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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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2
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Warren GM, Shuman S. Structure and in vivo psoralen DNA crosslink repair activity of mycobacterial Nei2. mBio 2024; 15:e0124824. [PMID: 39012146 PMCID: PMC11323726 DOI: 10.1128/mbio.01248-24] [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: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 07/17/2024] Open
Abstract
Mycobacterium smegmatis Nei2 is a monomeric enzyme with AP β-lyase activity on single-stranded DNA. Expression of Nei2, and its operonic neighbor Lhr (a tetrameric 3'-to-5' helicase), is induced in mycobacteria exposed to DNA damaging agents. Here, we find that nei2 deletion sensitizes M. smegmatis to killing by DNA inter-strand crosslinker trimethylpsoralen but not to crosslinkers mitomycin C and cisplatin. By contrast, deletion of lhr sensitizes to killing by all three crosslinking agents. We report a 1.45 Å crystal structure of recombinant Nei2, which is composed of N and C terminal lobes flanking a central groove suitable for DNA binding. The C lobe includes a tetracysteine zinc complex. Mutational analysis identifies the N-terminal proline residue (Pro2 of the ORF) and Lys51, but not Glu3, as essential for AP lyase activity. We find that Nei2 has 5-hydroxyuracil glycosylase activity on single-stranded DNA that is effaced by alanine mutations of Glu3 and Lys51 but not Pro2. Testing complementation of psoralen sensitivity by expression of wild-type and mutant nei2 alleles in ∆nei2 cells established that AP lyase activity is neither sufficient nor essential for crosslink repair. By contrast, complementation of psoralen sensitivity of ∆lhr cells by mutant lhr alleles depended on Lhr's ATPase/helicase activities and its tetrameric quaternary structure. The lhr-nei2 operon comprises a unique bacterial system to rectify inter-strand crosslinks.IMPORTANCEThe DNA inter-strand crosslinking agents mitomycin C, cisplatin, and psoralen-UVA are used clinically for the treatment of cancers and skin diseases; they have been invaluable in elucidating the pathways of inter-strand crosslink repair in eukaryal systems. Whereas DNA crosslinkers are known to trigger a DNA damage response in bacteria, the roster of bacterial crosslink repair factors is incomplete and likely to vary among taxa. This study implicates the DNA damage-inducible mycobacterial lhr-nei2 gene operon in protecting Mycobacterium smegmatis from killing by inter-strand crosslinkers. Whereas interdicting the activity of the Lhr helicase sensitizes mycobacteria to mitomycin C, cisplatin, and psoralen-UVA, the Nei2 glycosylase functions uniquely in evasion of damage caused by psoralen-UVA.
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Affiliation(s)
- Garrett M. Warren
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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3
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Kligfeld H, Han I, Abraham A, Shukla V. Alternative DNA structures in hematopoiesis and adaptive immunity. Adv Immunol 2024; 161:109-126. [PMID: 38763699 DOI: 10.1016/bs.ai.2024.03.002] [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] [Indexed: 05/21/2024]
Abstract
Besides the canonical B-form, DNA also adopts alternative non-B form conformations which are highly conserved in all domains of life. While extensive research over decades has centered on the genomic functions of B-form DNA, understanding how non-B-form conformations influence functional genomic states remains a fundamental and open question. Recent studies have ascribed alternative DNA conformations such as G-quadruplexes and R-loops as important functional features in eukaryotic genomes. This review delves into the biological importance of alternative DNA structures, with a specific focus on hematopoiesis and adaptive immunity. We discuss the emerging roles of G-quadruplex and R-loop structures, the two most well-studied alternative DNA conformations, in the hematopoietic compartment and present evidence for their functional roles in normal cellular physiology and associated pathologies.
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Affiliation(s)
- Heather Kligfeld
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Isabella Han
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, United States.
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4
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [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: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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5
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Bellani MA, Huang J, Zhang J, Gali H, Thazhathveetil AK, Pokharel D, Majumdar I, Shaik A, Seidman MM. Imaging the cellular response to an antigen tagged interstrand crosslinking agent. DNA Repair (Amst) 2023; 128:103525. [PMID: 37320956 PMCID: PMC10413329 DOI: 10.1016/j.dnarep.2023.103525] [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: 04/02/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
Immunofluorescence imaging is a standard experimental tool for monitoring the response of cellular factors to DNA damage. Visualizing the recruitment of DNA Damage Response (DDR) components requires high affinity antibodies, which are generally available. In contrast, reagents for the display of the lesions that induce the response are far more limited. Consequently, DDR factor accumulation often serves as a surrogate for damage, without reporting the actual inducing structure. This limitation has practical implications given the importance of the response to DNA reactive drugs such as those used in cancer therapy. These include interstrand crosslink (ICL) forming compounds which are frequently employed clinically. Among them are the psoralens, natural products that form ICLs upon photoactivation and applied therapeutically since antiquity. However, despite multiple attempts, antibodies against psoralen ICLs have not been developed. To overcome this limitation, we developed a psoralen tagged with an antigen for which there are commercial antibodies. In this report we describe our application of the tagged psoralen in imaging experiments, and the unexpected discoveries they revealed.
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Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Jing Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD 21703, USA
| | | | | | - Ishani Majumdar
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA.
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6
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Jha JS, Yin J, Haldar T, Wang Y, Gates KS. Reconsidering the Chemical Nature of Strand Breaks Derived from Abasic Sites in Cellular DNA: Evidence for 3'-Glutathionylation. J Am Chem Soc 2022; 144:10471-10482. [PMID: 35612610 DOI: 10.1021/jacs.2c02703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hydrolytic loss of coding bases from cellular DNA is a common and unavoidable reaction. The resulting abasic sites can undergo β-elimination of the 3'-phosphoryl group to generate a strand break with an electrophilic α,β-unsaturated aldehyde residue on the 3'-terminus. The work reported here provides evidence that the thiol residue of the cellular tripeptide glutathione rapidly adds to the alkenal group on the 3'-terminus of an AP-derived strand break. The resulting glutathionylated adduct is the only major cleavage product observed when β-elimination occurs at an AP site in the presence of glutathione. Formation of the glutathionylated cleavage product is reversible, but in the presence of physiological concentrations of glutathione, the adduct persists for days. Biochemical experiments provided evidence that the 3'-phosphodiesterase activity of the enzyme apurinic/apyrimidinic endonuclease (APE1) can remove the glutathionylated sugar remnant from an AP-derived strand break to generate the 3'OH residue required for repair via base excision or single-strand break repair pathways. The results suggest that a previously unrecognized 3'glutathionylated sugar remnant─and not the canonical α,β-unsaturated aldehyde end group─may be the true strand cleavage product arising from β-elimination at an abasic site in cellular DNA. This work introduces the 3'glutathionylated cleavage product as the major blocking group that must be trimmed to enable repair of abasic site-derived strand breaks by the base excision repair or single-strand break repair pathways.
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7
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Housh K, Jha JS, Yang Z, Haldar T, Johnson KM, Yin J, Wang Y, Gates KS. Formation and Repair of an Interstrand DNA Cross-Link Arising from a Common Endogenous Lesion. J Am Chem Soc 2021; 143:15344-15357. [PMID: 34516735 DOI: 10.1021/jacs.1c06926] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interstrand DNA cross-links (ICLs) are cytotoxic because they block the strand separation required for read-out and replication of the genetic information in duplex DNA. The unavoidable formation of ICLs in cellular DNA may contribute to aging, neurodegeneration, and cancer. Here, we describe the formation and properties of a structurally complex ICL derived from an apurinic/apyrimidinic (AP) site, which is one of the most common endogenous lesions in cellular DNA. The results characterize a cross-link arising from aza-Michael addition of the N2-amino group of a guanine residue to the electrophilic sugar remnant generated by spermine-mediated strand cleavage at an AP site in duplex DNA. An α,β-unsaturated iminium ion is the critical intermediate involved in ICL formation. Studies employing the bacteriophage φ29 polymerase provided evidence that this ICL can block critical DNA transactions that require strand separation. The results of biochemical studies suggest that this complex strand break/ICL might be repaired by a simple mechanism in which the 3'-exonuclease action of the enzyme apurinic/apyrimidinic endonuclease (APE1) unhooks the cross-link to initiate repair via the single-strand break repair pathway.
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Affiliation(s)
- Kurt Housh
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Jay S Jha
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Tuhin Haldar
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Kevin M Johnson
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Jiekai Yin
- Department of Chemistry University of California-Riverside Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry University of California-Riverside Riverside, California 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States.,University of Missouri Department of Biochemistry 125 Chemistry Building Columbia, Missouri 65211, United States
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8
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Zhang J, Bellani MA, Huang J, James RC, Pokharel D, Gichimu J, Gali H, Stewart G, Seidman MM. Replication of the Mammalian Genome by Replisomes Specific for Euchromatin and Heterochromatin. Front Cell Dev Biol 2021; 9:729265. [PMID: 34532320 PMCID: PMC8438199 DOI: 10.3389/fcell.2021.729265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
Abstract
Replisomes follow a schedule in which replication of DNA in euchromatin is early in S phase while sequences in heterochromatin replicate late. Impediments to DNA replication, referred to as replication stress, can stall replication forks triggering activation of the ATR kinase and downstream pathways. While there is substantial literature on the local consequences of replisome stalling-double strand breaks, reversed forks, or genomic rearrangements-there is limited understanding of the determinants of replisome stalling vs. continued progression. Although many proteins are recruited to stalled replisomes, current models assume a single species of "stressed" replisome, independent of genomic location. Here we describe our approach to visualizing replication fork encounters with the potent block imposed by a DNA interstrand crosslink (ICL) and our discovery of an unexpected pathway of replication restart (traverse) past an intact ICL. Additionally, we found two biochemically distinct replisomes distinguished by activity in different stages of S phase and chromatin environment. Each contains different proteins that contribute to ICL traverse.
