1
|
Li Y. DNA Adducts in Cancer Chemotherapy. J Med Chem 2024; 67:5113-5143. [PMID: 38552031 DOI: 10.1021/acs.jmedchem.3c02476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
DNA adducting drugs, including alkylating agents and platinum-containing drugs, are prominent in cancer chemotherapy. Their mechanisms of action involve direct interaction with DNA, resulting in the formation of DNA addition products known as DNA adducts. While these adducts are well-accepted to induce cancer cell death, understanding of their specific chemotypes and their role in drug therapy response remain limited. This perspective aims to address this gap by investigating the metabolic activation and chemical characterization of DNA adducts formed by the U.S. FDA-approved drugs. Moreover, clinical studies on DNA adducts as potential biomarkers for predicting patient responses to drug efficacy are examined. The overarching goal is to engage the interest of medicinal chemists and stimulate further research into the use of DNA adducts as biomarkers for guiding personalized cancer treatment.
Collapse
|
2
|
Guidolin V, Jacobs FC, MacMillan ML, Villalta PW, Balbo S. Liquid Chromatography-Mass Spectrometry Screening of Cyclophosphamide DNA Damage In Vitro and in Patients Undergoing Chemotherapy Treatment. Chem Res Toxicol 2023; 36:1278-1289. [PMID: 37490747 DOI: 10.1021/acs.chemrestox.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
DNA alkylating drugs have been used as frontline medications to treat cancer for decades. Their chemical reaction with DNA leads to the blockage of DNA replication, which impacts cell replication. While this impacts rapidly dividing cancerous cells, this process is not selective and results in highly variable and often severe side effects in patients undergoing alkylating-drug based therapies. The development of biomarkers to identify patients who effectively respond with tolerable toxicities vs patients who develop serious side effects is needed. Cyclophosphamide (CPA) is a commonly used chemotherapeutic drug and lacks biomarkers to evaluate its therapeutic effect and toxicity. Upon administration, CPA is metabolically activated and converted to phosphoramide mustard and acrolein, which are responsible for its efficacy and toxicity, respectively. Previous studies have explored the detection of the major DNA adduct of CPA, the interstrand DNA-DNA cross-link G-NOR-G, finding differences in the cross-link amount between Fanconi Anemia and non-Fanconi Anemia patients undergoing chemotherapy treatment. In this study, we take advantage of our DNA adductomic approach to comprehensively profile CPA's and its metabolites' reactions with DNA in vitro and in patients undergoing CPA-based chemotherapy. This investigation led to the detection of 40 DNA adducts in vitro and 20 DNA adducts in patients treated with CPA. Moreover, acrolein-derived DNA adducts were quantified in patient samples. The results suggest that CPA-DNA damage is very complex, and an evaluation of DNA adduct profiles is necessary when evaluating the relationship between CPA-DNA damage and patient outcome.
Collapse
Affiliation(s)
- Valeria Guidolin
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Foster C Jacobs
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Margaret L MacMillan
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Blood and Marrow Transplantation & Cellular Therapy Program, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
- School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
3
|
Bellamri M, Terrell JT, Brandt K, Gruppi F, Turesky RJ, Rizzo CJ. Anthracyclines React with Apurinic/Apyrimidinic Sites in DNA. ACS Chem Biol 2023; 18:1315-1323. [PMID: 37200590 PMCID: PMC10391585 DOI: 10.1021/acschembio.3c00033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The combination of doxorubicin (Adriamycin) and cyclophosphamide, referred to as AC chemotherapy, is commonly used for the clinical treatment of breast and other cancers. Both agents target DNA with cyclophosphamide causing alkylation damage and doxorubicin stabilizing the topoisomerase II-DNA complex. We hypothesize a new mechanism of action whereby both agents work in concert. DNA alkylating agents, such as nitrogen mustards, increase the number of apurinic/apyrimidinic (AP) sites through deglycosylation of labile alkylated bases. Herein, we demonstrate that anthracyclines with aldehyde-reactive primary and secondary amines form covalent Schiff base adducts with AP sites in a 12-mer DNA duplex, calf thymus DNA, and MDA-MB-231 human breast cancer cells treated with nor-nitrogen mustard and the anthracycline mitoxantrone. The anthracycline-AP site conjugates are characterized and quantified by mass spectrometry after NaB(CN)H3 or NaBH4 reduction of the Schiff base. If stable, the anthracycline-AP site conjugates represent bulky adducts that may block DNA replication and contribute to the cytotoxic mechanism of therapies involving combinations of anthracyclines and DNA alkylating agents.
