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Xia X, Chen Q, Zuo T, Liang Z, Xu G, Wei F, Yang J, Hu Q, Zhao Z, Tang BZ, Cen Y. DNA Robots for CRISPR/Cas12a Activity Management and Universal Platforms for Biosensing. Anal Chem 2024; 96:2620-2627. [PMID: 38217497 DOI: 10.1021/acs.analchem.3c05210] [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: 01/15/2024]
Abstract
The CRISPR/Cas12a system is a revolutionary genome editing technique that is widely employed in biosensing and molecular diagnostics. However, there are few reports on precisely managing the trans-cleavage activity of Cas12a by simple modification since the traditional methods to manage Cas12a often require difficult and rigorous regulation of core components. Hence, we developed a novel CRISPR/Cas12a regulatory mechanism, named DNA Robots for Enzyme Activity Management (DREAM), by introducing two simple DNA robots, apurinic/apyrimidinic site (AP site) or nick on target activator. First, we revealed the mechanism of how the DREAM strategy precisely regulated Cas12a through different binding affinities. Second, the DREAM strategy was found to improve the selectivity of Cas12a for identifying base mismatch. Third, a modular biosensor for base excision repair enzymes based on the DREAM strategy was developed by utilizing diversified generation ways of DNA robots, and a multi-signal output platform such as fluorescence, colorimetry, and visual lateral flow strip was constructed. Furthermore, we extended logic sensing circuits to overcome the barrier that Cas12a could not detect simultaneously in a single tube. Overall, the DREAM strategy not only provided new prospects for programmable Cas12a biosensing systems but also enabled portable, specific, and humanized detection with great potential for molecular diagnostics.
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Affiliation(s)
- Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Tongshan Zuo
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhigang Liang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zheng Zhao
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
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Jung KW, Kwon S, Jung JH, Lim S, Bahn YS. Functional Characterization of DNA N-Glycosylase Ogg1 and Ntg1 in DNA Damage Stress of Cryptococcus neoformans. J Microbiol 2023; 61:981-992. [PMID: 38055144 DOI: 10.1007/s12275-023-00092-y] [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: 10/05/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023]
Abstract
Reactive oxygen species induce DNA strand breaks and DNA oxidation. DNA oxidation leads to DNA mismatches, resulting in mutations in the genome if not properly repaired. Homologous recombination (HR) and non-homologous end-joining (NHEJ) are required for DNA strand breaks, whereas the base excision repair system mainly repairs oxidized DNAs, such as 8-oxoguanine and thymine glycol, by cleaving the glycosidic bond, inserting correct nucleotides, and sealing the gap. Our previous studies revealed that the Rad53-Bdr1 pathway mainly controls DNA strand breaks through the regulation of HR- and NHEJ-related genes. However, the functional roles of genes involved in the base excision repair system remain elusive in Cryptococcus neoformans. In the present study, we identified OGG1 and NTG1 genes in the base excision repair system of C. neoformans, which are involved in DNA oxidation repair. The expression of OGG1 was induced in a Hog1-dependent manner under oxidative stress. On the other hand, the expression of NTG1 was strongly induced by DNA damage stress in a Rad53-independent manner. We demonstrated that the deletion of NTG1, but not OGG1, resulted in elevated susceptibility to DNA damage agents and oxidative stress inducers. Notably, the ntg1Δ mutant showed growth defects upon antifungal drug treatment. Although deletion of OGG1 or NTG1 did not increase mutation rates, the mutation profile of each ogg1Δ and ntg1Δ mutant was different from that of the wild-type strain. Taken together, we found that DNA N-glycosylase Ntg1 is required for oxidative DNA damage stress and antifungal drug resistance in C. neoformans.
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Affiliation(s)
- Kwang-Woo Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Sunhak Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jong-Hyun Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
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Li J, Cui Z, Fan C, Zhou Y, Ren M, Zhou C. Photo-caged 2-butene-1,4-dial as an efficient, target-specific photo-crosslinker for covalent trapping of DNA-binding proteins. Chem Sci 2023; 14:10884-10891. [PMID: 37829010 PMCID: PMC10566456 DOI: 10.1039/d3sc03719c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Covalent trapping of DNA-binding proteins via photo-crosslinking is an advantageous method for studying DNA-protein interactions. However, traditional photo-crosslinkers generate highly reactive intermediates that rapidly and non-selectively react with nearby functional groups, resulting in low target-capture yields and high non-target background capture. Herein, we report that photo-caged 2-butene-1,4-dial (PBDA) is an efficient photo-crosslinker for trapping DNA-binding proteins. Photo-irradiation (360 nm) of PBDA-modified DNA generates 2-butene-1,4-dial (BDA), a small, long-lived intermediate that reacts selectively with Lys residues of DNA-binding proteins, leading in minutes to stable DNA-protein crosslinks in up to 70% yield. In addition, BDA exhibits high specificity for target proteins, leading to low non-target background capture. The high photo-crosslinking yield and target specificity make PBDA a powerful tool for studying DNA-protein interactions.
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Affiliation(s)
- Jiahui Li
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Zenghui Cui
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University Tianjin 300071 China
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Wu H, Zhang Y, Xu H, Xu B, Chen J, Guo L, Liu Q, Xie J. Urinary Profile of Alkylated DNA Adducts and DNA Oxidative Damage in Sulfur Mustard-Exposed Rats Revealed by Mass Spectrometry Quantification. Chem Res Toxicol 2023; 36:1495-1502. [PMID: 37625021 DOI: 10.1021/acs.chemrestox.3c00135] [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: 08/27/2023]
Abstract
Alkylation reagents, represented by sulfur mustard (SM), can damage DNA molecules directly as well as lead to oxidative stress, causing DNA lesions indirectly. Correspondingly, two types of biomarkers including alkylated DNA adducts and oxidative DNA adducts are commonly involved in the research of DNA damage evaluation caused by these agents. However, the correlations and differences of the occurrence, duration, severity, and traceability between alkylation and oxidation lesions on the DNA molecular level reflected by these two types of biomarkers have not been systematically studied. A simultaneous determination method for four alkylated DNA adducts, i.e., N7-(2-hydroxyethylthioethyl)2'-guanine (N7-HETEG), O6-(2-hydroxyethylthioethyl)-2'-guanine (O6-HETEG), N3-(2-hydroxyethylthioethyl)-2'-adenine (N3-HETEA), and bis(2-ethyl-N7-guanine)thioether (Bis-G), and the oxidative adduct 8-hydroxy-2'-deoxyguanosine (8-OH-dG) in urine samples by isotope-dilution high-performance liquid chromatography-tandem mass spectrometry (ID-HPLC-MS/MS) was built with a lower limit of detection of 0.02 ng/mL (except Bis-G, 0.05 ng/mL) and a recovery of 79-111%. The profile of these adducts was simultaneously monitored in urine samples after SD rats' dermal exposure to SM in three dose levels (1, 3, and 10 mg/kg). The time-effect and dose-effect experiments revealed that when exposed to SM, DNA alkylation lesions would happen earlier than those of oxidation. For the two types of biomarkers, alkylated DNA adducts showed an obvious dose-effect relationship and could be used as internal exposure dose and effect biomarkers, while 8-OH-dG did not show a correlation with exposure dose, demonstrating that it was more suitable as a biomarker for DNA oxidative lesions but not an indicator for the extent of cytotoxicity and internal exposure.
