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Xue P, Huang D, Pu J, Zhou Y. DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283. J Phys Chem B 2024; 128:6670-6683. [PMID: 38982772 DOI: 10.1021/acs.jpcb.4c01011] [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: 07/11/2024]
Abstract
DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesion─cyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5-C5 and C6-C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol-1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5-C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.
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Affiliation(s)
- Pei Xue
- Guangxi Key Laboratory for Polysaccharide Materials and Modification, Guangxi Higher Education Institutes Key Laboratory for New Chemical and Biological Transformation Process Technology, School of Chemistry and Chemical Engineering, Guangxi Minzu University, 188 Daxue East Road, Nanning, Guangxi 530006, China
| | - Donglian Huang
- Guangxi Key Laboratory for Polysaccharide Materials and Modification, Guangxi Higher Education Institutes Key Laboratory for New Chemical and Biological Transformation Process Technology, School of Chemistry and Chemical Engineering, Guangxi Minzu University, 188 Daxue East Road, Nanning, Guangxi 530006, China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, Indiana 46202, United States
| | - Yan Zhou
- Guangxi Key Laboratory for Polysaccharide Materials and Modification, Guangxi Higher Education Institutes Key Laboratory for New Chemical and Biological Transformation Process Technology, School of Chemistry and Chemical Engineering, Guangxi Minzu University, 188 Daxue East Road, Nanning, Guangxi 530006, China
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2
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Ortiz-Rodríguez LA, Caldero-Rodríguez NE, Seth SK, Díaz-González K, Crespo-Hernández CE. Electronic relaxation mechanism of 9-methyl-2,6-diaminopurine and 2,6-diaminopurine-2'-deoxyribose in solution. Photochem Photobiol 2024; 100:393-403. [PMID: 38018292 DOI: 10.1111/php.13887] [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: 08/30/2023] [Revised: 10/16/2023] [Accepted: 11/05/2023] [Indexed: 11/30/2023]
Abstract
Prolonged ultraviolet exposure results in the formation of cyclobutane pyrimidine dimers (CPDs) in RNA. Consequently, prebiotic photolesion repair mechanisms should have played an important role in the maintenance of the structural integrity of primitive nucleic acids. 2,6-Diaminopurine is a prebiotic nucleobase that repairs CPDs with high efficiency when incorporated into polymers. We investigate the electronic deactivation pathways of 2,6-diaminopurine-2'-deoxyribose and 9-methyl-2,6-diaminopurine in acetonitrile and aqueous solution to shed light on the photophysical and excited state properties of the 2,6-diaminopurine chromophore. Evidence is presented that both are photostable compounds exhibiting similar deactivation mechanisms upon the population of the S1 (ππ* La ) state at 290 nm. The mechanism involves deactivation through the C2- and C6-reaction coordinates and >99% of the excited state population decays through nonradiative pathways involving two conical intersections with the ground state. The radiative and nonradiative lifetimes are longer in aqueous solution compared to acetonitrile. While τ1 is similar in both derivatives, τ2 is ca. 1.5-fold longer in 2,6-diaminopurine-2'-deoxyribose due to a more efficient trapping in the S1 (ππ* La ) minimum. Therefore, 2,6-diaminopurine could have accumulated in significant quantities during prebiotic times to be incorporated into non-canonical RNA and play a significant role in its photoprotection.
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Affiliation(s)
| | | | - Sourav Kanti Seth
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
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3
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Tayanloo-Beik A, Hamidpour SK, Nikkhah A, Arjmand R, Mafi AR, Rezaei-Tavirani M, Larijani B, Gilany K, Arjmand B. DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37923882 DOI: 10.1007/5584_2023_791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amirabbas Nikkhah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasta Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Rezazadeh Mafi
- Department of Radiation Oncology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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4
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Hu ML, Pan YR, Yong YY, Liu Y, Yu L, Qin DL, Qiao G, Law BYK, Wu JM, Zhou XG, Wu AG. Poly (ADP-ribose) polymerase 1 and neurodegenerative diseases: Past, present, and future. Ageing Res Rev 2023; 91:102078. [PMID: 37758006 DOI: 10.1016/j.arr.2023.102078] [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: 02/13/2023] [Revised: 08/30/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a first responder that recognizes DNA damage and facilitates its repair. Neurodegenerative diseases, characterized by progressive neuron loss driven by various risk factors, including DNA damage, have increasingly shed light on the pivotal involvement of PARP1. During the early phases of neurodegenerative diseases, PARP1 experiences controlled activation to swiftly address mild DNA damage, thereby contributing to maintain brain homeostasis. However, in late stages, exacerbated PARP1 activation precipitated by severe DNA damage exacerbates the disease condition. Consequently, inhibition of PARP1 overactivation emerges as a promising therapeutic approach for neurodegenerative diseases. In this review, we comprehensively synthesize and explore the multifaceted role of PARP1 in neurodegenerative diseases, with a particular emphasis on its over-activation in the aggregation of misfolded proteins, dysfunction of the autophagy-lysosome pathway, mitochondrial dysfunction, neuroinflammation, and blood-brain barrier (BBB) injury. Additionally, we encapsulate the therapeutic applications and limitations intrinsic of PARP1 inhibitors, mainly including limited specificity, intricate pathway dynamics, constrained clinical translation, and the heterogeneity of patient cohorts. We also explore and discuss the potential synergistic implementation of these inhibitors alongside other agents targeting DNA damage cascades within neurodegenerative diseases. Simultaneously, we propose several recommendations for the utilization of PARP1 inhibitors within the realm of neurodegenerative disorders, encompassing factors like the disease-specific roles of PARP1, combinatorial therapeutic strategies, and personalized medical interventions. Lastly, the encompassing review presents a forward-looking perspective along with strategic recommendations that could guide future research endeavors in this field.
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Affiliation(s)
- Meng-Ling Hu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi-Ru Pan
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yuan-Yuan Yong
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi Liu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Lu Yu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Da-Lian Qin
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Gan Qiao
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Betty Yuen-Kwan Law
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Jian-Ming Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - Xiao-Gang Zhou
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - An-Guo Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China.
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5
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Stanfill SB, Hecht SS, Joerger AC, González PJ, Maia LB, Rivas MG, Moura JJG, Gupta AK, Le Brun NE, Crack JC, Hainaut P, Sparacino-Watkins C, Tyx RE, Pillai SD, Zaatari GS, Henley SJ, Blount BC, Watson CH, Kaina B, Mehrotra R. From cultivation to cancer: formation of N-nitrosamines and other carcinogens in smokeless tobacco and their mutagenic implications. Crit Rev Toxicol 2023; 53:658-701. [PMID: 38050998 DOI: 10.1080/10408444.2023.2264327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/20/2023] [Indexed: 12/07/2023]
Abstract
Tobacco use is a major cause of preventable morbidity and mortality globally. Tobacco products, including smokeless tobacco (ST), generally contain tobacco-specific N-nitrosamines (TSNAs), such as N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-butanone (NNK), which are potent carcinogens that cause mutations in critical genes in human DNA. This review covers the series of biochemical and chemical transformations, related to TSNAs, leading from tobacco cultivation to cancer initiation. A key aim of this review is to provide a greater understanding of TSNAs: their precursors, the microbial and chemical mechanisms that contribute to their formation in ST, their mutagenicity leading to cancer due to ST use, and potential means of lowering TSNA levels in tobacco products. TSNAs are not present in harvested tobacco but can form due to nitrosating agents reacting with tobacco alkaloids present in tobacco during certain types of curing. TSNAs can also form during or following ST production when certain microorganisms perform nitrate metabolism, with dissimilatory nitrate reductases converting nitrate to nitrite that is then released into tobacco and reacts chemically with tobacco alkaloids. When ST usage occurs, TSNAs are absorbed and metabolized to reactive compounds that form DNA adducts leading to mutations in critical target genes, including the RAS oncogenes and the p53 tumor suppressor gene. DNA repair mechanisms remove most adducts induced by carcinogens, thus preventing many but not all mutations. Lastly, because TSNAs and other agents cause cancer, previously documented strategies for lowering their levels in ST products are discussed, including using tobacco with lower nornicotine levels, pasteurization and other means of eliminating microorganisms, omitting fermentation and fire-curing, refrigerating ST products, and including nitrite scavenging chemicals as ST ingredients.