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Affiliation(s)
- Jing Zhang
- Department of Neurosurgery, Institute for Advanced Study, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Marina A. Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jing Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, China
| | - Ryan C. James
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Durga Pokharel
- Horizon Discovery Group plc, Lafayette, CO, United States
| | - Julia Gichimu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Grant Stewart
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, United Kingdom
| | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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9
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Baptista MS, Cadet J, Greer A, Thomas AH. Photosensitization Reactions of Biomolecules: Definition, Targets and Mechanisms. Photochem Photobiol 2021; 97:1456-1483. [PMID: 34133762 DOI: 10.1111/php.13470] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/13/2021] [Indexed: 02/07/2023]
Abstract
Photosensitization reactions have been demonstrated to be largely responsible for the deleterious biological effects of UV and visible radiation, as well as for the curative actions of photomedicine. A large number of endogenous and exogenous photosensitizers, biological targets and mechanisms have been reported in the past few decades. Evolving from the original definitions of the type I and type II photosensitized oxidations, we now provide physicochemical frameworks, classifications and key examples of these mechanisms in order to organize, interpret and understand the vast information available in the literature and the new reports, which are in vigorous growth. This review surveys in an extended manner all identified photosensitization mechanisms of the major biomolecule groups such as nucleic acids, proteins, lipids bridging the gap with the subsequent biological processes. Also described are the effects of photosensitization in cells in which UVA and UVB irradiation triggers enzyme activation with the subsequent delayed generation of superoxide anion radical and nitric oxide. Definitions of photosensitized reactions are identified in biomolecules with key insights into cells and tissues.
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Affiliation(s)
| | - Jean Cadet
- Département de Médecine Nucléaire et de Radiobiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, Brooklyn, NY, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Andrés H Thomas
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CCT La Plata-CONICET, La Plata, Argentina
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10
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Varela JG, Pierce LE, Guo X, Price NE, Johnson KM, Yang Z, Wang Y, Gates KS. Interstrand Cross-Link Formation Involving Reaction of a Mispaired Cytosine Residue with an Abasic Site in Duplex DNA. Chem Res Toxicol 2021; 34:1124-1132. [PMID: 33784065 PMCID: PMC8650171 DOI: 10.1021/acs.chemrestox.1c00004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of interstrand cross-links in duplex DNA is important in biology, medicine, and biotechnology. Interstrand cross-links arising from the reaction of the aldehyde residue of an abasic (apurinic or AP) site with the exocyclic amino groups of guanine or adenine residues on the opposing strand of duplex DNA have previously been characterized. The canonical nucleobase cytosine has an exocyclic amino group but its ability to form interstrand cross-links by reaction with an AP site has not been characterized before now. Here it is shown that substantial yields of interstrand cross-links are generated in sequences having a mispaired cytosine residue located one nucleotide to the 3'-side of the AP site on the opposing strand (e.g., 5'XA/5'CA, where X = AP). Formation of the dC-AP cross-link is pH-dependent, with significantly higher yields at pH 5 than pH 7. Once formed, the dC-AP cross-link is quite stable, showing less than 5% dissociation over the course of 96 h at pH 7 and 37 °C. No significant yields of cross-link are observed when the cytosine residue is paired with its Watson-Crick partner guanine. It was also shown that a single AP site can engage with multiple nucleobase cross-linking partners in some sequences. Specifically, the dG-AP and dC-AP cross-links coexist in dynamic equilibrium in the sequence 5'CXA/5'CAG (X = AP). In this sequence, the dC-AP cross-link dominates. However, in the presence of NaBH3CN, irreversible reduction of small amounts of the dG-AP cross-link present in the mixture shifts the equilibria away from the dC-AP cross-link toward good yields of the dG-APred cross-link.
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Affiliation(s)
- Jacqueline Gamboa Varela
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Luke E. Pierce
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Xu Guo
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Nathan E. Price
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
- Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Kevin M. Johnson
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Zhiyu Yang
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
- University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States
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11
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James RC, Bellani MA, Zhang J, Huang J, Shaik A, Pokharel D, Gali H, Gichimu J, Thazhathveetil AK, Seidman MM. Visualizing replication fork encounters with DNA interstrand crosslinks. Methods Enzymol 2021; 661:53-75. [PMID: 34776223 PMCID: PMC10035509 DOI: 10.1016/bs.mie.2021.08.015] [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] [Indexed: 03/25/2023]
Abstract
Replication forks encounter numerous challenges as they move through eu- and hetero-chromatin during S phase in mammalian cells. These include a variety of impediments to the unwinding of DNA by the replicative helicase such as alternate DNA structures, transcription complexes and R-loops, DNA-protein complexes, and DNA chemical adducts. Much of our knowledge of these events is based on analysis of markers of the replication stress and DNA Damage Response that follow stalling of replisomes. To examine consequences for the replisomes more directly, we developed an approach for imaging collisions of replication forks with the potent block presented by an interstrand crosslink (ICL). The strategy is based on the visualization on DNA fibers of the encounter of replication tracts and an antigen tagged ICL. Our studies revealed an unexpected restart of DNA synthesis past an intact ICL. In addition, and also unexpected, we found two distinct versions of the replisome, one biased toward euchromatin and the other more prominent in heterochromatin. Here, we present details of our experimental procedures that led to these observations.
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Affiliation(s)
- Ryan C James
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Marina A Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jing Huang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, China
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | | | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Julia Gichimu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | | | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States.
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12
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Hartman CJ, Mester JC, Hare PM, Cohen AI. Novel inactivation of the causative fungal pathogen of white-nose syndrome with methoxsalen plus ultraviolet A or B radiation. PLoS One 2020; 15:e0239001. [PMID: 32915896 PMCID: PMC7485863 DOI: 10.1371/journal.pone.0239001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/27/2020] [Indexed: 12/03/2022] Open
Abstract
White-nose syndrome is a fungal disease responsible for the rapid decline of North American bat populations. This study addressed a novel method for inactivating Pseudogymnoascus destructans, the causative agent of WNS, using ultraviolet A (UVA) or B (UVB) radiation in combination with methoxsalen, a photosensitizer from the furanocoumarin family of compounds. Fungal spore suspensions were diluted in micromolar concentrations of methoxsalen (50–500 μM), then exposed to fixed doses of UVA radiation (500–5000 mJ/cm2), followed by plating on germination media. These plates were examined for two to four weeks for evidence of spore germination or inactivation, along with resultant growth or inhibition of P. destructans colonies. Pretreatment of fungal spores with low doses of methoxsalen resulted in a UVA dose-dependent inactivation of the P. destructans spores. All doses of methoxsalen paired with 500 mJ/cm2 of UVA led to an approximate two-log10 (~99%) reduction in spore viability, and when paired with 1000 mJ/cm2, a four-log10 or greater (>99.99%) reduction in spore viability was observed. Additionally, actively growing P. destructans colonies treated directly with methoxsalen and either UVA or UVB radiation demonstrated UV dose-dependent inhibition and termination of colony growth. This novel approach of using a photosensitizer in combination with UV radiation to control fungal growth may have broad, practical application in the future.
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Affiliation(s)
- Colin J. Hartman
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Joseph C. Mester
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, United States of America
- * E-mail:
| | - Patrick M. Hare
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky, United States of America
| | - Alan I. Cohen
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, United States of America
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13
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Zhang Y, Zhang X, Zhang W, Zhang W. Effects of Psoralen on Histone-DNA Interactions Studied by Using Atomic Force Microscopy. Macromol Rapid Commun 2020; 41:e2000017. [PMID: 32686170 DOI: 10.1002/marc.202000017] [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: 01/07/2020] [Revised: 06/26/2020] [Indexed: 11/09/2022]
Abstract
The investigation of the DNA-histone interactions and factors that affect such interactions in the nucleosome is essential for understanding the role of chromatin organization in all cellular processes involved in the repair, transcription, and replication of the eukaryotic genome. As a kind of photosensitive molecule, psoralen (PSO) is used in the treatment of skin disease with ultraviolet light (PSO and ultra violet light, type A). The effect of treatment is remarkable, but the side effect is also obvious. PSO can be embedded in a 5' TA sequence in double-stranded DNA (dsDNA), and dsDNA is mainly wrapped around a histone octamer to form a nucleosome structure in human cells. Therefore, it is very necessary to explore the influence of PSO on DNA-histone interactions. To this end, the binding specificity and mode of DNA and histone in the presence or absence of PSO are investigated systematically. The results show that the presence of PSO (no matter if there is ultra violet light treatment) can increase the overall probability of histone binding to dsDNA while lowering the selectivity of histone binding to the specific DNA sequence in vitro. In addition, the increase of solution ionic strength can lower the ratio of histone binding to nonspecific DNA.
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Affiliation(s)
- Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Wei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
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14
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Sabatella M, Pines A, Slyskova J, Vermeulen W, Lans H. ERCC1-XPF targeting to psoralen-DNA crosslinks depends on XPA and FANCD2. Cell Mol Life Sci 2020; 77:2005-2016. [PMID: 31392348 PMCID: PMC7228994 DOI: 10.1007/s00018-019-03264-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/19/2019] [Accepted: 07/31/2019] [Indexed: 01/02/2023]
Abstract
The effectiveness of many DNA-damaging chemotherapeutic drugs depends on their ability to form monoadducts, intrastrand crosslinks and/or interstrand crosslinks (ICLs) that interfere with transcription and replication. The ERCC1-XPF endonuclease plays a critical role in removal of these lesions by incising DNA either as part of nucleotide excision repair (NER) or interstrand crosslink repair (ICLR). Engagement of ERCC1-XPF in NER is well characterized and is facilitated by binding to the XPA protein. However, ERCC1-XPF recruitment to ICLs is less well understood. Moreover, specific mutations in XPF have been found to disrupt its function in ICLR but not in NER, but whether this involves differences in lesion targeting is unknown. Here, we imaged GFP-tagged ERCC1, XPF and ICLR-defective XPF mutants to investigate how in human cells ERCC1-XPF is localized to different types of psoralen-induced DNA lesions, repaired by either NER or ICLR. Our results confirm its dependence on XPA in NER and furthermore show that its engagement in ICLR is dependent on FANCD2. Interestingly, we find that two ICLR-defective XPF mutants (R689S and S786F) are less well recruited to ICLs. These studies highlight the differential mechanisms that regulate ERCC1-XPF activity in DNA repair.