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Affiliation(s)
- Haijiang Wu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Yajiao Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Hua Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Bin Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jia Chen
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Qin Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
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Tong H, Liu N, Wei Y, Zhou Y, Li Y, Wu D, Jin M, Cui S, Li H, Li G, Zhou J, Yuan Y, Zhang H, Shi L, Yao X, Yang H. Programmable deaminase-free base editors for G-to-Y conversion by engineered glycosylase. Natl Sci Rev 2023; 10:nwad143. [PMID: 37404457 PMCID: PMC10317176 DOI: 10.1093/nsr/nwad143] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/13/2023] [Accepted: 05/13/2023] [Indexed: 07/06/2023] Open
Abstract
Current DNA base editors contain nuclease and DNA deaminase that enables deamination of cytosine (C) or adenine (A), but no method for guanine (G) or thymine (T) editing is available at present. Here we developed a deaminase-free glycosylase-based guanine base editor (gGBE) with G editing ability, by fusing Cas9 nickase with engineered N-methylpurine DNA glycosylase protein (MPG). By several rounds of MPG mutagenesis via unbiased and rational screening using an intron-split EGFP reporter, we demonstrated that gGBE with engineered MPG could increase G editing efficiency by more than 1500 fold. Furthermore, this gGBE exhibited high base editing efficiency (up to 81.2%) and high G-to-T or G-to-C (i.e. G-to-Y) conversion ratio (up to 0.95) in both cultured human cells and mouse embryos. Thus, we have provided a proof-of-concept of a new base editing approach by endowing the engineered DNA glycosylase the capability to selectively excise a new type of substrate.
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Affiliation(s)
| | | | | | | | | | | | - Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Shuna Cui
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Hengbin Li
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Jingxing Zhou
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Yuan Yuan
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Hainan Zhang
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Linyu Shi
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
| | - Xuan Yao
- HuidaGene Therapeutics Co., Ltd., Shanghai 200131, China
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Li J, Hu Z, Liu D, Wang P. Mass spectrometry-based assays for assessing replicative bypass and repair of DNA alkylation in cells. RSC Adv 2023; 13:15490-15497. [PMID: 37223415 PMCID: PMC10201546 DOI: 10.1039/d2ra08340j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
Endogenous metabolism and environmental exposure can give rise to DNA alkylation, which can elicit deleterious biological consequences. In the search for reliable and quantitative analytical methods to elucidate the impact of DNA alkylation on the flow of genetic information, mass spectrometry (MS) has attracted increasing attention, owing to its unambiguous determination of molecular mass. The MS-based assays obviate conventional colony-picking methods and Sanger sequencing procedures, and retained the high sensitivity of postlabeling methods. With the help of the CRISPR/Cas9 gene editing method, MS-based assays showed high potential in studying individual functions of repair proteins and translesion synthesis (TLS) polymerases in DNA replication. In this mini-review, we have summarized the development of MS-based competitive and replicative adduct bypass (CRAB) assays and their recent applications in assessing the impact of alkylation on DNA replication. With further development of MS instruments for high resolving power and high throughput, these assays should be generally applicable and efficient in quantitative measurement of the biological consequences and repair of other DNA lesions.
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Affiliation(s)
- Jiaxian Li
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Zhihai Hu
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Dandan Liu
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
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Ji TT, Xie NB, Ding JH, Wang M, Guo X, Chen YY, Yu SY, Feng YQ, Yuan BF. Enzymatic Cleavage-Mediated Extension Stalling Enables Accurate Recognition and Quantification of Locus-Specific Uracil Modification in DNA. Anal Chem 2023; 95:8384-8392. [PMID: 37192336 DOI: 10.1021/acs.analchem.3c01410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chemical modifications in DNA have profound influences on the structures and functions of DNA. Uracil, a naturally occurring DNA modification, can originate from the deamination of cytosine or arise from misincorporation of dUTP into DNA during DNA replication. Uracil in DNA will imperil genomic stability due to their potential in producing detrimental mutations. An in-depth understanding of the functions of uracil modification requires the accurate determination of its site as well as content in genomes. Herein, we characterized that a new member of the uracil-DNA glycosylase (UDG) family enzyme (UdgX-H109S) could selectively cleave both uracil-containing single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Based on this unique property of UdgX-H109S, we developed an enzymatic cleavage-mediated extension stalling (ECES) method for the locus-specific detection and quantification of uracil in genomic DNA. In the ECES method, UdgX-H109S specifically recognizes and cleaves the N-glycosidic bond of uracil from dsDNA and generates an apurinic/apyrimidinic (AP) site, which could be broken by APE1 to form a one-nucleotide gap. The specific cleavage by UdgX-H109S is then evaluated and quantified by qPCR. With the developed ECES approach, we demonstrated that the level of uracil at position Chr4:50566961 in genomic DNA of breast cancer tissues was significantly decreased. Collectively, the ECES method has been proved to be accurate and reproducible in the locus-specific quantification of uracil in genomic DNA from biological and clinical samples.
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Affiliation(s)
- Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Neng-Bin Xie
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Jiang-Hui Ding
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Ying-Ying Chen
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Si-Yu Yu
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Yu-Qi Feng
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan Research Center for Infectious Diseases and Cancer, Zhongnan Hospital of Wuhan University, Chinese Academy of Medical Sciences, Wuhan, Hubei 430071, China
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Eun HJ, Ishiuchi SI, Yoo IT, Heo J, Park JW, Fujii M, Kim NJ. Cryogenic Ion Spectroscopy of Protonated and Sodiated Methyladenine Derivatives. J Phys Chem A 2023; 127:2472-2480. [PMID: 36895090 DOI: 10.1021/acs.jpca.2c09083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Ultraviolet photodissociation (UVPD) spectra of protonated 9-methyladenine (H+9MA), protonated 7-methyl adenine (H+7MA), protonated 3-methyladenine (H+3MA), and sodiated 7-methyladenine (Na+7MA) near the origin bands of the S0-S1 transition were obtained using cryogenic ion spectroscopy. The UV-UV hole burning, infrared (IR) ion-dip, and IR-UV double resonance spectra showed that all the ions were present as single isomers in a cryogenic ion trap. The UVPD spectrum of H+9MA exhibited only a broad absorption band, whereas the spectra of H+7MA, H+3MA, and Na+7MA displayed moderately or well-resolved vibronic bands. Potential energy profiles were computed to understand the reason for the different bandwidths of the vibronic bands in the spectra. The broadening of the bands was correlated with the slopes between the Franck-Condon point and the conical intersection between the S1 and S0 states in the potential energy profiles, thus reflecting the deactivation rates in the S1 state.