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Affiliation(s)
- Stephen B Stanfill
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andreas C Joerger
- Structural Genomics Consortium (SGC), Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pablo J González
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - Luisa B Maia
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | - Maria G Rivas
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - José J G Moura
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | | | - Nick E Le Brun
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Jason C Crack
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Grenoble Alpes University, Grenoble, France
| | - Courtney Sparacino-Watkins
- University of Pittsburgh, School of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, PA, USA
| | - Robert E Tyx
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suresh D Pillai
- Department of Food Science & Technology, National Center for Electron Beam Research, Texas A&M University, College Station, TX, USA
| | - Ghazi S Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - S Jane Henley
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin C Blount
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clifford H Watson
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Ravi Mehrotra
- Centre for Health, Innovation and Policy Foundation, Noida, India
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6
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Maguina M, Kang PB, Tsai AC, Pacak CA. Peripheral neuropathies associated with DNA repair disorders. Muscle Nerve 2023; 67:101-110. [PMID: 36190439 PMCID: PMC10075233 DOI: 10.1002/mus.27721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 01/25/2023]
Abstract
Repair of genomic DNA is a fundamental housekeeping process that quietly maintains the health of our genomes. The consequences of a genetic defect affecting a component of this delicate mechanism are quite harmful, characterized by a cascade of premature aging that injures a variety of organs, including the nervous system. One part of the nervous system that is impaired in certain DNA repair disorders is the peripheral nerve. Chronic motor, sensory, and sensorimotor polyneuropathies have all been observed in affected individuals, with specific physiologies associated with different categories of DNA repair disorders. Cockayne syndrome has classically been linked to demyelinating polyneuropathies, whereas xeroderma pigmentosum has long been associated with axonal polyneuropathies. Three additional recessive DNA repair disorders are associated with neuropathies, including trichothiodystrophy, Werner syndrome, and ataxia-telangiectasia. Although plausible biological explanations exist for why the peripheral nerves are specifically vulnerable to impairments of DNA repair, specific mechanisms such as oxidative stress remain largely unexplored in this context, and bear further study. It is also unclear why different DNA repair disorders manifest with different types of neuropathy, and why neuropathy is not universally present in those diseases. Longitudinal physiological monitoring of these neuropathies with serial electrodiagnostic studies may provide valuable noninvasive outcome data in the context of future natural history studies, and thus the responses of these neuropathies may become sentinel outcome measures for future clinical trials of treatments currently in development such as adeno-associated virus gene replacement therapies.
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Affiliation(s)
- Melissa Maguina
- Medical Education Program, Nova Southeastern University, Fort Lauderdale, Florida
| | - Peter B Kang
- Department of Neurology, Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, Minnesota.,Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Ang-Chen Tsai
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida
| | - Christina A Pacak
- Department of Neurology, Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, Minnesota
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Akbari B, Baghaei-Yazdi N, Bahmaie M, Mahdavi Abhari F. The role of plant-derived natural antioxidants in reduction of oxidative stress. Biofactors 2022; 48:611-633. [PMID: 35229925 DOI: 10.1002/biof.1831] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/31/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022]
Abstract
Free radicals are a group of damaging molecules produced during the normal metabolism of cells in the human body. Exposure to ultraviolet radiation, cigarette smoking, and other environmental pollutants enhances free radicals in the human body. The destructive effects of free radicals may also cause harm to membranes, enzymes, and DNA, leading to several human diseases such as cancer, atherosclerosis, malaria, coronavirus disease (COVID-19), rheumatoid arthritis, and neurodegenerative illnesses. This process occurs when there is an imbalance between free radicals and antioxidant defenses. Since antioxidants scavenge free radicals and repair damaged cells, increasing the consumption of fruits and vegetables containing high antioxidant values is recommended to slow down oxidative stress in the body. Additionally, natural products demonstrated a wide range of biological impacts such as anti-inflammatory, anti-aging, anti-atherosclerosis, and anti-cancer properties. Hence, in this review article, our goal is to explore the role of natural therapeutic antioxidant effects to reduce oxidative stress in the diseases.
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Affiliation(s)
- Behnaz Akbari
- School of Medicine, Department of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | - Namdar Baghaei-Yazdi
- College of Liberal Arts & Sciences, School of Life Sciences, University of Westminster, London, UK
| | - Manochehr Bahmaie
- Department of Chemistry, Islamic Azad University, North Tehran Branch, Tehran, Iran
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Chikhaoui A, Kraoua I, Calmels N, Bouchoucha S, Obringer C, Zayoud K, Montagne B, M’rad R, Abdelhak S, Laugel V, Ricchetti M, Turki I, Yacoub-Youssef H. Heterogeneous clinical features in Cockayne syndrome patients and siblings carrying the same CSA mutations. Orphanet J Rare Dis 2022; 17:121. [PMID: 35248096 PMCID: PMC8898519 DOI: 10.1186/s13023-022-02257-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cockayne syndrome (CS) is a rare autosomal recessive disorder caused by mutations in ERCC6/CSB or ERCC8/CSA that participate in the transcription-coupled nucleotide excision repair (TC-NER) of UV-induced DNA damage. CS patients display a large heterogeneity of clinical symptoms and severities, the reason of which is not fully understood, and that cannot be anticipated in the diagnostic phase. In addition, little data is available for affected siblings, and this disease is largely undiagnosed in North Africa. Methods We report here the clinical description as well as genetic and functional characterization of eight Tunisian CS patients, including siblings. These patients, who belonged to six unrelated families, underwent complete clinical examination and biochemical analyses. Sanger sequencing was performed for the recurrent mutation in five families, and targeted gene sequencing was done for one patient of the sixth family. We also performed Recovery RNA Synthesis (RRS) to confirm the functional impairment of DNA repair in patient-derived fibroblasts. Results Six out of eight patients carried a homozygous indel mutation (c.598_600delinsAA) in exon 7 of ERCC8, and displayed a variable clinical spectrum including between siblings sharing the same mutation. The other two patients were siblings who carried a homozygous splice-site variant in ERCC8 (c.843+1G>C). This last pair presented more severe clinical manifestations, which are rarely associated with CSA mutations, leading to gastrostomy and hepatic damage. Impaired TC-NER was confirmed by RRS in six tested patients. Conclusions This study provides the first deep characterization of case series of CS patients carrying CSA mutations in North Africa. These mutations have been described only in this region and in the Middle-East. We also provide the largest characterization of multiple unrelated patients, as well as siblings, carrying the same mutation, providing a framework for dissecting elusive genotype–phenotype correlations in CS. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02257-1.
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Caldero-Rodríguez NE, Ortiz-Rodríguez LA, Gonzalez AA, Crespo-Hernández CE. Photostability of 2,6-diaminopurine and its 2'-deoxyriboside investigated by femtosecond transient absorption spectroscopy. Phys Chem Chem Phys 2022; 24:4204-4211. [PMID: 35119441 DOI: 10.1039/d1cp05269a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultraviolet radiation (UVR) from the sun is essential for the prebiotic syntheses of nucleotides, but it can also induce photolesions such as the cyclobutane pyrimidine dimers (CPDs) to RNA or DNA oligonucleotide in prebiotic Earth. 2,6-Diaminopurine (26DAP) has been proposed to repair CPDs in high yield under prebiotic conditions and be a key component in enhancing the photostability of higher-order prebiotic DNA structures. However, its electronic relaxation pathways have not been studied, which is necessary to know whether 26DAP could have survived the intense UV fluxes of the prebiotic Earth. We investigate the electronic relaxation mechanism of both 26DAP and its 2'-deoxyribonucleoside (26DAP-d) in aqueous solution using steady-state and femtosecond transient absorption measurements that are complemented with electronic-structure calculations. The results demonstrate that both purine derivatives are significantly photostable to UVR. It is shown that upon excitation at 287 nm, the lowest energy 1ππ* state is initially populated. The population then branches following two relaxation coordinates in the 1ππ* potential energy surface, which are identified as the C2- and C6-relaxation coordinates. The population following the C6-coordinate internally converts to the ground state nonradiatively through a nearly barrierless conical intersection within 0.7 ps in 26DAP or within 1.1 ps in 26DAP-d. The population that follows the C2-relaxation coordinate decays back to the ground state by a combination of nonradiative internal conversion via a conical intersection and fluorescence emission from the 1ππ* minimum in 43 ps and 1.8 ns for the N9 and N7 tautomers of 26DAP, respectively, or in 70 ps for 26DAP-d. Fluorescence quantum yields of 0.037 and 0.008 are determined for 26DAP and 26DAP-d, respectively. Collectively, it is demonstrated that most of the excited state population in 26DAP and 26DAP-d decays back to the ground state via both nonradiative and radiative relaxation pathways. This result lends support to the idea that 26DAP could have accumulated in large enough quantities during the prebiotic era to participate in the formation of prebiotic RNA or DNA oligomers and act as a key component in the protection of the prebiotic genetic alphabet.
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Affiliation(s)
| | | | - Andres A Gonzalez
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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10
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Hu H, Liu S, Chu A, Chen J, Xing C, Jing J. Comprehensive analysis of ceRNA network of ERCC4 in colorectal cancer. PeerJ 2022; 9:e12647. [PMID: 34993023 PMCID: PMC8679902 DOI: 10.7717/peerj.12647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Objective ERCC4 is one of the most significant molecules of Nucleotide Excision Repair (NER), which has been researched due to its high expression in colorectal cancer (CRC). This study aimed to find out the ceRNA (competitive endogenous RNA) network of ERCC4 in CRC. Methods and Materials Pan cancer mRNA expression of ERCC4 was evaluated using TCGA database. The protein expression of ERCC4 was evaluated based on the Human Protein Atlas (HPA). We screened DElncRNAs and DEmiRNAs in two groups of ERCC4high and ERCC4low expression in CRC. Then a lncRNA-miRNA-ERCC4 regulatory network was constructed based on DElncRNAs and DEmiRNAs using Starbase database and visualized by Cytoscape software. Kaplan-Meier analysis was performed to evaluate the prognostic value of the ceRNA network. Further, RT-PCR was performed to validate the expression of the representative molecules in the ceRNA network in CRC and normal tissues. The relationship between drug sensitivity and these molecules were also evaluated using RNAactDrug database. Results ERCC4 was overexpressed in a variety of tumors at mRNA levels, including CRC. High expression of ERCC4 was also observed on protein level in CRC. A total of 1,885 DElncRNAs and 68 DEmiRNAs were identified from CRC samples in ERCC4high and ERCC4low expression groups. Predicted by the Starbase database, we got interacting miRNAs and lncRNAs of ERCC4 from the DEmiRNAs and DElncRNAs, and a lncRNA-miRNA-ERCC4 regulatory network was constructed. Kaplan-Meier survival curves results showed that miR-200c-3p (hazard ratio [HR] = 0.62, P = 0.032), MALAT1 (HR = 1.54, P = 0.016), and AC005520.2 (hazard ratio [HR] = 1.75, P = 0.002) were significantly associated with the prognosis of CRC. After validation by RT-PCR, we found that ERCC4 and MALAT1 were up-regulated in CRC compared with normal tissues, while miR-200c-3p was down-regulated. A strong negative correlation was observed between MALAT1 and miR-200c-3p. Drug sensitivity analysis showed that ERCC4, miR-200c and MALAT1 were all associated with Cisplatin. Conclusion We constructed a ceRNA network of ERCC4 in CRC, of which the MALAT1-miR-200c-3p-ERCC4 axis may be involved in the development, prognosis and chemotherapy sensitivity of CRC. These findings might provide novel clues and insights on the molecular mechanisms of ERCC4 and NER pathway in CRC.