Collapse
|
4
|
Schmaltz LF, Koag MC, Kou Y, Zhang L, Lee S. Genotoxic effects of the major alkylation damage N7-methylguanine and methyl formamidopyrimidine. Biochem J 2023; 480:573-585. [PMID: 37078496 PMCID: PMC11061863 DOI: 10.1042/bcj20220460] [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: 08/31/2022] [Revised: 03/29/2023] [Accepted: 04/19/2023] [Indexed: 04/21/2023]
Abstract
Various alkylating agents are known to preferentially modify guanine in DNA, resulting in the formation of N7-alkylguanine (N7-alkylG) and the imidazole ring opened alkyl-formamidopyrimidine (alkyl-FapyG) lesions. Evaluating the mutagenic effects of N7-alkylG has been challenging due to the instability of the positively charged N7-alkylG. To address this issue, we developed a 2'-fluorine-mediated transition-state destabilization approach, which stabilizes N7-alkylG and prevents spontaneous depurination. We also developed a postsynthetic conversion of 2'-F-N7-alkylG DNA into 2'-F-alkyl-FapyG DNA. Using these methods, we incorporated site-specific N7-methylG and methyl-FapyG into pSP189 plasmid and determined their mutagenic properties in bacterial cells using the supF-based colony screening assay. The mutation frequency of N7-methylG was found to be less than 0.5%. Our crystal structure analysis revealed that N7-methylation did not significantly alter base pairing properties, as evidenced by a correct base pairing between 2'-F-N7-methylG and dCTP in Dpo4 polymerase catalytic site. In contrast, the mutation frequency of methyl-FapyG was 6.3%, highlighting the mutagenic nature of this secondary lesion. Interestingly, all mutations arising from methyl-FapyG in the 5'-GGT(methyl-FapyG)G-3' context were single nucleotide deletions at the 5'-G of the lesion. Overall, our results demonstrate that 2'-fluorination technology is a useful tool for studying the chemically labile N7-alkylG and alkyl-FapyG lesions.
Collapse
Affiliation(s)
- Lillian F Schmaltz
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Myong-Chul Koag
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Yi Kou
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Louis Zhang
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Seongmin Lee
- From the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, U.S.A
| |
Collapse
|
5
|
Guidolin V, Li Y, Jacobs FC, MacMillan ML, Villalta PW, Hecht SS, Balbo S. Characterization and quantitation of busulfan DNA adducts in the blood of patients receiving busulfan therapy. Mol Ther Oncolytics 2023; 28:197-210. [PMID: 36820303 PMCID: PMC9938526 DOI: 10.1016/j.omto.2023.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
DNA alkylating drugs have been used as cancer chemotherapy with variable outcomes. The establishment of predictive biomarkers to identify patients who will effectively respond to treatment would allow for the development of personalized therapies. As the degree of interaction of alkylating drug with DNA plays a key role in their mechanism of action, our hypothesis is that the measurement of the DNA adducts formed by alkylating drugs could be used to inform patient stratification. Beginning with busulfan, we took advantage of our DNA adductomic approach to characterize DNA adducts formed by reacting busulfan with calf-thymus DNA. Samples collected from six patients undergoing busulfan-based chemotherapy prior to allogeneic hematopoietic cell transplantation were analyzed for the presence of busulfan-derived DNA adducts. Among the 15 adducts detected in vitro, 12 were observed in the patient blood confirming the presence of a large profile of DNA adducts in vivo. Two of the detected adducts were structurally confirmed by comparison with synthetic standards and quantified in patients. These data confirm our ability to comprehensively characterize busulfan-derived DNA damage and set the stage for the development of methods to support personalized chemotherapy.
Collapse
Affiliation(s)
- Valeria Guidolin
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA,School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yupeng Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA,Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Foster C. Jacobs
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA,School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Margaret L. MacMillan
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA,Blood and Marrow Transplantation & Cellular Therapy Program, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Peter W. Villalta
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA,Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA,School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA,Corresponding author: Silvia Balbo, Masonic Cancer Center, University of Minnesota, 2231 6 Street SE - 2-145 CCRB, Minneapolis, MN 55455, USA.
| |
Collapse
|
6
|
Krassnig SC, Mäser M, Probst NA, Werner J, Schlett C, Schumann N, von Scheven G, Mangerich A, Bürkle A. Comparative analysis of chlorambucil-induced DNA lesion formation and repair in a spectrum of different human cell systems. Toxicol Rep 2023; 10:171-189. [PMID: 36714466 PMCID: PMC9881385 DOI: 10.1016/j.toxrep.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
Chlorambucil (CLB) belongs to the class of nitrogen mustards (NMs), which are highly reactive bifunctional alkylating agents and were the first chemotherapeutic agents developed. They form DNA interstrand crosslinks (ICLs), which cause a blockage of DNA strand separation, inhibiting essential processes in DNA metabolism like replication and transcription. In fast replicating cells, e.g., tumor cells, this can induce cell death. The upregulation of ICL repair is thought to be a key factor for the resistance of tumor cells to ICL-inducing cytostatic agents including NMs. To monitor induction and repair of CLB-induced ICLs, we adjusted the automated reversed fluorometric analysis of alkaline DNA unwinding assay (rFADU) for the detection of ICLs in adherent cells. For the detection of monoalkylated DNA bases we established an LC-MS/MS method. We performed a comparative analysis of adduct formation and removal in five human cell lines and in peripheral blood mononuclear cells (PBMCs) after treatment with CLB. Dose-dependent increases in adduct formation were observed, and suitable treatment concentrations were identified for each cell line, which were then used for monitoring the kinetics of adduct formation. We observed significant differences in the repair kinetics of the cell lines tested. For example, in A2780 cells, hTERT immortalized VH10 cells, and in PBMCs a time-dependent repair of the two main monoalkylated DNA-adducts was confirmed. Regarding ICLs, repair was observed in all cell systems except for PBMCs. In conclusion, LC-MS/MS analyses combined with the rFADU technique are powerful tools to study the molecular mechanisms of NM-induced DNA damage and repair. By applying these methods to a spectrum of human cell systems of different origin and transformation status, we obtained insight into the cell-type specific repair of different CLB-induced DNA lesions, which may help identify novel resistance mechanisms of tumors and define molecular targets for therapeutic interventions.