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Affiliation(s)
- Han Jun Eun
- Gas Metrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
| | - Shun-Ichi Ishiuchi
- Department of Chemistry, Tokyo Institute of Technology, Ookayama 2-12-1, Tokyo 152-8550, Japan
| | - Il Tae Yoo
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Jiyoung Heo
- Department of Green Chemical Engineering, Sangmyung University, Chungnam 31066, Korea
| | - Jae Woo Park
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama 226-8503, Japan
| | - Nam Joon Kim
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
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Petronek MS, Allen BG. Maintenance of genome integrity by the late-acting cytoplasmic iron-sulfur assembly (CIA) complex. Front Genet 2023; 14:1152398. [PMID: 36968611 PMCID: PMC10031043 DOI: 10.3389/fgene.2023.1152398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability.
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Hussain T, Kandeel M, Metwally E, Murtaza G, Kalhoro DH, Yin Y, Tan B, Chughtai MI, Yaseen A, Afzal A, Kalhoro MS. Unraveling the harmful effect of oxidative stress on male fertility: A mechanistic insight. Front Endocrinol (Lausanne) 2023; 14:1070692. [PMID: 36860366 PMCID: PMC9968806 DOI: 10.3389/fendo.2023.1070692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/02/2023] [Indexed: 02/16/2023] Open
Abstract
Male infertility is a widely debated issue that affects males globally. There are several mechanisms involved. Oxidative stress is accepted to be the main contributing factor, with sperm quality and quantity affected by the overproduction of free radicals. Excess reactive oxygen species (ROS) cannot be controlled by the antioxidant system and, thus, potentially impact male fertility and hamper sperm quality parameters. Mitochondria are the driving force of sperm motility; irregularities in their function may lead to apoptosis, alterations to signaling pathway function, and, ultimately, compromised fertility. Moreover, it has been observed that the prevalence of inflammation may arrest sperm function and the production of cytokines triggered by the overproduction of ROS. Further, oxidative stress interacts with seminal plasma proteomes that influence male fertility. Enhanced ROS production disturbs the cellular constituents, particularly DNA, and sperms are unable to impregnate the ovum. Here, we review the latest information to better understand the relationship between oxidative stress and male infertility, the role of mitochondria, the cellular response, inflammation and fertility, and the interaction of seminal plasma proteomes with oxidative stress, as well as highlight the influence of oxidative stress on hormones; collectively, all of these factors are assumed to be important for the regulation of male infertility. This article may help improve our understanding of male infertility and the strategies to prevent it.
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Affiliation(s)
- Tarique Hussain
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
- Animal Sciences Division, Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
- *Correspondence: Tarique Hussain, ; Bie Tan,
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
| | - Elsayed Metwally
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Ghulam Murtaza
- Department of Animal Reproduction, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, Sindh, Pakistan
| | - Dildar Hussain Kalhoro
- Department of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, Sindh, Pakistan
| | - Yulong Yin
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Bie Tan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
- *Correspondence: Tarique Hussain, ; Bie Tan,
| | - Muhammad Ismail Chughtai
- Animal Sciences Division, Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Anjaleena Yaseen
- Animal Sciences Division, Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Ali Afzal
- Department of Zoology, Minhaj University, Lahore, Pakistan
| | - Muhammad Saleem Kalhoro
- Food Engineering and Bioprocess Technology, Asian Institute of Technology, Bangkok, Thailand
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11
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Berdis A. Nucleobase-modified nucleosides and nucleotides: Applications in biochemistry, synthetic biology, and drug discovery. Front Chem 2022; 10:1051525. [PMID: 36531317 PMCID: PMC9748101 DOI: 10.3389/fchem.2022.1051525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
. DNA is often referred to as the "molecule of life" since it contains the genetic blueprint for all forms of life on this planet. The core building blocks composing DNA are deoxynucleotides. While the deoxyribose sugar and phosphate group are ubiquitous, it is the composition and spatial arrangement of the four natural nucleobases, adenine (A), cytosine (C), guanine (G), and thymine (T), that provide diversity in the coding information present in DNA. The ability of DNA to function as the genetic blueprint has historically been attributed to the formation of proper hydrogen bonding interactions made between complementary nucleobases. However, recent chemical and biochemical studies using nucleobase-modified nucleotides that contain "non-hydrogen bonding" functional groups have challenged many of the dogmatic views for the necessity of hydrogen-bonding interactions for DNA stability and function. Based on years of exciting research, this area has expanded tremendously and is thus too expansive to provide a comprehensive review on the topic. As such, this review article provides an opinion highlighting how nucleobase-modified nucleotides are being applied in diverse biomedical fields, focusing on three exciting areas of research. The first section addresses how these analogs are used as mechanistic probes for DNA polymerase activity and fidelity during replication. This section outlines the synthetic logic and medicinal chemistry approaches used to replace hydrogen-bonding functional groups to examine the contributions of shape/size, nucleobase hydrophobicity, and pi-electron interactions. The second section extends these mechanistic studies to provide insight into how nucleobase-modified nucleosides are used in synthetic biology. One example is through expansion of the genetic code in which changing the composition of DNA makes it possible to site-specifically incorporate unnatural amino acids bearing unique functional groups into enzymes and receptors. The final section describes results of pre-clinical studies using nucleobase-modified nucleosides as potential therapeutic agents against diseases such as cancer.