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Affiliation(s)
- Huixin Hu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Songyi Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Aining Chu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Jing Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
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11
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Qin N, Geng A, Xue R. Activated or Impaired: An Overview of DNA Repair in Neurodegenerative Diseases. Aging Dis 2022; 13:987-1004. [PMID: 35855336 PMCID: PMC9286913 DOI: 10.14336/ad.2021.1212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022] Open
Abstract
As the population ages, age-related neurodegenerative diseases have become a major challenge in health science. Currently, the pathology of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease, is still not fully understood. Remarkably, emerging evidence indicates a role of genomic DNA damage and repair in various neurodegenerative disorders. Here, we summarized the current understanding of the function of DNA damage repair, especially base excision repair and double strand break repair pathways, in a variety of neurodegenerative diseases. We concluded that exacerbation of DNA lesions is found in almost all types of neurodegenerative diseases, whereas the activities of different DNA repair pathways demonstrate distinct trends, depending on disease type and even brain region. Specifically, key enzymes involved in base excision repair are likely impaired in Alzheimer's disease and amyotrophic lateral sclerosis but activated in Parkinson's disease, while nonhomologous end joining is likely downregulated in most types of neurodegenerative diseases. Hence, impairment of nonhomologous end joining is likely a common etiology for most neurodegenerative diseases, while defects in base excision repair are likely involved in the pathology of Alzheimer's disease and amyotrophic lateral sclerosis but are Parkinson's disease, based on current findings. Although there are still discrepancies and further studies are required to completely elucidate the exact roles of DNA repair in neurodegeneration, the current studies summarized here provide crucial insights into the pathology of neurodegenerative diseases and may reveal novel drug targets for corresponding neurodegenerative diseases.
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Affiliation(s)
| | | | - Renhao Xue
- Correspondence should be addressed to: Dr. Renhao Xue (), 311 Research Building, 550 Hunan Road, Shanghai First Maternity & Infant Hospital, Pudong, Shanghai 201204, China
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12
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Bouchal T, Durník I, Illík V, Réblová K, Kulhánek P. Importance of base-pair opening for mismatch recognition. Nucleic Acids Res 2020; 48:11322-11334. [PMID: 33080020 PMCID: PMC7672436 DOI: 10.1093/nar/gkaa896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/09/2020] [Accepted: 09/30/2020] [Indexed: 01/04/2023] Open
Abstract
Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.
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Affiliation(s)
- Tomáš Bouchal
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Durník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Viktor Illík
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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13
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Sadeghi F, Asgari M, Matloubi M, Ranjbar M, Karkhaneh Yousefi N, Azari T, Zaki-Dizaji M. Molecular contribution of BRCA1 and BRCA2 to genome instability in breast cancer patients: review of radiosensitivity assays. Biol Proced Online 2020; 22:23. [PMID: 33013205 PMCID: PMC7528506 DOI: 10.1186/s12575-020-00133-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/04/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND DNA repair pathways, cell cycle arrest checkpoints, and cell death induction are present in cells to process DNA damage and prevent genomic instability caused by various extrinsic and intrinsic ionizing factors. Mutations in the genes involved in these pathways enhances the ionizing radiation sensitivity, reduces the individual's capacity to repair DNA damages, and subsequently increases susceptibility to tumorigenesis. BODY BRCA1 and BRCA2 are two highly penetrant genes involved in the inherited breast cancer and contribute to different DNA damage pathways and cell cycle and apoptosis cascades. Mutations in these genes have been associated with hypersensitivity and genetic instability as well as manifesting severe radiotherapy complications in breast cancer patients. The genomic instability and DNA repair capacity of breast cancer patients with BRCA1/2 mutations have been analyzed in different studies using a variety of assays, including micronucleus assay, comet assay, chromosomal assay, colony-forming assay, γ -H2AX and 53BP1 biomarkers, and fluorescence in situ hybridization. The majority of studies confirmed the enhanced spontaneous & radiation-induced radiosensitivity of breast cancer patients compared to healthy controls. Using G2 micronucleus assay and G2 chromosomal assay, most studies have reported the lymphocyte of healthy carriers with BRCA1 mutation are hypersensitive to invitro ionizing radiation compared to non-carriers without a history of breast cancer. However, it seems this approach is not likely to be useful to distinguish the BRCA carriers from non-carrier with familial history of breast cancer. CONCLUSION In overall, breast cancer patients are more radiosensitive compared to healthy control; however, inconsistent results exist about the ability of current radiosensitive techniques in screening BRCA1/2 carriers or those susceptible to radiotherapy complications. Therefore, developing further radiosensitivity assay is still warranted to evaluate the DNA repair capacity of individuals with BRCA1/2 mutations and serve as a predictive factor for increased risk of cancer mainly in the relatives of breast cancer patients. Moreover, it can provide more evidence about who is susceptible to manifest severe complication after radiotherapy.
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Affiliation(s)
- Fatemeh Sadeghi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Digestive Diseases Research Institute, Digestive Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Asgari
- Rheumatology Research Center, Tehran University of Medical Sciences, Shariati Hospital, Kargar Ave, Tehran, Iran
| | - Mojdeh Matloubi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maral Ranjbar
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nahid Karkhaneh Yousefi
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahereh Azari
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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14
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Guo J, Yi GZ, Liu Z, Sun X, Yang R, Guo M, Li Y, Li K, Li K, Wang X, Song H, Qi S, Huang G, Liu Y. Quantitative Proteomics Analysis Reveals Nuclear Perturbation in Human Glioma U87 Cells treated with Temozolomide. Cell Biochem Funct 2019; 38:185-194. [PMID: 31833081 DOI: 10.1002/cbf.3459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/23/2019] [Accepted: 10/24/2019] [Indexed: 01/12/2023]
Abstract
Glioblastoma (GBM) is the most malignant and aggressive glioma, which has a very poor prognosis. Temozolomide (TMZ) is still a first-line treatment, but resistance is inevitable even in MGMT-deficient glioblastoma cells. The aims of this study were to comprehend the effect of TMZ on nucleus and the underlying mechanism of acquired TMZ resistance in MGMT-deficient GBM. We show the changes of nuclear proteome in the MGMT-deficient GBM U87 cells treated with TMZ for 1 week. Label-free-based quantitative proteomics were used to investigate nuclear protein abundance change. Subsequently, gene ontology function annotation, KEGG pathway analysis, protein-protein interaction (PPI) network construction analysis of DAPs, and immunofluorescence were applied to validate the quality of proteomics. In total, 457 (455 gene products) significant DAPs were identified, of which 327 were up-regulated and 128 were down-regulated. Bioinformatics analysis uncovered RAD50, MRE11, UBR5, MSH2, MSH6, DDB1, DDB2, RPA1, RBX1, CUL4A, and CUL4B mainly enriched in DNA damage repair related pathway and constituted a protein-protein interaction network. Ribosomal proteins were down-regulated. Cells were in a stress-responsive state, while the entire metabolic level was lowered. SIGNIFICANCE OF THE STUDY: In U87 cell treated with TMZ for 1 week, which resulted in DNA damage, we found various proteins dysregulated in the nucleus. Some proteins related to the DNA damage repair pathway were up-regulated, and there was a strong interaction. We believe this is the potential clues of chemotherapy resistance in tumour cells. These proteins can be used as indicators of tumour resistance screening in the future.