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Affiliation(s)
- Mariangela Sabatella
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
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15
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Slowly Repaired Bulky DNA Damages Modulate Cellular Redox Environment Leading to Premature Senescence. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:5367102. [PMID: 32104534 PMCID: PMC7035574 DOI: 10.1155/2020/5367102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/23/2020] [Indexed: 11/17/2022]
Abstract
Treatments on neoplastic diseases and cancer using genotoxic drugs often cause long-term health problems related to premature aging. The underlying mechanism is poorly understood. Based on the study of a long-lasting senescence-like growth arrest (10-12 weeks) of human dermal fibroblasts induced by psoralen plus UVA (PUVA) treatment, we here revealed that slowly repaired bulky DNA damages can serve as a “molecular scar” leading to reduced cell proliferation through persistent endogenous production of reactive oxygen species (ROS) that caused accelerated telomere erosion. The elevated levels of ROS were the results of mitochondrial dysfunction and the activation of NADPH oxidase (NOX). A combined inhibition of DNA-PK and PARP1 could suppress the level of ROS. Together with a reduced expression level of BRCA1 as well as the upregulation of PP2A and 53BP1, these data suggest that the NHEJ repair of DNA double-strand breaks may be the initial trigger of metabolic changes leading to ROS production. Further study showed that stimulation of the pentose phosphate pathway played an important role for NOX activation, and ROS could be efficiently suppressed by modulating the NADP/NADPH ratio. Interestingly, feeding cells with ribose-5-phosphate, a precursor for nucleotide biosynthesis that produced through the PPP, could evidently suppress the ROS level and prevent the cell enlargement related to mitochondrial biogenesis. Taken together, these results revealed an important signaling pathway between DNA damage repair and the cell metabolism, which contributed to the premature aging effects of PUVA, and may be generally applicable for a large category of chemotherapeutic reagents including many cancer drugs.
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16
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Pathogen reduction of blood components during outbreaks of infectious diseases in the European Union: an expert opinion from the European Centre for Disease Prevention and Control consultation meeting. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2019; 17:433-448. [PMID: 31846608 DOI: 10.2450/2019.0288-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022]
Abstract
Pathogen reduction (PR) of selected blood components is a technology that has been adopted in practice in various ways. Although they offer great advantages in improving the safety of the blood supply, these technologies have limitations which hinder their broader use, e.g. increased costs. In this context, the European Centre for Disease Prevention and Control (ECDC), in co-operation with the Italian National Blood Centre, organised an expert consultation meeting to discuss the potential role of pathogen reduction technologies (PRT) as a blood safety intervention during outbreaks of infectious diseases for which (in most cases) laboratory screening of blood donations is not available. The meeting brought together 26 experts and representatives of national competent authorities for blood from thirteen European Union and European Economic Area (EU/EEA) Member States (MS), Switzerland, the World Health Organization, the European Directorate for the Quality of Medicines and Health Care of the Council of Europe, the US Food and Drug Administration, and the ECDC. During the meeting, the current use of PRTs in the EU/EEA MS and Switzerland was verified, with particular reference to emerging infectious diseases (see Appendix). In this article, we also present expert discussions and a common view on the potential use of PRT as a part of both preparedness and response to threats posed to blood safety by outbreaks of infectious disease.
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17
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Mutreja K, Krietsch J, Hess J, Ursich S, Berti M, Roessler FK, Zellweger R, Patra M, Gasser G, Lopes M. ATR-Mediated Global Fork Slowing and Reversal Assist Fork Traverse and Prevent Chromosomal Breakage at DNA Interstrand Cross-Links. Cell Rep 2019; 24:2629-2642.e5. [PMID: 30184498 PMCID: PMC6137818 DOI: 10.1016/j.celrep.2018.08.019] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/26/2018] [Accepted: 08/07/2018] [Indexed: 01/02/2023] Open
Abstract
Interstrand cross-links (ICLs) are toxic DNA lesions interfering with DNA metabolism that are induced by widely used anticancer drugs. They have long been considered absolute roadblocks for replication forks, implicating complex DNA repair processes at stalled or converging replication forks. Recent evidence challenged this view, proposing that single forks traverse ICLs by yet elusive mechanisms. Combining ICL immunolabeling and single-molecule approaches in human cells, we now show that ICL induction leads to global replication fork slowing, involving forks not directly challenged by ICLs. Active fork slowing is linked to rapid recruitment of RAD51 to replicating chromatin and to RAD51/ZRANB3-mediated fork reversal. This global modulation of fork speed and architecture requires ATR activation, promotes single-fork ICL traverse—here, directly visualized by electron microscopy—and prevents chromosomal breakage by untimely ICL processing. We propose that global fork slowing by remodeling provides more time for template repair and promotes bypass of residual lesions, limiting fork-associated processing. Fork slowing and reversal are also observed at forks not directly challenged by ICLs Fork reversal assists ICL traverse and limits DSBs associated with ICL unhooking ICL traverse can be directly visualized in human cells by electron microscopy ATR mediates global fork slowing and reversal upon different genotoxic treatments
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Affiliation(s)
- Karun Mutreja
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jeannine Hess
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Sebastian Ursich
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Matteo Berti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Fabienne K Roessler
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Center for Microscopy and Image Analysis, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ralph Zellweger
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Malay Patra
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Gilles Gasser
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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18
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Kremis SA, Baev DS, Lipeeva AV, Shults EE, Tolstikova TG, Sinitsyna OI, Kochetov AV, Frolova TS. Genotoxic activity of 1,2,3-triazolyl modified furocoumarins and 2,3-dihydrofurocoumarins. J Biochem Mol Toxicol 2019; 33:e22396. [PMID: 31557364 DOI: 10.1002/jbt.22396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/21/2019] [Accepted: 09/12/2019] [Indexed: 11/12/2022]
Abstract
The furocoumarin backbone is a promising platform for chemical modifications aimed at creating new pharmaceutical agents. However, the high level of biological activity of furocoumarins is associated with a number of negative effects. For example, some of the naturally occurring ones and their derivatives can show genotoxic and mutagenic properties as a result of their forming crosslinks with DNA molecules. Therefore, a particularly important area for the chemical modification of natural furocoumarins is to reduce the negative aspects of their bioactivity. By studying a group of 21 compounds-1,2,3-triazolyl modified derivatives of furocoumarin and peucedanin-using the SOS chromotest, the Ames test, and DNA-comet assays, we revealed modifications that can neutralize the structure's genotoxic properties. Theoretical aspects of the interaction of the compound library were studied using molecular modeling and this identified the leading role of the polyaromatic molecular core that takes part in stacking-interactions with the pi-systems of the nitrogenous bases of DNA.
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Affiliation(s)
- Stepan A Kremis
- Federal Research Center of Fundamental and Translational Medicine SB RAS, Novosibirsk, Russia
| | - Dmitry S Baev
- Novosibirsk State University, Novosibirsk, Russia.,Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Alla V Lipeeva
- Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Elvira E Shults
- Novosibirsk State University, Novosibirsk, Russia.,Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Tatiana G Tolstikova
- Novosibirsk State University, Novosibirsk, Russia.,Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Olga I Sinitsyna
- Novosibirsk State University, Novosibirsk, Russia.,Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Alexey V Kochetov
- Novosibirsk State University, Novosibirsk, Russia.,Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Tatiana S Frolova
- Federal Research Center of Fundamental and Translational Medicine SB RAS, Novosibirsk, Russia.,Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia.,Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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19
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Nejad MI, Price NE, Haldar T, Lewis C, Wang Y, Gates KS. Interstrand DNA Cross-Links Derived from Reaction of a 2-Aminopurine Residue with an Abasic Site. ACS Chem Biol 2019; 14:1481-1489. [PMID: 31259519 DOI: 10.1021/acschembio.9b00208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Efficient methods for the site-specific installation of structurally defined interstrand cross-links in duplex DNA may be useful in a wide variety of fields. The work described here developed a high-yield synthesis of chemically stable interstrand cross-links resulting from a reductive amination reaction between an abasic site and the noncanonical nucleobase 2-aminopurine in duplex DNA. Results from footprinting, liquid chromatography-mass spectrometry, and stability studies support the formation of an N2-alkylamine attachment between the 2-aminopurine residue and the Ap site. The reaction performs best when the 2-aminopurine residue on the opposing strand is offset 1 nt to the 5'-side of the abasic site. The cross-link confers substantial resistance to thermal denaturation (melting). The cross-linking reaction is fast (complete in 4 h), employs only commercially available reagents, and can be used to generate cross-linked duplexes in sufficient quantities for biophysical, structural, and DNA repair studies.
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Affiliation(s)
- Maryam Imani Nejad
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Tuhin Haldar
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Calvin Lewis
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
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20
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Bellani MA, Huang J, Paramasivam M, Pokharel D, Gichimu J, Zhang J, Seidman MM. Imaging cellular responses to antigen tagged DNA damage. DNA Repair (Amst) 2018; 71:183-189. [PMID: 30166246 PMCID: PMC6340790 DOI: 10.1016/j.dnarep.2018.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Repair pathways of covalent DNA damage are understood in considerable detail due to decades of brilliant biochemical studies by many investigators. An important feature of these experiments is the defined adduct location on oligonucleotide or plasmid substrates that are incubated with purified proteins or cell free extracts. With some exceptions, this certainty is lost when the inquiry shifts to the response of living mammalian cells to the same adducts in genomic DNA. This reflects the limitation of assays, such as those based on immunofluorescence, that are widely used to follow responding proteins in cells exposed to a DNA reactive compound. The lack of effective reagents for adduct detection means that the proximity between responding proteins and an adduct must be assumed. Since these assumptions can be incorrect, models based on in vitro systems may fail to account for observations made in vivo. Here we discuss the use of a detection tag to address the problem of lesion location, as illustrated by our recent work on replication dependent and independent responses to interstrand crosslinks.
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Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Jing Huang
- Institute of Chemical Biology and Nanomedicine, College of Biology, Hunan University, Changsha, 410082, China
| | - Manikandan Paramasivam
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Durga Pokharel
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Julia Gichimu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Jing Zhang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States.
