 through chromatin immunoprecipitation. Activation of STAT3 through phosphorylation at Y705 by cytokine (IL-6) signaling increases the expression of XRCC1 and the occupancy of STAT3 within the XRCC1 promoter. In triple negative breast cancer, the constitutive activation of STAT3 upregulates XRCC1 gene and protein expression levels. Increased expression of XRCC1 is associated with aggressiveness and resistance to DNA damaging chemotherapeutics. Thus, we propose that activated STAT3 regulates XRCC1 under stress and growth conditions, but constitutive activation in cancers results in dysregulation of XRCC1 and subsequently BER and SSBR.
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Affiliation(s)
- Griffin Wright
- Department of Physiology and Cell Biology, University of South Alabama College of Medicine, 307 N University Blvd, Mobile, AL 36688, USA; (G.W.); (M.S.)
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
| | - Manoj Sonavane
- Department of Physiology and Cell Biology, University of South Alabama College of Medicine, 307 N University Blvd, Mobile, AL 36688, USA; (G.W.); (M.S.)
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
| | - Natalie R. Gassman
- Department of Physiology and Cell Biology, University of South Alabama College of Medicine, 307 N University Blvd, Mobile, AL 36688, USA; (G.W.); (M.S.)
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
- Correspondence:
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14
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Chauhan AK, Sun Y, Zhu Q, Wani AA. Timely upstream events regulating nucleotide excision repair by ubiquitin-proteasome system: ubiquitin guides the way. DNA Repair (Amst) 2021; 103:103128. [PMID: 33991872 DOI: 10.1016/j.dnarep.2021.103128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/15/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays crucial roles in regulation of multiple DNA repair pathways, including nucleotide excision repair (NER), which eliminates a broad variety of helix-distorting DNA lesions that can otherwise cause deleterious mutations and genomic instability. In mammalian NER, DNA damage sensors, DDB and XPC acting in global genomic NER (GG-NER), and, CSB and RNAPII acting in transcription-coupled NER (TC-NER) sub-pathways, undergo an array of post-translational ubiquitination at the DNA lesion sites. Accumulating evidence indicates that ubiquitination orchestrates the productive assembly of NER preincision complex by driving well-timed compositional changes in DNA damage-assembled sensor complexes. Conversely, the deubiquitination is also intimately involved in regulating the damage sensing aftermath, via removal of degradative ubiquitin modification on XPC and CSB to prevent their proteolysis for the factor recycling. This review summaries the relevant research efforts and latest findings in our understanding of ubiquitin-mediated regulation of NER and active participation by new regulators of NER, e.g., Cullin-Ring ubiquitin ligases (CRLs), ubiquitin-specific proteases (USPs) and ubiquitin-dependent segregase, valosin-containing protein (VCP)/p97. We project hypothetical step-by-step models in which VCP/p97-mediated timely extraction of damage sensors is integral to overall productive NER. The USPs and proteasome subtly counteract in fine-tuning the vital stability and function of NER damage sensors.
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Affiliation(s)
- Anil K Chauhan
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States
| | - Yingming Sun
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States
| | - Qianzheng Zhu
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States.
| | - Altaf A Wani
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States; Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH, 43210, United States; James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, 43210, United States.
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15
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Sadoughi F, Mirsafaei L, Dana PM, Hallajzadeh J, Asemi Z, Mansournia MA, Montazer M, Hosseinpour M, Yousefi B. The role of DNA damage response in chemo- and radio-resistance of cancer cells: Can DDR inhibitors sole the problem? DNA Repair (Amst) 2021; 101:103074. [PMID: 33640757 DOI: 10.1016/j.dnarep.2021.103074] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Up to now, many improvements have been made in providing more therapeutic strategies for cancer patients. The lack of susceptibility to common therapies like chemo- and radio-therapy is one of the reasons why we need more methods in the field of cancer therapy. DNA damage response (DDR) is a set of mechanisms which identifies DNA lesions and triggers the repair process for restoring DNA after causing an arrest in the cell cycle. The ability of DDR in maintaining the genome stability and integrity can be favorable to cancerous cells which are exposed to radiation therapy or are treated with chemotherapeutic agents. When DDR mechanisms are error-free in cancer cells, they can escape the expected cellular death and display resistance to treatment. In this regard, targeting different components of DDR can help to increase the susceptibility of advanced tumors to chemo- and radio-therapy.
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Affiliation(s)
- Fatemeh Sadoughi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Liaosadat Mirsafaei
- Department of Cardiology, Ramsar Campus, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Parisa Maleki Dana
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Jamal Hallajzadeh
- Department of Biochemistry and Nutrition, Research Center for Evidence-Based Health Management, Maragheh University of Medical Sciences, Maragheh, Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Mohammad Ali Mansournia
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Majid Montazer
- Department of Thorax Surgery, Tuberculosis and Lung Disease Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Hosseinpour
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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16
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Tomkinson AE, Naila T, Khattri Bhandari S. Altered DNA ligase activity in human disease. Mutagenesis 2021; 35:51-60. [PMID: 31630206 DOI: 10.1093/mutage/gez026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
The joining of interruptions in the phosphodiester backbone of DNA is critical to maintain genome stability. These breaks, which are generated as part of normal DNA transactions, such as DNA replication, V(D)J recombination and meiotic recombination as well as directly by DNA damage or due to DNA damage removal, are ultimately sealed by one of three human DNA ligases. DNA ligases I, III and IV each function in the nucleus whereas DNA ligase III is the sole enzyme in mitochondria. While the identification of specific protein partners and the phenotypes caused either by genetic or chemical inactivation have provided insights into the cellular functions of the DNA ligases and evidence for significant functional overlap in nuclear DNA replication and repair, different results have been obtained with mouse and human cells, indicating species-specific differences in the relative contributions of the DNA ligases. Inherited mutations in the human LIG1 and LIG4 genes that result in the generation of polypeptides with partial activity have been identified as the causative factors in rare DNA ligase deficiency syndromes that share a common clinical symptom, immunodeficiency. In the case of DNA ligase IV, the immunodeficiency is due to a defect in V(D)J recombination whereas the cause of the immunodeficiency due to DNA ligase I deficiency is not known. Overexpression of each of the DNA ligases has been observed in cancers. For DNA ligase I, this reflects increased proliferation. Elevated levels of DNA ligase III indicate an increased dependence on an alternative non-homologous end-joining pathway for the repair of DNA double-strand breaks whereas elevated level of DNA ligase IV confer radioresistance due to increased repair of DNA double-strand breaks by the major non-homologous end-joining pathway. Efforts to determine the potential of DNA ligase inhibitors as cancer therapeutics are on-going in preclinical cancer models.
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Affiliation(s)
- Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Tasmin Naila
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Seema Khattri Bhandari
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
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17
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Hammel M, Rashid I, Sverzhinsky A, Pourfarjam Y, Tsai MS, Ellenberger T, Pascal JM, Kim IK, Tainer JA, Tomkinson AE. An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex. Nucleic Acids Res 2021; 49:306-321. [PMID: 33330937 PMCID: PMC7797052 DOI: 10.1093/nar/gkaa1188] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/21/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ishtiaque Rashid
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Yasin Pourfarjam
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tom Ellenberger
- Department of Biochemistry, Washington University, St. Louis, MO, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - John A Tainer
- Departments of Cancer Biology and Molecular & Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
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18
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Zhou J, Zhou XA, Zhang N, Wang J. Evolving insights: how DNA repair pathways impact cancer evolution. Cancer Biol Med 2020; 17:805-827. [PMID: 33299637 PMCID: PMC7721097 DOI: 10.20892/j.issn.2095-3941.2020.0177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
Viewing cancer as a large, evolving population of heterogeneous cells is a common perspective. Because genomic instability is one of the fundamental features of cancer, this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation, development, metastasis, and relapse. With the increased mutation rate and abundant diversity of the gene pool, this heterogeneity leads to cancer evolution, which is the major obstacle in the clinical treatment of cancer. Cells rely on the integrity of DNA repair machineries to maintain genomic stability, but these machineries often do not function properly in cancer cells. The deficiency of DNA repair could contribute to the generation of cancer genomic instability, and ultimately promote cancer evolution. With the rapid advance of new technologies, such as single-cell sequencing in recent years, we have the opportunity to better understand the specific processes and mechanisms of cancer evolution, and its relationship with DNA repair. Here, we review recent findings on how DNA repair affects cancer evolution, and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.