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Affiliation(s)
- Anthony Berdis
- Department of Chemistry, Cleveland State University, Cleveland, OH, United States
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12
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Kim DH, Kim JS, Mok CS, Chang EH, Choi J, Lim J, Kim CH, Park AR, Bae YJ, Koo BS, Lee HC. dTMP imbalance through thymidylate 5'-phosphohydrolase activity induces apoptosis in triple-negative breast cancers. Sci Rep 2022; 12:20027. [PMID: 36414668 PMCID: PMC9681768 DOI: 10.1038/s41598-022-24706-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Immunotherapy has a number of advantages over traditional anti-tumor therapy but can cause severe adverse reactions due to an overactive immune system. In contrast, a novel metabolic treatment approach can induce metabolic vulnerability through multiple cancer cell targets. Here, we show a therapeutic effect by inducing nucleotide imbalance and apoptosis in triple negative breast cancer cells (TNBC), by treating with cytosolic thymidylate 5'-phosphohydrolase (CT). We show that a sustained consumption of dTMP by CT could induce dNTP imbalance, leading to apoptosis as tricarboxylic acid cycle intermediates were depleted to mitigate this imbalance. These cytotoxic effects appeared to be different, depending on substrate specificity of the 5' nucleotide or metabolic dependency of the cancer cell lines. Using representative TNBC cell lines, we reveal how the TNBC cells were affected by CT-transfection through extracellular acidification rate (ECAR)/oxygen consumption rate (OCR) analysis and differential transcription/expression levels. We suggest a novel approach for treating refractory TNBC by an mRNA drug that can exploit metabolic dependencies to exacerbate cell metabolic vulnerability.
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Affiliation(s)
- Dae-Ho Kim
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea ,grid.251916.80000 0004 0532 3933Department of Molecular Science and Technology, Ajou University, Suwon, 16499 Republic of Korea ,grid.251916.80000 0004 0532 3933Department of Otolaryngology, Ajou University School of Medicine, Suwon, 16499 Republic of Korea
| | - Jin-Sook Kim
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Chang-Soo Mok
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea ,grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University Biomedi Campus, Gyeonggi-do, 10326 Republic of Korea
| | - En-Hyung Chang
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Jiwon Choi
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Junsub Lim
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Chul-Ho Kim
- grid.251916.80000 0004 0532 3933Department of Otolaryngology, Ajou University School of Medicine, Suwon, 16499 Republic of Korea
| | | | | | - Bong-Seong Koo
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
| | - Hyeon-Cheol Lee
- Research Center, BPgene Co, Ltd, Seoul, 03127 Republic of Korea
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13
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Guo S, Li L, Yu K, Tan Y, Wang Y. LC-MS/MS for Assessing the Incorporation and Repair of N2-Alkyl-2'-deoxyguanosine in Genomic DNA. Chem Res Toxicol 2022; 35:1814-1820. [PMID: 35584366 PMCID: PMC9588702 DOI: 10.1021/acs.chemrestox.2c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding the occurrence, repair, and biological consequences of DNA damage is important in environmental toxicology and risk assessment. The most common way to assess DNA damage elicited by exogenous sources in a laboratory setting is to expose cells or experimental animals with chemicals that modify DNA. Owing to the lack of reaction specificities of DNA damaging agents, the approach frequently does not allow for induction of a specific DNA lesion. Herein, we employed metabolic labeling to selectively incorporate N2-methyl-dG (N2-MedG) and N2-n-butyl-dG (N2-nBudG) into genomic DNA of cultured mammalian cells, and investigated how the levels of the two lesions in cellular DNA are modulated by different DNA repair factors. Our results revealed that nucleotide excision repair (NER) exert moderate effects on the removal of N2-MedG and N2-nBudG from genomic DNA. We also observed that DNA polymerases κ and η contribute to the incorporation of N2-MedG into genomic DNA and modulate its repair in human cells. In addition, loss of ALKBH3 resulted in higher frequencies of N2-MedG and N2-nBuG incorporation into genomic DNA, suggesting a role of oxidative dealkylation in the reversal of these lesions. Together, our study provided new insights into the repair of minor-groove N2-alkyl-dG lesions in mammalian cells.
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Affiliation(s)
- Su Guo
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Kailin Yu
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Ying Tan
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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14
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Li CC, Liu WX, Jiang S, Liu M, Luo X, Zhang CY. Construction of Bioluminescent Sensors for Label-Free, Template-Free, Separation-Free, and Sequence-Independent Detection of both Clustered and Isolated Damage in Genomic DNA. Anal Chem 2022; 94:14716-14724. [PMID: 36223141 DOI: 10.1021/acs.analchem.2c03134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA damage induced by endogenous/exogenous factors may cause various diseases, and the genomic DNA damage has become an important biomarker for clinical diagnosis and risk assessment, but it remains a great challenge to accurately quantify both clustered and isolated damage because of their random locations, large diversity, and low abundance. Herein, we demonstrate the development of bioluminescent sensors for label-free, template-free, separation-free, and sequence-independent detection of both clustered and isolated damage in genomic DNA based on the base-excision repair (BER) pathway and terminal transferase (TdT)-initiated template-free isothermal cyclic amplification. The damaged bases are cleaved by DNA glycosylase to generate a new 3'-OH terminus, and subsequently, TdT catalyzes the repeated incorporation of dTTPs into the 3'-OH terminus to produce poly-T structures which can hybridize with the signal probe to form a poly-T sequence/signal probe duplex. Under the lambda exonuclease hydrolysis, a large number of adenosine monophosphate (AMP) molecules are produced to generate a high bioluminescence signal through the cyclic interconversion of AMP-adenosine triphosphate (ATP)-AMP in the presence of luciferin and firefly luciferase. Moreover, the introduction of APE1-induced cyclic cleavage signal amplification can greatly improve the detection sensitivity. The proposed strategy can detect both clustered and isolated damage in genomic DNA with extremely high sensitivity and excellent specificity, and it can even distinguish 0.001% DNA damage in the mixture. Importantly, it can detect the cellular DNA damage with a detection limit of 0.011 ng and further extend to measure various DNA damage with the integration of appropriate DNA repair enzymes.
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Affiliation(s)
- Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Wan-Xin Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Zichuan Experimental Middle School, Zibo 255100, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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15
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Lodato MA, Ziegenfuss JS. The two faces of DNA oxidation in genomic and functional mosaicism during aging in human neurons. FRONTIERS IN AGING 2022; 3:991460. [PMID: 36313183 PMCID: PMC9596766 DOI: 10.3389/fragi.2022.991460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022]
Abstract
Maintaining genomic integrity in post-mitotic neurons in the human brain is paramount because these cells must survive for an individual's entire lifespan. Due to life-long synaptic plasticity and electrochemical transmission between cells, the brain engages in an exceptionally high level of mitochondrial metabolic activity. This activity results in the generation of reactive oxygen species with 8-oxo-7,8-dihydroguanine (8-oxoG) being one of the most prevalent oxidation products in the cell. 8-oxoG is important for the maintenance and transfer of genetic information into proper gene expression: a low basal level of 8-oxoG plays an important role in epigenetic modulation of neurodevelopment and synaptic plasticity, while a dysregulated increase in 8-oxoG damages the genome leading to somatic mutations and transcription errors. The slow yet persistent accumulation of DNA damage in the background of increasing cellular 8-oxoG is associated with normal aging as well as neurological disorders such as Alzheimer's disease and Parkinson's disease. This review explores the current understanding of how 8-oxoG plays a role in brain function and genomic instability, highlighting new methods being used to advance pathological hallmarks that differentiate normal healthy aging and neurodegenerative disease.
