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Tian Z, Huang K, Yang W, Chen Y, Lyv W, Zhu B, Yang X, Ma P, Tong Z. Exogenous and endogenous formaldehyde-induced DNA damage in the aging brain: mechanisms and implications for brain diseases. Cell Biol Toxicol 2024; 40:83. [PMID: 39367211 PMCID: PMC11452425 DOI: 10.1007/s10565-024-09926-w] [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: 06/02/2024] [Accepted: 10/02/2024] [Indexed: 10/06/2024]
Abstract
Exogenous gaseous formaldehyde (FA) is recognized as a significant indoor air pollutant due to its chemical reactivity and documented mutagenic and carcinogenic properties, particularly in its capacity to damage DNA and impact human health. Despite increasing attention on the adverse effects of exogenous FA on human health, the potential detrimental effects of endogenous FA in the brain have been largely neglected in current research. Endogenous FA have been observed to accumulate in the aging brain due to dysregulation in the expression and activity of enzymes involved in FA metabolism. Surprisingly, excessive FA have been implicated in the development of neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and brain cancers. Notably, FA has the ability to not only initiate DNA double strand breaks but also induce the formation of crosslinks of DNA-DNA, DNA-RNA, and DNA-protein, which further exacerbate the progression of these brain diseases. However, recent research has identified that FA-resistant gene exonuclease-1 (EXO1) and FA scavengers can potentially mitigate FA toxicity, offering a promising strategy for mitigating or repairing FA-induced DNA damage. The present review offers novel insights into the impact of FA metabolism on brain ageing and the contribution of FA-damaged DNA to the progression of neurological disorders.
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Affiliation(s)
- Zixi Tian
- Beijing Geriatric Hospital, Beijing, 100049, China
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Kai Huang
- Beijing Geriatric Hospital, Beijing, 100049, China
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Wanting Yang
- Beijing Geriatric Hospital, Beijing, 100049, China
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Ying Chen
- Beijing Geriatric Hospital, Beijing, 100049, China
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Wanjia Lyv
- Key Laboratory of Environmental Related Diseases and One Health, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, China
| | - Beilei Zhu
- Beijing Geriatric Hospital, Beijing, 100049, China
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xu Yang
- Key Laboratory of Environmental Related Diseases and One Health, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, China
| | - Ping Ma
- Beijing Geriatric Hospital, Beijing, 100049, China.
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China.
- Key Laboratory of Environmental Related Diseases and One Health, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, China.
| | - Zhiqian Tong
- Beijing Geriatric Hospital, Beijing, 100049, China.
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China.
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2
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Cheng J, Liu H, Yu W, Dong X, Sai Y, Ye F, Dan G, Chen M, Zhao Y, Zhang X, Zou Z. Nitrogen mustard induces dynamic nuclear protein spectrum change and DNA-protein crosslinking, with p97 mediating repair. Heliyon 2024; 10:e37401. [PMID: 39290288 PMCID: PMC11407038 DOI: 10.1016/j.heliyon.2024.e37401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 09/01/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Nitrogen mustard (NM) is a chemotherapeutic agent capable of alkylating nucleophilic proteins and DNA, causing severe cell damage. However, no reports have been on the dynamic changes in proteomics induced by NM. In this study, we established a model of acute exposure to NM for 1 h and a continuous cultured model for 24 h after NM removal (repair stage) using 16HBE cells. The nuclear protein spectrum and nuclear proteins crosslinked with DNA were analyzed, and the function of p97 during NM damage was examined. An hour of NM exposure resulted in severe changes in the nuclear protein spectrum and protein into the cell nucleus, which is mainly involved in nuclear acid-related issues. After 24 h, the return to normal process of the types and amounts of differentially expressed proteins was inhibited by si-p97. The main processes involved in si-p97 intervention were nucleocytoplasmic transport, processing in the endoplasmic reticulum, metabolic abnormalities, and DNA-response; however. An hour of exposure to NM increased DNA-protein crosslinking (DPC), total-H2AX, and p-H2AX. In contrast, si-p97 only further increased or maintained their levels at 24 h yet not at 1 h. The effect of the proteasome inhibitor, MG132, was similar to that of si-p97. The siRNA of DVC1, a partner of p97, also increased the DPC content. Both si-p97 and si-DVC1 increased the cytoplasmic levels of the proteasome (PSMD2). These results suggest acute NM exposure induces severe nuclear protein spectral changes, rapid protein influx into the nucleus, DPC formation, and DNA double-strand breaks. Furthermore, our data indicated that p97 is involved in normal protein spectrum maintenance and DPC removal after NM withdrawal, requiring the participation of DVC1 and the proteasome.