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Affiliation(s)
- Jiadong Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ning Zhang
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Biomedical Pioneering Innovation Center (BIOPIC) and Translational Cancer Research Center, School of Life Sciences, First Hospital, Peking University, Beijing 100871, China
| | - Jiadong Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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19
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The Dark Side of UV-Induced DNA Lesion Repair. Genes (Basel) 2020; 11:genes11121450. [PMID: 33276692 PMCID: PMC7761550 DOI: 10.3390/genes11121450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented.
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20
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Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
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Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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21
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Establishment of Acquired Cisplatin Resistance in Ovarian Cancer Cell Lines Characterized by Enriched Metastatic Properties with Increased Twist Expression. Int J Mol Sci 2020; 21:ijms21207613. [PMID: 33076245 PMCID: PMC7589258 DOI: 10.3390/ijms21207613] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal of the gynecologic cancers, and platinum-based treatment is a part of the standard first-line chemotherapy regimen. However, rapid development of acquired cisplatin resistance remains the main cause of treatment failure, and the underlying mechanism of resistance in OC treatment remains poorly understood. Faced with this problem, our aim in this study was to generate cisplatin-resistant (CisR) OC cell models in vitro and investigate the role of epithelial–mesenchymal transition (EMT) transcription factor Twist on acquired cisplatin resistance in OC cell models. To achieve this aim, OC cell lines OV-90 and SKOV-3 were exposed to cisplatin using pulse dosing and stepwise dose escalation methods for a duration of eight months, and a total of four CisR sublines were generated, two for each cell line. The acquired cisplatin resistance was confirmed by determination of 50% inhibitory concentration (IC50) and clonogenic survival assay. Furthermore, the CisR cells were studied to assess their respective characteristics of metastasis, EMT phenotype, DNA repair and endoplasmic reticulum stress-mediated cell death. We found the IC50 of CisR cells to cisplatin was 3–5 times higher than parental cells. The expression of Twist and metastatic ability of CisR cells were significantly greater than those of sensitive cells. The CisR cells displayed an EMT phenotype with decreased epithelial cell marker E-cadherin and increased mesenchymal proteins N-cadherin and vimentin. We observed that CisR cells showed significantly higher expression of DNA repair proteins, X-ray repair cross-complementing protein 1 (XRCC1) and poly (ADP-ribose) polymerases 1 (PARP1), with significantly reduced endoplasmic reticulum (ER) stress-mediated cell death. Moreover, Twist knockdown reduced metastatic ability of CisR cells by suppressing EMT, DNA repair and inducing ER stress-induced cell death. In conclusion, we highlighted the utilization of an acquired cisplatin resistance model to identify the potential role of Twist as a therapeutic target to reverse acquired cisplatin resistance in OC.
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22
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DuPrez K, He F, Chen Z, Hilario E, Fan L. Structural basis of the XPB-Bax1 complex as a dynamic helicase-nuclease machinery for DNA repair. Nucleic Acids Res 2020; 48:6326-6339. [PMID: 32374860 PMCID: PMC7293015 DOI: 10.1093/nar/gkaa324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures of XPB in complex with Bax1 from Archaeoglobus fulgidus (Af) and Sulfolobus tokodaii (St). These structures reveal for the first time four domains in Bax1, which interacts with XPB mainly through its N-terminal domain. A Cas2-like domain likely helps to position Bax1 at the forked DNA allowing the nuclease domain to incise one arm of the fork. Bax1 exists in monomer or homodimer but forms a heterodimer exclusively with XPB. StBax1 keeps StXPB in a closed conformation and stimulates ATP hydrolysis by XPB while AfBax1 maintains AfXPB in the open conformation and reduces its ATPase activity. Bax1 contains two distinguished nuclease active sites to presumably incise DNA damage. Our results demonstrate that protein-protein interactions regulate the activities of XPB ATPase and Bax1 nuclease. These structures provide a platform to understand the XPB-nuclease interactions important for the coordination of DNA unwinding and damage incision in eukaryotic NER.
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Affiliation(s)
- Kevin DuPrez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Feng He
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Zhenhang Chen
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Eduardo Hilario
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Li Fan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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23
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Pu Y, Zhao L, Dai N, Xu M. Comprehensive analysis of the correlation between base-excision repair gene SNPs and esophageal squamous cell carcinoma risk in a Chinese Han population. Mol Clin Oncol 2020; 13:228-236. [PMID: 32714550 DOI: 10.3892/mco.2020.2066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/04/2020] [Indexed: 11/06/2022] Open
Abstract
This study sought to assess the relationship between single nucleotide polymorphisms (SNPs) affecting DNA base-excision repair (BER) genes and esophageal squamous cell carcinoma (ESCC) risk in a Han Chinese population. Genes screened for such SNPs included 8-oxoguanine DNA glycosylase (OGG1), apurinic/apyrimidinic endonuclease 1 (APE1) and X-ray repair cross-complementing group 1 protein (XRCC1). Blood samples that had been collected in a prospective manner were used for DNA extraction, with all DNA samples then being subjected to PCR-restriction fragment length polymorphism genotyping for BER gene SNPs, including APE1 Asp148Glu and -141T/G, OGG1 Ser326Cys, and XRCC1 Arg399Gln. The relationship between these SNPs and ESCC risk was then assessed, with the comparability of the case and control groups being enhanced via propensity score matching (PSM). This study initially included 642 healthy controls and 321 ESCC patients, with PSM optimization leading to a final analyzed total of 311 matched subjects per group (311 total). Factors associated with elevated ESCC risk in this analysis included advanced age, being male and smoking. We further identified that the XRCC1 399 Gln/Gln genotype was associated with a significant reduction in ESCC risk prior to propensity matching (odds ratio=0.48; 95% CI: 0.23-1.00; P<0.05), although this did not remain true following matching. For the remaining analyzed SNPs, no significant associations between genotype and ESCC risk were detected prior to or following propensity matching. A multivariate analysis incorporating patient age, sex, smoking status and drinking status failed to detect any relationship between the four tested genotypes and ESCC risk. In conclusion, being male, a smoker or of advanced age was associated with an elevated ESCC risk. However, we did not detect any significant relationship between ESCC risk and BER polymorphisms in XRCC1, OGG1, APE1 or the APE1 promoter region in a Han Chinese population.