Collapse
Key Words
- BER, base excision repair
- CLB, chlorambucil
- Chlorambucil
- DNA repair kinetics
- ICL, interstrand crosslink
- Interstrand crosslink
- MS, mass spectrometry
- Mass spectrometry
- Monoalkylated DNA adducts
- NER, nucleotide excision repair
- NM, Nitrogen mustard
- Nitrogen mustard
- PBMCs, peripheral blood mononuclear cells
- PI, propidium iodide
- RPE-1, human retinal pigment epithelial
- SD, standard deviation
- VH10, human foreskin fibroblasts
- dG, 2'-deoxyguanosine
- hTERT, human telomerase reverse transcriptase
- rFADU, reverse fluorometric analysis of alkaline DNA unwinding
Collapse
Affiliation(s)
- Sarah Ceylan Krassnig
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Marina Mäser
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Nicola Anna Probst
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Jens Werner
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Charlotte Schlett
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Nina Schumann
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Gudrun von Scheven
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Aswin Mangerich
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany,Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, D-14558 Nuthetal, Germany
| | - Alexander Bürkle
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany,Corresponding author.
| |
Collapse
|
7
|
Pujari SS, Jokipii Krueger CC, Chao C, Hutchins S, Hurben AK, Boysen G, Tretyakova N. DEB-FAPy-dG Adducts of 1,3-Butadiene: Synthesis, Structural Characterization, and Formation in 1,2,3,4-Diepoxybutane Treated DNA. Chemistry 2022; 28:e202103245. [PMID: 34767297 PMCID: PMC10603587 DOI: 10.1002/chem.202103245] [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: 09/07/2021] [Indexed: 11/10/2022]
Abstract
Metabolic activation of the human carcinogen 1,3-butadiene (BD) by cytochrome 450 monooxygenases gives rise to a genotoxic diepoxide, 1,2,3,4-diepoxybutane (DEB). This reactive electrophile alkylates guanine bases in DNA to produce N7-(2-hydroxy-3,4-epoxy-1-yl)-dG (N7-DE-dG) adducts. Because of the positive charge at the N7 position of the purine heterocycle, N7-DEB-dG adducts are inherently unstable and can undergo spontaneous depurination or base-catalyzed imidazole ring opening to give N6 -[2-deoxy-D-erythro-pentofuranosyl]-2,6-diamino-3,4-dihydro-4-oxo-5-N-1-(oxiran-2-yl)propan-1-ol-formamidopyrimidine (DEB-FAPy-dG) adducts. Here we report the first synthesis and structural characterization of DEB-FAPy-dG adducts. Authentic standards of DEB-FAPy-dG and its 15 N3 -labeled analogue were used for the development of a quantitative nanoLC-ESI+ -HRMS/MS method, allowing for adduct detection in DEB-treated calf thymus DNA. DEB-FAPy-dG formation in DNA was dependent on DEB concentration and pH, with higher numbers observed under alkaline conditions.
Collapse
Affiliation(s)
- Suresh S Pujari
- Department of Medicinal Chemistry, College of Pharmacy, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Caitlin C Jokipii Krueger
- Department of Medicinal Chemistry, College of Pharmacy, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Christopher Chao
- Department of Medicinal Chemistry, College of Pharmacy, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Spencer Hutchins
- Department of Medicinal Chemistry, College of Pharmacy, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Alexander K Hurben
- Department of Medicinal Chemistry, College of Pharmacy, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Gunnar Boysen
- Department of Environmental and Occupational Health and the Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 West Markham St., Slot 820, Little Rock, AR, 72205, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, College of Pharmacy, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| |
Collapse
|
8
|
Leškovskis K, Zaķis JM, Novosjolova I, Turks M. Applications of Purine Ring Opening in the Synthesis of Imidazole, Pyrimidine, and New Purine Derivatives. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kristaps Leškovskis
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry Riga Technical University P. Valdena Str. 3 Riga LV-1048 Latvia
| | - Jānis Miķelis Zaķis
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry Riga Technical University P. Valdena Str. 3 Riga LV-1048 Latvia
| | - Irina Novosjolova
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry Riga Technical University P. Valdena Str. 3 Riga LV-1048 Latvia
| | - Māris Turks
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry Riga Technical University P. Valdena Str. 3 Riga LV-1048 Latvia
| |
Collapse
|
9
|
Abstract
DNA interstrand cross-links (ICLs) covalently connect the two strands of the double helix and are extremely cytotoxic. Defective ICL repair causes the bone marrow failure and cancer predisposition syndrome, Fanconi anemia, and upregulation of repair causes chemotherapy resistance in cancer. The central event in ICL repair involves resolving the cross-link (unhooking). In this review, we discuss the chemical diversity of ICLs generated by exogenous and endogenous agents. We then describe how proliferating and nonproliferating vertebrate cells unhook ICLs. We emphasize fundamentally new unhooking strategies, dramatic progress in the structural analysis of the Fanconi anemia pathway, and insights into how cells govern the choice between different ICL repair pathways. Throughout, we highlight the many gaps that remain in our knowledge of these fascinating DNA repair pathways.