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Affiliation(s)
- Jinglin Guo
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guo-Zhong Yi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China.,Nanfang Glioma Center, Guangzhou, China
| | - Zhifeng Liu
- Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou, China
| | - Xuegang Sun
- The Key Laboratory of Molecular Biology, State Administration of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Southern Medical University, Guangdong, China
| | - Runwei Yang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Manlan Guo
- The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yaomin Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ke Li
- The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kaishu Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiran Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haimin Song
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China.,Nanfang Glioma Center, Guangzhou, China
| | - Guanglong Huang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Nanfang Glioma Center, Guangzhou, China
| | - Yawei Liu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The Laboratory for Precision Neurosurgery Nanfang Hospital, Southern Medical University, Guangzhou, China
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15
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Pfitzer L, Moser C, Gegenfurtner F, Arner A, Foerster F, Atzberger C, Zisis T, Kubisch-Dohmen R, Busse J, Smith R, Timinszky G, Kalinina OV, Müller R, Wagner E, Vollmar AM, Zahler S. Targeting actin inhibits repair of doxorubicin-induced DNA damage: a novel therapeutic approach for combination therapy. Cell Death Dis 2019; 10:302. [PMID: 30944311 PMCID: PMC6447524 DOI: 10.1038/s41419-019-1546-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/20/2019] [Accepted: 03/22/2019] [Indexed: 01/22/2023]
Abstract
Severe side effects often restrict clinical application of the widely used chemotherapeutic drug doxorubicin. In order to decrease required substance concentrations, new concepts for successful combination therapy are needed. Since doxorubicin causes DNA damage, combination with compounds that modulate DNA repair could be a promising strategy. Very recently, a role of nuclear actin for DNA damage repair has been proposed, making actin a potential target for cancer therapy in combination with DNA-damaging therapeutics. This is of special interest, since actin-binding compounds have not yet found their way into clinics. We find that low-dose combination treatment of doxorubicin with the actin polymerizer chondramide B (ChB) synergistically inhibits tumor growth in vivo. On the cellular level we demonstrate that actin binders inhibit distinctive double strand break (DSB) repair pathways. Actin manipulation impairs the recruitment of replication factor A (RPA) to the site of damage, a process crucial for homologous recombination. In addition, actin binders reduce autophosphorylation of DNA-dependent protein kinase (DNA-PK) during nonhomologous end joining. Our findings substantiate a direct involvement of actin in nuclear DSB repair pathways, and propose actin as a therapeutic target for combination therapy with DNA-damaging agents such as doxorubicin.
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Affiliation(s)
- Lisa Pfitzer
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Christina Moser
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Florian Gegenfurtner
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Anja Arner
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Florian Foerster
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Carina Atzberger
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Themistoklis Zisis
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Rebekka Kubisch-Dohmen
- Department of Pharmacy, Pharmaceutical Biology and Biotechnology-Biotechnology and Nanomedicine, Ludwig Maximilian University Munich, Munich, Germany
| | - Johanna Busse
- Department of Pharmacy, Pharmaceutical Biology and Biotechnology-Biotechnology and Nanomedicine, Ludwig Maximilian University Munich, Munich, Germany
| | - Rebecca Smith
- Department of Physiological Chemistry, Ludwig Maximilian University, Munich, Germany.,CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes)-UMR 6290, Univ Rennes, 35000, Rennes, France
| | - Gyula Timinszky
- Department of Physiological Chemistry, Ludwig Maximilian University, Munich, Germany.,MTA SZBK Lendület DNA Damage and Nuclear Dynamics Research Group, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Olga V Kalinina
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Ernst Wagner
- Department of Pharmacy, Pharmaceutical Biology and Biotechnology-Biotechnology and Nanomedicine, Ludwig Maximilian University Munich, Munich, Germany
| | - Angelika M Vollmar
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany
| | - Stefan Zahler
- Department of Pharmacy, Pharmaceutical Biology, Ludwig Maximilian University Munich, Munich, Germany.
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16
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Huang D, Chen S, Pu J, Tan X, Zhou Y. Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically. J Phys Chem A 2019; 123:2025-2039. [PMID: 30776239 DOI: 10.1021/acs.jpca.8b12345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cyclobutane pyrimidine dimer (CPD) is a major photoproduct of deoxyribonucleic acid (DNA) that is damaged by ultraviolet light. This DNA lesion can be repaired by DNA photolyase with the aid of UV light and two cofactors. To understand the repair mechanism of CPD and whether protonation of CPD participates in the DNA repair process, the cycloreversion reactions of four CPD models and proton transfers between the adjacent residue Glu283 and CPD models were explored through the quantum mechanical method. Two-dimensional maps of potential energy surface in a vacuum and in implicit water solution were calculated at the ωB97XD/6-311++G(2df,2pd) level. One-dimensional potential energy profiles were computed for proton transfer reactions. Among the models that have been considered, both in a vacuum and in water solution, the results indicate that the most likely repair mechanism involves CPD•2- radical anion splitting in a stepwise manner. C5-C5' splits first, and C6-C6' splits later. The computed free energies of activation of the two splitting steps are 0.9 and 3.1 kcal/mol, respectively. The adjacent Glu283 may stabilize the CPD•2- radical anion through hydrogen bond and increase the quantum yield; however, protonating the CPD radical anion by Glu283 cannot accelerate the rate of ring opening.
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Affiliation(s)
- Donglian Huang
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
| | - Shanfeng Chen
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology , Indiana University-Purdue University Indianapolis , 402 N. Blackford St. , Indianapolis , Indiana 46202 , United States
| | - Xuecai Tan
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
| | - Yan Zhou
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
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17
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Tezuka S, Ueno M, Kobayashi S, Morimoto M, Ohkawa S, Hirotani A, Tozuka Y, Moriya S, Nakamura Y, Miyagi Y, Sugimori M, Maeda S. Predictive value of ERCC1, ERCC2, ERCC4, and glutathione S-Transferase Pi expression for the efficacy and safety of FOLFIRINOX in patients with unresectable pancreatic cancer. Am J Cancer Res 2018; 8:2096-2105. [PMID: 30416859 PMCID: PMC6220150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/14/2018] [Indexed: 06/09/2023] Open
Abstract
The platinum-based chemotherapy regimen FOLFIRINOX (leucovorin, fluorouracil, irinotecan, and oxaliplatin) is currently used as a standard treatment for patients with unresectable pancreatic cancer. FOLFIRINOX is associated with severe toxicities, including neutropenia, febrile neutropenia, and anorexia; however, there are currently no reliable biomarkers to predict its efficacy and safety. Several studies of patients with various cancers have shown that tumor expression of excision repair cross-complementing (ERCC) proteins and glutathione S-transferase Pi (GSTPi) correlates with the response to platinum-based chemotherapies. Therefore, in this study, we examined the associations between expression of ERCC proteins and GSTPi and the safety and efficacy of FOLFIRINOX in 34 patients with unresectable pancreatic cancer. ERCC1, ERCC2, ERCC4, and GSTPi expression were examined by immunohistochemical staining of tumor specimens and the results were correlated with overall survival, progression-free survival, response rate, disease control rate, and the frequency of grade 3-4 neutropenia and non-hematologic toxicities. We found that ERCC1, ERCC2, ERCC4, and GSTPi were expressed in tumor samples from 64%, 24%, 18%, and 64% of patients, respectively. Notably, there were no statistically significant associations between the expression pattern of any of the proteins and either the clinical outcomes or the frequency of grade 3-4 neutropenia or grade 3-4 anorexia. Collectively, these data indicate that tumor expression of ERCC1, ERCC2, ERCC4, and GSTPi does not predict the safety or efficacy of FOLFIRINOX in patients with pancreatic cancer.
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Affiliation(s)
- Shun Tezuka
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Makoto Ueno
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Satoshi Kobayashi
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Manabu Morimoto
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Shinichi Ohkawa
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Akane Hirotani
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Yuichiro Tozuka
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Satoshi Moriya
- Department of Hepatobiliary and Pancreatic Medical Oncology, Kanagawa Cancer CenterYokohama, Japan
| | - Yoshiyasu Nakamura
- Department of Molecular Pathology and Genetics, Kanagawa Cancer Center Research InstituteYokohama, Japan
| | - Yohei Miyagi
- Department of Molecular Pathology and Genetics, Kanagawa Cancer Center Research InstituteYokohama, Japan
| | - Makoto Sugimori
- Department of Gastroenterology, Yokohama City University Graduate School of MedicineYokohama, Japan
| | - Shin Maeda
- Department of Gastroenterology, Yokohama City University Graduate School of MedicineYokohama, Japan
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18
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Kim JK, McCormick MA, Gallaher CM, Gallaher DD, Trudo SP. Apiaceous Vegetables and Cruciferous Phytochemicals Reduced PhIP-DNA Adducts in Prostate but Not in Pancreas of Wistar Rats. J Med Food 2018; 21:199-202. [PMID: 29451459 DOI: 10.1089/jmf.2017.0043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We previously showed rats fed with apiaceous vegetables, but not with their putative chemopreventive phytochemicals, reduced colonic DNA adducts formed by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a dietary procarcinogen. We report here the effects of feeding apiaceous and cruciferous vegetables versus their purified predominant phytochemicals, either alone or combined, on prostate and pancreatic PhIP-DNA adduct formation. In experiment I, male Wistar rats received three supplemented diets: CRU (cruciferous vegetables), API (apiaceous vegetables), and CRU+API (both types of vegetables). In experiment II, rats received three diets supplemented with phytochemicals matched to their levels in the vegetables from experiment I: P + I (phenethyl isothiocyanate and indole-3-carbinol), FC (furanocoumarins; 5-methoxypsoralen, 8-methoxypsoralen, and isopimpinellin), and COMBO (P + I and FC combined). After 6 days of feeding, PhIP was injected (10 mg/kg body weight) and animals were killed on day 7. PhIP-DNA adducts were analyzed by LC-MS/MS. In prostate, PhIP-DNA adducts were reduced by API (33%, P < .05), P + I (45%, P < .001), and COMBO (30%, P < .01). There were no effects observed in pancreas. Our results suggest that fresh vegetables and purified phytochemicals lower PhIP-DNA adducts and may influence cancer risk.