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21
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Jalili Z, Saleh M, Bouzari S, Pooya M. Characterization of killed but metabolically active uropathogenic Escherichia coli strain as possible vaccine candidate for urinary tract infection. Microb Pathog 2018; 122:184-190. [DOI: 10.1016/j.micpath.2018.06.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/28/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022]
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22
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Cole JM, Acott JD, Courcelle CT, Courcelle J. Limited Capacity or Involvement of Excision Repair, Double-Strand Breaks, or Translesion Synthesis for Psoralen Cross-Link Repair in Escherichia coli. Genetics 2018; 210:99-112. [PMID: 30045856 PMCID: PMC6116958 DOI: 10.1534/genetics.118.301239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/18/2018] [Indexed: 02/06/2023] Open
Abstract
DNA interstrand cross-links are complex lesions that covalently bind complementary strands of DNA and whose mechanism of repair remains poorly understood. In Escherichia coli, several gene products have been proposed to be involved in cross-link repair based on the hypersensitivity of mutants to cross-linking agents. However, cross-linking agents induce several forms of DNA damage, making it challenging to attribute mutant hypersensitivity specifically to interstrand cross-links. To address this, we compared the survival of UVA-irradiated repair mutants in the presence of 8-methoxypsoralen-which forms interstrand cross-links and monoadducts-to that of angelicin-a congener forming only monoadducts. We show that incision by nucleotide excision repair is not required for resistance to interstrand cross-links. In addition, neither RecN nor DNA polymerases II, IV, or V is required for interstrand cross-link survival, arguing against models that involve critical roles for double-strand break repair or translesion synthesis in the repair process. Finally, estimates based on Southern analysis of DNA fragments in alkali agarose gels indicate that lethality occurs in wild-type cells at doses producing as few as one to two interstrand cross-links per genome. These observations suggest that E. coli may lack an efficient repair mechanism for this form of damage.
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Affiliation(s)
- Jessica M Cole
- Department of Biology, Portland State University, Oregon 97201
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23
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Feys HB, Van Aelst B, Compernolle V. Biomolecular Consequences of Platelet Pathogen Inactivation Methods. Transfus Med Rev 2018; 33:29-34. [PMID: 30021699 DOI: 10.1016/j.tmrv.2018.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/21/2022]
Abstract
Pathogen inactivation (PI) for platelet concentrates (PC) is a fairly recent development in transfusion medicine that is intended to decrease infectious disease transmission from the donor to the receiving patient. Effective inactivation of viruses, bacteria and eukaryotic parasites adds a layer of safety, protecting the blood supply against customary and emerging pathogens. Three PI methods have been described for platelets. These are based on photochemical damage of nucleic acids which prevents replication of most infectious pathogens and contaminating donor leukocytes. Because platelets do not replicate, the collateral damage to platelet function is considered low to non-existing. This is disputable however because photochemistry is not specific for nucleic acids and significantly affects platelet biomolecules as well. The impact of these biomolecular changes on platelet function and hemostasis is not well understood, but is increasingly being studied. The results of these studies can help explain current and future clinical observations with PI platelets, including the impact on transfusion yield and bleeding. This review summarizes the biomolecular effects of PI treatment on platelets. We conclude that despite a comparable principle of photochemical inactivation, all three methods affect platelets in different ways. This knowledge can help blood banks and transfusion specialists to guide their choice when considering the implementation or clinical use of PI treated platelets.
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Affiliation(s)
- Hendrik B Feys
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Britt Van Aelst
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Blood Service of the Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Veerle Compernolle
- Transfusion Research Center, Belgian Red Cross-Flanders, Ghent, Belgium; Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Blood Service of the Belgian Red Cross-Flanders, Mechelen, Belgium
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24
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Chesner LN, Degner A, Sangaraju D, Yomtoubian S, Wickramaratne S, Malayappan B, Tretyakova N, Campbell C. Cellular Repair of DNA-DNA Cross-Links Induced by 1,2,3,4-Diepoxybutane. Int J Mol Sci 2017; 18:ijms18051086. [PMID: 28524082 PMCID: PMC5454995 DOI: 10.3390/ijms18051086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/04/2017] [Accepted: 05/11/2017] [Indexed: 11/25/2022] Open
Abstract
Xenobiotic-induced interstrand DNA–DNA cross-links (ICL) interfere with transcription and replication and can be converted to toxic DNA double strand breaks. In this work, we investigated cellular responses to 1,4-bis-(guan-7-yl)-2,3-butanediol (bis-N7G-BD) cross-links induced by 1,2,3,4-diepoxybutane (DEB). High pressure liquid chromatography electrospray ionization tandem mass spectrometry (HPLC-ESI+-MS/MS) assays were used to quantify the formation and repair of bis-N7G-BD cross-links in wild-type Chinese hamster lung fibroblasts (V79) and the corresponding isogenic clones V-H1 and V-H4, deficient in the XPD and FANCA genes, respectively. Both V-H1 and V-H4 cells exhibited enhanced sensitivity to DEB-induced cell death and elevated bis-N7G-BD cross-links. However, relatively modest increases of bis-N7G-BD adduct levels in V-H4 clones did not correlate with their hypersensitivity to DEB. Further, bis-N7G-BD levels were not elevated in DEB-treated human clones with defects in the XPA or FANCD2 genes. Comet assays and γ-H2AX focus analyses conducted with hamster cells revealed that ICL removal was associated with chromosomal double strand break formation, and that these breaks persisted in V-H4 cells as compared to control cells. Our findings suggest that ICL repair in cells with defects in the Fanconi anemia repair pathway is associated with aberrant re-joining of repair-induced double strand breaks, potentially resulting in lethal chromosome rearrangements.
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Affiliation(s)
- Lisa N Chesner
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Amanda Degner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Dewakar Sangaraju
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Shira Yomtoubian
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Susith Wickramaratne
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Bhaskar Malayappan
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA.
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25
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Huang J, Gali H, Gichimu J, Bellani MA, Pokharel D, Paramasivam M, Seidman MM. Single Molecule Analysis of Laser Localized Psoralen Adducts. J Vis Exp 2017. [PMID: 28448050 DOI: 10.3791/55541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The DNA Damage Response (DDR) has been extensively characterized in studies of double strand breaks (DSBs) induced by laser micro beam irradiation in live cells. The DDR to helix distorting covalent DNA modifications, including interstrand DNA crosslinks (ICLs), is not as well defined. We have studied the DDR stimulated by ICLs, localized by laser photoactivation of immunotagged psoralens, in the nuclei of live cells. In order to address fundamental questions about adduct distribution and replication fork encounters, we combined laser localization with two other technologies. DNA fibers are often used to display the progress of replication forks by immunofluorescence of nucleoside analogues incorporated during short pulses. Immunoquantum dots have been widely employed for single molecule imaging. In the new approach, DNA fibers from cells carrying laser localized ICLs are spread onto microscope slides. The tagged ICLs are displayed with immunoquantum dots and the inter-lesion distances determined. Replication fork collisions with ICLs can be visualized and different encounter patterns identified and quantitated.
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Affiliation(s)
- Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Himabindu Gali
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Julia Gichimu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Durga Pokharel
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Manikandan Paramasivam
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health;
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26
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Yang Z, Nejad MI, Varela JG, Price NE, Wang Y, Gates KS. A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand DNA cross-links derived from psoralen and abasic sites. DNA Repair (Amst) 2017; 52:1-11. [PMID: 28262582 PMCID: PMC5424475 DOI: 10.1016/j.dnarep.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
Abstract
Interstrand DNA-DNA cross-links are highly toxic lesions that are important in medicinal chemistry, toxicology, and endogenous biology. In current models of replication-dependent repair, stalling of a replication fork activates the Fanconi anemia pathway and cross-links are "unhooked" by the action of structure-specific endonucleases such as XPF-ERCC1 that make incisions flanking the cross-link. This process generates a double-strand break, which must be subsequently repaired by homologous recombination. Recent work provided evidence for a new, incision-independent unhooking mechanism involving intrusion of a base excision repair (BER) enzyme, NEIL3, into the world of cross-link repair. The evidence suggests that the glycosylase action of NEIL3 unhooks interstrand cross-links derived from an abasic site or the psoralen derivative trioxsalen. If the incision-independent NEIL3 pathway is blocked, repair reverts to the incision-dependent route. In light of the new model invoking participation of NEIL3 in cross-link repair, we consider the possibility that various BER glycosylases or other DNA-processing enzymes might participate in the unhooking of chemically diverse interstrand DNA cross-links.
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Affiliation(s)
- Zhiyu Yang
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Maryam Imani Nejad
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Jacqueline Gamboa Varela
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Nathan E Price
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Yinsheng Wang
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States; University of Missouri Department of Biochemistry, 125 Chemistry Building Columbia, MO 65211, United States.
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Douki T, von Koschembahr A, Cadet J. Insight in DNA Repair of UV-induced Pyrimidine Dimers by Chromatographic Methods. Photochem Photobiol 2017; 93:207-215. [PMID: 27935042 DOI: 10.1111/php.12685] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/21/2016] [Indexed: 01/15/2023]
Abstract
UV-induced formation of pyrimidine dimers in DNA is a major deleterious event in both eukaryotic and prokaryotic cells. Accumulation of cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts can lead to cell death or be at the origin of mutations. In skin, UV induction of DNA damage is a major initiating event in tumorigenesis. To counteract these deleterious effects, all cell types possess DNA repair machinery, such as nucleotide excision repair and, in some cell types, direct reversion. Different analytical approaches were used to assess the efficiency of repair and decipher the enzymatic mechanisms. We presently review the information provided by chromatographic methods, which are complementary to biochemical assays, such as immunological detection and electrophoresis-based techniques. Chromatographic assays are interesting in their ability to provide quantitative data on a wide range of damage and are also valuable tools for the identification of repair intermediates.