Collapse
Affiliation(s)
- Daniel R Semlow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Current affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
10
|
Cheng X, Liu C, Yang Y, Liang L, Chen B, Yu H, Xia J, Liu S, Li Y. Advances in sulfur mustard-induced DNA adducts: Characterization and detection. Toxicol Lett 2021; 344:46-57. [PMID: 33705862 DOI: 10.1016/j.toxlet.2021.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Sulfur mustard (SM) is a blister chemical warfare agent with severe cytotoxicity and genotoxicity. It can extensively alkylate important macromolecules in organisms, such as proteins, DNA, and lipids, and produce a series of metabolites, among which the characteristic ones can be used as biomarkers. The exact toxicological mechanisms of SM remain unclear but mainly involve the DNA lesions induced by alkylation and oxidative stress caused by glutathione depletion. Various methods have been used to analyze DNA damage caused by SM. Among these methods, liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology stands out and makes it possible to observe damage in view of biomarkers induced by SM. Sample preparation is critical for detection by LC-MS/MS and mainly includes DNA isolation, adduct hydrolysis, and adduct purification. Moreover, optimization of chromatographic conditions, selection of MS transitions, and quantitative strategies are also essential. SM-DNA adducts are generally considered to be N7-HETEG, O6-HETEG, N7-BisG, and N3-HETEA. This article proposes some other possibilities of SM-DNA adducts for the identification of SM genotoxicity.
Collapse
Affiliation(s)
- Xi Cheng
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, PR China; State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Changcai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Yang Yang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Longhui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Bo Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Huilan Yu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Junmei Xia
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Shilei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China.
| | - Yihe Li
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, PR China.
| |
Collapse
|
11
|
Ullmann R, Becker BV, Rothmiller S, Schmidt A, Thiermann H, Kaatsch HL, Schrock G, Müller J, Jakobi J, Obermair R, Port M, Scherthan H. Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation. Int J Mol Sci 2021; 22:ijms22031146. [PMID: 33498964 PMCID: PMC7865644 DOI: 10.3390/ijms22031146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022] Open
Abstract
Sulfur mustard (SM) is a chemical warfare agent that can damage DNA via alkylation and oxidative stress. Because of its genotoxicity, SM is cancerogenic and the progenitor of many chemotherapeutics. Previously, we developed an SM-resistant cell line via chronic exposure of the popular keratinocyte cell line HaCaT to increasing doses of SM over a period of 40 months. In this study, we compared the genomic landscape of the SM-resistant cell line HaCaT/SM to its sensitive parental line HaCaT in order to gain insights into genetic changes associated with continuous alkylation and oxidative stress. We established chromosome numbers by cytogenetics, analyzed DNA copy number changes by means of array Comparative Genomic Hybridization (array CGH), employed the genome-wide chromosome conformation capture technique Hi-C to detect chromosomal translocations, and derived mutational signatures by whole-genome sequencing. We observed that chronic SM exposure eliminated the initially prevailing hypotetraploid cell population in favor of a hyperdiploid one, which contrasts with previous observations that link polyploidization to increased tolerance and adaptability toward genotoxic stress. Furthermore, we observed an accumulation of chromosomal translocations, frequently flanked by DNA copy number changes, which indicates a high rate of DNA double-strand breaks and their misrepair. HaCaT/SM-specific single-nucleotide variants showed enrichment of C > A and T > A transversions and a lower rate of deaminated cytosines in the CpG dinucleotide context. Given the frequent use of HaCaT in toxicology, this study provides a valuable data source with respect to the original genotype of HaCaT and the mutational signatures associated with chronic alkylation and oxidative stress.
Collapse
Affiliation(s)
- Reinhard Ullmann
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
- Correspondence:
| | - Benjamin Valentin Becker
- Bundeswehr Central Hospital, Department of Radiology and Neuroradiology, Rübenacherstrasse 170, D-56072 Koblenz, Germany;
| | - Simone Rothmiller
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstr. 11, D-80937 Munich, Germany; (S.R.); (A.S.); (H.T.)
| | - Annette Schmidt
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstr. 11, D-80937 Munich, Germany; (S.R.); (A.S.); (H.T.)
| | - Horst Thiermann
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstr. 11, D-80937 Munich, Germany; (S.R.); (A.S.); (H.T.)
| | - Hanns Leonhard Kaatsch
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
| | - Gerrit Schrock
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
| | - Jessica Müller
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
| | - Julia Jakobi
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
| | - Richard Obermair
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
| | - Matthias Port
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
| | - Harry Scherthan
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, D-80937 Munich, Germany; (H.L.K.); (G.S.); (J.M.); (J.J.); (R.O.); (M.P.); (H.S.)
| |
Collapse
|
12
|
Chen H, Cui Z, Hejazi L, Yao L, Walmsley SJ, Rizzo CJ, Turesky RJ. Kinetics of DNA Adducts and Abasic Site Formation in Tissues of Mice Treated with a Nitrogen Mustard. Chem Res Toxicol 2020; 33:988-998. [PMID: 32174110 DOI: 10.1021/acs.chemrestox.0c00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nitrogen mustards (NM) are an important class of chemotherapeutic drugs used in the treatment of malignant tumors. The accepted mechanism of action of NM is through the alkylation of DNA bases. NM-adducts block DNA replication in cancer cells by forming cytotoxic DNA interstrand cross-links. We previously characterized several adducts formed by reaction of bis(2-chloroethyl)ethylamine (NM) with calf thymus (CT) DNA and the MDA-MB-231 mammary tumor cell line. The monoalkylated N7-guanine (NM-G) adduct and its cross-link (G-NM-G) were major lesions. The cationic NM-G undergoes a secondary reaction through depurination to form an apurinic (AP) site or reacts with hydroxide to yield the stable ring-opened N5-substituted formamidopyrimidine (NM-Fapy-G) adduct. Both of these lesions are mutagenic and may contribute to secondary tumor development, a major clinical limitation of NM chemotherapy. We established a kinetic model with NM-treated female mice and measured the rates of formation and removal of NM-DNA adducts and AP sites. We employed liquid chromatography-mass spectrometry (LC-MS) to measure NM-G, G-NM-G, and NM-Fapy-G adducts in liver, lung, and spleen over 168 h. NM-G reached a maximum level within 6 h in all organs and then rapidly declined. The G-NM-G cross-link and NM-FapyG were more persistent with half-lives over three-times longer than NM-G. We quantified AP site lesions in the liver and showed that NM treatment increased AP site levels by 3.7-fold over the basal levels at 6 h. The kinetics of AP site repair closely followed the rate of removal of NM-G; however, AP sites remained 1.3-fold above basal levels 168 h post-treatment with NM. Our data provide new insights into NM-induced DNA damage and biological processing in vivo. The quantitative measurement of the spectrum of NM adducts and AP sites can serve as biomarkers in the design and assessment of the efficacy of novel chemotherapeutic regimens.