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16
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Zhang Q, Zhao R, Li CC, Zhang Y, Tang C, Luo X, Ma F, Zhang CY. Construction of an Entropy-Driven Dumbbell-Type DNAzyme Assembly Circuit for Lighting Up Uracil-DNA Glycosylase in Living Cells. Anal Chem 2022; 94:13978-13986. [PMID: 36179339 DOI: 10.1021/acs.analchem.2c03223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sensitive monitoring of intracellular uracil-DNA glycosylase (UDG) in living cells is essential to understanding the DNA repair pathways and discovery of anticancer drugs. Herein, we demonstrate the construction of an entropy-driven dumbbell-type DNAzyme assembly circuit for lighting up UDG in living cells via the integration of entropy-driven DNA catalysis (EDC) with the DNAzyme biocatalyst. Target UDG excises the damaged uracil base, causing the breakage of detection probe and the release of trigger. The released trigger can initiate the downstream EDC reaction to form two catalytically active DNAzyme units. The resultant dual Mg2+-DNAzyme units serve as the signal transducers to cyclically cleave the fluorophore/quenched-modified reporters, generating an enhanced fluorescence signal. In contrast to the single-layered EDC method with a linear amplification, the proposed doublet EDC-DNAzyme strategy exhibits high signal gain and achieves a detection limit of 8.71 × 10-6 U/mL. Notably, this assay can be performed in one-step manner at room temperature without the requirement of strict temperature control and complicated reaction procedures, and it can further screen the UDG inhibitors, measure kinetic parameters, and discriminate cancer cells from normal cells. Moreover, this strategy can monitor intracellular UDG activity with improved signal gain, and it may be exploited for sensing and imaging of other types of DNA modifying enzymes with the integration of the corresponding detection substrate, providing a facile and robust approach for biological research studies and clinical diagnosis.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Ran Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chen-Chen Li
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chunying Tang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiliang Luo
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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17
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Lu Y, Cong P, Kuang S, Tang L, Li Y, Dong J, Song W. Long-term excessive application of K 2SO 4 fertilizer alters bacterial community and functional pathway of tobacco-planting soil. FRONTIERS IN PLANT SCIENCE 2022; 13:1005303. [PMID: 36247599 PMCID: PMC9554487 DOI: 10.3389/fpls.2022.1005303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 05/31/2023]
Abstract
To improve tobacco leaf quality, excessive K2SO4 fertilizers were applied to soils in major tobacco-planting areas in China. However, the effects of K2SO4 application on soil microbial community and functions are still unclear. An eight-year field experiment with three kinds of K2SO4 amounts (low amount, K2O 82.57 kg hm-2, LK; moderate amount, K2O 165.07 kg hm-2, MK; high amount, K2O 247.58 kg hm-2, HK) was established to assess the effects of K2SO4 application on the chemical and bacterial characteristics of tobacco-planting soil using 16S rRNA gene and metagenomic sequencing approaches. Results showed that HK led to lower pH and higher nitrogen (N), potassium (K), sulfur(S) and organic matter contents of the soil than LK. The bacterial community composition of HK was significantly different from those of MK and LK, while these of MK and LK were similar. Compared to LK, HK increased the relative abundance of predicted copiotrophic groups (e.g. Burkholderiaceae, Rhodospirillaceae families and Ellin6067 genus) and potentially beneficial bacteria (e.g. Gemmatimonadetes phylum and Bacillus genus) associated with pathogens and heavy metal resistance, N fixation, dissolution of phosphorus and K. While some oligotrophic taxa (e.g. Acidobacteria phylum) related to carbon, N metabolism exhibited adverse responses to HK. Metagenomic analysis suggested that the improvement of pathways related to carbohydrate metabolism and genetic information processing by HK might be the self-protection mechanism of microorganisms against environmental stress. Besides, the redundancy analysis and variation partitioning analysis showed that soil pH, available K and S were the primary soil factors in shifting the bacterial community and KEGG pathways. This study provides a clear understanding of the responses of soil microbial communities and potential functions to excessive application of K2SO4 in tobacco-planting soil.
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Affiliation(s)
- Ya Lu
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ping Cong
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Shuai Kuang
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lina Tang
- Tobacco Science Research Institute, Fujian Tobacco Monopoly Administration, Fuzhou, China
| | - Yuyi Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianxin Dong
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wenjing Song
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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18
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The Role of NLRP3 Inflammasome Activation and Oxidative Stress in Varicocele-Mediated Male Hypofertility. Int J Mol Sci 2022; 23:ijms23095233. [PMID: 35563625 PMCID: PMC9102453 DOI: 10.3390/ijms23095233] [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: 04/15/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/11/2022] Open
Abstract
Varicocele (VC) is the most common abnormality identified in men evaluated for hypofertility. Increased levels of reactive oxygen species (ROS) and reduced antioxidants concentrations are key contributors in varicocele-mediated hypofertility. Moreover, inflammation and alterations in testicular immunity negatively impact male fertility. In particular, NLRP3 inflammasome activation was hypothesized to lead to seminal inflammation, in which the levels of specific cytokines, such as IL-1β and IL-18, are overexpressed. In this review, we described the role played by oxidative stress (OS), inflammation, and NLRP3 inflammasome activation in VC disease. The consequences of ROS overproduction in testis, including inflammation, lipid peroxidation, mitochondrial dysfunction, chromatin damage, and sperm DNA fragmentation, leading to abnormal testicular function and failed spermatogenesis, were highlighted. Finally, we described some therapeutic antioxidant strategies, with recognized beneficial effects in counteracting OS and inflammation in testes, as possible therapeutic drugs against varicocele-mediated hypofertility.