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Affiliation(s)
- Thierry Douki
- Univ. Grenoble Alpes, INAC, LCIB, LAN, Grenoble, France.,CEA, INAC, SyMMES, LAN, Grenoble, France
| | - Anne von Koschembahr
- Univ. Grenoble Alpes, INAC, LCIB, LAN, Grenoble, France.,CEA, INAC, SyMMES, LAN, Grenoble, France
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
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28
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Van Aelst B, Devloo R, Zachée P, t'Kindt R, Sandra K, Vandekerckhove P, Compernolle V, Feys HB. Psoralen and Ultraviolet A Light Treatment Directly Affects Phosphatidylinositol 3-Kinase Signal Transduction by Altering Plasma Membrane Packing. J Biol Chem 2016; 291:24364-24376. [PMID: 27687726 DOI: 10.1074/jbc.m116.735126] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/17/2016] [Indexed: 01/15/2023] Open
Abstract
Psoralen and ultraviolet A light (PUVA) are used to kill pathogens in blood products and as a treatment of aberrant cell proliferation in dermatitis, cutaneous T-cell lymphoma, and graft-versus-host disease. DNA damage is well described, but the direct effects of PUVA on cell signal transduction are poorly understood. Because platelets are anucleate and contain archetypal signal transduction machinery, they are ideally suited to address this. Lipidomics on platelet membrane extracts showed that psoralen forms adducts with unsaturated carbon bonds of fatty acyls in all major phospholipid classes after PUVA. Such adducts increased lipid packing as measured by a blue shift of an environment-sensitive fluorescent probe in model liposomes. Furthermore, the interaction of these liposomes with lipid order-sensitive proteins like amphipathic lipid-packing sensor and α-synuclein was inhibited by PUVA. In platelets, PUVA caused poor membrane binding of Akt and Bruton's tyrosine kinase effectors following activation of the collagen glycoprotein VI and thrombin protease-activated receptor (PAR) 1. This resulted in defective Akt phosphorylation despite unaltered phosphatidylinositol 3,4,5-trisphosphate levels. Downstream integrin activation was furthermore affected similarly by PUVA following PAR1 (effective half-maximal concentration (EC50), 8.4 ± 1.1 versus 4.3 ± 1.1 μm) and glycoprotein VI (EC50, 1.61 ± 0.85 versus 0.26 ± 0.21 μg/ml) but not PAR4 (EC50, 50 ± 1 versus 58 ± 1 μm) signal transduction. Our findings were confirmed in T-cells from graft-versus-host disease patients treated with extracorporeal photopheresis, a form of systemic PUVA. In conclusion, PUVA increases the order of lipid phases by covalent modification of phospholipids, thereby inhibiting membrane recruitment of effector kinases.
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Affiliation(s)
- Britt Van Aelst
- From the Transfusion Research Center, Belgian Red Cross-Flanders, 9000 Ghent, Belgium
| | - Rosalie Devloo
- From the Transfusion Research Center, Belgian Red Cross-Flanders, 9000 Ghent, Belgium
| | - Pierre Zachée
- the Department of Hematology, Hospital Network Antwerp, 2000 Antwerp, Belgium
| | - Ruben t'Kindt
- the Research Institute for Chromatography, 8500 Kortrijk, Belgium
| | - Koen Sandra
- the Research Institute for Chromatography, 8500 Kortrijk, Belgium
| | - Philippe Vandekerckhove
- the Blood Service of the Belgian Red Cross-Flanders, 2800 Mechelen, Belgium,; the Department of Public Health and Primary Care, KULeuven, 3000 Leuven, Belgium, and; the Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Veerle Compernolle
- From the Transfusion Research Center, Belgian Red Cross-Flanders, 9000 Ghent, Belgium,; the Blood Service of the Belgian Red Cross-Flanders, 2800 Mechelen, Belgium,; the Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Hendrik B Feys
- From the Transfusion Research Center, Belgian Red Cross-Flanders, 9000 Ghent, Belgium,.
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Schmidt AE, Refaai MA, Blumberg N. Past, present and forecast of transfusion medicine: What has changed and what is expected to change? Presse Med 2016; 45:e253-72. [PMID: 27474234 DOI: 10.1016/j.lpm.2016.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Blood transfusion is the second most used medical procedures in health care systems worldwide. Over the last few decades, significant changes have been evolved in transfusion medicine practices. These changes were mainly needed to increase safety, efficacy, and availability of blood products as well as reduce recipients' unnecessary exposure to allogeneic blood. Blood products collection, processing, and storage as well as transfusion practices throughout all patient populations were the main stream of these changes. Health care systems across the world have adopted some or most of these changes to reduce transfusion risks, to improve overall patients' outcome, and to reduce health care costs. In this article, we are going to present and discuss some of these recent modifications and their impact on patients' safety.
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Affiliation(s)
- Amy E Schmidt
- University of Rochester medical center, department of pathology and laboratory medicine, 14642 Rochester, NY, USA
| | - Majed A Refaai
- University of Rochester medical center, department of pathology and laboratory medicine, 14642 Rochester, NY, USA
| | - Neil Blumberg
- University of Rochester medical center, department of pathology and laboratory medicine, 14642 Rochester, NY, USA.
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30
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Huang J, Gali H, Paramasivam M, Muniandy P, Gichimu J, Bellani MA, Seidman MM. Single Molecule Analysis of Laser Localized Interstrand Crosslinks. Front Genet 2016; 7:84. [PMID: 27242893 PMCID: PMC4860505 DOI: 10.3389/fgene.2016.00084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
DNA interstrand crosslinks (ICLs) block unwinding of the double helix, and have always been regarded as major challenges to replication and transcription. Compounds that form these lesions are very toxic and are frequently used in cancer chemotherapy. We have developed two strategies, both based on immunofluorescence (IF), for studying cellular responses to ICLs. The basis of each is psoralen, a photoactive (by long wave ultraviolet light, UVA) DNA crosslinking agent, to which we have linked an antigen tag. In the one approach, we have taken advantage of DNA fiber and immuno-quantum dot technologies for visualizing the encounter of replication forks with ICLs induced by exposure to UVA lamps. In the other, psoralen ICLs are introduced into nuclei in live cells in regions of interest defined by a UVA laser. The antigen tag can be displayed by conventional IF, as can the recruitment and accumulation of DNA damage response proteins to the laser localized ICLs. However, substantial difference between the technologies creates considerable uncertainty as to whether conclusions from one approach are applicable to those of the other. In this report, we have employed the fiber/quantum dot methodology to determine lesion density and spacing on individual DNA molecules carrying laser localized ICLs. We have performed the same measurements on DNA fibers with ICLs induced by exposure of psoralen to UVA lamps. Remarkably, we find little difference in the adduct distribution on fibers prepared from cells exposed to the different treatment protocols. Furthermore, there is considerable similarity in patterns of replication in the vicinity of the ICLs introduced by the two techniques.
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Affiliation(s)
- Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Himabindu Gali
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Manikandan Paramasivam
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Parameswary Muniandy
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Julia Gichimu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health Baltimore, MD, USA
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31
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Evison BJ, Actis ML, Fujii N. A clickable psoralen to directly quantify DNA interstrand crosslinking and repair. Bioorg Med Chem 2016; 24:1071-8. [PMID: 26833244 DOI: 10.1016/j.bmc.2016.01.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/06/2016] [Accepted: 01/17/2016] [Indexed: 11/26/2022]
Abstract
DNA interstrand crosslinks (ICLs) represent physical obstacles to advancing replication forks and transcription complexes. A range of ICL-inducing agents have successfully been incorporated into cancer therapeutics. While studies have adopted UVA-activated psoralens as model ICL-inducing agents for investigating ICL repair, direct detection of the lesion has often been tempered by tagging the psoralen scaffold with a relatively large reporter group that may perturb the biological activity of the parent psoralen. Here a minimally-modified psoralen probe was prepared featuring a small alkyne handle suitable for click chemistry. The psoralen probe, designated 8-propargyloxypsoralen (8-POP), can be activated by UVA in vitro to generate ICLs that are susceptible to post-labeling with an azide-tagged fluorescent reporter via a copper-catalyzed reaction. A modified alkaline comet assay demonstrated that UVA-activated 8-POP proficiently generated ICLs in cells. Cellular 8-POP-DNA lesions were amenable to click-mediated ligation to fluorescent reporters in situ, which permitted their detection and quantitation by fluorescence microscopy and flow cytometry. Small molecule DNA repair inhibitors to 8-POP-treated cells attenuated the removal of 8-POP-DNA lesions, validating 8-POP as an appropriate probe for investigating cellular ICL repair. The post-labeling strategy applied in this study is inexpensive, rapid and highly modular in nature with the potential for multiple applications in DNA repair studies.
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Affiliation(s)
- Benjamin J Evison
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marcelo L Actis
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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32
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Improving platelet transfusion safety: biomedical and technical considerations. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2015; 14:109-22. [PMID: 26674828 DOI: 10.2450/2015.0042-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/16/2015] [Indexed: 12/25/2022]
Abstract
Platelet concentrates account for near 10% of all labile blood components but are responsible for more than 25% of the reported adverse events. Besides factors related to patients themselves, who may be particularly at risk of side effects because of their underlying illness, there are aspects of platelet collection and storage that predispose to adverse events. Platelets for transfusion are strongly activated by collection through disposal equipment, which can stress the cells, and by preservation at 22 °C with rotation or rocking, which likewise leads to platelet activation, perhaps more so than storage at 4 °C. Lastly, platelets constitutively possess a very large number of bioactive components that may elicit pro-inflammatory reactions when infused into a patient. This review aims to describe approaches that may be crucial to minimising side effects while optimising safety and quality. We suggest that platelet transfusion is complex, in part because of the complexity of the "material" itself: platelets are highly versatile cells and the transfusion process adds a myriad of variables that present many challenges for preserving basal platelet function and preventing dysfunctional activation of the platelets. The review also presents information showing--after years of exhaustive haemovigilance--that whole blood buffy coat pooled platelet components are extremely safe compared to the gold standard (i.e. apheresis platelet components), both in terms of acquired infections and of immunological/inflammatory hazards.