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Affiliation(s)
- Jae Kyeom Kim
- Department of Food Science and Nutrition, University of Minnesota , St. Paul, MN, USA
| | - Marissa A McCormick
- Department of Food Science and Nutrition, University of Minnesota , St. Paul, MN, USA
| | - Cynthia M Gallaher
- Department of Food Science and Nutrition, University of Minnesota , St. Paul, MN, USA
| | - Daniel D Gallaher
- Department of Food Science and Nutrition, University of Minnesota , St. Paul, MN, USA
| | - Sabrina P Trudo
- Department of Food Science and Nutrition, University of Minnesota , St. Paul, MN, USA
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19
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Apiaceous vegetable intake modulates expression of DNA damage response genes and microRNA in the rat colon. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Kim C, Yang J, Jeong SH, Kim H, Park GH, Shin HB, Ro M, Kim KY, Park Y, Kim KP, Kwack K. Yeast-based assays for characterization of the functional effects of single nucleotide polymorphisms in human DNA repair genes. PLoS One 2018; 13:e0193823. [PMID: 29522548 PMCID: PMC5844570 DOI: 10.1371/journal.pone.0193823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/20/2018] [Indexed: 01/03/2023] Open
Abstract
DNA repair mechanisms maintain genomic integrity upon exposure to various types of DNA damage, which cause either single- or double-strand breaks in the DNA. Here, we propose a strategy for the functional study of single nucleotide polymorphisms (SNPs) in the human DNA repair genes XPD/ERCC2, RAD18, and KU70/XRCC6 and the checkpoint activation gene ATR that are essentially involved in the cell cycle and DNA damage repair. We analyzed the mutational effects of the DNA repair genes under DNA-damaging conditions, including ultraviolet irradiation and treatment with genotoxic reagents, using a Saccharomyces cerevisiae system to overcome the limitations of the human cell-based assay. We identified causal variants from selected SNPs in the present analyses. (i) R594C SNP in RAD3 (human XPD/ERCC2) caused severe reductions in the growth rate of mutant cells upon short-wavelength UV irradiation or chemical reagent treatment. (ii) The growth rates of the selected variants in RAD18, YKU70, and MEC1 were similar to those of wild-type cells on methyl methanesulfonate and hydroxyurea treated media. (iii) We also assessed the structural impact of the SNPs by analyzing differences in the structural conformation and calculating the root mean square deviation, which is a measure of the discordance of the Cα atoms between protein structures. Based on the above results, we propose that these analytical approaches serve as efficient methods for the identification of causal variants of human disease-causing genes and elucidation of yeast-cell based molecular mechanisms.
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Affiliation(s)
- Changshin Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jinmo Yang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Su-Hyun Jeong
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Hayoung Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Geun-hee Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Hwa Beom Shin
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - MyungJa Ro
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Kyoung-Yeon Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Keun Pil Kim
- Department of Life Sciences, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
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21
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Zhang Y, Cao J, Meng Y, Qu C, Shen F, Xu L. Overexpression of xeroderma pigmentosum group C decreases the chemotherapeutic sensitivity of colorectal carcinoma cells to cisplatin. Oncol Lett 2018; 15:6336-6344. [PMID: 29616110 PMCID: PMC5876430 DOI: 10.3892/ol.2018.8127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 11/20/2017] [Indexed: 11/09/2022] Open
Abstract
Xeroderma pigmentosum group C (XPC) is a DNA-damage-recognition gene active at the early stage of DNA repair. XPC also participates in regulation of cell-cycle checkpoint and DNA-damage-induced apoptosis. In the present study, the expression levels of genes involved in nucleotide excision repair (NER) were assessed in human colorectal cancer (CRC) tissue. This analysis revealed that expression of XPC mRNA significantly increased in colorectal carcinoma tissues compared with matched normal controls. Expression of XPC gradually increased along with the degree of progression of CRC. In vitro, an XTT assay demonstrated that small interfering RNA (siRNA) targeting XPC significantly increased the sensitivity of CRC SW480 cells to cisplatin, whereas cells transfected with a XPC-overexpression plasmid became more resistant to cisplatin. Furthermore, flow cytometry revealed that the proportion of apoptotic cells significantly increased in XPC-knockdown cells upon cisplatin treatment. However, the overexpression XPC significantly increased the resistance of cells to cisplatin. In vivo, tumor growth was significantly reduced in tumor-bearing mice when the XPC gene was knocked down. Upregulation of the expression of pro-apoptotic Bcl-associated X and downregulation of the anti-apoptotic B-cell lymphoma 2 proteins was observed in the implanted tumor tissue. In conclusion, XPC serves a key role in chemotherapeutic sensitivity of CRC to cisplatin, meaning that it may be a potential target for chemotherapy of CRC.
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Affiliation(s)
- Yi Zhang
- Department of Digestive Endoscopic Diagnosis and Treatment, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Jia Cao
- Department of Digestive Endoscopic Diagnosis and Treatment, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Yanni Meng
- Department of Digestive Endoscopic Diagnosis and Treatment, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Chunying Qu
- Department of Digestive Endoscopic Diagnosis and Treatment, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Feng Shen
- Department of Digestive Endoscopic Diagnosis and Treatment, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Leiming Xu
- Department of Digestive Endoscopic Diagnosis and Treatment, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
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22
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Sar D, Kim B, Ostadhossein F, Misra SK, Pan D. Revisiting Polyarenes and Related Molecules: An Update of Synthetic Approaches and Structure-Activity-Mechanistic Correlation for Carcinogenesis. CHEM REC 2018; 18:619-658. [DOI: 10.1002/tcr.201700110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/05/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Dinabandhu Sar
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
| | | | - Fatemeh Ostadhossein
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
| | - Santosh K. Misra
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
| | - Dipanjan Pan
- Department of Bioengineering; University of Illinois at Urbana-Champaign; Biomedical Research Center, Office 3304; 3rd Floor, Mills Breast Cancer Institute, Carle Foundation Hospital; 502 N. Busey Urbana IL 61801 USA
- Mills Breast Cancer Institute and Carle Foundation Hospital; 502 North Busey Urbana, Illinois 61801 USA
- Department of Materials Science and Engineering; University of Illinois at Urbana-Champaign, Urbana, Illinois; 61801 USA
- Beckman Institute; University of Illinois at Urbana-Champaign; Urbana, Illinois 61801 USA
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23
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Zhu B, Chen S, Wang H, Yin C, Han C, Peng C, Liu Z, Wan L, Zhang X, Zhang J, Lian CG, Ma P, Xu ZX, Prince S, Wang T, Gao X, Shi Y, Liu D, Liu M, Wei W, Wei Z, Pan J, Wang Y, Xuan Z, Hess J, Hayward NK, Goding CR, Chen X, Zhou J, Cui R. The protective role of DOT1L in UV-induced melanomagenesis. Nat Commun 2018; 9:259. [PMID: 29343685 PMCID: PMC5772495 DOI: 10.1038/s41467-017-02687-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 12/13/2017] [Indexed: 11/09/2022] Open
Abstract
The DOT1L histone H3 lysine 79 (H3K79) methyltransferase plays an oncogenic role in MLL-rearranged leukemogenesis. Here, we demonstrate that, in contrast to MLL-rearranged leukemia, DOT1L plays a protective role in ultraviolet radiation (UVR)-induced melanoma development. Specifically, the DOT1L gene is located in a frequently deleted region and undergoes somatic mutation in human melanoma. Specific mutations functionally compromise DOT1L methyltransferase enzyme activity leading to reduced H3K79 methylation. Importantly, in the absence of DOT1L, UVR-induced DNA damage is inefficiently repaired, so that DOT1L loss promotes melanoma development in mice after exposure to UVR. Mechanistically, DOT1L facilitates DNA damage repair, with DOT1L-methylated H3K79 involvement in binding and recruiting XPC to the DNA damage site for nucleotide excision repair (NER). This study indicates that DOT1L plays a protective role in UVR-induced melanomagenesis.
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Affiliation(s)
- Bo Zhu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, 250014, Jinan, China
| | - Shuyang Chen
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Hongshen Wang
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Chengqian Yin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Institute of Life Science, Jiangsu University, 212013, Zhenjiang, China
| | - Changpeng Han
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Cong Peng
- Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Zhaoqian Liu
- Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Xiaoyang Zhang
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Jie Zhang
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Christine G Lian
- Department of Pathology, The Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA
| | - Peilin Ma
- Department of Pathology, Indiana University School of Medicine, 340 West 10th Street, Fairbanks 6200, Indianapolis, IN, 46202, USA
| | - Zhi-Xiang Xu
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - Sharon Prince
- Department of Human Biology, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Tao Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 300193, Tianjin, China
| | - Xiumei Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 300193, Tianjin, China
| | - Yujiang Shi
- Department of Medicine, Endocrinology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Min Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, 250014, Jinan, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Jingxuan Pan
- Cancer Pharmacology Research Institute, Jinan University, 510632, Guangzhou, China
| | - Yongjun Wang
- Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Jay Hess
- Department of Pathology, Indiana University School of Medicine, 340 West 10th Street, Fairbanks 6200, Indianapolis, IN, 46202, USA
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane City, QLD, 4006, Australia
| | - Colin R Goding
- Ludwig Institute for Cancer Research, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Xiang Chen
- Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China.