Collapse
Affiliation(s)
| | | | | | | | | | - Carmelo J Rizzo
- Departments of Chemistry and Biochemistry, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37067, United States
| | | |
Collapse
|
13
|
Yun BH, Guo J, Bellamri M, Turesky RJ. DNA adducts: Formation, biological effects, and new biospecimens for mass spectrometric measurements in humans. MASS SPECTROMETRY REVIEWS 2020; 39:55-82. [PMID: 29889312 PMCID: PMC6289887 DOI: 10.1002/mas.21570] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/25/2018] [Indexed: 05/18/2023]
Abstract
Hazardous chemicals in the environment and diet or their electrophilic metabolites can form adducts with genomic DNA, which can lead to mutations and the initiation of cancer. In addition, reactive intermediates can be generated in the body through oxidative stress and damage the genome. The identification and measurement of DNA adducts are required for understanding exposure and the causal role of a genotoxic chemical in cancer risk. Over the past three decades, 32 P-postlabeling, immunoassays, gas chromatography/mass spectrometry, and liquid chromatography/mass spectrometry (LC/MS) methods have been established to assess exposures to chemicals through measurements of DNA adducts. It is now possible to measure some DNA adducts in human biopsy samples, by LC/MS, with as little as several milligrams of tissue. In this review article, we highlight the formation and biological effects of DNA adducts, and highlight our advances in human biomonitoring by mass spectrometric analysis of formalin-fixed paraffin-embedded tissues, untapped biospecimens for carcinogen DNA adduct biomarker research.
Collapse
Affiliation(s)
- Byeong Hwa Yun
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Jingshu Guo
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Robert J. Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| |
Collapse
|
14
|
Emerging Technologies in Mass Spectrometry-Based DNA Adductomics. High Throughput 2019; 8:ht8020013. [PMID: 31091740 PMCID: PMC6630665 DOI: 10.3390/ht8020013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/19/2019] [Accepted: 05/09/2019] [Indexed: 12/11/2022] Open
Abstract
The measurement of DNA adducts, the covalent modifications of DNA upon the exposure to the environmental and dietary genotoxicants and endogenously produced electrophiles, provides molecular evidence for DNA damage. With the recent improvements in the sensitivity and scanning speed of mass spectrometry (MS) instrumentation, particularly high-resolution MS, it is now feasible to screen for the totality of DNA damage in the human genome through DNA adductomics approaches. Several MS platforms have been used in DNA adductomic analysis, each of which has its strengths and limitations. The loss of 2′-deoxyribose from the modified nucleoside upon collision-induced dissociation is the main transition feature utilized in the screening of DNA adducts. Several advanced data-dependent and data-independent scanning techniques originated from proteomics and metabolomics have been tailored for DNA adductomics. The field of DNA adductomics is an emerging technology in human exposure assessment. As the analytical technology matures and bioinformatics tools become available for analysis of the MS data, DNA adductomics can advance our understanding about the role of chemical exposures in DNA damage and disease risk.
Collapse
|
15
|
Chen H, Yao L, Brown C, Rizzo CJ, Turesky RJ. Quantitation of Apurinic/Apyrimidinic Sites in Isolated DNA and in Mammalian Tissue with a Reduced Level of Artifacts. Anal Chem 2019; 91:7403-7410. [PMID: 31055913 DOI: 10.1021/acs.analchem.9b01351] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The apurinic/apyrimidinic (AP) site is a common lesion of DNA damage. The levels of AP sites reported in the literature cover a wide range, which is primarily due to the artifactual generation or loss of AP sites during processing of the DNA. Herein, we have developed a method for quantitating AP sites with a largely reduced level of artifacts by derivatizing AP sites before DNA isolation. A rapid digestion of nuclear protein was performed to minimize enzymatic DNA repair, followed by direct derivatization of AP sites in the nuclear lysate with O-(pyridin-3-yl-methyl)hydroxylamine, yielding an oxime derivative that is stable through the subsequent DNA processing steps. Quantitation was done using highly selective and sensitive liquid chromatography-tandem mass spectrometry, with a limit of quantitation at 2.2 lesions per 108 nucleotides (nts, 0.9 fmol on column). The method was applied in vivo to measure AP sites in rats undergoing oxidative stress [liver, 3.31 ± 0.47/107 nts (dosed) vs 0.91 ± 0.06/107 nts (control); kidney, 1.60 ± 0.07/107 nts (dosed) vs 1.13 ± 0.12/107 nts (control)]. The basal AP level was significantly lower than literature values. The method was also used to measure AP sites induced by the chemotherapeutic nitrogen mustard in vitro.