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33
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Liu S, Wang Y. Mass spectrometry for the assessment of the occurrence and biological consequences of DNA adducts. Chem Soc Rev 2015; 44:7829-54. [PMID: 26204249 PMCID: PMC4787602 DOI: 10.1039/c5cs00316d] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exogenous and endogenous sources of chemical species can react, directly or after metabolic activation, with DNA to yield DNA adducts. If not repaired, DNA adducts may compromise cellular functions by blocking DNA replication and/or inducing mutations. Unambiguous identification of the structures and accurate measurements of the levels of DNA adducts in cellular and tissue DNA constitute the first and important step towards understanding the biological consequences of these adducts. The advances in mass spectrometry (MS) instrumentation in the past 2-3 decades have rendered MS an important tool for structure elucidation, quantification, and revelation of the biological consequences of DNA adducts. In this review, we summarized the development of MS techniques on these fronts for DNA adduct analysis. We placed our emphasis of discussion on sample preparation, the combination of MS with gas chromatography- or liquid chromatography (LC)-based separation techniques for the quantitative measurement of DNA adducts, and the use of LC-MS along with molecular biology tools for understanding the human health consequences of DNA adducts. The applications of mass spectrometry-based DNA adduct analysis for predicting the therapeutic outcome of anti-cancer agents, for monitoring the human exposure to endogenous and environmental genotoxic agents, and for DNA repair studies were also discussed.
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Affiliation(s)
- Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California, USA and Department of Chemistry, University of California, Riverside, CA 92521-0403, USA.
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34
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Synthesis of 1H-1,2,3-triazole linked aryl(arylamidomethyl) - dihydrofurocoumarin hybrids and analysis of their cytotoxicity. Eur J Med Chem 2015; 100:119-28. [PMID: 26079088 DOI: 10.1016/j.ejmech.2015.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/30/2015] [Accepted: 05/11/2015] [Indexed: 01/02/2023]
Abstract
A series of 2-(4-R-triazolyl)substituted 3-oxo-2,3-dihydrofurocoumarins have been synthesized by a regioselective cycloaddition of 2-azidooreoselone 1 or 2-azido-9-[(4-methylpiperazin-1-yl)methyl]oreoselone 2 with various alkynes in the presence of Cu(II)/ascorbate in water/methylene chloride reaction medium. The structure of 2-azidooreoselone was established by X-ray structure analysis. The cytotoxicity of 2-substituted dihydrofurocoumarins was determined against three cancer cell lines (CEM-13, MT-4, U-937) using the conventional MTT assays. Among the tested molecules, most of the analogs displayed better cytotoxic activity then the parent natural furocoumarin peucedanin 3. The activity and selectivity to the cell line increased even further in the series of 2-(4-{2,3-dihydrobenzo[b][1,4]dioxine}triazolyl)-3-oxo-2,3-dihydrofurocoumarins and 2-(4-aryltriazolyl)-3-oxo-2,3-dihydrofurocoumarins having the (4-methylpiperazin-1-ylmethyl) substituent in the 9-th position. The most active compound 20 contain the 4-hydroxy-3-methoxybenzamidomethyl substituent in the 4-th position at the triazole ring of 2-(triazol-1-yl)dihydrofurocoumarins. The obtained 2-triazolyl substituted dihydrofurocoumarins were studied as inhibitors of phosphodiesterase (PDE-4B) using docking experiments. As a result of virtual screening 3 compounds are selected based on minimum binding energy. The interactions of the most active compound and amino acid residues in the binding site were studied.
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35
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Abonnenc M, Sonego G, Crettaz D, Aliotta A, Prudent M, Tissot JD, Lion N. In vitro study of platelet function confirms the contribution of the ultraviolet B (UVB) radiation in the lesions observed in riboflavin/UVB-treated platelet concentrates. Transfusion 2015; 55:2219-30. [DOI: 10.1111/trf.13123] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 02/24/2015] [Accepted: 02/28/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Mélanie Abonnenc
- Laboratoire de Recherche sur les Produits Sanguins Epalinges; Transfusion Interrégionale CRS; Epalinges Switzerland
| | - Giona Sonego
- Laboratoire de Recherche sur les Produits Sanguins Epalinges; Transfusion Interrégionale CRS; Epalinges Switzerland
| | - David Crettaz
- Laboratoire de Recherche sur les Produits Sanguins Epalinges; Transfusion Interrégionale CRS; Epalinges Switzerland
| | - Alessandro Aliotta
- Laboratoire de Recherche sur les Produits Sanguins Epalinges; Transfusion Interrégionale CRS; Epalinges Switzerland
| | - Michel Prudent
- Laboratoire de Recherche sur les Produits Sanguins Epalinges; Transfusion Interrégionale CRS; Epalinges Switzerland
| | - Jean-Daniel Tissot
- Laboratoire de Recherche sur les Produits Sanguins Epalinges; Transfusion Interrégionale CRS; Epalinges Switzerland
| | - Niels Lion
- Laboratoire de Recherche sur les Produits Sanguins Epalinges; Transfusion Interrégionale CRS; Epalinges Switzerland
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36
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Catalano MJ, Liu S, Andersen N, Yang Z, Johnson KM, Price NE, Wang Y, Gates KS. Chemical structure and properties of interstrand cross-links formed by reaction of guanine residues with abasic sites in duplex DNA. J Am Chem Soc 2015; 137:3933-45. [PMID: 25710271 DOI: 10.1021/jacs.5b00669] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A new type of interstrand cross-link resulting from the reaction of a DNA abasic site with a guanine residue on the opposing strand of the double helix was recently identified, but the chemical connectivity of the cross-link was not rigorously established. The work described here was designed to characterize the chemical structure and properties of dG-AP cross-links generated in duplex DNA. The approach involved characterization of the nucleoside cross-link "remnant" released by enzymatic digestion of DNA duplexes containing the dG-AP cross-link. We first carried out a chemical synthesis and complete spectroscopic structure determination of the putative cross-link remnant 9b composed of a 2-deoxyribose adduct attached to the exocyclic N(2)-amino group of dG. A reduced analogue of the cross-link remnant was also prepared (11b). Liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis revealed that the retention times and mass spectral properties of synthetic standards 9b and 11b matched those of the authentic cross-link remnants released by enzymatic digestion of duplexes containing the native and reduced dG-AP cross-link, respectively. These results establish the chemical connectivity of the dG-AP cross-link released from duplex DNA and provide a foundation for detection of this lesion in biological samples. The dG-AP cross-link in duplex DNA was remarkably stable, decomposing with a half-life of 22 days at pH 7 and 23 °C. The intrinsic chemical stability of the dG-AP cross-link suggests that this lesion in duplex DNA may have the power to block DNA-processing enzymes involved in transcription and replication.
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Affiliation(s)
| | - Shuo Liu
- ‡Environmental Toxicology Graduate Program and Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Nisana Andersen
- ‡Environmental Toxicology Graduate Program and Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | | | | | | | - Yinsheng Wang
- ‡Environmental Toxicology Graduate Program and Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
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37
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Kaiser-Guignard J, Canellini G, Lion N, Abonnenc M, Osselaer JC, Tissot JD. The clinical and biological impact of new pathogen inactivation technologies on platelet concentrates. Blood Rev 2014; 28:235-41. [PMID: 25192602 DOI: 10.1016/j.blre.2014.07.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/14/2014] [Indexed: 01/01/2023]
Abstract
Since 1990, several techniques have been developed to photochemically inactivate pathogens in platelet concentrates, potentially leading to safer transfusion therapy. The three most common methods are amotosalen/UVA (INTERCEPT Blood System), riboflavin/UVA-UVB (MIRASOL PRT), and UVC (Theraflex-UV). We review the biology of pathogen inactivation methods, present their efficacy in reducing pathogens, discuss their impact on the functional aspects of treated platelets, and review clinical studies showing the clinical efficiency of the pathogen inactivation methods and their possible toxicity.
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Affiliation(s)
| | - Giorgia Canellini
- Service régional vaudois de transfusion, Route de la Corniche 2, 1066 Epalinges, Switzerland.
| | - Niels Lion
- Service régional vaudois de transfusion, Route de la Corniche 2, 1066 Epalinges, Switzerland.
| | - Mélanie Abonnenc
- Service régional vaudois de transfusion, Route de la Corniche 2, 1066 Epalinges, Switzerland.
| | - Jean-Claude Osselaer
- Service régional vaudois de transfusion, Route de la Corniche 2, 1066 Epalinges, Switzerland.
| | - Jean-Daniel Tissot
- Service régional vaudois de transfusion, Route de la Corniche 2, 1066 Epalinges, Switzerland.
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38
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Prudent M, Sonego G, Abonnenc M, Tissot JD, Lion N. LC-MS/MS analysis and comparison of oxidative damages on peptides induced by pathogen reduction technologies for platelets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:651-661. [PMID: 24470194 DOI: 10.1007/s13361-013-0813-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/21/2013] [Accepted: 12/13/2013] [Indexed: 06/03/2023]
Abstract
Pathogen reduction technologies (PRT) are photochemical processes that use a combination of photosensitizers and UV-light to inactivate pathogens in platelet concentrates (PCs), a blood-derived product used to prevent hemorrhage. However, different studies have questioned the impact of PRT on platelet function and transfusion efficacy, and several proteomic analyses revealed possible oxidative damages to proteins. The present work focused on the oxidative damages produced by the two main PRT on peptides. Model peptides containing residues prone to oxidation (tyrosine, histidine, tryptophane, and cysteine) were irradiated with a combination of amotosalen/UVA (Intercept process) or riboflavin/UVB (Mirasol-like process). Modifications were identified and quantified by liquid chromatography coupled to tandem mass spectrometry. Cysteine-containing peptides formed disulfide bridges (R-SS-R, -2 Da; favored following amotosalen/UVA), sulfenic and sulfonic acids (R-SOH, +16 Da, R-SO3H, +48 Da, favored following riboflavin/UVB) upon treatment and the other amino acids exhibited different oxidations revealed by mass shifts from +4 to +34 Da involving different mechanisms; no photoadducts were detected. These amino acids were not equally affected by the PRT and the combination riboflavin/UVB generated more oxidation than amotosalen/UVA. This work identifies the different types and sites of peptide oxidations under the photochemical treatments and demonstrates that the two PRT may behave differently. The potential impact on proteins and platelet functions may thus be PRT-dependent.