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Affiliation(s)
- Jin Cheng
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
- Department of Clinic, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Haoyin Liu
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Wenpei Yu
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Xunhu Dong
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Yan Sai
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Feng Ye
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Guorong Dan
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Mingliang Chen
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Yuanpeng Zhao
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Xi Zhang
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
| | - Zhongmin Zou
- Department of Chemical Defense Medicine, School of Preventive Medicine, The Third Military Medical University Army Medical University, Chongqing, China
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3
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Blouin T, Saini N. Aldehyde-induced DNA-protein crosslinks- DNA damage, repair and mutagenesis. Front Oncol 2024; 14:1478373. [PMID: 39328207 PMCID: PMC11424613 DOI: 10.3389/fonc.2024.1478373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Aldehyde exposure has been shown to lead to the formation of DNA damage comprising of DNA-protein crosslinks (DPCs), base adducts and interstrand or intrastrand crosslinks. DPCs have recently drawn more attention because of recent advances in detection and quantification of these adducts. DPCs are highly deleterious to genome stability and have been shown to block replication forks, leading to wide-spread mutagenesis. Cellular mechanisms to prevent DPC-induced damage include excision repair pathways, homologous recombination, and specialized proteases involved in cleaving the covalently bound proteins from DNA. These pathways were first discovered in formaldehyde-treated cells, however, since then, various other aldehydes have been shown to induce formation of DPCs in cells. Defects in DPC repair or aldehyde clearance mechanisms lead to various diseases including Ruijs-Aalfs syndrome and AMeD syndrome in humans. Here, we discuss recent developments in understanding how aldehydes form DPCs, how they are repaired, and the consequences of defects in these repair pathways.
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Affiliation(s)
- Thomas Blouin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
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4
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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5
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Oka Y, Nakazawa Y, Shimada M, Ogi T. Endogenous aldehyde-induced DNA-protein crosslinks are resolved by transcription-coupled repair. Nat Cell Biol 2024; 26:784-796. [PMID: 38600234 PMCID: PMC11098742 DOI: 10.1038/s41556-024-01401-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
DNA-protein crosslinks (DPCs) induced by aldehydes interfere with replication and transcription. Hereditary deficiencies in DPC repair and aldehyde clearance processes cause progeria, including Ruijs-Aalfs syndrome (RJALS) and AMeD syndrome (AMeDS) in humans. Although the elimination of DPC during replication has been well established, how cells overcome DPC lesions in transcription remains elusive. Here we show that endogenous aldehyde-induced DPC roadblocks are efficiently resolved by transcription-coupled repair (TCR). We develop a high-throughput sequencing technique to measure the genome-wide distribution of DPCs (DPC-seq). Using proteomics and DPC-seq, we demonstrate that the conventional TCR complex as well as VCP/p97 and the proteasome are required for the removal of formaldehyde-induced DPCs. TFIIS-dependent cleavage of RNAPII transcripts protects against transcription obstacles. Finally, a mouse model lacking both aldehyde clearance and TCR confirms endogenous DPC accumulation in actively transcribed regions. Collectively, our data provide evidence that transcription-coupled DPC repair (TC-DPCR) as well as aldehyde clearance are crucial for protecting against metabolic genotoxin, thus explaining the molecular pathogenesis of AMeDS and other disorders associated with defects in TCR, such as Cockayne syndrome.