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Affiliation(s)
- Yu Pu
- Cancer Center, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - Liang Zhao
- Cancer Center, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - Nan Dai
- Cancer Center, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - Mingfang Xu
- Cancer Center, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
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24
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Rajapakse A, Suraweera A, Boucher D, Naqi A, O'Byrne K, Richard DJ, Croft LV. Redox Regulation in the Base Excision Repair Pathway: Old and New Players as Cancer Therapeutic Targets. Curr Med Chem 2020; 27:1901-1921. [PMID: 31258058 DOI: 10.2174/0929867326666190430092732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/09/2019] [Accepted: 04/05/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Reactive Oxygen Species (ROS) are by-products of normal cellular metabolic processes, such as mitochondrial oxidative phosphorylation. While low levels of ROS are important signalling molecules, high levels of ROS can damage proteins, lipids and DNA. Indeed, oxidative DNA damage is the most frequent type of damage in the mammalian genome and is linked to human pathologies such as cancer and neurodegenerative disorders. Although oxidative DNA damage is cleared predominantly through the Base Excision Repair (BER) pathway, recent evidence suggests that additional pathways such as Nucleotide Excision Repair (NER) and Mismatch Repair (MMR) can also participate in clearance of these lesions. One of the most common forms of oxidative DNA damage is the base damage 8-oxoguanine (8-oxoG), which if left unrepaired may result in G:C to A:T transversions during replication, a common mutagenic feature that can lead to cellular transformation. OBJECTIVE Repair of oxidative DNA damage, including 8-oxoG base damage, involves the functional interplay between a number of proteins in a series of enzymatic reactions. This review describes the role and the redox regulation of key proteins involved in the initial stages of BER of 8-oxoG damage, namely Apurinic/Apyrimidinic Endonuclease 1 (APE1), human 8-oxoguanine DNA glycosylase-1 (hOGG1) and human single-stranded DNA binding protein 1 (hSSB1). Moreover, the therapeutic potential and modalities of targeting these key proteins in cancer are discussed. CONCLUSION It is becoming increasingly apparent that some DNA repair proteins function in multiple repair pathways. Inhibiting these factors would provide attractive strategies for the development of more effective cancer therapies.
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Affiliation(s)
- Aleksandra Rajapakse
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,School of Natural Sciences, Griffith University, Nathan, QLD, Australia
| | - Amila Suraweera
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Didier Boucher
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Ali Naqi
- Department of Chemistry, Pennsylvania State University, United States
| | - Kenneth O'Byrne
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,Cancer Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J Richard
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Laura V Croft
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
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25
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Distinct roles of XRCC1 in genome integrity in Xenopus egg extracts. Biochem J 2020; 476:3791-3804. [PMID: 31808793 DOI: 10.1042/bcj20190798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023]
Abstract
Oxidative DNA damage represents one of the most abundant DNA lesions. It remains unclear how DNA repair and DNA damage response (DDR) pathways are co-ordinated and regulated following oxidative stress. While XRCC1 has been implicated in DNA repair, it remains unknown how exactly oxidative DNA damage is repaired and sensed by XRCC1. In this communication, we have demonstrated evidence that XRCC1 is dispensable for ATR-Chk1 DDR pathway following oxidative stress in Xenopus egg extracts. Whereas APE2 is essential for SSB repair, XRCC1 is not required for the repair of defined SSB and gapped plasmids with a 5'-OH or 5'-P terminus, suggesting that XRCC1 and APE2 may contribute to SSB repair via different mechanisms. Neither Polymerase beta nor Polymerase alpha is important for the repair of defined SSB structure. Nonetheless, XRCC1 is important for the repair of DNA damage following oxidative stress. Our observations suggest distinct roles of XRCC1 for genome integrity in oxidative stress in Xenopus egg extracts.
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26
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Saha LK, Wakasugi M, Akter S, Prasad R, Wilson SH, Shimizu N, Sasanuma H, Huang SYN, Agama K, Pommier Y, Matsunaga T, Hirota K, Iwai S, Nakazawa Y, Ogi T, Takeda S. Topoisomerase I-driven repair of UV-induced damage in NER-deficient cells. Proc Natl Acad Sci U S A 2020; 117:14412-14420. [PMID: 32513688 PMCID: PMC7321995 DOI: 10.1073/pnas.1920165117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nucleotide excision repair (NER) removes helix-destabilizing adducts including ultraviolet (UV) lesions, cyclobutane pyrimidine dimers (CPDs), and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). In comparison with CPDs, 6-4PPs have greater cytotoxicity and more strongly destabilizing properties of the DNA helix. It is generally believed that NER is the only DNA repair pathway that removes the UV lesions as evidenced by the previous data since no repair of UV lesions was detected in NER-deficient skin fibroblasts. Topoisomerase I (TOP1) constantly creates transient single-strand breaks (SSBs) releasing the torsional stress in genomic duplex DNA. Stalled TOP1-SSB complexes can form near DNA lesions including abasic sites and ribonucleotides embedded in chromosomal DNA. Here we show that base excision repair (BER) increases cellular tolerance to UV independently of NER in cancer cells. UV lesions irreversibly trap stable TOP1-SSB complexes near the UV damage in NER-deficient cells, and the resulting SSBs activate BER. Biochemical experiments show that 6-4PPs efficiently induce stable TOP1-SSB complexes, and the long-patch repair synthesis of BER removes 6-4PPs downstream of the SSB. Furthermore, NER-deficient cancer cell lines remove 6-4PPs within 24 h, but not CPDs, and the removal correlates with TOP1 expression. NER-deficient skin fibroblasts weakly express TOP1 and show no detectable repair of 6-4PPs. Remarkably, the ectopic expression of TOP1 in these fibroblasts led them to completely repair 6-4PPs within 24 h. In conclusion, we reveal a DNA repair pathway initiated by TOP1, which significantly contributes to cellular tolerance to UV-induced lesions particularly in malignant cancer cells overexpressing TOP1.
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Affiliation(s)
- Liton Kumar Saha
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Mitsuo Wakasugi
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 920-1192 Kanazawa, Japan
| | - Salma Akter
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Naoto Shimizu
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Tsukasa Matsunaga
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 920-1192 Kanazawa, Japan
| | - Kouji Hirota
- Department of Chemistry, Tokyo Metropolitan University, 192-0397 Tokyo, Japan
| | - Shigenori Iwai
- Biological Chemistry Group, Graduate School of Engineering Science, Osaka University, 565-0871 Osaka, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, 464-8601 Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, 464-8601 Nagoya, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan;
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27
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Lerner LK, Moreno NC, Rocha CRR, Munford V, Santos V, Soltys DT, Garcia CCM, Sarasin A, Menck CFM. XPD/ERCC2 mutations interfere in cellular responses to oxidative stress. Mutagenesis 2020; 34:341-354. [PMID: 31348825 DOI: 10.1093/mutage/gez020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/10/2019] [Indexed: 01/28/2023] Open
Abstract
Nucleotide excision repair (NER) is a conserved, flexible mechanism responsible for the removal of bulky, helix-distorting DNA lesions, like ultraviolet damage or cisplatin adducts, but its role in the repair of lesions generated by oxidative stress is still not clear. The helicase XPD/ERCC2, one of the two helicases of the transcription complex IIH, together with XPB, participates both in NER and in RNA pol II-driven transcription. In this work, we investigated the responses of distinct XPD-mutated cell lines to the oxidative stress generated by photoactivated methylene blue (MB) and KBrO3 treatments. The studied cells are derived from patients with XPD mutations but expressing different clinical phenotypes, including xeroderma pigmentosum (XP), XP and Cockayne syndrome (XP-D/CS) and trichothiodystrophy (TTD). We show by different approaches that all XPD-mutated cell lines tested were sensitive to oxidative stress, with those from TTD patients being the most sensitive. Host cell reactivation (HCR) assays showed that XP-D/CS and TTD cells have severely impaired repair capacity of oxidised lesions in plasmid DNA, and alkaline comet assays demonstrated the induction of significantly higher amounts of DNA strand breaks after treatment with photoactivated MB in these cells compared to wild-type cells. All XPD-mutated cells presented strong S/G2 arrest and persistent γ-H2AX staining after photoactivated MB treatment. Taken together, these results indicate that XPD participates in the repair of lesions induced by the redox process, and that XPD mutations lead to differences in the response to oxidatively induced damage.