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, 250014, Jinan, China.
| | - Rutao Cui
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.
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24
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Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS. Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science 2017; 356:189-194. [PMID: 28408603 DOI: 10.1126/science.aak9787] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 02/03/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Single-cell genomics is important for biology and medicine. However, current whole-genome amplification (WGA) methods are limited by low accuracy of copy-number variation (CNV) detection and low amplification fidelity. Here we report an improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI), which outperforms existing methods, enabling micro-CNV detection with kilobase resolution. This allowed direct observation of stochastic firing of DNA replication origins, which differs from cell to cell. We also show that the predominant cytosine-to-thymine mutations observed in single-cell genomics often arise from the artifact of cytosine deamination upon cell lysis. However, identifying single-nucleotide variations (SNVs) can be accomplished by sequencing kindred cells. We determined the spectrum of SNVs in a single human cell after ultraviolet radiation, revealing their nonrandom genome-wide distribution.
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Affiliation(s)
- Chongyi Chen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dong Xing
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Longzhi Tan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Heng Li
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Guangyu Zhou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lei Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. .,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
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25
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Association of DNA repair genes polymorphisms and mutations with increased risk of head and neck cancer: a review. Med Oncol 2017; 34:197. [PMID: 29143133 PMCID: PMC5688183 DOI: 10.1007/s12032-017-1057-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022]
Abstract
DNA repair mechanisms allow maintain genomic stability and proper functioning within the cells. Any aberrations may cause an increased risk of many diseases such as cancer. The most crucial risk factors for head and neck squamous cell carcinoma are behavioral factors, predominantly chronic exposure to tobacco, alcohol addiction, and infection with human papillomavirus or Epstein–Barr virus. These agents can induce DNA damage; therefore, cells must activate appropriate mechanisms in order to function correctly. Cancer cells are marked with genomic instability, which is associated with a greater tendency for the accumulation of a DNA damage and increased chemo- and radioresistance. Multiple studies have assessed the correlation of increased head and neck cancer (HNC) risk with polymorphism in the DNA repair genes. However, they suggest that interaction of DNA repair genes mutations with susceptibility to HNC depends on a patient’s race and risk factors, especially tobacco smoking. Further identification of these sequence variations must be performed. In this review, we discuss the current knowledge about the DNA repair genes mutations and polymorphisms associated with the high risk of head and neck treatment.
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26
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Kim K, Kim JH, Kim YH, Hong SE, Lee SH. Pathway profiles based on gene-set enrichment analysis in the honey bee Apis mellifera under brood rearing-suppressed conditions. Genomics 2017; 110:43-49. [PMID: 28803879 DOI: 10.1016/j.ygeno.2017.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/25/2017] [Accepted: 08/09/2017] [Indexed: 11/29/2022]
Abstract
Perturbation of normal behaviors in honey bee colonies by any external factor can immediately reduce the colony's capacity for brood rearing, which can eventually lead to colony collapse. To investigate the effects of brood-rearing suppression on the biology of honey bee workers, gene-set enrichment analysis of the transcriptomes of worker bees with or without suppressed brood rearing was performed. When brood rearing was suppressed, pathways associated with both protein degradation and synthesis were simultaneously over-represented in both nurses and foragers, and their overall pathway representation profiles resembled those of normal foragers and nurses, respectively. Thus, obstruction of normal labor induced over-representation in pathways related with reshaping of worker bee physiology, suggesting that transition of labor is physiologically reversible. In addition, some genes associated with the regulation of neuronal excitability, cellular and nutritional stress and aggressiveness were over-expressed under brood rearing suppression perhaps to manage in-hive stress under unfavorable conditions.
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Affiliation(s)
- Kyungmun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Ju Hyeon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Young Ho Kim
- Department of Applied Biology, College of Ecology & Environmental Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - Seong-Eui Hong
- Theragen Etex, Bio Institute, Suwon, Gyeonggi-do, Republic of Korea
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea; Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
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27
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Huestis J, Zhou X, Chen L, Feng C, Hudson LG, Liu KJ. Kinetics and thermodynamics of zinc(II) and arsenic(III) binding to XPA and PARP-1 zinc finger peptides. J Inorg Biochem 2016; 163:45-52. [PMID: 27521476 PMCID: PMC5096954 DOI: 10.1016/j.jinorgbio.2016.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022]
Abstract
Inhibition of DNA repair is an established mechanism of arsenic co-carcinogenesis, and may be perpetuated by the binding of As(III) to key zinc finger (zf) DNA repair proteins. Validated molecular targets of As(III) include the first zinc finger domain of Poly (ADP-Ribose) Polymerase 1 (PARP-1), and the zinc finger domain of Xeroderma Pigmentosum Complementation Group A (XPA). In order to gain an understanding of the thermodynamic and kinetic parameters of the interaction of As(III) with these two zinc finger motifs, a fluorescence based approach was used to investigate Zn(II) and As(III) binding to synthetic model peptides corresponding to the zf motif of XPA and first zf motif of PARP-1, referred to in this paper as XPAzf and PARP-1zf-1, respectively. While XPAzf and PARP-1zf-1 display similar relative affinities for As(III), PARP-1zf-1 shows a potential kinetic advantage over XPAzf for As(III) binding, with a rate constant for the fast phase of formation of As(III)-PARP-1zf-1 approximately 4-fold higher than for As(III)-XPAzf. However, the binding of Zn(II) with either peptide proceeds at a faster rate than As(III). Notably, XPAzf demonstrates comparable affinities for binding both metals, while PARP-1zf-1 shows a slightly higher affinity for Zn(II), suggesting that the relative concentrations of Zn(II) and As(III) in a system may significantly influence which species predominates in zinc finger occupancy. These results provide insight into the mechanisms underlying interactions between zinc finger structures and As(III), and highlight the potential utility of zinc supplementation in mitigating adverse effects of As(III) on zinc finger functions in vivo.
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Affiliation(s)
- Juliana Huestis
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
| | - Xixi Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
| | - Li Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
| | - Changjian Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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28
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Yagi T, Fujikawa Y, Sawai T, Takamura-Enya T, Ito-Harashima S, Kawanishi M. Error-Prone and Error-Free Translesion DNA Synthesis over Site-Specifically Created DNA Adducts of Aryl Hydrocarbons (3-Nitrobenzanthrone and 4-Aminobiphenyl). Toxicol Res 2015; 33:265-272. [PMID: 29071010 PMCID: PMC5654197 DOI: 10.5487/tr.2017.33.4.265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 09/20/2017] [Accepted: 09/25/2017] [Indexed: 01/05/2023] Open
Abstract
Aryl hydrocarbons such as 3-nitrobenzanthrone (NBA), 4-aminobiphenyl (ABP), acetylaminofluorene (AAF), benzo(a)pyrene (BaP), and 1-nitropyrene (NP) form bulky DNA adducts when absorbed by mammalian cells. These chemicals are metabolically activated to reactive forms in mammalian cells and preferentially get attached covalently to the N2 or C8 positions of guanine or the N6 position of adenine. The proportion of N2 and C8 guanine adducts in DNA differs among chemicals. Although these adducts block DNA replication, cells have a mechanism allowing to continue replication by bypassing these adducts: translesion DNA synthesis (TLS). TLS is performed by translesion DNA polymerases—Pol η, κ, ι, and ζ and Rev1—in an error-free or error-prone manner. Regarding the NBA adducts, namely, 2-(2′-deoxyguanosin-N2-yl)-3-aminobenzanthrone (dG-N2-ABA) and N-(2′-deoxyguanosin-8-yl)-3-aminobenzanthrone (dG-C8-ABA), dG-N2-ABA is produced more often than dG-C8-ABA, whereas dG-C8-ABA blocks DNA replication more strongly than dG-N2-ABA. dG-N2-ABA allows for a less error-prone bypass than dG-C8-ABA does. Pol η and κ are stronger contributors to TLS over dG-C8-ABA, and Pol κ bypasses dG-C8-ABA in an error-prone manner. TLS efficiency and error-proneness are affected by the sequences surrounding the adduct, as demonstrated in our previous study on an ABP adduct, N-(2′-deoxyguanosine-8-yl)-4-aminobiphenyl (dG-C8-ABP). Elucidation of the general mechanisms determining efficiency, error-proneness, and the polymerases involved in TLS over various adducts is the next step in the research on TLS. These TLS studies will clarify the mechanisms underlying aryl hydrocarbon mutagenesis and carcinogenesis in more detail.
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Affiliation(s)
- Takashi Yagi
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Yoshihiro Fujikawa
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Tomoko Sawai
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takeji Takamura-Enya
- Department of Applied Chemistry, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Sayoko Ito-Harashima
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Masanobu Kawanishi
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
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29
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Zhou T, Chen P, Gu J, Bishop AJR, Scott LM, Hasty P, Rebel VI. Potential relationship between inadequate response to DNA damage and development of myelodysplastic syndrome. Int J Mol Sci 2015; 16:966-89. [PMID: 25569081 PMCID: PMC4307285 DOI: 10.3390/ijms16010966] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/22/2014] [Indexed: 12/29/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are responsible for the continuous regeneration of all types of blood cells, including themselves. To ensure the functional and genomic integrity of blood tissue, a network of regulatory pathways tightly controls the proliferative status of HSCs. Nevertheless, normal HSC aging is associated with a noticeable decline in regenerative potential and possible changes in other functions. Myelodysplastic syndrome (MDS) is an age-associated hematopoietic malignancy, characterized by abnormal blood cell maturation and a high propensity for leukemic transformation. It is furthermore thought to originate in a HSC and to be associated with the accrual of multiple genetic and epigenetic aberrations. This raises the question whether MDS is, in part, related to an inability to adequately cope with DNA damage. Here we discuss the various components of the cellular response to DNA damage. For each component, we evaluate related studies that may shed light on a potential relationship between MDS development and aberrant DNA damage response/repair.