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Affiliation(s)
- Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan.
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Division of Animal Medical Science, Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Japan.
- Division of Molecular Physiology and Dynamics, Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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6
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Krawic C, Luczak MW, Valiente S, Zhitkovich A. Atypical genotoxicity of carcinogenic nickel(II): Linkage to dNTP biosynthesis, DNA-incorporated rNMPs, and impaired repair of TOP1-DNA crosslinks. J Biol Chem 2023; 299:105385. [PMID: 37890780 PMCID: PMC10692736 DOI: 10.1016/j.jbc.2023.105385] [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: 05/15/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Cancer is a genetic disease requiring multiple mutations for its development. However, many carcinogens are DNA-unreactive and nonmutagenic and consequently described as nongenotoxic. One of such carcinogens is nickel, a global environmental pollutant abundantly emitted by burning of coal. We investigated activation of DNA damage responses by Ni and identified this metal as a replication stressor. Genotoxic stress markers indicated the accumulation of ssDNA and stalled replication forks, and Ni-treated cells were dependent on ATR for suppression of DNA damage and long-term survival. Replication stress by Ni resulted from destabilization of RRM1 and RRM2 subunits of ribonucleotide reductase and the resulting deficiency in dNTPs. Ni also increased DNA incorporation of rNMPs (detected by a specific fluorescent assay) and strongly enhanced their genotoxicity as a result of repressed repair of TOP1-DNA protein crosslinks (TOP1-DPC). The DPC-trap assay found severely impaired SUMOylation and K48-polyubiquitination of DNA-crosslinked TOP1 due to downregulation of specific enzymes. Our findings identified Ni as the human carcinogen inducing genome instability via DNA-embedded ribonucleotides and accumulation of TOP1-DPC which are carcinogenic abnormalities with poor detectability by the standard mutagenicity tests. The discovered mechanisms for Ni could also play a role in genotoxicity of other protein-reactive carcinogens.
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Affiliation(s)
- Casey Krawic
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Michal W Luczak
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Sophia Valiente
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA.
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7
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Zhao Y, Wei L, Tagmount A, Loguinov A, Sobh A, Hubbard A, McHale CM, Chang CJ, Vulpe CD, Zhang L. Applying genome-wide CRISPR to identify known and novel genes and pathways that modulate formaldehyde toxicity. CHEMOSPHERE 2021; 269:128701. [PMID: 33189395 PMCID: PMC7904579 DOI: 10.1016/j.chemosphere.2020.128701] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/18/2020] [Indexed: 05/09/2023]
Abstract
Formaldehyde (FA), a ubiquitous environmental pollutant, is classified as a Group I human carcinogen by the International Agency for Research on Cancer. Previously, we reported that FA induced hematotoxicity and chromosomal aneuploidy in exposed workers and toxicity in bone marrow and hematopoietic stem cells of experimental animals. Using functional toxicogenomic profiling in yeast, we identified genes and cellular processes modulating eukaryotic FA cytotoxicity. Although we validated some of these findings in yeast, many specific genes, pathways and mechanisms of action of FA in human cells are not known. In the current study, we applied genome-wide, loss-of-function CRISPR screening to identify modulators of FA toxicity in the human hematopoietic K562 cell line. We assessed the cellular genetic determinants of susceptibility and resistance to FA at 40, 100 and 150 μM (IC10, IC20 and IC60, respectively) at two time points, day 8 and day 20. We identified multiple candidate genes that increase sensitivity (e.g. ADH5, ESD and FANC family) or resistance (e.g. FASN and KDM6A) to FA when disrupted. Pathway analysis revealed a major role for the FA metabolism and Fanconi anemia pathway in FA tolerance, consistent with findings from previous studies. Additional network analyses revealed potential new roles for one-carbon metabolism, fatty acid synthesis and mTOR signaling in modulating FA toxicity. Validation of these novel findings will further enhance our understanding of FA toxicity in human cells. Our findings support the utility of CRISPR-based functional genomics screening of environmental chemicals.