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19
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Barańska A, Woźniak A, Mokra K, Michałowicz J. Genotoxic Mechanism of Action of TBBPA, TBBPS and Selected Bromophenols in Human Peripheral Blood Mononuclear Cells. Front Immunol 2022; 13:869741. [PMID: 35493487 PMCID: PMC9039255 DOI: 10.3389/fimmu.2022.869741] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/21/2022] [Indexed: 11/27/2022] Open
Abstract
Bromophenolic flame retardants (BFRs) are a large group of synthetic substances used in the industry in order to reduce the flammability of synthetic materials used in electrical and electronic devices, textiles, furniture and other everyday products. The presence of BFRs has been documented in the environment, food, drinking water, inhaled dust and the human body. Due to the widespread exposure of the general population to BFRs and insufficient knowledge on their toxic action, including genotoxic potential, we have compared the effect of tetrabromobisphenol A (TBBPA), tetrabromobisphenol S (TBBPS), 2,4,6,-tribromophenol (2,4,6-TBP) and pentabromophenol (PBP) on DNA damage in human peripheral blood mononuclear cells (PBMCs) (playing a crucial role in the immune system) as well as examined underlying mechanism of action of these substances. The cells were incubated for 24 h with studied compounds in the concentrations ranging from 0.01 to 10 µg/mL. The study has shown that examined BFRs induced single and, to a lesser extent, double strand-breaks formation and caused oxidative damage to pyrimidines, and particularly to purines in the incubated cells. PBMCs efficiently repaired the DNA strand-breaks induced by BFRs, but they were unable to remove completely damaged DNA (except cells treated with TBBPS). The greatest changes in the above-mentioned parameters were observed in cells incubated with TBBPA, while the smallest in PBMCs treated with TBBPS. The results have also revealed that tested compounds do not form adducts with DNA in PBMCs, while the observed changes were the most probably induced by indirect DNA-damaging agents, such as ROS and other reactive species.
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Affiliation(s)
- Anna Barańska
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Agnieszka Woźniak
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Katarzyna Mokra
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jaromir Michałowicz
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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20
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Shadfar S, Brocardo M, Atkin JD. The Complex Mechanisms by Which Neurons Die Following DNA Damage in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23052484. [PMID: 35269632 PMCID: PMC8910227 DOI: 10.3390/ijms23052484] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 01/18/2023] Open
Abstract
Human cells are exposed to numerous exogenous and endogenous insults every day. Unlike other molecules, DNA cannot be replaced by resynthesis, hence damage to DNA can have major consequences for the cell. The DNA damage response contains overlapping signalling networks that repair DNA and hence maintain genomic integrity, and aberrant DNA damage responses are increasingly described in neurodegenerative diseases. Furthermore, DNA repair declines during aging, which is the biggest risk factor for these conditions. If unrepaired, the accumulation of DNA damage results in death to eliminate cells with defective genomes. This is particularly important for postmitotic neurons because they have a limited capacity to proliferate, thus they must be maintained for life. Neuronal death is thus an important process in neurodegenerative disorders. In addition, the inability of neurons to divide renders them susceptible to senescence or re-entry to the cell cycle. The field of cell death has expanded significantly in recent years, and many new mechanisms have been described in various cell types, including neurons. Several of these mechanisms are linked to DNA damage. In this review, we provide an overview of the cell death pathways induced by DNA damage that are relevant to neurons and discuss the possible involvement of these mechanisms in neurodegenerative conditions.
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Affiliation(s)
- Sina Shadfar
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
| | - Mariana Brocardo
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
| | - Julie D. Atkin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW 2109, Australia; (S.S.); (M.B.)
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
- Correspondence:
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21
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Xiang D, Jia B, Guo J, Shao Q, Hong Q, Wei H, Quan G, Wu G. Transcriptome Analysis of mRNAs and Long Non-Coding RNAs During Subsequent Embryo Development of Porcine Cloned Zygotes After Vitrification. Front Genet 2022; 12:753327. [PMID: 34976007 PMCID: PMC8718616 DOI: 10.3389/fgene.2021.753327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/17/2021] [Indexed: 11/15/2022] Open
Abstract
Cryopreservation of porcine cloned zygotes has important implications for biotechnology and biomedicine research; however, lower embryo developmental potential remains an urgent problem to be resolved. For exploring the sublethal cryodamages during embryo development, this study was designed to acquire the mRNA and long non-coding RNA (lncRNA) profiles of 2-cells, 4-cells and blastocysts derived from vitrified porcine cloned zygotes using transcriptome sequencing. We identified 167 differentially expressed (DE) mRNAs and 516 DE lncRNAs in 2-cell stage, 469 DE mRNAs and 565 lncRNAs in 4-cell stage, and 389 DE mRNAs and 816 DE lncRNAs in blastocyst stage. Functional enrichment analysis revealed that the DE mRNAs during embryo development were involved in many regulatory mechanisms related to cell cycle, cell proliferation, apoptosis, metabolism and others. Moreover, the target genes of DE lncRNAs in the three embryonic stages were also enriched in many key GO terms or pathways such as “defense response”, “linoleic acid metabolic process”, “embryonic axis specification”, “negative regulation of protein neddylation”, etc., In conclusion, the present study provided comprehensive transcriptomic data about mRNAs and lncRNAs for the vitrified porcine cloned zygotes during different developmental stages, which contributed to further understand the potential cryodamage mechanisms responsible for impaired embryo development.
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Affiliation(s)
- Decai Xiang
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Baoyu Jia
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Jianxiong Guo
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Qingyong Shao
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Qionghua Hong
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Hongjiang Wei
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Guobo Quan
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Guoquan Wu
- Yunnan Provincial Genebank of Livestock and Poultry Genetic Resources, Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Animal Science and Veterinary Institute, Kunming, China
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22
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Alexeeva M, Moen MN, Xu XM, Rasmussen A, Leiros I, Kirpekar F, Klungland A, Alsøe L, Nilsen H, Bjelland S. Intrinsic Strand-Incision Activity of Human UNG: Implications for Nick Generation in Immunoglobulin Gene Diversification. Front Immunol 2021; 12:762032. [PMID: 35003074 PMCID: PMC8730318 DOI: 10.3389/fimmu.2021.762032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/17/2021] [Indexed: 12/05/2022] Open
Abstract
Uracil arises in cellular DNA by cytosine (C) deamination and erroneous replicative incorporation of deoxyuridine monophosphate opposite adenine. The former generates C → thymine transition mutations if uracil is not removed by uracil-DNA glycosylase (UDG) and replaced by C by the base excision repair (BER) pathway. The primary human UDG is hUNG. During immunoglobulin gene diversification in activated B cells, targeted cytosine deamination by activation-induced cytidine deaminase followed by uracil excision by hUNG is important for class switch recombination (CSR) and somatic hypermutation by providing the substrate for DNA double-strand breaks and mutagenesis, respectively. However, considerable uncertainty remains regarding the mechanisms leading to DNA incision following uracil excision: based on the general BER scheme, apurinic/apyrimidinic (AP) endonuclease (APE1 and/or APE2) is believed to generate the strand break by incising the AP site generated by hUNG. We report here that hUNG may incise the DNA backbone subsequent to uracil excision resulting in a 3´-α,β-unsaturated aldehyde designated uracil-DNA incision product (UIP), and a 5´-phosphate. The formation of UIP accords with an elimination (E2) reaction where deprotonation of C2´ occurs via the formation of a C1´ enolate intermediate. UIP is removed from the 3´-end by hAPE1. This shows that the first two steps in uracil BER can be performed by hUNG, which might explain the significant residual CSR activity in cells deficient in APE1 and APE2.