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Affiliation(s)
- Leticia K Lerner
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Natália C Moreno
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Clarissa R R Rocha
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Valquíria Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Daniela T Soltys
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Camila C M Garcia
- Department of Biological Sciences, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - Alain Sarasin
- CNRS-UMR8200, Institut Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
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28
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Borsos BN, Majoros H, Pankotai T. Emerging Roles of Post-Translational Modifications in Nucleotide Excision Repair. Cells 2020; 9:cells9061466. [PMID: 32549338 PMCID: PMC7349741 DOI: 10.3390/cells9061466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleotide excision repair (NER) is a versatile DNA repair pathway which can be activated in response to a broad spectrum of UV-induced DNA damage, such as bulky adducts, including cyclobutane-pyrimidine dimers (CPDs) and 6–4 photoproducts (6–4PPs). Based on the genomic position of the lesion, two sub-pathways can be defined: (I) global genomic NER (GG-NER), involved in the ablation of damage throughout the whole genome regardless of the transcription activity of the damaged DNA locus, and (II) transcription-coupled NER (TC-NER), activated at DNA regions where RNAPII-mediated transcription takes place. These processes are tightly regulated by coordinated mechanisms, including post-translational modifications (PTMs). The fine-tuning modulation of the balance between the proteins, responsible for PTMs, is essential to maintain genome integrity and to prevent tumorigenesis. In this review, apart from the other substantial PTMs (SUMOylation, PARylation) related to NER, we principally focus on reversible ubiquitylation, which involves E3 ubiquitin ligase and deubiquitylase (DUB) enzymes responsible for the spatiotemporally precise regulation of NER.
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29
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Gsell C, Richly H, Coin F, Naegeli H. A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions. Nucleic Acids Res 2020; 48:1652-1668. [PMID: 31930303 PMCID: PMC7038933 DOI: 10.1093/nar/gkz1229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The excision of mutagenic DNA adducts by the nucleotide excision repair (NER) pathway is essential for genome stability, which is key to avoiding genetic diseases, premature aging, cancer and neurologic disorders. Due to the need to process an extraordinarily high damage density embedded in the nucleosome landscape of chromatin, NER activity provides a unique functional caliper to understand how histone modifiers modulate DNA damage responses. At least three distinct lysine methyltransferases (KMTs) targeting histones have been shown to facilitate the detection of ultraviolet (UV) light-induced DNA lesions in the difficult to access DNA wrapped around histones in nucleosomes. By methylating core histones, these KMTs generate docking sites for DNA damage recognition factors before the chromatin structure is ultimately relaxed and the offending lesions are effectively excised. In view of their function in priming nucleosomes for DNA repair, mutations of genes coding for these KMTs are expected to cause the accumulation of DNA damage promoting cancer and other chronic diseases. Research on the question of how KMTs modulate DNA repair might pave the way to the development of pharmacologic agents for novel therapeutic strategies.
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Affiliation(s)
- Corina Gsell
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Holger Richly
- Boehringer Ingelheim Pharma, Department of Molecular Biology, Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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30
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Ngo LP, Owiti NA, Swartz C, Winters J, Su Y, Ge J, Xiong A, Han J, Recio L, Samson LD, Engelward B. Sensitive CometChip assay for screening potentially carcinogenic DNA adducts by trapping DNA repair intermediates. Nucleic Acids Res 2020; 48:e13. [PMID: 31822921 PMCID: PMC7026589 DOI: 10.1093/nar/gkz1077] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 10/08/2019] [Accepted: 11/19/2019] [Indexed: 12/27/2022] Open
Abstract
Genotoxicity testing is critical for predicting adverse effects of pharmaceutical, industrial, and environmental chemicals. The alkaline comet assay is an established method for detecting DNA strand breaks, however, the assay does not detect potentially carcinogenic bulky adducts that can arise when metabolic enzymes convert pro-carcinogens into a highly DNA reactive products. To overcome this, we use DNA synthesis inhibitors (hydroxyurea and 1-β-d-arabinofuranosyl cytosine) to trap single strand breaks that are formed during nucleotide excision repair, which primarily removes bulky lesions. In this way, comet-undetectable bulky lesions are converted into comet-detectable single strand breaks. Moreover, we use HepaRG™ cells to recapitulate in vivo metabolic capacity, and leverage the CometChip platform (a higher throughput more sensitive comet assay) to create the 'HepaCometChip', enabling the detection of bulky genotoxic lesions that are missed by current genotoxicity screens. The HepaCometChip thus provides a broadly effective approach for detection of bulky DNA adducts.
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Affiliation(s)
- Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Norah A Owiti
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carol Swartz
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - John Winters
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - Yang Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aoli Xiong
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Jongyoon Han
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
- Department of Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leslie Recio
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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31
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Kim DV, Makarova AV, Miftakhova RR, Zharkov DO. Base Excision DNA Repair Deficient Cells: From Disease Models to Genotoxicity Sensors. Curr Pharm Des 2020; 25:298-312. [PMID: 31198112 DOI: 10.2174/1381612825666190319112930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022]
Abstract
Base excision DNA repair (BER) is a vitally important pathway that protects the cell genome from many kinds of DNA damage, including oxidation, deamination, and hydrolysis. It involves several tightly coordinated steps, starting from damaged base excision and followed by nicking one DNA strand, incorporating an undamaged nucleotide, and DNA ligation. Deficiencies in BER are often embryonic lethal or cause morbid diseases such as cancer, neurodegeneration, or severe immune pathologies. Starting from the early 1980s, when the first mammalian cell lines lacking BER were produced by spontaneous mutagenesis, such lines have become a treasure trove of valuable information about the mechanisms of BER, often revealing unexpected connections with other cellular processes, such as antibody maturation or epigenetic demethylation. In addition, these cell lines have found an increasing use in genotoxicity testing, where they provide increased sensitivity and representativity to cell-based assay panels. In this review, we outline current knowledge about BER-deficient cell lines and their use.
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Affiliation(s)
- Daria V Kim
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., Moscow 123182, Russian Federation
| | - Regina R Miftakhova
- Kazan Federal University, 18 Kremlevsakaya St., Kazan 420008, Russian Federation
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation.,SB RAS Institute of Chemical Biology and Fu ndamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russian Federation
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32
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Kent T, Gracias D, Shepherd S, Clynes D. Alternative Lengthening of Telomeres in Pediatric Cancer: Mechanisms to Therapies. Front Oncol 2020; 9:1518. [PMID: 32039009 PMCID: PMC6985284 DOI: 10.3389/fonc.2019.01518] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/17/2019] [Indexed: 12/26/2022] Open
Abstract
Achieving replicative immortality is a crucial step in tumorigenesis and requires both bypassing cell cycle checkpoints and the extension of telomeres, sequences that protect the distal ends of chromosomes during replication. In the majority of cancers this is achieved through the enzyme telomerase, however a subset of cancers instead utilize a telomerase-independent mechanism of telomere elongation-the Alternative Lengthening of Telomeres (ALT) pathway. Recent work has aimed to decipher the exact mechanism that underlies this pathway. To this end, this pathway has now been shown to extend telomeres through exploitation of DNA repair machinery in a unique process that may present a number of druggable targets. The identification of such targets, and the subsequent development or repurposing of therapies to these targets may be crucial to improving the prognosis for many ALT-positive cancers, wherein mean survival is lower than non-ALT counterparts and the cancers themselves are particularly unresponsive to standard of care therapies. In this review we summarize the recent identification of many aspects of the ALT pathway, and the therapies that may be employed to exploit these new targets.
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Affiliation(s)
- Thomas Kent
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Deanne Gracias
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Samuel Shepherd
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - David Clynes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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33
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CRL4 Ubiquitin Pathway and DNA Damage Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:225-239. [PMID: 31898231 DOI: 10.1007/978-981-15-1025-0_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
DNA damage occurs in a human cell at an average frequency of 10,000 incidences per day by means of external and internal culprits, damage that triggers sequential cellular responses and stalls the cell cycle while activating specific DNA repair pathways. Failure to remove DNA lesions would compromise genomic integrity, leading to human diseases such as cancer and premature aging. If DNA damage is extensive and cannot be repaired, cells undergo apoptosis. DNA damage response (DDR) often entails posttranslational modifications of key DNA repair and DNA damage checkpoint proteins, including phosphorylation and ubiquitination. Cullin-RING ligase 4 (CRL4) enzyme has been found to target multiple DDR proteins for ubiquitination. In this chapter, we will discuss key repair and checkpoint proteins that are subject to ubiquitin-dependent regulation by members of the CRL4 family during ultraviolet light (UV)-induced DNA damage.
