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Chao MR, Chang YJ, Cooke MS, Hu CW. Multi-adductomics: Advancing mass spectrometry techniques for comprehensive exposome characterization. Trends Analyt Chem 2024; 180:117900. [PMID: 39246549 PMCID: PMC11375889 DOI: 10.1016/j.trac.2024.117900] [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: 09/10/2024]
Abstract
Adductomics, an emerging field within the 'omics sciences, focuses on the formation and prevalence of DNA, RNA, and protein adducts induced by endogenous and exogenous agents in biological systems. These modifications often result from exposure to environmental pollutants, dietary components, and xenobiotics, impacting cellular functions and potentially leading to diseases such as cancer. This review highlights advances in mass spectrometry (MS) that enhance the detection of these critical modifications and discusses current and emerging trends in adductomics, including developments in MS instrument use, screening techniques, and the study of various biomolecular modifications from mono-adducts to complex hybrid crosslinks between different types of biomolecules. The review also considers challenges, including the need for specialized MS spectra databases and multi-omics integration, while emphasizing techniques to distinguish between exogenous and endogenous modifications. The future of adductomics possesses significant potential for enhancing our understanding of health in relation to environmental exposures and precision medicine.
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Affiliation(s)
- Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
- Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan
- Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan
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2
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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. Repair of genomic interstrand crosslinks. DNA Repair (Amst) 2024; 141:103739. [PMID: 39106540 DOI: 10.1016/j.dnarep.2024.103739] [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: 03/12/2024] [Revised: 07/11/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024]
Abstract
Genomic interstrand crosslinks (ICLs) are formed by reactive species generated during normal cellular metabolism, produced by the microbiome, and employed in cancer chemotherapy. While there are multiple options for replication dependent and independent ICL repair, the crucial step for each is unhooking one DNA strand from the other. Much of our insight into mechanisms of unhooking comes from powerful model systems based on plasmids with defined ICLs introduced into cells or cell free extracts. Here we describe the properties of exogenous and endogenous ICL forming compounds and provide an historical perspective on early work on ICL repair. We discuss the modes of unhooking elucidated in the model systems, the concordance or lack thereof in drug resistant tumors, and the evolving view of DNA adducts, including ICLs, formed by metabolic aldehydes.
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Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ishani Majumdar
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chen Ling
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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3
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Anticevic I, Otten C, Popovic M. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) repairs DNA-protein crosslinks and protects against double strand breaks in vivo. Front Cell Dev Biol 2024; 12:1394531. [PMID: 39228401 PMCID: PMC11369425 DOI: 10.3389/fcell.2024.1394531] [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: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 09/05/2024] Open
Abstract
DNA-protein crosslinks pose a significant challenge to genome stability and cell viability. Efficient repair of DPCs is crucial for preserving genomic integrity and preventing the accumulation of DNA damage. Despite recent advances in our understanding of DPC repair, many aspects of this process, especially at the organismal level, remain elusive. In this study, we used zebrafish as a model organism to investigate the role of TDP2 (Tyrosyl-DNA phosphodiesterase 2) in DPC repair. We characterized the two tdp2 orthologs in zebrafish using phylogenetic, syntenic and expression analysis and investigated the phenotypic consequences of tdp2 silencing in zebrafish embryos. We then quantified the effects of tdp2a and tdp2b silencing on cellular DPC levels and DSB accumulation in zebrafish embryos. Our findings revealed that tdp2b is the main ortholog during embryonic development, while both orthologs are ubiquitously present in adult tissues. Notably, the tdp2b ortholog is phylogenetically closer to human TDP2. Silencing of tdp2b, but not tdp2a, resulted in the loss of Tdp2 activity in zebrafish embryos, accompanied by the accumulation of DPCs and DSBs. Our findings contribute to a more comprehensive understanding of DPC repair at the organismal level and underscore the significance of TDP2 in maintaining genome stability.