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Affiliation(s)
- Yun Zhao
- School of Public Health, University of California, Berkeley, CA, United States; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Linqing Wei
- School of Public Health, University of California, Berkeley, CA, United States
| | - Abderrahmane Tagmount
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Alex Loguinov
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Amin Sobh
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Alan Hubbard
- School of Public Health, University of California, Berkeley, CA, United States
| | - Cliona M McHale
- School of Public Health, University of California, Berkeley, CA, United States
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, CA, United States
| | - Chris D Vulpe
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.
| | - Luoping Zhang
- School of Public Health, University of California, Berkeley, CA, United States.
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8
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Kühbacher U, Duxin JP. How to fix DNA-protein crosslinks. DNA Repair (Amst) 2020; 94:102924. [PMID: 32683310 PMCID: PMC7511601 DOI: 10.1016/j.dnarep.2020.102924] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/18/2022]
Abstract
Proteins that act on DNA, or are in close proximity to it, can become inadvertently crosslinked to DNA and form highly toxic lesions, known as DNA-protein crosslinks (DPCs). DPCs are generated by different chemotherapeutics, environmental or endogenous sources of crosslinking agents, or by lesions on DNA that stall the catalytic cycle of certain DNA processing enzymes. These bulky adducts impair processes on DNA such as DNA replication or transcription, and therefore pose a serious threat to genome integrity. The large diversity of DPCs suggests that there is more than one canonical mechanism to repair them. Indeed, many different enzymes have been shown to act on DPCs by either processing the protein, the DNA or the crosslink itself. In addition, the cell cycle stage or cell type are likely to dictate pathway choice. In recent years, a detailed understanding of DPC repair during S phase has started to emerge. Here, we review the current knowledge on the mechanisms of replication-coupled DPC repair, and describe and also speculate on possible pathways that remove DPCs outside of S phase. Moreover, we highlight a recent paradigm shifting finding that indicates that DPCs are not always detrimental, but can also play a protective role, preserving the genome from more deleterious forms of DNA damage.
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Affiliation(s)
- Ulrike Kühbacher
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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9
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Kim CH, Lee DH. KAT5 Negatively regulates the proliferation of prostate cancer LNCaP cells via the caspase 3-dependent apoptosis pathway. Anim Cells Syst (Seoul) 2019; 23:253-259. [PMID: 31489246 PMCID: PMC6711033 DOI: 10.1080/19768354.2019.1644372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 12/26/2022] Open
Abstract
Prostate cancer is one of the most common cancers in men over the age of sixty. Lysine acetyltransferase 5 (KAT5) is a histone acetyltransferase involved in transcriptional regulation, DNA repair, and cell signaling pathways. Previous studies have shown that KAT5 expression is reduced in the cytoplasm of the prostate cancer cell line LNCaP when exposed to androgen. Moreover, KAT5 has been reported to have a role in the molecular pathway leading to androgen-independent prostate cancer after long-term androgen deprivation therapy. Here, we showed that KAT5 expression was significantly reduced in prostate cancer tissues and cell lines by using the public databases Oncomine and Human Protein Atlas. Reduced KAT5 expression was significantly associated with high mortality in prostate cancer patients. Furthermore, KAT5 overexpression increased the level of apoptotic markers, such as cleaved-caspase 3, in LNCaP cells, thus enhancing the apoptotic death of LNCaP cells. Taken together, KAT5 induced apoptosis in prostate cancer cells via the caspase-3 pathway, indicating that KAT5 could be a gene therapy target for prostate cancer.