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34
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Mota MBS, Carvalho MA, Monteiro ANA, Mesquita RD. DNA damage response and repair in perspective: Aedes aegypti, Drosophila melanogaster and Homo sapiens. Parasit Vectors 2019; 12:533. [PMID: 31711518 PMCID: PMC6849265 DOI: 10.1186/s13071-019-3792-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/05/2019] [Indexed: 01/18/2023] Open
Abstract
Background The maintenance of genomic integrity is the responsibility of a complex network, denominated the DNA damage response (DDR), which controls the lesion detection and DNA repair. The main repair pathways are base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination repair (HR) and non-homologous end joining repair (NHEJ). They correct double-strand breaks (DSB), single-strand breaks, mismatches and others, or when the damage is quite extensive and repair insufficient, apoptosis is activated. Methods In this study we used the BLAST reciprocal best-hit methodology to search for DDR orthologs proteins in Aedes aegypti. We also provided a comparison between Ae. aegypti, D. melanogaster and human DDR network. Results Our analysis revealed the presence of ATR and ATM signaling, including the H2AX ortholog, in Ae. aegypti. Key DDR proteins (orthologs to RAD51, Ku and MRN complexes, XP-components, MutS and MutL) were also identified in this insect. Other proteins were not identified in both Ae. aegypti and D. melanogaster, including BRCA1 and its partners from BRCA1-A complex, TP53BP1, PALB2, POLk, CSA, CSB and POLβ. In humans, their absence affects DSB signaling, HR and sub-pathways of NER and BER. Seven orthologs not known in D. melanogaster were found in Ae. aegypti (RNF168, RIF1, WRN, RAD54B, RMI1, DNAPKcs, ARTEMIS). Conclusions The presence of key DDR proteins in Ae. aegypti suggests that the main DDR pathways are functional in this insect, and the identification of proteins not known in D. melanogaster can help fill gaps in the DDR network. The mapping of the DDR network in Ae. aegypti can support mosquito biology studies and inform genetic manipulation approaches applied to this vector.
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Affiliation(s)
- Maria Beatriz S Mota
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcelo Alex Carvalho
- Instituto Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro, RJ, Brazil
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rafael D Mesquita
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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35
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Sharifi Z, Faranoush M, Mohseni A, Rostami S, Ramzi M, Sharifi MJ. Genetic variants of nucleotide excision repair pathway and outcomes of induction therapy in acute myeloid leukemia. Per Med 2019; 16:479-490. [PMID: 31647372 DOI: 10.2217/pme-2018-0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Acute myeloid leukemia (AML) is a heterogeneous disease in pathogenesis and response to therapy. Nucleotide excision repair (NER) pathway has a major role in the elimination of genotoxic effects of chemotherapeutic agents. We aimed to clarify the effects of selected variants of XPD, XPC, ERCC5 and ERCC1 genes on the outcomes of induction therapy. Materials & methods: The prevalence of NER genetic variants was evaluated in 67 subjects with AML and their effects on clinical outcomes were analyzed by χ2 test. Results: The XPD 751 Lys variant was associated with improved response to chemotherapy compared with XPD 751 Gln and Lys/Gln variants (p = 0.023; odds ratio: 4.5; 95% CI: 1.14-17.73). There were no associations between other genotypes and any outcomes. Conclusion: Current findings suggest that XPD Lys751Gln variant could be considered as a prognostic factor in AML.
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Affiliation(s)
- Zohreh Sharifi
- Blood Transfusion Research Center, High Institute for Research & Education in Transfusion Medicine, Tehran, Iran
| | - Mohammad Faranoush
- Rasool Akram Complex Medical Center, Iran University ofMedical Sciences, Tehran, Iran
| | - Alireza Mohseni
- Thalassemia Research Center, Hemoglobinopthy Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shahrbano Rostami
- Haematology-Oncology & Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran,Iran
| | - Mani Ramzi
- Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Mohammad J Sharifi
- Blood Transfusion Research Center, High Institute for Research & Education in Transfusion Medicine, Tehran, Iran.,Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences & Health Services, Isfahan, Iran
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36
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Lee KJ, Piett CG, Andrews JF, Mann E, Nagel ZD, Gassman NR. Defective base excision repair in the response to DNA damaging agents in triple negative breast cancer. PLoS One 2019; 14:e0223725. [PMID: 31596905 PMCID: PMC6785058 DOI: 10.1371/journal.pone.0223725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/26/2019] [Indexed: 01/08/2023] Open
Abstract
DNA repair defects have been increasingly focused on as therapeutic targets. In hormone-positive breast cancer, XRCC1-deficient tumors have been identified and proposed as targets for combination therapies that damage DNA and inhibit DNA repair pathways. XRCC1 is a scaffold protein that functions in base excision repair (BER) by mediating essential interactions between DNA glycosylases, AP endonuclease, poly(ADP-ribose) polymerase 1, DNA polymerase β (POL β), and DNA ligases. Loss of XRCC1 confers BER defects and hypersensitivity to DNA damaging agents. BER defects have not been evaluated in triple negative breast cancers (TNBC), for which new therapeutic targets and therapies are needed. To evaluate the potential of XRCC1 as an indicator of BER defects in TNBC, we examined XRCC1 expression in the TCGA database and its expression and localization in TNBC cell lines. The TCGA database revealed high XRCC1 expression in TNBC tumors and TNBC cell lines show variable, but mostly high expression of XRCC1. XRCC1 localized outside of the nucleus in some TNBC cell lines, altering their ability to repair base lesions and single-strand breaks. Subcellular localization of POL β also varied and did not correlate with XRCC1 localization. Basal levels of DNA damage correlated with observed changes in XRCC1 expression, localization, and measure repair capacity. The results confirmed that XRCC1 expression changes indicate DNA repair capacity changes but emphasize that basal DNA damage levels along with protein localization are better indicators of DNA repair defects. Given the observed over-expression of XRCC1 in TNBC preclinical models and tumors, XRCC1 expression levels should be assessed when evaluating treatment responses of TNBC preclinical model cells.
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Affiliation(s)
- Kevin J. Lee
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States of America
- University of South Alabama College of Medicine, Mobile, AL, United States of America
| | - Cortt G. Piett
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Joel F. Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States of America
- University of South Alabama College of Medicine, Mobile, AL, United States of America
| | - Elise Mann
- University of South Alabama College of Medicine, Mobile, AL, United States of America
| | - Zachary D. Nagel
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Natalie R. Gassman
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States of America
- University of South Alabama College of Medicine, Mobile, AL, United States of America
- * E-mail:
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37
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Steurer B, Turkyilmaz Y, van Toorn M, van Leeuwen W, Escudero-Ferruz P, Marteijn JA. Fluorescently-labelled CPD and 6-4PP photolyases: new tools for live-cell DNA damage quantification and laser-assisted repair. Nucleic Acids Res 2019; 47:3536-3549. [PMID: 30698791 PMCID: PMC6468286 DOI: 10.1093/nar/gkz035] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/29/2018] [Accepted: 01/15/2019] [Indexed: 01/02/2023] Open
Abstract
UV light induces cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (6-4PPs), which can result in carcinogenesis and aging, if not properly repaired by nucleotide excision repair (NER). Assays to determine DNA damage load and repair rates are invaluable tools for fundamental and clinical NER research. However, most current assays to quantify DNA damage and repair cannot be performed in real time. To overcome this limitation, we made use of the damage recognition characteristics of CPD and 6-4PP photolyases (PLs). Fluorescently-tagged PLs efficiently recognize UV-induced DNA damage without blocking NER activity, and therefore can be used as sensitive live-cell damage sensors. Importantly, FRAP-based assays showed that PLs bind to damaged DNA in a highly sensitive and dose-dependent manner, and can be used to quantify DNA damage load and to determine repair kinetics in real time. Additionally, PLs can instantly reverse DNA damage by 405 nm laser-assisted photo-reactivation during live-cell imaging, opening new possibilities to study lesion-specific NER dynamics and cellular responses to damage removal. Our results show that fluorescently-tagged PLs can be used as a versatile tool to sense, quantify and repair DNA damage, and to study NER kinetics and UV-induced DNA damage response in living cells.