Collapse
Affiliation(s)
- Haoqing Chen
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Lihua Yao
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Christina Brown
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Carmelo J Rizzo
- Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| |
Collapse
|
16
|
Minko IG, Christov PP, Li L, Stone MP, McCullough AK, Lloyd RS. Processing of N 5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3. DNA Repair (Amst) 2018; 73:49-54. [PMID: 30448017 DOI: 10.1016/j.dnarep.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 12/29/2022]
Abstract
A variety of agents cause DNA base alkylation damage, including the known hepatocarcinogen aflatoxin B1 (AFB1) and chemotherapeutic drugs derived from nitrogen mustard (NM). The N7 site of guanine is the primary site of alkylation, with some N7-deoxyguanosine adducts undergoing imidazole ring-opening to stable mutagenic N5-alkyl formamidopyrimidine (Fapy-dG) adducts. These adducts exist as a mixture of canonical β- and unnatural α-anomeric forms. The β species are predominant in double-stranded (ds) DNA. Recently, we have demonstrated that the DNA glycosylase NEIL1 can initiate repair of AFB1-Fapy-dG adducts both in vitro and in vivo, with Neil1-/- mice showing an increased susceptibility to AFB1-induced hepatocellular carcinoma. Here, we hypothesized that NEIL1 could excise NM-Fapy-dG and that NEIL3, a closely related DNA glycosylase, could excise both NM-Fapy-dG and AFB1-Fapy-dG. Product formation from the reaction of human NEIL1 with ds oligodeoxynucleotides containing a unique NM-Fapy-dG followed a bi-component exponential function under single turnover conditions. Thus, two adduct conformations were differentially recognized by hNEIL1. The excision rate of the major form (∼13.0 min-1), presumed to be the β-anomer, was significantly higher than that previously reported for 5-hydroxycytosine, 5-hydroxyuracil, thymine glycol (Tg), and AFB1-Fapy-dG. Product generation from the minor form was much slower (∼0.4 min-1), likely reflecting the rate of conversion of the α anomer into the β anomer. Mus musculus NEIL3 (MmuNEIL3Δ324) excised NM-Fapy-dG from single-stranded (ss) DNA (turnover rate of ∼0.4 min-1), but not from ds DNA. Product formation from ss substrate was incomplete, presumably because of a substantial presence of the α anomer. MmuNEIL3Δ324 could not initiate repair of AFB1-Fapy-dG in either ds or ss DNA. Overall, the data suggest that both NEIL1 and NEIL3 may protect cells against cytotoxic and mutagenic effects of NM-Fapy-dG, but NEIL1 may have a unique role in initiation of base excision repair of AFB1-Fapy-dG.
Collapse
Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Plamen P Christov
- Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN 37235, United States
| | - Liang Li
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Michael P Stone
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, United States.
| |
Collapse
|
17
|
Groehler AS, Najjar D, Pujari SS, Sangaraju D, Tretyakova NY. N 6-(2-Deoxy-d- erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-(2-hydroxy-3-buten-1-yl)-formamidopyrimidine Adducts of 1,3-Butadiene: Synthesis, Structural Identification, and Detection in Human Cells. Chem Res Toxicol 2018; 31:885-897. [PMID: 30016111 DOI: 10.1021/acs.chemrestox.8b00123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
1,3-Butadiene (BD) is an environmental and occupational toxicant classified as a human carcinogen. BD is metabolically activated by cytochrome P450 monooxygenases to 3,4-epoxy-1-butene (EB), which alkylates DNA to form a range of nucleobase adducts. Among these, the most abundant are the hydrolytically labile N7-guanine adducts such as N7-(2-hydroxy-3-buten-1-yl)-guanine (N7-EB-dG). We now report that N7-EB-dG can be converted to the corresponding ring open N6-(2-deoxy-d- erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-(2-hydroxy-3-buten-1-yl)-formamidopyrimidine (EB-Fapy-dG) adducts. EB-Fapy-dG lesions were detected in EB-treated calf thymus DNA and in EB-treated mammalian cells using quantitative isotope dilution nanoLC-ESI+-MS/MS. EB-Fapy-dG adduct formation in EB-treated calf thymus DNA was concentration dependent and was greatly accelerated at an increased pH. EB-FAPy-dG adduct amounts were 2-fold higher in base excision repair-deficient NEIL1-/- mouse embryonic fibroblasts (MEF) as compared to isogenic controls (NEIL1+/+), suggesting that this lesion may be a substrate for NEIL1. Furthermore, NEIL1-/- cells were sensitized to EB treatment as compared to NEIL1+/+ fibroblasts. Overall, our results indicate that ring-opened EB-FAPy-dG adducts form under physiological conditions, prompting future studies to determine their contributions to genotoxicity and mutagenicity of BD.