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Affiliation(s)
- Chul-Hong Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Dong Ho Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
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10
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Larsen NB, Gao AO, Sparks JL, Gallina I, Wu RA, Mann M, Räschle M, Walter JC, Duxin JP. Replication-Coupled DNA-Protein Crosslink Repair by SPRTN and the Proteasome in Xenopus Egg Extracts. Mol Cell 2018; 73:574-588.e7. [PMID: 30595436 PMCID: PMC6375733 DOI: 10.1016/j.molcel.2018.11.024] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/20/2018] [Accepted: 11/15/2018] [Indexed: 01/19/2023]
Abstract
DNA-protein crosslinks (DPCs) are bulky lesions that interfere with DNA metabolism and therefore threaten genomic integrity. Recent studies implicate the metalloprotease SPRTN in S phase removal of DPCs, but how SPRTN is targeted to DPCs during DNA replication is unknown. Using Xenopus egg extracts that recapitulate replication-coupled DPC proteolysis, we show that DPCs can be degraded by SPRTN or the proteasome, which act as independent DPC proteases. Proteasome recruitment requires DPC polyubiquitylation, which is partially dependent on the ubiquitin ligase activity of TRAIP. In contrast, SPRTN-mediated DPC degradation does not require DPC polyubiquitylation but instead depends on nascent strand extension to within a few nucleotides of the lesion, implying that polymerase stalling at the DPC activates SPRTN on both leading and lagging strand templates. Our results demonstrate that SPRTN and proteasome activities are coupled to DNA replication by distinct mechanisms that promote replication across immovable protein barriers.
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Affiliation(s)
- Nicolai B Larsen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Alan O Gao
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Justin L Sparks
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Irene Gallina
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthias Mann
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Markus Räschle
- Department of Molecular Biotechnology and Systems Biology, Technical University of Kaiserslautern, 67653 Kaiserslautern, Germany
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Julien P Duxin
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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11
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Klages-Mundt NL, Li L. Formation and repair of DNA-protein crosslink damage. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1065-1076. [PMID: 29098631 DOI: 10.1007/s11427-017-9183-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/26/2017] [Indexed: 12/15/2022]
Abstract
DNA is constantly exposed to a wide array of genotoxic agents, generating a variety of forms of DNA damage. DNA-protein crosslinks (DPCs)-the covalent linkage of proteins with a DNA strand-are one of the most deleterious and understudied forms of DNA damage, posing as steric blockades to transcription and replication. If not properly repaired, these lesions can lead to mutations, genomic instability, and cell death. DPCs can be induced endogenously or through environmental carcinogens and chemotherapeutic agents. Endogenously, DPCs are commonly derived through reactions with aldehydes, as well as through trapping of various enzymatic intermediates onto the DNA. Proteolytic cleavage of the protein moiety of a DPC is a general strategy for removing the lesion. This can be accomplished through a DPC-specific protease and and/or proteasome-mediated degradation. Nucleotide excision repair and homologous recombination are each involved in repairing DPCs, with their respective roles likely dependent on the nature and size of the adduct. The Fanconi anemia pathway may also have a role in processing DPC repair intermediates. In this review, we discuss how these lesions are formed, strategies and mechanisms for their removal, and diseases associated with defective DPC repair.
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Affiliation(s)
- Naeh L Klages-Mundt
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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12
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Luczak MW, Zhitkovich A. Nickel-induced HIF-1α promotes growth arrest and senescence in normal human cells but lacks toxic effects in transformed cells. Toxicol Appl Pharmacol 2017; 331:94-100. [PMID: 28552779 DOI: 10.1016/j.taap.2017.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 02/09/2023]
Abstract
Nickel is a human carcinogen that acts as a hypoxia mimic by activating the transcription factor HIF-1α and hypoxia-like transcriptomic responses. Hypoxia and elevated HIF-1α are typically associated with drug resistance in cancer cells, which is caused by increased drug efflux and other mechanisms. Here we examined the role of HIF-1α in uptake of soluble Ni(II) and Ni(II)-induced cell fate outcomes using si/shRNA knockdowns and gene deletion models. We found that HIF-1α had no effect on accumulation of Ni(II) in two transformed (H460, A549) and two normal human cell lines (IMR90, WI38). The loss of HIF-1α also produced no significant impact on p53-dependent and p53-independent apoptotic responses or clonogenic survival of Ni(II)-treated transformed cells. In normal human cells, HIF-1α enhanced the ability of Ni(II) to inhibit cell proliferation and cause a permanent growth arrest (senescence). Consistent with its growth-suppressive effects, HIF-1α was important for upregulation of the cell cycle inhibitors p21 (CDKN1A) and p27 (CDKN1B). Irrespective of HIF-1α status, Ni(II) strongly increased levels of MYC protein but did not change protein expression of the cell cycle-promoting phosphatase CDC25A or the CDK inhibitor p16. Our findings indicate that HIF-1α limits propagation of Ni(II)-damaged normal cells, suggesting that it may act in a tumor suppressor-like manner during early stages of Ni(II) carcinogenesis.