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Affiliation(s)
- Marina Alexeeva
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Marivi Nabong Moen
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Xiang Ming Xu
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Anette Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ingar Leiros
- Department of Chemistry, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Lene Alsøe
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
- *Correspondence: Svein Bjelland, ; Hilde Nilsen,
| | - Svein Bjelland
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
- Section of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
- *Correspondence: Svein Bjelland, ; Hilde Nilsen,
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23
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Carroll BL, Zahn KE, Hanley JP, Wallace SS, Dragon JA, Doublié S. Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis. Nucleic Acids Res 2021; 49:13165-13178. [PMID: 34871433 PMCID: PMC8682792 DOI: 10.1093/nar/gkab1162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/02/2021] [Accepted: 12/03/2021] [Indexed: 01/08/2023] Open
Abstract
Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.
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Affiliation(s)
- Brittany L Carroll
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Karl E Zahn
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - John P Hanley
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Julie A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
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24
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Hindi NN, Elsakrmy N, Ramotar D. The base excision repair process: comparison between higher and lower eukaryotes. Cell Mol Life Sci 2021; 78:7943-7965. [PMID: 34734296 PMCID: PMC11071731 DOI: 10.1007/s00018-021-03990-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 01/01/2023]
Abstract
The base excision repair (BER) pathway is essential for maintaining the stability of DNA in all organisms and defects in this process are associated with life-threatening diseases. It is involved in removing specific types of DNA lesions that are induced by both exogenous and endogenous genotoxic substances. BER is a multi-step mechanism that is often initiated by the removal of a damaged base leading to a genotoxic intermediate that is further processed before the reinsertion of the correct nucleotide and the restoration of the genome to a stable structure. Studies in human and yeast cells, as well as fruit fly and nematode worms, have played important roles in identifying the components of this conserved DNA repair pathway that maintains the integrity of the eukaryotic genome. This review will focus on the components of base excision repair, namely, the DNA glycosylases, the apurinic/apyrimidinic endonucleases, the DNA polymerase, and the ligases, as well as other protein cofactors. Functional insights into these conserved proteins will be provided from humans, Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans, and the implications of genetic polymorphisms and knockouts of the corresponding genes.
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Affiliation(s)
- Nagham Nafiz Hindi
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Noha Elsakrmy
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar.
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25
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Park SH, Kim Y, Ra JS, Wie MW, Kang MS, Kang S, Myung K, Lee KY. Timely termination of repair DNA synthesis by ATAD5 is important in oxidative DNA damage-induced single-strand break repair. Nucleic Acids Res 2021; 49:11746-11764. [PMID: 34718749 PMCID: PMC8599757 DOI: 10.1093/nar/gkab999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) generate oxidized bases and single-strand breaks (SSBs), which are fixed by base excision repair (BER) and SSB repair (SSBR), respectively. Although excision and repair of damaged bases have been extensively studied, the function of the sliding clamp, proliferating cell nuclear antigen (PCNA), including loading/unloading, remains unclear. We report that, in addition to PCNA loading by replication factor complex C (RFC), timely PCNA unloading by the ATPase family AAA domain-containing protein 5 (ATAD5)-RFC-like complex is important for the repair of ROS-induced SSBs. We found that PCNA was loaded at hydrogen peroxide (H2O2)-generated direct SSBs after the 3'-terminus was converted to the hydroxyl moiety by end-processing enzymes. However, PCNA loading rarely occurred during BER of oxidized or alkylated bases. ATAD5-depleted cells were sensitive to acute H2O2 treatment but not methyl methanesulfonate treatment. Unexpectedly, when PCNA remained on DNA as a result of ATAD5 depletion, H2O2-induced repair DNA synthesis increased in cancerous and normal cells. Based on higher H2O2-induced DNA breakage and SSBR protein enrichment by ATAD5 depletion, we propose that extended repair DNA synthesis increases the likelihood of DNA polymerase stalling, shown by increased PCNA monoubiquitination, and consequently, harmful nick structures are more frequent.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Youyoung Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Min Woo Wie
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
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26
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Evans EPP, Scholten JTM, Mzyk A, Reyes-San-Martin C, Llumbet AE, Hamoh T, Arts EGJM, Schirhagl R, Cantineau AEP. Male subfertility and oxidative stress. Redox Biol 2021; 46:102071. [PMID: 34340027 PMCID: PMC8342954 DOI: 10.1016/j.redox.2021.102071] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 02/08/2023] Open
Abstract
To date 15% of couples are suffering from infertility with 45-50% of males being responsible. With an increase in paternal age as well as various environmental and lifestyle factors worsening these figures are expected to increase. As the so-called free radical theory of infertility suggests, free radicals or reactive oxygen species (ROS) play an essential role in this process. However, ROS also fulfill important functions for instance in sperm maturation. The aim of this review article is to discuss the role reactive oxygen species play in male fertility and how these are influenced by lifestyle, age or disease. We will further discuss how these ROS are measured and how they can be avoided during in-vitro fertilization.
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Affiliation(s)
- Emily P P Evans
- Department of Biomedical Engineering, Groningen University University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW, Groningen, the Netherlands
| | - Jorien T M Scholten
- Department of Biomedical Engineering, Groningen University University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW, Groningen, the Netherlands
| | - Aldona Mzyk
- Department of Biomedical Engineering, Groningen University University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW, Groningen, the Netherlands; Institute of Metallurgy and Materials Science, Polish Academy of Sciences, Reymonta 25, 30-059, Krakow, Poland
| | - Claudia Reyes-San-Martin
- Department of Biomedical Engineering, Groningen University University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW, Groningen, the Netherlands
| | - Arturo E Llumbet
- Department of Biomedical Engineering, Groningen University University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW, Groningen, the Netherlands; Laboratory of Genomic of Germ Cells, Biomedical Sciences Institute, Faculty of Medicine, University of Chile. Independencia, 1027, Independencia Santiago, Chile
| | - Thamir Hamoh
- Department of Biomedical Engineering, Groningen University University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW, Groningen, the Netherlands
| | - Eus G J M Arts
- Department of Obstetrics and Gynaecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Romana Schirhagl
- Department of Biomedical Engineering, Groningen University University Medical Center Groningen, Antonius Deusinglaan 1, 9713AW, Groningen, the Netherlands.