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Affiliation(s)
| | | | - Marta Popovic
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruder Boskovic, Zagreb, Croatia
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4
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Torrecilla I, Ruggiano A, Kiianitsa K, Aljarbou F, Lascaux P, Hoslett G, Song W, Maizels N, Ramadan K. Isolation and detection of DNA-protein crosslinks in mammalian cells. Nucleic Acids Res 2024; 52:525-547. [PMID: 38084926 PMCID: PMC10810220 DOI: 10.1093/nar/gkad1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 01/26/2024] Open
Abstract
DNA-protein crosslinks (DPCs) are toxic DNA lesions wherein a protein is covalently attached to DNA. If not rapidly repaired, DPCs create obstacles that disturb DNA replication, transcription and DNA damage repair, ultimately leading to genome instability. The persistence of DPCs is associated with premature ageing, cancer and neurodegeneration. In mammalian cells, the repair of DPCs mainly relies on the proteolytic activities of SPRTN and the 26S proteasome, complemented by other enzymes including TDP1/2 and the MRN complex, and many of the activities involved are essential, restricting genetic approaches. For many years, the study of DPC repair in mammalian cells was hindered by the lack of standardised assays, most notably assays that reliably quantified the proteins or proteolytic fragments covalently bound to DNA. Recent interest in the field has spurred the development of several biochemical methods for DPC analysis. Here, we critically analyse the latest techniques for DPC isolation and the benefits and drawbacks of each. We aim to assist researchers in selecting the most suitable isolation method for their experimental requirements and questions, and to facilitate the comparison of results across different laboratories using different approaches.
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Affiliation(s)
- Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Nancy Maizels
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
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Anticevic I, Otten C, Vinkovic L, Jukic L, Popovic M. Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinks in vivo. Open Biol 2023; 13:230113. [PMID: 37788708 PMCID: PMC10547559 DOI: 10.1098/rsob.230113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
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Affiliation(s)
- Ivan Anticevic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Cecile Otten
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Vinkovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Jukic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Marta Popovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
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6
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Sun Y, Nitiss JL, Pommier Y. Editorial: The repair of DNA-protein crosslinks. Front Mol Biosci 2023; 10:1203479. [PMID: 37187895 PMCID: PMC10175854 DOI: 10.3389/fmolb.2023.1203479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Affiliation(s)
- Yilun Sun
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss, ; Yves Pommier,
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7
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Abstract
Topoisomerases are enzymes that play essential roles in DNA replication, transcription, chromosome segregation, and recombination. All cells have two major forms of DNA topoisomerases: type I enzymes, which make single-stranded cuts in DNA, and type II enzymes, which cut and decatenate double-stranded DNA. DNA topoisomerases are important targets of approved and experimental anti-cancer agents. Provided in this article are protocols to assess activities of topoisomerases and their inhibitors. Included are an assay for topoisomerase I activity based on relaxation of supercoiled DNA; an assay for topoisomerase II based on the decatenation of double-stranded DNA; and approaches for enriching and quantifying DNA-protein covalent complexes formed as obligatory intermediates in the reactions of type I and II topoisomerases with DNA; and assays for measuring DNA cleavage in vitro. Topoisomerases are not the only proteins that form covalent adducts with DNA in living cells, and the approaches described here are likely to find use in characterizing other protein-DNA adducts and exploring their utility as targets for therapy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Assay of topoisomerase I activity Basic Protocol 2: Assay of topoisomerase II activity Basic Protocol 3: In vivo determination of topoisomerase covalent complexes using the in vivo complex of enzyme (ICE) assay Support Protocol 1: Preparation of mouse tissue for determination of topoisomerase covalent complexes using the ICE assay Support Protocol 2: Using recombinant topoisomerase standard for absolute quantification of cellular TOP2CC Basic Protocol 4: Quantification of topoisomerase-DNA covalent complexes by RADAR/ELISA: The rapid approach to DNA adduct recovery (RADAR) combined with the enzyme-linked immunosorbent assay (ELISA) Basic Protocol 5: Analysis of protein-DNA covalent complexes by RADAR/Western Support Protocol 3: Adduct-Seq to characterize adducted DNA Support Protocol 4: Nuclear fractionation and RNase treatment to reduce sample complexity Basic Protocol 6: Determination of DNA cleavage by purified topoisomerase I Basic Protocol 7: Determination of inhibitor effects on DNA cleavage by topoisomerase II using a plasmid linearization assay Alternate Protocol: Gel electrophoresis determination of topoisomerase II cleavage.