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Affiliation(s)
- Michel Prudent
- Service Régional Vaudois de Transfusion Sanguine, Unité de Recherche et Développement, Lausanne, Switzerland
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39
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Li L, Zhao L, Zhong R. Quantification of DNA interstrand crosslinks induced by ACNU in NIH/3T3 and L1210 cells using high-performance liquid chromatography/electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:439-447. [PMID: 24497281 DOI: 10.1002/rcm.6800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/28/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Chloroethylnitrosoureas (CENUs) are important alkylating agents employed for the clinical treatment of cancer. The cellular toxicity of CENUs is primarily due to induction of DNA interstrand crosslinks (ICLs), which has been characterized as l-(3-deoxycytidyl), 2-(l-deoxyguanosinyl)ethane (dG-dC). However, the formation of dG-dC crosslinks can be prevented by O(6) -alkylguanine-DNA alkyltransferase (AGT), which removes the O(6) -chloroethyl group from O(6) -chloroethylguanine (O(6) -ClEt-Gua), and ultimately its increased expression can result in drug resistance. Differing levels of AGT expression can lead to varying amounts of dG-dC crosslinking, which influences the sensitivity of cells to CENUs. METHODS In this work, a sensitive method for the quantitation of dG-dC crosslinks in cellular DNA has been established using high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). RESULTS The limit of detection (LOD) and limit of quantitation (LOQ) of the method were determined to be 2 fmol and 8 fmol on-column, respectively, and the recovery ranged from 96% to 105% with the relative standard deviation (RSD) below 5%. Using this method, the levels of dG-dC crosslink induced by 1-(4-amino-2-methyl-5-pyrimidinyl)methyl-3-(2-chloroethyl)-3-nitrosourea hydrochloride (ACNU) were determined in NIH/3T3 fibroblasts cells (high level of expression of AGT) and L1210 leukemia cells (low level of expression of AGT). The time-course profile indicated that the levels of dG-dC crosslink uniformly increased in the early incubation period and reached the maximum at 12 h. Subsequently, the amount of dG-dC crosslinking decreased to very low levels presumably owing to the repair of O(6) -ClEt-Gua by AGT. The crosslinking levels in L1210 cells were significantly higher than those in NIH/3T3 cells at each time point. This provides strong evidence that high express of AGT in CENU-resistant cells inhibits the formation of dG-dC crosslinks. CONCLUSIONS This work will contribute to the further understanding of the drug resistance of CENUs, and will provide a means to evaluate the anticancer activity of new bifunctional anticancer agents.
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Affiliation(s)
- Lili Li
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Sciences and Bioengineering, Beijing University of Technology, Beijing, 100124, P.R., China
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40
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Price N, Johnson KM, Wang J, Fekry MI, Wang Y, Gates KS. Interstrand DNA-DNA cross-link formation between adenine residues and abasic sites in duplex DNA. J Am Chem Soc 2014; 136:3483-90. [PMID: 24506784 PMCID: PMC3954461 DOI: 10.1021/ja410969x] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Indexed: 01/28/2023]
Abstract
The loss of a coding nucleobase from the structure of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an equilibrating mixture of a cyclic hemiacetal and a ring-opened aldehyde. Aldehydes are electrophilic functional groups that can form covalent adducts with nucleophilic sites in DNA. Thus, Ap sites present a potentially reactive aldehyde as part of the internal structure of DNA. Here we report evidence that the aldehyde group of Ap sites in duplex DNA can form a covalent adduct with the N(6)-amino group of adenine residues on the opposing strand. The resulting interstrand DNA-DNA cross-link occurs at 5'-ApT/5'-AA sequences in remarkably high yields (15-70%) under physiologically relevant conditions. This naturally occurring DNA-templated reaction has the potential to generate cross-links in the genetic material of living cells.
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Affiliation(s)
- Nathan
E. Price
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Jin Wang
- Department
of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Mostafa I. Fekry
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Yinsheng Wang
- Department
of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Kent S. Gates
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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Vare D, Johansson F, Persson JO, Erixon K, Jenssen D. Quantification and repair of psoralen-induced interstrand crosslinks in human cells. Toxicol Lett 2014; 226:343-50. [PMID: 24508309 DOI: 10.1016/j.toxlet.2014.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 01/13/2014] [Accepted: 01/14/2014] [Indexed: 11/17/2022]
Abstract
Bi-functional alkylating agents that cause crosslinks are commonly used in chemotherapy. However, there is no conclusive knowledge for human cells regarding the number of induced interstrand crosslinks (ICLs) and the unhooking rate when the lesion is removed from one of the DNA strand. Using a newly developed method, we quantified the number of induced ICLs for the five furocoumarins; psoralen, 5-methoxypsoralen, 8-methoxypsoralen, tri-methoxypsoralen and angelicin. In quantitative terms, the results were in agreement with the values found by others. In kinetic studies using mammalian cells, we found that half of the psoralen-induced ICLs were unhooked within 2.5h. The rate in normal human diploid fibroblasts was found to be 20,000 ICLs/h/cell. In comparison to survival, 2500 ICLs per cell led to 50% toxicity, indicating that the unhooking of the ICLs is not the crucial step for ICL tolerance. Surprisingly, only 3500 ICLs per cell corresponded to a significant delay in the replication fork elongation. The results indicate involvements of additional pathway(s) for the delay since the effect on replication elongation could be monitored when only 10% of the replication forks encounter an ICL.
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Affiliation(s)
- Daniel Vare
- Department of Molecular Biosciences, The Wenner-Gren Institute, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Fredrik Johansson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Jan-Olov Persson
- Department of Mathematics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Klaus Erixon
- Department of Molecular Biosciences, The Wenner-Gren Institute, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Dag Jenssen
- Department of Molecular Biosciences, The Wenner-Gren Institute, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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Manayi A, Saeidnia S, Gohari AR, Abdollahi M. Methods for the discovery of new anti-aging products--targeted approaches. Expert Opin Drug Discov 2014; 9:383-405. [PMID: 24494592 DOI: 10.1517/17460441.2014.885014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Aging is considered to be one of the most complicated and heterogeneous phenomena and is the main risk factor for most chronic diseases, disabilities and declining health. Aging cells cease to divide and drive the progression of illness through various pathways. Over the years, a number of anti-aging medicines of natural and synthetic origin have been introduced. Indeed, some studies have identified senescent cells as potential therapeutic targets in the treatment of aging and age-related diseases. AREAS COVERED In this review, the authors highlight and critically review the possible mechanisms of the aging process and related illnesses. The authors give particular attention to illnesses, including Alzheimer's disease, Parkinson's disease, skin aging and cardiovascular diseases. EXPERT OPINION Several reports have highlighted that mitochondria are a key factor in the progression of aging and neurodegenerative illnesses. This is due to their production of extra amounts of reactive oxygen species, which leads into progressive caspase-dependent apoptosis and cell death. Therefore, strategies to prevent/reduce oxidative stress-mediated aging, whether environmental, nutritional and pharmacological, need to be taken into account. Presently, Drosophila melanogaster and Caenorhabditis elegans, which focus on the evolutionary and genetic foundations of aging, have helped to establish the screening of several synthetic and natural compounds with large cohorts in a quick manner. However, there is yet to be any efficient experimental evidence to prove the exact role of senescent cells in age-related dysfunction and further studies are required to better understand these processes.
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Affiliation(s)
- Azadeh Manayi
- Tehran University of Medical Sciences, Faculty of Pharmacy, Medicinal Plants Research Center , Tehran 1417614411 , Iran
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Vatansever F, Ferraresi C, de Sousa MVP, Yin R, Rineh A, Sharma SK, Hamblin MR. Can biowarfare agents be defeated with light? Virulence 2013; 4:796-825. [PMID: 24067444 PMCID: PMC3925713 DOI: 10.4161/viru.26475] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 09/10/2013] [Accepted: 09/12/2013] [Indexed: 02/08/2023] Open
Abstract
Biological warfare and bioterrorism is an unpleasant fact of 21st century life. Highly infectious and profoundly virulent diseases may be caused in combat personnel or in civilian populations by the appropriate dissemination of viruses, bacteria, spores, fungi, or toxins. Dissemination may be airborne, waterborne, or by contamination of food or surfaces. Countermeasures may be directed toward destroying or neutralizing the agents outside the body before infection has taken place, by destroying the agents once they have entered the body before the disease has fully developed, or by immunizing susceptible populations against the effects. A range of light-based technologies may have a role to play in biodefense countermeasures. Germicidal UV (UVC) is exceptionally active in destroying a wide range of viruses and microbial cells, and recent data suggests that UVC has high selectivity over host mammalian cells and tissues. Two UVA mediated approaches may also have roles to play; one where UVA is combined with titanium dioxide nanoparticles in a process called photocatalysis, and a second where UVA is combined with psoralens (PUVA) to produce "killed but metabolically active" microbial cells that may be particularly suitable for vaccines. Many microbial cells are surprisingly sensitive to blue light alone, and blue light can effectively destroy bacteria, fungi, and Bacillus spores and can treat wound infections. The combination of photosensitizing dyes such as porphyrins or phenothiaziniums and red light is called photodynamic therapy (PDT) or photoinactivation, and this approach cannot only kill bacteria, spores, and fungi, but also inactivate viruses and toxins. Many reports have highlighted the ability of PDT to treat infections and stimulate the host immune system. Finally pulsed (femtosecond) high power lasers have been used to inactivate pathogens with some degree of selectivity. We have pointed to some of the ways light-based technology may be used to defeat biological warfare in the future.