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Affiliation(s)
- Barbara Steurer
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Yasemin Turkyilmaz
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Marvin van Toorn
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Wessel van Leeuwen
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Paula Escudero-Ferruz
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
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Abstract
The nucleotide excision repair (NER) system removes a variety of types of helix-distorting lesions from DNA through a dual incision mechanism, in which the damaged nucleotide bases are excised in the form of a small, excised, damage-containing single-stranded DNA oligonucleotide (sedDNA). Damage removal leaves a gap in the DNA template that must then be filled in by the action of a DNA polymerase and ligated to the downstream phosphodiester backbone in the DNA to complete the repair reaction. Defects in damage removal, sedDNA processing, or gap filling have the potential to be mutagenic and lethal to cells, and thus several human pathologies, including cancer and aging, are associated with defects in NER. This review summarizes our current understanding of NER with a focus on the enzymes that excise sedDNAs and restore the duplex DNA to its native state in human cells.
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Affiliation(s)
- Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH, United States.
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Slyskova J, Sabatella M, Ribeiro-Silva C, Stok C, Theil AF, Vermeulen W, Lans H. Base and nucleotide excision repair facilitate resolution of platinum drugs-induced transcription blockage. Nucleic Acids Res 2019; 46:9537-9549. [PMID: 30137419 PMCID: PMC6182164 DOI: 10.1093/nar/gky764] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
Sensitivity and resistance of cells to platinum drug chemotherapy are to a large extent determined by activity of the DNA damage response (DDR). Combining chemotherapy with inhibition of specific DDR pathways could therefore improve treatment efficacy. Multiple DDR pathways have been implicated in removal of platinum-DNA lesions, but it is unclear which exact pathways are most important to cellular platinum drug resistance. Here, we used CRISPR/Cas9 screening to identify DDR proteins that protect colorectal cancer cells against the clinically applied platinum drug oxaliplatin. We find that besides the expected homologous recombination, Fanconi anemia and translesion synthesis pathways, in particular also transcription-coupled nucleotide excision repair (TC-NER) and base excision repair (BER) protect against platinum-induced cytotoxicity. Both repair pathways are required to overcome oxaliplatin- and cisplatin-induced transcription arrest. In addition to the generation of DNA crosslinks, exposure to platinum drugs leads to reactive oxygen species production that induces oxidative DNA lesions, explaining the requirement for BER. Our findings highlight the importance of transcriptional integrity in cells exposed to platinum drugs and suggest that both TC-NER and BER should be considered as targets for novel combinatorial treatment strategies.
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Affiliation(s)
- Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Mariangela Sabatella
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Colin Stok
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- To whom correspondence should be addressed. Tel: +31 10 7038169; Fax: +31 10 7044743;
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Li W, Liu W, Kakoki A, Wang R, Adebali O, Jiang Y, Sancar A. Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells. J Biol Chem 2019; 294:5914-5922. [PMID: 30808711 DOI: 10.1074/jbc.ra119.007861] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/22/2019] [Indexed: 11/06/2022] Open
Abstract
Embryonic stem cells can self-renew and differentiate, holding great promise for regenerative medicine. They also employ multiple mechanisms to preserve the integrity of their genomes. Nucleotide excision repair, a versatile repair mechanism, removes bulky DNA adducts from the genome. However, the dynamics of the capacity of nucleotide excision repair during stem cell differentiation remain unclear. Here, using immunoslot blot assay, we measured repair rates of UV-induced DNA damage during differentiation of human embryonic carcinoma (NTERA-2) cells into neurons and muscle cells. Our results revealed that the capacity of nucleotide excision repair increases as cell differentiation progresses. We also found that inhibition of the apoptotic signaling pathway has no effect on nucleotide excision repair capacity. Furthermore, RNA-Seq-based transcriptomic analysis indicated that expression levels of four core repair factors, xeroderma pigmentosum (XP) complementation group A (XPA), XPC, XPG, and XPF-ERCC1, are progressively up-regulated during differentiation, but not those of replication protein A (RPA) and transcription factor IIH (TFIIH). Together, our findings reveal that increase of nucleotide excision repair capacity accompanies cell differentiation, supported by the up-regulated transcription of genes encoding DNA repair enzymes during differentiation of two distinct cell lineages.
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Affiliation(s)
- Wentao Li
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Wenjie Liu
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599; School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian 361102 China
| | - Ayano Kakoki
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Rujin Wang
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Ogun Adebali
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956 Turkey
| | - Yuchao Jiang
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599; Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Aziz Sancar
- From the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599.
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Mullenders LHF. Solar UV damage to cellular DNA: from mechanisms to biological effects. Photochem Photobiol Sci 2018; 17:1842-1852. [PMID: 30065996 DOI: 10.1039/c8pp00182k] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Solar ultraviolet (UV) radiation generates bulky photodimers at di-pyrimidine sites that pose stress to cells and organisms by hindering DNA replication and transcription. In addition, solar UV also induces various types of oxidative DNA lesions and single strand DNA breaks. Relieving toxicity and maintenance of genomic integrity are of clinical importance in relation to erythema/edema and diseases such as cancer, neurodegeneration and premature ageing, respectively. Following solar UV radiation, a network of DNA damage response mechanisms triggers a signal transduction cascade to regulate various genome-protection pathways including DNA damage repair, cell cycle control, apoptosis, transcription and chromatin remodeling. The effects of UVC and UVB radiation on cellular DNA are predominantly accounted for by the formation of photodimers at di-pyrimidine sites. These photodimers are mutagenic: UVC, UVB and also UVA radiation induce a broadly similar pattern of transition mutations at di-pyrimidine sites. The mutagenic potency of solar UV is counteracted by efficient repair of photodimers involving global genome nucleotide excision repair (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER); the latter is a specialized repair pathway to remove transcription-blocking photodimers and restore UV-inhibited transcription. On the molecular level these processes are facilitated and regulated by various post-translational modifications of NER factors and the chromatin substrate. Inherited defects in NER are manifested in different diseases including xeroderma pigmentosum (XP), Cockayne syndrome (CS), UV sensitive syndrome (UVsS) and the photosensitive form of trichothiodystrophy (TTD). XP patients are prone to sunlight-induced skin cancer. UVB irradiated XP and CS knockout mouse models unveiled that only TC-NER counteracts erythema/edema, whereas both GG-NER and TC-NER protect against UVB-induced cancer. Additionally, UVA radiation induces mutations characterized by oxidation-linked signature at non-di-pyrimidine sites. The biological relevance of oxidation damage is demonstrated by the cancer susceptibility of UVB-irradiated mice deficient in repair of oxidation damage, i.e., 8-oxoguanine.