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Affiliation(s)
- John L Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, Illinois
| | - Kostantin Kiianitsa
- Departments of Immunology and Biochemistry, University of Washington, Seattle, Washington
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Karin C Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, Illinois.,Biomedical Sciences Department, University of Illinois College of Medicine, Rockford, Illinois
| | - Nancy Maizels
- Departments of Immunology and Biochemistry, University of Washington, Seattle, Washington
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8
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Bin-Jumah M, Abdel-Fattah AFM, Saied EM, El-Seedi HR, Abdel-Daim MM. Acrylamide-induced peripheral neuropathy: manifestations, mechanisms, and potential treatment modalities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:13031-13046. [PMID: 33484463 DOI: 10.1007/s11356-020-12287-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/28/2020] [Indexed: 05/10/2023]
Abstract
Acrylamide is a chemical monomer; its polymer compounds are used in the manufacture of plastic, papers, adhesive tapes, dyes, and food packaging. Lately, scientists found that cooking (mainly roasting, baking, and frying) yields acrylamide. In addition to fried/baked potatoes, coffee and bakery products still contain substantial amounts of acrylamide. Acrylamide has toxic effects on different body systems include genitourinary, reproductive, nervous system, along with being a carcinogenic substance. The neurotoxicity of acrylamide includes central and peripheral neuropathy. In humans, the clinical manifestations include sensory or motor peripheral neuropathy, drowsiness, or cerebellar ataxia. Likewise, it presents with skeletal muscle weakness, hindlimb dysfunction, ataxia, and weight loss in animals. The suggested mechanisms for acrylamide neurotoxicity include direct inhibition of neurotransmission, cellular changes, inhibition of key cellular enzymes, and bonding of kinesin-based fast axonal transport. Moreover, it is suggested that acrylamide's molecular effect on SNARE core kinetics is carried out through the adduction of NSF and/or SNARE proteins. Lately, scientists showed disruption of focal adhesion kinase (FAK) and proline-rich tyrosine kinase 2 (Pyk2) cell signaling pathways in human differentiating neuroblastoma SH-SY5Y cells, exposed to acrylamide. Different treatment modalities have been revealed to shield against or hasten recovery from acrylamide-induced neuropathy in preclinical studies, including phytochemical, biological, and vitamin-based compounds. Still, additional studies are needed to elucidate the pathogenesis and to identify the best treatment modality.
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Affiliation(s)
- May Bin-Jumah
- Biology Department, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Essa M Saied
- Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - Hesham R El-Seedi
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, BMC, Uppsala University, SE-751 23, Uppsala, Sweden
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang, 212013, China
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom, 32511, Egypt
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt.
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
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9
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Kiianitsa K, Zhang Y, Maizels N. Treatment of human cells with 5-aza-dC induces formation of PARP1-DNA covalent adducts at genomic regions targeted by DNMT1. DNA Repair (Amst) 2020; 96:102977. [PMID: 33039802 DOI: 10.1016/j.dnarep.2020.102977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022]
Abstract
The nucleoside analog 5-aza-2'-deoxycytidine (5-aza-dC) is used to treat some hematopoietic malignancies. The mechanism of cell killing depends upon DNMT1, but is otherwise not clearly defined. Here we show that PARP1 forms covalent DNA adducts in human lymphoblast or fibroblasts treated with 5-aza-dC. Some adducts recovered from 5-aza-dC-treated cells have undergone cleavage by apoptotic caspases 3/7. Mapping of PARP1-DNA adducts, by a new method, "Adduct-Seq", demonstrates adduct enrichment at CpG-dense genomic locations that are targets of maintenance methylation by DNMT1. Covalent protein-DNA adducts can arrest replication and induce apoptosis, and these results raise the possibility that induction of PARP1-DNA adducts may contribute to cell killing in response to treatment with 5-aza-dC.
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Affiliation(s)
| | - Yinbo Zhang
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
| | - Nancy Maizels
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
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Sinha D, Kiianitsa K, Sherman DR, Maizels N. Rapid, direct detection of bacterial topoisomerase 1-DNA adducts by RADAR/ELISA. Anal Biochem 2020; 608:113827. [PMID: 32738213 DOI: 10.1016/j.ab.2020.113827] [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: 04/02/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 10/23/2022]
Abstract
Topoisomerases are proven drug targets, but antibiotics that poison bacterial Topoisomerase 1 (Top1) have yet to be discovered. We have developed a rapid and direct assay for quantification of Top1-DNA adducts that is suitable for high throughput assays. Adducts are recovered by "RADAR fractionation", a quick, convenient approach in which cells are lysed in chaotropic salts and detergent and nucleic acids and covalently bound adducts then precipitated with alcohol. Here we show that RADAR fractionation followed by ELISA immunodetection can quantify adducts formed by wild-type and mutant Top1 derivatives encoded by two different bacterial pathogens, Y. pestis and M. tuberculosis, expressed in E. coli or M. smegmatis, respectively. For both enzymes, quantification of adducts by RADAR/ELISA produces results comparable to the more cumbersome classical approach of CsCl density gradient fractionation. The experiments reported here establish that RADAR/ELISA assay offers a simple way to characterize Top1 mutants and analyze kinetics of adduct formation and repair. They also provide a foundation for discovery and optimization of drugs that poison bacterial Top1 using standard high-throughput approaches.
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Affiliation(s)
- Devapriya Sinha
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA.
| | - David R Sherman
- Department of Microbiology, University of Washington, 815 Republican St., Seattle, WA, 98102, USA
| | - Nancy Maizels
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA; Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
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