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Affiliation(s)
- Fatma Vatansever
- Wellman Center for Photomedicine; Massachusetts General Hospital; Boston MA USA
- Harvard Medical School; Department of Dermatology; Boston, MA USA
| | - Cleber Ferraresi
- Wellman Center for Photomedicine; Massachusetts General Hospital; Boston MA USA
- Laboratory of Electro-thermo-phototherapy; Department of Physical Therapy; Federal University of São Carlos; São Paulo, Brazil
- Post-Graduation Program in Biotechnology; Federal University of São Carlos; São Paulo, Brazil
- Optics Group; Physics Institute of Sao Carlos; University of São Paulo; São Carlos, Brazil
| | - Marcelo Victor Pires de Sousa
- Wellman Center for Photomedicine; Massachusetts General Hospital; Boston MA USA
- Laboratory of Radiation Dosimetry and Medical Physics; Institute of Physics, São Paulo University, São Paulo, Brazil
| | - Rui Yin
- Wellman Center for Photomedicine; Massachusetts General Hospital; Boston MA USA
- Harvard Medical School; Department of Dermatology; Boston, MA USA
- Department of Dermatology; Southwest Hospital; Third Military Medical University; Chongqing, PR China
| | - Ardeshir Rineh
- Wellman Center for Photomedicine; Massachusetts General Hospital; Boston MA USA
- School of Chemistry; University of Wollongong; Wollongong, NSW Australia
| | - Sulbha K Sharma
- Wellman Center for Photomedicine; Massachusetts General Hospital; Boston MA USA
- Raja Ramanna Centre for Advanced Technology; Indore, India
| | - Michael R Hamblin
- Wellman Center for Photomedicine; Massachusetts General Hospital; Boston MA USA
- Harvard Medical School; Department of Dermatology; Boston, MA USA
- Harvard-MIT Division of Health Sciences and Technology; Cambridge, MA USA
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Huang J, Liu S, Bellani MA, Thazhathveetil AK, Ling C, de Winter JP, Wang Y, Wang W, Seidman MM. The DNA translocase FANCM/MHF promotes replication traverse of DNA interstrand crosslinks. Mol Cell 2013; 52:434-46. [PMID: 24207054 DOI: 10.1016/j.molcel.2013.09.021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/09/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The replicative machinery encounters many impediments, some of which can be overcome by lesion bypass or replication restart pathways, leaving repair for a later time. However, interstrand crosslinks (ICLs), which preclude DNA unwinding, are considered absolute blocks to replication. Current models suggest that fork collisions, either from one or both sides of an ICL, initiate repair processes required for resumption of replication. To test these proposals, we developed a single-molecule technique for visualizing encounters of replication forks with ICLs as they occur in living cells. Surprisingly, the most frequent patterns were consistent with replication traverse of an ICL, without lesion repair. The traverse frequency was strongly reduced by inactivation of the translocase and DNA binding activities of the FANCM/MHF complex. The results indicate that translocase-based mechanisms enable DNA synthesis to continue past ICLs and that these lesions are not always absolute blocks to replication.
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Affiliation(s)
- Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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Buhimschi AD, Gasparro FP. UVA and UVB-Induced 8-Methoxypsoralen Photoadducts and a Novel Method for their Detection by Surface-Enhanced Laser Desorption Ionization Time-of-Flight Mass Spectrometry (SELDI-TOF MS). Photochem Photobiol 2013; 90:241-6. [DOI: 10.1111/php.12171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022]
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46
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Liu S, Wang Y. A quantitative mass spectrometry-based approach for assessing the repair of 8-methoxypsoralen-induced DNA interstrand cross-links and monoadducts in mammalian cells. Anal Chem 2013; 85:6732-9. [PMID: 23789926 DOI: 10.1021/ac4012232] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interstrand cross-links (ICLs) are highly toxic DNA lesions that block transcription and replication by preventing strand separation. ICL-inducing agents were among the earliest and are still the most widely used forms of chemotherapeutic drugs. Because of the repair of DNA ICLs, the therapeutic efficacy of the DNA cross-linking agents is often reduced by the development of chemoresistance in patients. Thus, it is very important to understand how various DNA ICLs are repaired. Such studies are currently hampered by the lack of an analytical method for monitoring directly the repair of DNA ICLs in cells. Here we report a high-performance liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method, together with the isotope dilution technique, for assessing the repair of 8-methoxypsoralen (8-MOP)-induced DNA ICLs, as well as monoadducts (MAs), in cultured mammalian cells. We found that, while there were substantial decreases in the levels of ICL and MAs in repair-competent cells 24 h after 8-MOP/UVA treatment, there was little repair of 8-MOP-ICLs and -MAs in xeroderma pigmentosum, complementation group A-deficient human skin fibroblasts and excision repair cross-complementing rodent repair deficiency, complementation group 1-deficient Chinese hamster ovary cells over a 24 h period. This result provided unequivocal evidence supporting the notion that the 8-MOP photoadducts are substrates for nucleotide excision repair in mammalian cells. This is one of the first few reports about the application of LC-MS/MS for assessing the repair of DNA ICLs. The analytical method developed here, when combined with genetic manipulation, will also facilitate the assessment of the roles of other DNA repair pathways in removing these DNA lesions, and the method can also be generally applicable for investigating the repair of other types of DNA ICLs in mammalian cells.
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Affiliation(s)
- Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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Silvestri C, Brodbelt JS. Tandem mass spectrometry for characterization of covalent adducts of DNA with anticancer therapeutics. MASS SPECTROMETRY REVIEWS 2013; 32:247-66. [PMID: 23150278 PMCID: PMC3578003 DOI: 10.1002/mas.21363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 05/17/2023]
Abstract
The chemotherapeutic activities of many anticancer and antibacterial drugs arise from their interactions with nucleic acid substrates. Some of these ligands interact with DNA in a way that causes conformational changes or damage to the nucleic acid targets, ultimately altering recognition by key DNA-specific enzymes, interfering with DNA transcription or prohibiting replication, and terminating cell growth and proliferation. The design and synthesis of ligands that bind to nucleic acids remains a dynamic field in medicinal chemistry and pharmaceutical research. The quest for more selective and efficacious DNA-interactive anticancer chemotherapeutics has likewise catalyzed the need for sensitive analytical methods that can provide structural information about the nature of the resulting DNA adducts and provide insight into the mechanistic pathways of the DNA/drug interactions and the impact on the cellular processes in biological systems. This review focuses on the array of tandem mass spectrometric strategies developed and applied for characterization of covalent adducts formed between DNA and anticancer ligands.
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Affiliation(s)
- Catherine Silvestri
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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48
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Huang X, Zhang R. A Theoretical Rationale why Furan-side Monoadduct is More Favorable Toward Diadduct Formation in 8-Methoxypsoralen and Thymine Complexes. Photochem Photobiol 2013; 89:891-9. [DOI: 10.1111/php.12067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/26/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Xuebin Huang
- Key Laboratory of Cluster Science; School of Chemistry; Beijing Institute of Technology; Beijing; China
| | - Rubo Zhang
- Key Laboratory of Cluster Science; School of Chemistry; Beijing Institute of Technology; Beijing; China
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McNeill DR, Paramasivam M, Baldwin J, Huang J, Vyjayanti VN, Seidman MM, Wilson DM. NEIL1 responds and binds to psoralen-induced DNA interstrand crosslinks. J Biol Chem 2013; 288:12426-36. [PMID: 23508956 DOI: 10.1074/jbc.m113.456087] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent evidence suggests a role for base excision repair (BER) proteins in the response to DNA interstrand crosslinks, which block replication and transcription, and lead to cell death and genetic instability. Employing fluorescently tagged fusion proteins and laser microirradiation coupled with confocal microscopy, we observed that the endonuclease VIII-like DNA glycosylase, NEIL1, accumulates at sites of oxidative DNA damage, as well as trioxsalen (psoralen)-induced DNA interstrand crosslinks, but not to angelicin monoadducts. While recruitment to the oxidative DNA lesions was abrogated by the anti-oxidant N-acetylcysteine, this treatment did not alter the accumulation of NEIL1 at sites of interstrand crosslinks, suggesting distinct recognition mechanisms. Consistent with this conclusion, recruitment of the NEIL1 population variants, G83D, C136R, and E181K, to oxidative DNA damage and psoralen-induced interstrand crosslinks was differentially affected by the mutation. NEIL1 recruitment to psoralen crosslinks was independent of the nucleotide excision repair recognition factor, XPC. Knockdown of NEIL1 in LN428 glioblastoma cells resulted in enhanced recruitment of XPC, a more rapid removal of digoxigenin-tagged psoralen adducts, and decreased cellular sensitivity to trioxsalen plus UVA, implying that NEIL1 and BER may interfere with normal cellular processing of interstrand crosslinks. While exhibiting no enzymatic activity, purified NEIL1 protein bound stably to psoralen interstrand crosslink-containing synthetic oligonucleotide substrates in vitro. Our results indicate that NEIL1 recognizes specifically and distinctly interstrand crosslinks in DNA, and can obstruct the efficient removal of lethal crosslink adducts.
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Affiliation(s)
- Daniel R McNeill
- Laboratory of Molecular Gerontology, Biomedical Research Center, NIA, National Institutes of Health, Baltimore, Maryland 21224, USA
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50
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Moskalev AA, Shaposhnikov MV, Plyusnina EN, Zhavoronkov A, Budovsky A, Yanai H, Fraifeld VE. The role of DNA damage and repair in aging through the prism of Koch-like criteria. Ageing Res Rev 2013; 12:661-84. [PMID: 22353384 DOI: 10.1016/j.arr.2012.02.001] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 01/27/2012] [Accepted: 02/06/2012] [Indexed: 12/21/2022]
Abstract
Since the first publication on Somatic Mutation Theory of Aging (Szilárd, 1959), a great volume of knowledge in the field has been accumulated. Here we attempted to organize the evidence "for" and "against" the hypothesized causal role of DNA damage and mutation accumulation in aging in light of four Koch-like criteria. They are based on the assumption that some quantitative relationship between the levels of DNA damage/mutations and aging rate should exist, so that (i) the longer-lived individuals or species would have a lower rate of damage than the shorter-lived, and (ii) the interventions that modulate the level of DNA damage and repair capacity should also modulate the rate of aging and longevity and vice versa. The analysis of how the existing data meets the proposed criteria showed that many gaps should still be filled in order to reach a clear-cut conclusion. As a perspective, it seems that the main emphasis in future studies should be put on the role of DNA damage in stem cell aging.
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