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Faridounnia M, Folkers GE, Boelens R. Function and Interactions of ERCC1-XPF in DNA Damage Response. Molecules 2018; 23:E3205. [PMID: 30563071 PMCID: PMC6320978 DOI: 10.3390/molecules23123205] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/27/2018] [Accepted: 12/01/2018] [Indexed: 12/28/2022] Open
Abstract
Numerous proteins are involved in the multiple pathways of the DNA damage response network and play a key role to protect the genome from the wide variety of damages that can occur to DNA. An example of this is the structure-specific endonuclease ERCC1-XPF. This heterodimeric complex is in particular involved in nucleotide excision repair (NER), but also in double strand break repair and interstrand cross-link repair pathways. Here we review the function of ERCC1-XPF in various DNA repair pathways and discuss human disorders associated with ERCC1-XPF deficiency. We also overview our molecular and structural understanding of XPF-ERCC1.
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Affiliation(s)
- Maryam Faridounnia
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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43
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cAMP-mediated regulation of melanocyte genomic instability: A melanoma-preventive strategy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 115:247-295. [PMID: 30798934 DOI: 10.1016/bs.apcsb.2018.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Malignant melanoma of the skin is the leading cause of death from skin cancer and ranks fifth in cancer incidence among all cancers in the United States. While melanoma mortality has remained steady for the past several decades, melanoma incidence has been increasing, particularly among fair-skinned individuals. According to the American Cancer Society, nearly 10,000 people in the United States will die from melanoma this year. Individuals with dark skin complexion are protected damage generated by UV-light due to the high content of UV-blocking melanin pigment in their epidermis as well as better capacity for melanocytes to cope with UV damage. There is now ample evidence that suggests that the melanocortin 1 receptor (MC1R) is a major melanoma risk factor. Inherited loss-of-function mutations in MC1R are common in melanoma-prone persons, correlating with a less melanized skin complexion and poorer recovery from mutagenic photodamage. We and others are interested in the MC1R signaling pathway in melanocytes, its mechanisms of enhancing genomic stability and pharmacologic opportunities to reduce melanoma risk based on those insights. In this chapter, we review melanoma risk factors, the MC1R signaling pathway, and the relationship between MC1R signaling and DNA repair.
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Maffucci P, Chavez J, Jurkiw TJ, O’Brien PJ, Abbott JK, Reynolds PR, Worth A, Notarangelo LD, Felgentreff K, Cortes P, Boisson B, Radigan L, Cobat A, Dinakar C, Ehlayel M, Ben-Omran T, Gelfand EW, Casanova JL, Cunningham-Rundles C. Biallelic mutations in DNA ligase 1 underlie a spectrum of immune deficiencies. J Clin Invest 2018; 128:5489-5504. [PMID: 30395541 PMCID: PMC6264644 DOI: 10.1172/jci99629] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/04/2018] [Indexed: 12/30/2022] Open
Abstract
We report the molecular, cellular, and clinical features of 5 patients from 3 kindreds with biallelic mutations in the autosomal LIG1 gene encoding DNA ligase 1. The patients exhibited hypogammaglobulinemia, lymphopenia, increased proportions of circulating γδT cells, and erythrocyte macrocytosis. Clinical severity ranged from a mild antibody deficiency to a combined immunodeficiency requiring hematopoietic stem cell transplantation. Using engineered LIG1-deficient cell lines, we demonstrated chemical and radiation defects associated with the mutant alleles, which variably impaired the DNA repair pathway. We further showed that these LIG1 mutant alleles are amorphic or hypomorphic, and exhibited variably decreased enzymatic activities, which lead to premature release of unligated adenylated DNA. The variability of the LIG1 genotypes in the patients was consistent with that of their immunological and clinical phenotypes. These data suggest that different forms of autosomal recessive, partial DNA ligase 1 deficiency underlie an immunodeficiency of variable severity.
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Affiliation(s)
- Patrick Maffucci
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
- Graduate School of Biomedical Sciences, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jose Chavez
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
| | - Thomas J. Jurkiw
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick J. O’Brien
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Jordan K. Abbott
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Paul R. Reynolds
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Austen Worth
- Department of Pediatric Medicine, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kerstin Felgentreff
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Science, CUNY School of Medicine, City College of New York, New York, New York, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Paris Descartes University, Imagine Institute, Paris, France
| | - Lin Radigan
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
| | - Aurélie Cobat
- Paris Descartes University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Chitra Dinakar
- Allergy, Asthma & Immunodeficiency, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Mohammad Ehlayel
- Section of Pediatric Allergy-Immunology, Department of Pediatrics, Weill Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Tawfeg Ben-Omran
- Department of Clinical and Metabolic Genetics, Department of Pediatrics, Weill Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Erwin W. Gelfand
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Paris Descartes University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
| | - Charlotte Cunningham-Rundles
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
- Graduate School of Biomedical Sciences, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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45
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The Histone Chaperone FACT Coordinates H2A.X-Dependent Signaling and Repair of DNA Damage. Mol Cell 2018; 72:888-901.e7. [PMID: 30344095 PMCID: PMC6292839 DOI: 10.1016/j.molcel.2018.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/27/2018] [Accepted: 09/07/2018] [Indexed: 02/07/2023]
Abstract
Safeguarding cell function and identity following a genotoxic stress challenge entails a tight coordination of DNA damage signaling and repair with chromatin maintenance. How this coordination is achieved and with what impact on chromatin integrity remains elusive. Here, we address these questions by investigating the mechanisms governing the distribution in mammalian chromatin of the histone variant H2A.X, a central player in damage signaling. We reveal that H2A.X is deposited de novo at sites of DNA damage in a repair-coupled manner, whereas the H2A.Z variant is evicted, thus reshaping the chromatin landscape at repair sites. Our mechanistic studies further identify the histone chaperone FACT (facilitates chromatin transcription) as responsible for the deposition of newly synthesized H2A.X. Functionally, we demonstrate that FACT potentiates H2A.X-dependent signaling of DNA damage. We propose that new H2A.X deposition in chromatin reflects DNA damage experience and may help tailor DNA damage signaling to repair progression. H2A.X is deposited de novo at sites of DNA damage repair, whereas H2A.Z is evicted FACT promotes new H2A.X deposition coupled to repair synthesis FACT stimulates H2A.X-dependent signaling of DNA damage H2A.X is not only a starting point of damage signaling but also an output of repair
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Ali R, Al-Kawaz A, Toss MS, Green AR, Miligy IM, Mesquita KA, Seedhouse C, Mirza S, Band V, Rakha EA, Madhusudan S. Targeting PARP1 in XRCC1-Deficient Sporadic Invasive Breast Cancer or Preinvasive Ductal Carcinoma In Situ Induces Synthetic Lethality and Chemoprevention. Cancer Res 2018; 78:6818-6827. [PMID: 30297533 DOI: 10.1158/0008-5472.can-18-0633] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/03/2018] [Accepted: 09/26/2018] [Indexed: 11/16/2022]
Abstract
: Targeting PARP1 for synthetic lethality is a new strategy for breast cancers harboring germline mutations in BRCA. However, these mutations are rare, and reactivation of BRCA-mediated pathways may result in eventual resistance to PARP1 inhibitor therapy. Alternative synthetic lethality approaches targeting more common sporadic breast cancers and preinvasive ductal carcinoma in situ (DCIS) are desirable. Here we show that downregulation of XRCC1, which interacts with PARP1 and coordinates base excision repair, is an early event in human breast cancer pathogenesis. XRCC1-deficient DCIS were aggressive and associated with increased risk of local recurrence. Human invasive breast cancers deficient in XRCC1 and expressing high PARP1 levels also manifested aggressive features and poor outcome. The PARP1 inhibitor olaparib was synthetically lethal in XRCC1-deficient DCIS and invasive breast cancer cells. We conclude that targeting PARP1 is an attractive strategy for synthetic lethality and chemoprevention in XRCC1-deficient breast cancers, including preinvasive DCIS. SIGNIFICANCE: These findings show that loss of XRCC1, which is associated with more malignant DCIS, can be exploited by PARP inhibition, suggesting its application as a promising therapeutic and chemoprevention strategy in XRCC1-deficient tumor cells.