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Affiliation(s)
- Ting Zhou
- Greehey Children's Cancer Research Center, University of Texas Health Science Center San Antonio (UTHSCSA), 8403 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Peishuai Chen
- Greehey Children's Cancer Research Center, University of Texas Health Science Center San Antonio (UTHSCSA), 8403 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Jian Gu
- Department of Hematology, Northern Jiangsu People's Hospital, Yangzhou 225001, China.
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Center, University of Texas Health Science Center San Antonio (UTHSCSA), 8403 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Linda M Scott
- The University of Queensland Diamantina Institute, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
| | - Paul Hasty
- The Cancer Therapy Research Center, UTHSCSA, 7979 Wurzbach Road, San Antonio, TX 78229, USA.
| | - Vivienne I Rebel
- Greehey Children's Cancer Research Center, University of Texas Health Science Center San Antonio (UTHSCSA), 8403 Floyd Curl Drive, San Antonio, TX 78229, USA.
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Hocevar BA, Kamendulis LM, Pu X, Perkins SM, Wang ZY, Johnston EL, DeWitt JM, Li L, Loehrer PJ, Klaunig JE, Chiorean EG. Contribution of environment and genetics to pancreatic cancer susceptibility. PLoS One 2014; 9:e90052. [PMID: 24651674 PMCID: PMC3961224 DOI: 10.1371/journal.pone.0090052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/27/2014] [Indexed: 12/20/2022] Open
Abstract
Several risk factors have been identified as potential contributors to pancreatic cancer development, including environmental and lifestyle factors, such as smoking, drinking and diet, and medical conditions such as diabetes and pancreatitis, all of which generate oxidative stress and DNA damage. Oxidative stress status can be modified by environmental factors and also by an individual's unique genetic makeup. Here we examined the contribution of environment and genetics to an individual's level of oxidative stress, DNA damage and susceptibility to pancreatic cancer in a pilot study using three groups of subjects: a newly diagnosed pancreatic cancer group, a healthy genetically-unrelated control group living with the case subject, and a healthy genetically-related control group which does not reside with the subject. Oxidative stress and DNA damage was evaluated by measuring total antioxidant capacity, direct and oxidative DNA damage by Comet assay, and malondialdehyde levels. Direct DNA damage was significantly elevated in pancreatic cancer patients (age and sex adjusted mean ± standard error: 1.00 ± 0.05) versus both healthy unrelated and related controls (0.70 ± 0.06, p<0.001 and 0.82 ± 0.07, p = 0.046, respectively). Analysis of 22 selected SNPs in oxidative stress and DNA damage genes revealed that CYP2A6 L160H was associated with pancreatic cancer. In addition, DNA damage was found to be associated with TNFA -308G>A and ERCC4 R415Q polymorphisms. These results suggest that measurement of DNA damage, as well as select SNPs, may provide an important screening tool to identify individuals at risk for development of pancreatic cancer.
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Affiliation(s)
- Barbara A. Hocevar
- Department of Environmental Health, Indiana University, Bloomington, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Lisa M. Kamendulis
- Department of Environmental Health, Indiana University, Bloomington, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Xinzhu Pu
- Department of Environmental Health, Indiana University, Bloomington, Indiana, United States of America
| | - Susan M. Perkins
- Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Zheng-Yu Wang
- Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Erica L. Johnston
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - John M. DeWitt
- Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Lang Li
- Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Patrick J. Loehrer
- Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - James E. Klaunig
- Department of Environmental Health, Indiana University, Bloomington, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- * E-mail: (JEK); (EGC)
| | - E. Gabriela Chiorean
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- University of Washington, Seattle, Washington, United States of America
- * E-mail: (JEK); (EGC)
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31
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A short review on the implications of base excision repair pathway for neurons: relevance to neurodegenerative diseases. Mitochondrion 2013; 16:38-49. [PMID: 24220222 DOI: 10.1016/j.mito.2013.10.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/31/2013] [Accepted: 10/31/2013] [Indexed: 12/13/2022]
Abstract
Oxidative DNA damage results from the attack by reactive oxygen and nitrogen species (ROS/RNS) on human genome. This includes base modifications such as oxidized bases, abasic (AP) sites, and single-strand breaks (SSBs), all of which are repaired by the base excision repair (BER) pathway, one among the six known repair pathways. BER-pathway in mammalian cells involves several evolutionarily conserved proteins and is also linked to genome replication and transcription. The BER-pathway enzymes, namely, DNA glycosylases (DGs) and the end-processing proteins such as abasic endonuclease (APE1), form complexes with downstream repair enzymes via protein-protein and DNA-protein interactions. An emerging concept for BER proteins is their involvement in non-canonical functions associated to RNA metabolism, which is opening new interesting perspectives. Various mechanisms that are underlined in maintaining neuronal cell genome integrity are identified, but are inconclusive in providing protection against oxidative damage in neurodegenerative disorders, main emphasis is given towards the role played by the proteins of BER-pathway that is discussed. In addition, mechanisms of action of BER-pathway in nuclear vs. mitochondria as well as the non-canonical functions are discussed in connection to human neurodegenerative diseases.
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32
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Deciphering signatures of mutational processes operative in human cancer. Cell Rep 2013; 3:246-59. [PMID: 23318258 PMCID: PMC3588146 DOI: 10.1016/j.celrep.2012.12.008] [Citation(s) in RCA: 858] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/07/2012] [Accepted: 12/13/2012] [Indexed: 11/24/2022] Open
Abstract
The genome of a cancer cell carries somatic mutations that are the cumulative consequences of the DNA damage and repair processes operative during the cellular lineage between the fertilized egg and the cancer cell. Remarkably, these mutational processes are poorly characterized. Global sequencing initiatives are yielding catalogs of somatic mutations from thousands of cancers, thus providing the unique opportunity to decipher the signatures of mutational processes operative in human cancer. However, until now there have been no theoretical models describing the signatures of mutational processes operative in cancer genomes and no systematic computational approaches are available to decipher these mutational signatures. Here, by modeling mutational processes as a blind source separation problem, we introduce a computational framework that effectively addresses these questions. Our approach provides a basis for characterizing mutational signatures from cancer-derived somatic mutational catalogs, paving the way to insights into the pathogenetic mechanism underlying all cancers.
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Tillhon M, Cazzalini O, Nardo T, Necchi D, Sommatis S, Stivala LA, Scovassi AI, Prosperi E. p300/CBP acetyl transferases interact with and acetylate the nucleotide excision repair factor XPG. DNA Repair (Amst) 2012; 11:844-52. [PMID: 22954786 DOI: 10.1016/j.dnarep.2012.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 07/03/2012] [Accepted: 08/03/2012] [Indexed: 01/01/2023]
Abstract
Nucleotide excision repair (NER) is an important DNA repair mechanism through which cells remove bulky DNA lesions. Following DNA damage, the histone acetyltransferase (HAT) p300 (also referred to as lysine acetyltransferase or KAT) is known to associate with proliferating cell nuclear antigen (PCNA), a master regulator of DNA replication and repair processes. This interaction, which results in HAT inhibition, may be dissociated by the cell cycle inhibitor p21(CDKN1A), thereby restoring p300 activity; however, the role of this protein interplay is still unclear. Here, we report that silencing p300 or its homolog CREB-binding protein (CBP) by RNA interference (RNAi) significantly reduces DNA repair synthesis in human fibroblasts. In addition, we determined whether p300 and CBP may associate with and acetylate specific NER factors such as XPG, the 3'-endonuclease that is involved in the incision/excision step and is known to interact with PCNA. Our results show that p300 and CBP interact with XPG, which has been found to be acetylated in vivo. XPG is acetylated by p300 in vitro, and this reaction is inhibited by PCNA. Knocking down both p300/CBP by RNAi or by chemical inhibition with curcumin greatly reduced XPG acetylation, and a concomitant accumulation of the protein at DNA damage sites was observed. The ability of p21 to bind PCNA was found to regulate the interaction between p300 and XPG, and an abnormal accumulation of XPG at DNA damage sites was also found in p21(-/-) fibroblasts. These results indicate an additional function of p300/CBP in NER through the acetylation of XPG protein in a PCNA-p21 dependent manner.