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Affiliation(s)
- Michal W Luczak
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA.
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13
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Vaz B, Popovic M, Ramadan K. DNA-Protein Crosslink Proteolysis Repair. Trends Biochem Sci 2017; 42:483-495. [PMID: 28416269 DOI: 10.1016/j.tibs.2017.03.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 01/18/2023]
Abstract
Proteins that are covalently bound to DNA constitute a specific type of DNA lesion known as DNA-protein crosslinks (DPCs). DPCs represent physical obstacles to the progression of DNA replication. If not repaired, DPCs cause stalling of DNA replication forks that consequently leads to DNA double-strand breaks, the most cytotoxic DNA lesion. Although DPCs are common DNA lesions, the mechanism of DPC repair was unclear until now. Recent work unveiled that DPC repair is orchestrated by proteolysis performed by two distinct metalloproteases, SPARTAN in metazoans and Wss1 in yeast. This review summarizes recent discoveries on two proteases in DNA replication-coupled DPC repair and establishes DPC proteolysis repair as a separate DNA repair pathway for genome stability and protection from accelerated aging and cancer.
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Affiliation(s)
- Bruno Vaz
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Marta Popovic
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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14
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Ortega-Atienza S, Krawic C, Watts L, McCarthy C, Luczak MW, Zhitkovich A. 20S immunoproteasomes remove formaldehyde-damaged cytoplasmic proteins suppressing caspase-independent cell death. Sci Rep 2017; 7:654. [PMID: 28381880 PMCID: PMC5429636 DOI: 10.1038/s41598-017-00757-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/09/2017] [Indexed: 01/08/2023] Open
Abstract
Immunoproteasomes are known for their involvement in antigen presentation. However, their broad tissue presence and other evidence are indicative of nonimmune functions. We examined a role for immunoproteasomes in cellular responses to the endogenous and environmental carcinogen formaldehyde (FA) that binds to cytosolic and nuclear proteins producing proteotoxic stress and genotoxic DNA-histone crosslinks. We found that immunoproteasomes were important for suppression of a caspase-independent cell death and the long-term survival of FA-treated cells. All major genotoxic responses to FA, including replication inhibition and activation of the transcription factor p53 and the apical ATM and ATR kinases, were unaffected by immunoproteasome inactivity. Immunoproteasome inhibition enhanced activation of the cytosolic protein damage sensor HSF1, elevated levels of K48-polyubiquitinated cytoplasmic proteins and increased depletion of unconjugated ubiquitin. We further found that FA induced the disassembly of 26S immunoproteasomes, but not standard 26S proteasomes, releasing the 20S catalytic immunoproteasome. FA-treated cells also had higher amounts of small activators PA28αβ and PA28γ bound to 20S particles. Our findings highlight the significance of nonnuclear damage in FA injury and reveal a major role for immunoproteasomes in elimination of FA-damaged cytoplasmic proteins through ubiquitin-independent proteolysis.
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Affiliation(s)
- Sara Ortega-Atienza
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
| | - Casey Krawic
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
| | - Lauren Watts
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
| | - Caitlin McCarthy
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
| | - Michal W Luczak
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA.