Collapse
Affiliation(s)
- Arnold S Groehler
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Dominic Najjar
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Suresh S Pujari
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Dewakar Sangaraju
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| |
Collapse
|
18
|
Bamberger SN, Malik CK, Voehler MW, Brown SK, Pan H, Johnson-Salyard TL, Rizzo CJ, Stone MP. Configurational and Conformational Equilibria of N 6-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG) Lesion in DNA. Chem Res Toxicol 2018; 31:924-935. [PMID: 30169026 DOI: 10.1021/acs.chemrestox.8b00135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The most common lesion in DNA occurring due to clinical treatment with Temozolomide or cellular exposures to other methylating agents is 7-methylguanine (N7-Me-dG). It can undergo a secondary reaction to form N6-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5- N-methylformamidopyrimidine (MeFapy-dG). MeFapy-dG undergoes epimerization in DNA to produce either α or β deoxyribose anomers. Additionally, conformational rotation around the formyl bond, C5- N5 bond, and glycosidic bond may occur. To characterize and quantitate the mixture of these isomers in DNA, a 13C-MeFapy-dG lesion, in which the CH3 group of the MeFapy-dG was isotopically labeled, was incorporated into the trimer 5'-TXT-3' and the dodecamer 5'-CATXATGACGCT-3' (X = 13C-MeFapy-dG). NMR spectroscopy of both the trimer and dodecamer revealed that the MeFapy-dG lesion exists in single strand DNA as ten configurationally and conformationally discrete species, eight of which may be unequivocally assigned. In the duplex dodecamer, the MeFapy-dG lesion exists as six configurationally and conformationally discrete species. Analyses of NMR data in the single strand trimer confirm that for each deoxyribose anomer, atropisomerism occurs around the C5- N5 bond to produce R a and S a atropisomers. Each atropisomer exhibits geometrical isomerism about the formyl bond yielding E and Z conformations. 1H NMR experiments allow the relative abundances of the species to be determined. For the single strand trimer, the α and β anomers exist in a 3:7 ratio, favoring the β anomer. For the β anomer, with respect to the C5- N5 bond, the R a and S a atropisomers are equally populated. However, the Z geometrical isomer of the formyl moiety is preferred. For the α anomer, the E- S a isomer is present at 12%, whereas all other isomers are present at 5-7%. DNA processing enzymes may differentially recognize different isomers of the MeFapy-dG lesion. Moreover, DNA sequence-specific differences in the populations of configurational and conformational species may modulate biological responses to the MeFapy-dG lesion.
Collapse
Affiliation(s)
- Stephanie N Bamberger
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Chanchal K Malik
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Markus W Voehler
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Summer K Brown
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Hope Pan
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Tracy L Johnson-Salyard
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Carmelo J Rizzo
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Michael P Stone
- Department of Chemistry , Vanderbilt University Center for Structural Biology, Vanderbilt Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University , Nashville , Tennessee 37235 , United States
| |
Collapse
|
19
|
Affiliation(s)
- Yang Yu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yuxiang Cui
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| |
Collapse
|
20
|
Minko IG, Rizzo CJ, Lloyd RS. Mutagenic potential of nitrogen mustard-induced formamidopyrimidine DNA adduct: Contribution of the non-canonical α-anomer. J Biol Chem 2017; 292:18790-18799. [PMID: 28972137 DOI: 10.1074/jbc.m117.802520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/15/2017] [Indexed: 12/14/2022] Open
Abstract
Nitrogen mustards (NMs) are DNA-alkylating compounds that represent the earliest anticancer drugs. However, clinical use of NMs is limited because of their own mutagenic properties. The mechanisms of NM-induced mutagenesis remain unclear. The major product of DNA alkylation by NMs is a cationic NM-N7-dG adduct that can yield the imidazole ring-fragmented lesion, N5-NM-substituted formamidopyrimidine (NM-Fapy-dG). Characterization of this adduct is complicated because it adopts different conformations, including both a canonical β- and an unnatural α-anomeric configuration. Although formation of NM-Fapy-dG in cellular DNA has been demonstrated, its potential role in NM-induced mutagenesis is unknown. Here, we created site-specifically modified single-stranded vectors for replication in primate (COS7) or Escherichia coli cells. In COS7 cells, NM-Fapy-dG caused targeted mutations, predominantly G → T transversions, with overall frequencies of ∼11-12%. These frequencies were ∼2-fold higher than that induced by 8-oxo-dG adduct. Replication in E. coli was essentially error-free. To elucidate the mechanisms of bypass of NM-Fapy-dG, we performed replication assays in vitro with a high-fidelity DNA polymerase, Saccharomyces cerevisiae polymerase (pol) δ. It was found that pol δ could catalyze high-fidelity synthesis past NM-Fapy-dG, but only on a template subpopulation, presumably containing the β-anomeric adduct. Consistent with the low mutagenic potential of the β-anomer in vitro, the mutation frequency was significantly reduced when conditions for vector preparation were modified to favor this configuration. Collectively, these data implicate the α-anomer as a major contributor to NM-Fapy-dG-induced mutagenesis in primate cells.
Collapse
Affiliation(s)
- Irina G Minko
- From the Oregon Institute of Occupational Health Sciences and
| | - Carmelo J Rizzo
- the Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - R Stephen Lloyd
- From the Oregon Institute of Occupational Health Sciences and .,the Departments of Molecular and Medical Genetics and Physiology and Pharmacology, Oregon Health & Science University, Portland, Oregon 97239 and
| |
Collapse
|
21
|
Pujari SS, Tretyakova N. Chemical Biology of N 5-Substituted Formamidopyrimidine DNA Adducts. Chem Res Toxicol 2016; 30:434-452. [PMID: 27959490 DOI: 10.1021/acs.chemrestox.6b00392] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA nucleobases are the prime targets for chemical modifications by endogenous and exogenous electrophiles. Alkylation of the N7 position of guanine and adenine in DNA triggers base-catalyzed imidazole ring opening and the formation of N5-substituted formamidopyrimidine (N5-R-FAPy) lesions. Me-FAPy-dG adducts induced by exposure to methylating agents and AFB-FAPy-dG lesions formed by aflatoxin B1 have been shown to persist in cells and to contribute to toxicity and mutagenicity. In contrast, the biological outcomes of other N5-substituted FAPy lesions have not been fully elucidated. To enable their structural and biological evaluation, N5-R-FAPy adducts must be site-specifically incorporated into synthetic DNA strands using phosphoramidite building blocks, which can be complicated by their unusual structural complexity. N5-R-FAPy exist as a mixture of rotamers and can undergo isomerization between α, β anomers and furanose-pyranose forms. In this Perspective, we will discuss the main types of N5-R-FAPy adducts and summarize the strategies for their synthesis and structural elucidation. We will also summarize the chemical biology studies conducted with N5-R-FAPy-containing DNA to elucidate their effects on DNA replication and to identify the mechanisms of N5-R-FAPy repair.