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Affiliation(s)
- Micol Tillhon
- Istituto di Genetica Molecolare (IGM) del CNR, Pavia, Italy
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Fuss JO, Tainer JA. XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair (Amst) 2011; 10:697-713. [PMID: 21571596 DOI: 10.1016/j.dnarep.2011.04.028] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Helicases must unwind DNA at the right place and time to maintain genomic integrity or gene expression. Biologically critical XPB and XPD helicases are key members of the human TFIIH complex; they anchor CAK kinase (cyclinH, MAT1, CDK7) to TFIIH and open DNA for transcription and for repair of duplex distorting damage by nucleotide excision repair (NER). NER is initiated by arrested RNA polymerase or damage recognition by XPC-RAD23B with or without DDB1/DDB2. XP helicases, named for their role in the extreme sun-mediated skin cancer predisposition xeroderma pigmentosum (XP), are then recruited to asymmetrically unwind dsDNA flanking the damage. XPB and XPD genetic defects can also cause premature aging with profound neurological defects without increased cancers: Cockayne syndrome (CS) and trichothiodystrophy (TTD). XP helicase patient phenotypes cannot be predicted from the mutation position along the linear gene sequence and adjacent mutations can cause different diseases. Here we consider the structural biology of DNA damage recognition by XPC-RAD23B, DDB1/DDB2, RNAPII, and ATL, and of helix unwinding by the XPB and XPD helicases plus the bacterial repair helicases UvrB and UvrD in complex with DNA. We then propose unified models for TFIIH assembly and roles in NER. Collective crystal structures with NMR and electron microscopy results reveal functional motifs, domains, and architectural elements that contribute to biological activities: damaged DNA binding, translocation, unwinding, and ATP driven changes plus TFIIH assembly and signaling. Coupled with mapping of patient mutations, these combined structural analyses provide a framework for integrating and unifying the rich biochemical and cellular information that has accumulated over forty years of study. This integration resolves puzzles regarding XP helicase functions and suggests that XP helicase positions and activities within TFIIH detect and verify damage, select the damaged strand for incision, and coordinate repair with transcription and cell cycle through CAK signaling.
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Affiliation(s)
- Jill O Fuss
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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35
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Zhao X, Krishnamurthy N, Burrows CJ, David SS. Mutation versus repair: NEIL1 removal of hydantoin lesions in single-stranded, bulge, bubble, and duplex DNA contexts. Biochemistry 2010; 49:1658-66. [PMID: 20099873 DOI: 10.1021/bi901852q] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human DNA glycosylase NEIL1 exhibits a superior ability to remove oxidized guanine lesions guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from duplex DNA in comparison to other substrates. In this work, Gh and Sp lesions in bubble, bulge, and single-stranded DNA were found to be good substrates for NEIL1 but were typically excised at much slower rates than from canonical duplex substrates. A notable exception was the activity of NEIL1 on removal of Gh in bubble structures which approaches that of the normal duplex substrate. The cleavage of Gh in the template strand of a replication or transcription bubble may prevent mutations associated with Gh during replication or transcription. However, removal of hydantoin lesions in the absence of an opposite base may also result in strand breaks and potentially deletion and frameshift mutations. Consistent with this as a potential mechanism leading to an N-1 frameshift mutation, the nick left after the removal of the Gh lesion in a DNA bulge by NEIL1 was efficiently religated in the presence of polynucleotide kinase (PNK) and human DNA ligase III (Lig III). These results indicate that NEIL1 does not require a base opposite to identify and remove hydantoin lesions. Depending on the context, the glycosylase activity of NEIL1 may stall replication and prevent mutations or lead to inappropriate removal that may contribute to the mutational spectrum of these unusual lesions.
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Affiliation(s)
- Xiaobei Zhao
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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36
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Recent insights into the molecular mechanisms involved in aging and the malignant transformation of adult stem/progenitor cells and their therapeutic implications. Ageing Res Rev 2009; 8:94-112. [PMID: 19114129 DOI: 10.1016/j.arr.2008.12.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 12/04/2008] [Indexed: 02/07/2023]
Abstract
Recent advancements in tissue-resident adult stem/progenitor cell research have revealed that enhanced telomere attrition, oxidative stress, ultraviolet radiation exposure and oncogenic events leading to severe DNA damages and genomic instability may occur in these immature and regenerative cells during chronological aging. Particularly, the alterations in key signaling components controlling their self-renewal capacity and an up-regulation of tumor suppressor gene products such as p16(INK4A), p19(ARF), ataxia-telangiectasia mutated (ATM) kinase, p53 and/or the forkhead box O (FOXOs) family of transcription factors may result in their dysfunctions, growth arrest and senescence or apoptotic death during the aging process. These molecular events may culminate in a progressive decline in the regenerative functions and the number of tissue-resident adult stem/progenitor cells, and age-related disease development. Conversely, the telomerase re-activation and accumulation of numerous genetic and/or epigenetic alterations in adult stem/progenitor cells with advancing age may result in their immortalization and malignant transformation into highly leukemic or tumorigenic cancer-initiating cells and cancer initiation. Therefore, the cell-replacement and gene therapies and molecular targeting of aged and dysfunctional adult stem/progenitor cells including their malignant counterpart, cancer-initiating cells, hold great promise for treating and even curing diverse devastating human diseases. These diseases include premature aging diseases, hematopoietic, cardiovascular, musculoskeletal, pulmonary, ocular, urogenital, neurodegenerative and skin disorders and aggressive and recurrent cancers.
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37
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Krishnamurthy N, Zhao X, Burrows CJ, David SS. Superior removal of hydantoin lesions relative to other oxidized bases by the human DNA glycosylase hNEIL1. Biochemistry 2008; 47:7137-46. [PMID: 18543945 DOI: 10.1021/bi800160s] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The DNA glycosylase hNEIL1 initiates the base excision repair (BER) of a diverse array of lesions, including ring-opened purines and saturated pyrimidines. Of these, the hydantoin lesions, guanidinohydantoin (Gh) and the two diastereomers of spiroiminodihydantoin (Sp1 and Sp2), have garnered much recent attention due to their unusual structures, high mutagenic potential, and detection in cells. In order to provide insight into the role of repair, the excision efficiency by hNEIL1 of these hydantoin lesions relative to other known substrates was determined. Most notably, quantitative examination of the substrate specificity with hNEIL1 revealed that the hydantoin lesions are excised much more efficiently (>100-fold faster) than the reported standard substrates thymine glycol (Tg) and 5-hydroxycytosine (5-OHC). Importantly, the glycosylase and beta,delta-lyase reactions are tightly coupled such that the rate of the lyase activity does not influence the observed substrate specificity. The activity of hNEIL1 is also influenced by the base pair partner of the lesion, with both Gh and Sp removal being more efficient when paired with T, G, or C than when paired with A. Notably, the most efficient removal is observed with the Gh or Sp paired in the unlikely physiological context with T; indeed, this may be a consequence of the unstable nature of base pairs with T. However, the facile removal via BER in promutagenic base pairs that are reasonably formed after replication (such as Gh.G) may be a factor that modulates the mutagenic profile of these lesions. In addition, hNEIL1 excises Sp1 faster than Sp2, indicating the enzyme can discriminate between the two diastereomers. This is the first time that a BER glycosylase has been shown to be able to preferentially excise one diastereomer of Sp. This may be a consequence of the architecture of the active site of hNEIL1 and the structural uniqueness of the Sp lesion. These results indicate that the hydantoin lesions are the best substrates identified thus far for hNEIL1 and suggest that repair of these lesions may be a critical function of the hNEIL1 enzyme in vivo.
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Affiliation(s)
- Nirmala Krishnamurthy
- Department of Chemistry, University of Utah, 315 South, 1400 East, Salt Lake City, Utah 84112, USA
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38
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Melov S, Tarnopolsky MA, Beckman K, Felkey K, Hubbard A. Resistance exercise reverses aging in human skeletal muscle. PLoS One 2007; 2:e465. [PMID: 17520024 PMCID: PMC1866181 DOI: 10.1371/journal.pone.0000465] [Citation(s) in RCA: 209] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 04/25/2007] [Indexed: 01/07/2023] Open
Abstract
Human aging is associated with skeletal muscle atrophy and functional impairment (sarcopenia). Multiple lines of evidence suggest that mitochondrial dysfunction is a major contributor to sarcopenia. We evaluated whether healthy aging was associated with a transcriptional profile reflecting mitochondrial impairment and whether resistance exercise could reverse this signature to that approximating a younger physiological age. Skeletal muscle biopsies from healthy older (N = 25) and younger (N = 26) adult men and women were compared using gene expression profiling, and a subset of these were related to measurements of muscle strength. 14 of the older adults had muscle samples taken before and after a six-month resistance exercise-training program. Before exercise training, older adults were 59% weaker than younger, but after six months of training in older adults, strength improved significantly (P<0.001) such that they were only 38% lower than young adults. As a consequence of age, we found 596 genes differentially expressed using a false discovery rate cut-off of 5%. Prior to the exercise training, the transcriptome profile showed a dramatic enrichment of genes associated with mitochondrial function with age. However, following exercise training the transcriptional signature of aging was markedly reversed back to that of younger levels for most genes that were affected by both age and exercise. We conclude that healthy older adults show evidence of mitochondrial impairment and muscle weakness, but that this can be partially reversed at the phenotypic level, and substantially reversed at the transcriptome level, following six months of resistance exercise training.
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Affiliation(s)
- Simon Melov
- Buck Institute for Age Research, Novato, California, United States of America
- * To whom correspondence should be addressed. E-mail: (SM); (MT)
| | - Mark A. Tarnopolsky
- McMaster University, Department of Pediatrics and Medicine, Hamilton, Canada
- * To whom correspondence should be addressed. E-mail: (SM); (MT)
| | - Kenneth Beckman
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Krysta Felkey
- Buck Institute for Age Research, Novato, California, United States of America
| | - Alan Hubbard
- Buck Institute for Age Research, Novato, California, United States of America
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