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15
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Cheng J, Zhang L, Tang Y, Li Z. The toxicity of continuous long-term low-dose formaldehyde inhalation in mice. Immunopharmacol Immunotoxicol 2017; 38:495-501. [PMID: 27819568 DOI: 10.1080/08923973.2016.1248844] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although the toxicity of high-dose formaldehyde (FA) inhalation has been extensively analyzed in animals, the effect of continuous long-term exposure to low-dose FA has not been well documented. This study aims to evaluate the toxicity of continuous long-term low-dose FA inhalation in mice. Forty-eight Kunming male mice were equally randomized to three groups according to the dose of FA inhalation exposure: a control (0 mg/m3) group, a low-dose (0.08 mg/m3) group and a high-dose (0.8 mg/m3) group. The mice have been selected to expose to FA for different consecutive days at 24 h/day. The learning and memory functions, pathological changes in the lung and liver, and the percentage of CD4 + T and CD8 + T cells were observed and analyzed. It was found that continuous long-term inhalation of FA at relatively low doses could impair the learning and memory functions and induce pathological changes in the lung and liver, but did not seem to significantly affect the number of immune (CD4 + T and CD8 + T) cells.
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Affiliation(s)
- Jiaying Cheng
- a Department of Building Science , Tsinghua University , Beijing , China
| | - Long Zhang
- b Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military University , Shanghai , China
| | - Yufu Tang
- b Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military University , Shanghai , China
| | - Zhenhai Li
- c Department of Mechanical Energy , Tongji University , Shanghai , China
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16
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Ortega-Atienza S, Rubis B, McCarthy C, Zhitkovich A. Formaldehyde Is a Potent Proteotoxic Stressor Causing Rapid Heat Shock Transcription Factor 1 Activation and Lys48-Linked Polyubiquitination of Proteins. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:2857-2868. [PMID: 27639166 DOI: 10.1016/j.ajpath.2016.06.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 05/24/2016] [Accepted: 06/30/2016] [Indexed: 11/29/2022]
Abstract
Endogenous and exogenous formaldehyde (FA) has been linked to cancer, neurotoxicity, and other pathophysiologic effects. Molecular and cellular mechanisms that underlie FA-induced damage are poorly understood. In this study, we investigated whether proteotoxicity is an important, unrecognized factor in cell injury caused by FA. We found that irrespective of their cell cycle phases, all FA-treated human cells rapidly accumulated large amounts of proteins with proteasome-targeting K48-linked polyubiquitin, which was comparable with levels of polyubiquitination in proteasome-inhibited MG132 controls. Both nuclear and cytoplasmic proteins were damaged and underwent K48-polyubiquitination. There were no significant changes in the nonproteolytic K63-polyubiquitination of soluble and insoluble cellular proteins. FA also rapidly induced nuclear accumulation and Ser326 phosphorylation of the main heat shock-responsive transcription factor HSF1, which was not a result of protein polyubiquitination. Consistent with the activation of the functional heat shock response, FA strongly elevated the expression of HSP70 genes. In contrast to the responsiveness of the cytoplasmic protein damage sensor HSF1, FA did not activate the unfolded protein response in either the endoplasmic reticulum or mitochondria. Inhibition of HSP90 chaperone activity increased the levels of K48-polyubiquitinated proteins and diminished cell viability after FA treatment. Overall, our results indicate that FA is a strong proteotoxic agent, which helps explain its diverse pathologic effects, including injury in nonproliferative tissues.
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Affiliation(s)
- Sara Ortega-Atienza
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Blazej Rubis
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Caitlin McCarthy
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island.