Collapse
Affiliation(s)
- Suresh S Pujari
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| |
Collapse
|
22
|
AbdulSalam SF, Thowfeik FS, Merino EJ. Excessive Reactive Oxygen Species and Exotic DNA Lesions as an Exploitable Liability. Biochemistry 2016; 55:5341-52. [PMID: 27582430 DOI: 10.1021/acs.biochem.6b00703] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although the terms "excessive reactive oxygen species (ROS)" and "oxidative stress" are widely used, the implications of oxidative stress are often misunderstood. ROS are not a single species but a variety of compounds, each with unique biochemical properties and abilities to react with biomolecules. ROS cause activation of growth signals through thiol oxidation and may lead to DNA damage at elevated levels. In this review, we first discuss a conceptual framework for the interplay of ROS and antioxidants. This review then describes ROS signaling using FLT3-mediated growth signaling as an example. We then focus on ROS-mediated DNA damage. High concentrations of ROS result in various DNA lesions, including 8-oxo-7,8-dihydro-guanine, oxazolone, DNA-protein cross-links, and hydantoins, that have unique biological impacts. Here we delve into the biochemistry of nine well-characterized DNA lesions. Within each lesion, the types of repair mechanisms, the mutations induced, and their effects on transcription and replication are discussed. Finally, this review will discuss biochemically inspired implications for cancer therapy. Several teams have put forward designs to harness the excessive ROS and the burdened DNA repair systems of tumor cells for treating cancer. We discuss inhibition of the antioxidant system, the targeting of DNA repair, and ROS-activated prodrugs.
Collapse
Affiliation(s)
- Safnas F AbdulSalam
- Department of Chemistry, University of Cincinnati , 404 Crosley Tower, Cincinnati, Ohio 45221-0172, United States
| | - Fathima Shazna Thowfeik
- Department of Chemistry, University of Cincinnati , 404 Crosley Tower, Cincinnati, Ohio 45221-0172, United States
| | - Edward J Merino
- Department of Chemistry, University of Cincinnati , 404 Crosley Tower, Cincinnati, Ohio 45221-0172, United States
| |
Collapse
|
23
|
Ishiguro K, Zhu YL, Lin ZP, Penketh PG, Shyam K, Zhu R, Baumann RP, Sartorelli AC, Rutherford TJ, Ratner ES. Cataloging antineoplastic agents according to their effectiveness against platinum-resistant and platinum-sensitive ovarian carcinoma cell lines. JOURNAL OF TRANSLATIONAL SCIENCE 2016; 2:117-124. [PMID: 27076919 DOI: 10.15761/jts.1000127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although epithelial ovarian cancers (EOCs) are initially treated with platinum-based chemotherapy, EOCs vary in platinum responsiveness. Cataloging antineoplastic agents according to their effectiveness against platinum-resistant and platinum-sensitive EOC cell lines is valuable for development of therapeutic strategies to avoid platinum inefficacy and to exploit platinum sensitivity. TOV-21G devoid of FANCF expression, OV-90 and SKOV-3 were employed as examples of platinum-sensitive, platinum-intermediate and platinum-resistant cell lines, respectively. Antineoplastic agents examined included mitomycin C, doxorubicin, etoposide, gemcitabine, chlorambucil, paclitaxel, triapine and X-rays. Their effectiveness against cell lines was analyzed by clonogenic assays. Cytotoxic profiles of mitomycin C and carboplatin were similar, with mitomycin C exhibiting greater potency and selectivity against TOV-21G than carboplatin. Cytotoxic profiles of doxorubicin, etoposide and X-rays overlapped with that of carboplatin, while OV-90 overexpressing Rad51 was more resistant to chlorambucil than SKOV-3. The efficacy of paclitaxel and triapine was independent of platinum sensitivity or resistance. Consistent with these cytotoxic profiles, cisplatin/mitomycin C, triapine, and paclitaxel differed in the capacity to induce phosphorylation of H2AX, and produced unique inhibitory patterns of DNA/RNA syntheses in HL-60 human leukemia cells. Paclitaxel and triapine in combination produced additive antitumor effects in M109 murine lung carcinoma. In conclusion, mitomycin C is potentially more effective against Fanconi anemia pathway-deficient EOCs than carboplatin. Doxorubicin and etoposide, because of their overlapping cytotoxic properties with carboplatin, are unlikely to be efficacious against platinum-refractory EOCs. Paclitaxel and triapine are effective regardless of platinum sensitivity status, and promising in combination for both platinum-sensitive and platinum-refractory EOCs.
Collapse
Affiliation(s)
- Kimiko Ishiguro
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Yong-Lian Zhu
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Z Ping Lin
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Philip G Penketh
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Krishnamurthy Shyam
- Department of Pharmacology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Rui Zhu
- Department of Pharmacology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Raymond P Baumann
- Department of Pharmacology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Alan C Sartorelli
- Department of Pharmacology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Thomas J Rutherford
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Elena S Ratner
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, United States
| |
Collapse
|