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Affiliation(s)
- Reem Ali
- Translational Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Abdulbaqi Al-Kawaz
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Michael S Toss
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Andrew R Green
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Islam M Miligy
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Katia A Mesquita
- Translational Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Claire Seedhouse
- Academic Haematology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Centre, Nebraska Medical Centre, Omaha, Nebraska
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Centre, Nebraska Medical Centre, Omaha, Nebraska
| | - Emad A Rakha
- Department of Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom.
| | - Srinivasan Madhusudan
- Translational Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, United Kingdom. .,Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham, United Kingdom
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47
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Mu H, Geacintov NE, Broyde S, Yeo JE, Schärer OD. Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair. DNA Repair (Amst) 2018; 71:33-42. [PMID: 30174301 DOI: 10.1016/j.dnarep.2018.08.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Global genome nucleotide excision repair (GG-NER) is the main pathway for the removal of bulky lesions from DNA and is characterized by an extraordinarily wide substrate specificity. Remarkably, the efficiency of lesion removal varies dramatically and certain lesions escape repair altogether and are therefore associated with high levels of mutagenicity. Central to the multistep mechanism of damage recognition in NER is the sensing of lesion-induced thermodynamic and structural alterations of DNA by the XPC-RAD23B protein and the verification of the damage by the transcription/repair factor TFIIH. Additional factors contribute to the process: UV-DDB, for the recognition of certain UV-induced lesions in particular in the context of chromatin, while the XPA protein is believed to have a role in damage verification and NER complex assembly. Here we consider the molecular mechanisms that determine repair efficiency in GG-NER based on recent structural, computational, biochemical, cellular and single molecule studies of XPC-RAD23B and its yeast ortholog Rad4. We discuss how the actions of XPC-RAD23B are integrated with those of other NER proteins and, based on recent high-resolution structures of TFIIH, present a structural model of how XPC-RAD23B and TFIIH cooperate in damage recognition and verification.
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Affiliation(s)
- Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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48
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Azuara-Liceaga E, Betanzos A, Cardona-Felix CS, Castañeda-Ortiz EJ, Cárdenas H, Cárdenas-Guerra RE, Pastor-Palacios G, García-Rivera G, Hernández-Álvarez D, Trasviña-Arenas CH, Diaz-Quezada C, Orozco E, Brieba LG. The Sole DNA Ligase in Entamoeba histolytica Is a High-Fidelity DNA Ligase Involved in DNA Damage Repair. Front Cell Infect Microbiol 2018; 8:214. [PMID: 30050869 PMCID: PMC6052137 DOI: 10.3389/fcimb.2018.00214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/07/2018] [Indexed: 01/03/2023] Open
Abstract
The protozoan parasite Entamoeba histolytica is exposed to reactive oxygen and nitric oxide species that have the potential to damage its genome. E. histolytica harbors enzymes involved in DNA repair pathways like Base and Nucleotide Excision Repair. The majority of DNA repairs pathways converge in their final step in which a DNA ligase seals the DNA nicks. In contrast to other eukaryotes, the genome of E. histolytica encodes only one DNA ligase (EhDNAligI), suggesting that this ligase is involved in both DNA replication and DNA repair. Therefore, the aim of this work was to characterize EhDNAligI, its ligation fidelity and its ability to ligate opposite DNA mismatches and oxidative DNA lesions, and to study its expression changes and localization during and after recovery from UV and H2O2 treatment. We found that EhDNAligI is a high-fidelity DNA ligase on canonical substrates and is able to discriminate erroneous base-pairing opposite DNA lesions. EhDNAligI expression decreases after DNA damage induced by UV and H2O2 treatments, but it was upregulated during recovery time. Upon oxidative DNA damage, EhDNAligI relocates into the nucleus where it co-localizes with EhPCNA and the 8-oxoG adduct. The appearance and disappearance of 8-oxoG during and after both treatments suggest that DNA damaged was efficiently repaired because the mainly NER and BER components are expressed in this parasite and some of them were modulated after DNA insults. All these data disclose the relevance of EhDNAligI as a specialized and unique ligase in E. histolytica that may be involved in DNA repair of the 8-oxoG lesions.
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Affiliation(s)
- Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico,*Correspondence: Elisa Azuara-Liceaga
| | - Abigail Betanzos
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Cesar S. Cardona-Felix
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | | | - Helios Cárdenas
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Rosa E. Cárdenas-Guerra
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Guillermo Pastor-Palacios
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - David Hernández-Álvarez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Carlos H. Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico,Luis G. Brieba
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Xu W, Zhou B, Zhao X, Zhu L, Xu J, Jiang Z, Chen D, Wei Q, Han M, Feng L, Wang S, Wang X, Zhou J, Jin H. KDM5B demethylates H3K4 to recruit XRCC1 and promote chemoresistance. Int J Biol Sci 2018; 14:1122-1132. [PMID: 29989047 PMCID: PMC6036731 DOI: 10.7150/ijbs.25881] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/03/2018] [Indexed: 12/15/2022] Open
Abstract
Chemotherapy is the main treatment for human cancers including gastric cancer. However, in response to chemotherapeutic drugs, tumor cells can develop drug resistance by reprogramming intracellular metabolic and epigenetic networks to maintain their intrinsic homeostasis. Previously, we have established cisplatin-resistant gastric cancer cells as a drug resistant model, and elucidated the XRCC1 as the core DNA repair mechanism of drug resistance. This study investigated the regulation of XRCC1 by lysine demethylase 5B (KDM5B) in drug resistance. We found that the methylation level of H3K4 decreased significantly in drug-resistant cells. The chemical inhibitor of H3K4 demethylases, JIB-04, restored the methylation of H3K4 and blocked the co-localization of XRCC1 and γH2AX, eventually improved drug sensitivity. We further found that the expression level of KDM5B increased significantly in drug-resistant cells. Knockdown of KDM5B increased the methylation level of H3K4 and blocked the localization of XRCC1 to the DNA damage site, leads to increased drug sensitivity. In the sensitive cells, overexpression of KDM5B suppressed H3K4 methylation levels, which resulted to resistance to cisplatin. Moreover, we found that the posttranslational modification of KDM5B is responsible for its high expression in drug-resistant cells. Through mass spectrometry screening and co-immunoprecipitation validation, we found that the molecular chaperone HSP90 forms a complex with KDM5B in drug resistance cells. Interestingly, HSP90 inhibitor 17-AAG induced KDM5B degradation in a time-and-dose-dependent manner, indicating that HSP90 protected KDM5B from protein degradation. Targeting inhibition of HSP90 and KDM5B reversed drug resistance both in vitro and in vivo. Taken together, molecular chaperon HSP90 interacted with KDM5B to protect it from ubiquitin-dependent proteasomal degradation. Increased KDM5B demethylated H3K4 and facilitated the recruitment of XRCC1 to repair damaged DNA. Therefore, inhibition of HSP90 or KDM5B represented a novel approach to reverse chemoresistance in human cancers.
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Affiliation(s)
- Wenxia Xu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Bingluo Zhou
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Xiaoya Zhao
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Liyuan Zhu
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Jinye Xu
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Dingwei Chen
- Department of general surgery, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Qi Wei
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Mengjiao Han
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Lifeng Feng
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Shouyu Wang
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw hospital, Medical School of Zhejiang University, China
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50
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Abstract
The local UV irradiation technique enables detection, kinetic measurements of recruitment, and quantification of DNA Damage Response (DDR) proteins at the site of UV-induced DNA damage.Using Isopore filters with high density pores of a broad range of sizes, it is possible to UV irradiate and damage only a very small portion of the nucleus of a cell by letting UV light pass only through the pores. Immunofluorescent analyses of modified DNA nucleotides, proteins, or fluorescently tagged versions of target factors can be used as markers to label and study UV-induced lesions and their repair.
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