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17
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Ortega-Atienza S, Wong VC, DeLoughery Z, Luczak MW, Zhitkovich A. ATM and KAT5 safeguard replicating chromatin against formaldehyde damage. Nucleic Acids Res 2016; 44:198-209. [PMID: 26420831 PMCID: PMC4705693 DOI: 10.1093/nar/gkv957] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/09/2015] [Accepted: 09/10/2015] [Indexed: 01/18/2023] Open
Abstract
Many carcinogens damage both DNA and protein constituents of chromatin, and it is unclear how cells respond to this compound injury. We examined activation of the main DNA damage-responsive kinase ATM and formation of DNA double-strand breaks (DSB) by formaldehyde (FA) that forms histone adducts and replication-blocking DNA-protein crosslinks (DPC). We found that low FA doses caused a strong and rapid activation of ATM signaling in human cells, which was ATR-independent and restricted to S-phase. High FA doses inactivated ATM via its covalent dimerization and formation of larger crosslinks. FA-induced ATM signaling showed higher CHK2 phosphorylation but much lower phospho-KAP1 relative to DSB inducers. Replication blockage by DPC did not produce damaged forks or detectable amounts of DSB during the main wave of ATM activation, which did not require MRE11. Chromatin-monitoring KAT5 (Tip60) acetyltransferase was responsible for acetylation and activation of ATM by FA. KAT5 and ATM were equally important for triggering of intra-S-phase checkpoint and ATM signaling promoted recovery of normal human cells after low-dose FA. Our results revealed a major role of the KAT5-ATM axis in protection of replicating chromatin against damage by the endogenous carcinogen FA.
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Affiliation(s)
- Sara Ortega-Atienza
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Victor C Wong
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Zachary DeLoughery
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Michal W Luczak
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
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18
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Al-Anati L, Viluksela M, Strid A, Bergman Å, Andersson PL, Stenius U, Högberg J. Hydroxyl metabolite of PCB 180 induces DNA damage signaling and enhances the DNA damaging effect of benzo[a]pyrene. Chem Biol Interact 2015; 239:164-73. [PMID: 26148434 DOI: 10.1016/j.cbi.2015.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/16/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
Abstract
Non-dioxin-like (NDL) polychlorinated biphenyls (PCBs) and their hydroxyl metabolites (OH-PCBs) are ubiquitous environmental contaminants in human tissues and blood. The toxicological impact of these metabolites is poorly understood. In this study rats were exposed to ultrapure PCB180 (10-1000mg/kgbw) for 28days and induction of genotoxic stress in liver was investigated. DNA damage signaling proteins (pChk1Ser317 and γH2AXSer319) were increased dose dependently in female rats. This increase was paralleled by increasing levels of the metabolite 3'-OH-PCB180. pChk1 was the most sensitive marker. In in vitro studies HepG2 cells were exposed to 1μM of PCB180 and 3'-OH-PCB180 or the positive control benzo[a]pyrene (BaP, 5μM). 3'-OH-PCB180, but not PCB180, induced CYP1A1 mRNA and γH2AX. CYP1A1 mRNA induction was seen at 1h, and γH2AX at 3h. The anti-oxidant N-Acetyl-l-Cysteine (NAC) completely prevented, and 17β-estradiol amplified the γH2AX induction by 3'-OH-PCB180. As 3'-OH-PCB180 induced CYP1A1, a major BaP-metabolizing and activating enzyme, interactions between 3'-OH-PCB180 and BaP was also studied. The metabolite amplified the DNA damage signaling response to BaP. In conclusion, metabolism of PCB180 to its hydroxyl metabolite and the subsequent induction of CYP1A1 seem important for DNA damage induced by PCB180 in vivo. Amplification of the response with estradiol may explain why DNA damage was only seen in female rats.
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Affiliation(s)
- Lauy Al-Anati
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Matti Viluksela
- Chemicals and Health Unit, National Institute for Health and Welfare (THL), P.O. Box 95, FI-70701 Kuopio, Finland; Department of Environmental Science, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Anna Strid
- Analytical and Toxicological Chemistry Unit, Department of Environmental Science and Analytical Chemistry, Stockholm University, SE 106-91 Stockholm, Sweden
| | - Åke Bergman
- Analytical and Toxicological Chemistry Unit, Department of Environmental Science and Analytical Chemistry, Stockholm University, SE 106-91 Stockholm, Sweden; Swedish Toxicology Sciences Research Center (Swetox), Forskargatan 20, 151 36 Södertälje, Sweden
| | | | - Ulla Stenius
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Johan Högberg
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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