| | - Astrid E P Cantineau
- Department of Obstetrics and Gynaecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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27
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Vadivel Gnanasundram S, Bonczek O, Wang L, Chen S, Fahraeus R. p53 mRNA Metabolism Links with the DNA Damage Response. Genes (Basel) 2021; 12:genes12091446. [PMID: 34573428 PMCID: PMC8465283 DOI: 10.3390/genes12091446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/14/2022] Open
Abstract
Human cells are subjected to continuous challenges by different genotoxic stress attacks. DNA damage leads to erroneous mutations, which can alter the function of oncogenes or tumor suppressors, resulting in cancer development. To circumvent this, cells activate the DNA damage response (DDR), which mainly involves cell cycle regulation and DNA repair processes. The tumor suppressor p53 plays a pivotal role in the DDR by halting the cell cycle and facilitating the DNA repair processes. Various pathways and factors participating in the detection and repair of DNA have been described, including scores of RNA-binding proteins (RBPs) and RNAs. It has become increasingly clear that p53’s role is multitasking, and p53 mRNA regulation plays a prominent part in the DDR. This review is aimed at covering the p53 RNA metabolism linked to the DDR and highlights the recent findings.
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Affiliation(s)
- Sivakumar Vadivel Gnanasundram
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- Correspondence: (S.V.G.); (R.F.)
| | - Ondrej Bonczek
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656-53 Brno, Czech Republic
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
| | - Sa Chen
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
| | - Robin Fahraeus
- Department of Medical Biosciences, Umeå University, 901-87 Umeå, Sweden; (O.B.); (L.W.); (S.C.)
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656-53 Brno, Czech Republic
- Inserm UMRS1131, Institut de Genetique Moleculaire, Universite Paris 7, Hopital St Louis, F-75010 Paris, France
- International Centre for Cancer Vaccine Science, University of Gdansk, 80-822 Gdansk, Poland
- Correspondence: (S.V.G.); (R.F.)
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28
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Genomic Mosaicism Formed by Somatic Variation in the Aging and Diseased Brain. Genes (Basel) 2021; 12:genes12071071. [PMID: 34356087 PMCID: PMC8305509 DOI: 10.3390/genes12071071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past 20 years, analyses of single brain cell genomes have revealed that the brain is composed of cells with myriad distinct genomes: the brain is a genomic mosaic, generated by a host of DNA sequence-altering processes that occur somatically and do not affect the germline. As such, these sequence changes are not heritable. Some processes appear to occur during neurogenesis, when cells are mitotic, whereas others may also function in post-mitotic cells. Here, we review multiple forms of DNA sequence alterations that have now been documented: aneuploidies and aneusomies, smaller copy number variations (CNVs), somatic repeat expansions, retrotransposons, genomic cDNAs (gencDNAs) associated with somatic gene recombination (SGR), and single nucleotide variations (SNVs). A catch-all term of DNA content variation (DCV) has also been used to describe the overall phenomenon, which can include multiple forms within a single cell’s genome. A requisite step in the analyses of genomic mosaicism is ongoing technology development, which is also discussed. Genomic mosaicism alters one of the most stable biological molecules, DNA, which may have many repercussions, ranging from normal functions including effects of aging, to creating dysfunction that occurs in neurodegenerative and other brain diseases, most of which show sporadic presentation, unlinked to causal, heritable genes.
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29
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Zonneville J, Wang M, Alruwaili MM, Smith B, Melnick M, Eng KH, Melendy T, Park BH, Iyer R, Fountzilas C, Bakin AV. Selective therapeutic strategy for p53-deficient cancer by targeting dysregulation in DNA repair. Commun Biol 2021; 4:862. [PMID: 34253820 PMCID: PMC8275734 DOI: 10.1038/s42003-021-02370-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Breast carcinomas commonly carry mutations in the tumor suppressor p53, although therapeutic efforts to target mutant p53 have previously been unfruitful. Here we report a selective combination therapy strategy for treatment of p53 mutant cancers. Genomic data revealed that p53 mutant cancers exhibit high replication activity and express high levels of the Base-Excision Repair (BER) pathway, whereas experimental testing showed substantial dysregulation in BER. This defect rendered accumulation of DNA damage in p53 mutant cells upon treatment with deoxyuridine analogues. Notably, inhibition of poly (ADP-ribose) polymerase (PARP) greatly enhanced this response, whereas normal cells responded with activation of the p53-p21 axis and cell cycle arrest. Inactivation of either p53 or p21/CDKN1A conferred the p53 mutant phenotype. Preclinical animal studies demonstrated a greater anti-neoplastic efficacy of the drug combination (deoxyuridine analogue and PARP inhibitor) than either drug alone. This work illustrates a selective combination therapy strategy for p53 mutant cancers that will improve survival rates and outcomes for thousands of breast cancer patients.
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Affiliation(s)
- Justin Zonneville
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Moyi Wang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mohammed M Alruwaili
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Medical Laboratory Technology Department, Northern Border University, Arar City, Saudi Arabia
| | - Brandon Smith
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Megan Melnick
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Thomas Melendy
- Department of Microbiology & Immunology and Biochemistry, University at Buffalo, Buffalo, NY, USA
| | - Ben Ho Park
- The Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Renuka Iyer
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christos Fountzilas
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andrei V Bakin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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30
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Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain. Int J Mol Sci 2021; 22:ijms22126308. [PMID: 34208390 PMCID: PMC8231204 DOI: 10.3390/ijms22126308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
APE1 (DNA (apurinic/apyrimidinic site) endonuclease 1) is a key enzyme of one of the major DNA repair routes, the BER (base excision repair) pathway. APE1 fulfils additional functions, acting as a redox regulator of transcription factors and taking part in RNA metabolism. The mechanisms regulating APE1 are still being deciphered. Structurally, human APE1 consists of a well-characterized globular catalytic domain responsible for its endonuclease activity, preceded by a conformationally flexible N-terminal extension, acquired along evolution. This N-terminal tail appears to play a prominent role in the modulation of APE1 and probably in BER coordination. Thus, it is primarily involved in mediating APE1 localization, post-translational modifications, and protein–protein interactions, with all three factors jointly contributing to regulate the enzyme. In this review, recent insights on the regulatory role of the N-terminal region in several aspects of APE1 function are covered. In particular, interaction of this region with nucleophosmin (NPM1) might modulate certain APE1 activities, representing a paradigmatic example of the interconnection between various regulatory factors.
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31
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Wang LJ, Liang L, Liu BJ, Jiang B, Zhang CY. A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases. Chem Sci 2021; 12:5544-5554. [PMID: 34168791 PMCID: PMC8179622 DOI: 10.1039/d1sc00189b] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Genomic oxidation and alkylation are two of the most important forms of cytotoxic damage that may induce mutagenesis, carcinogenicity, and teratogenicity. Human 8-oxoguanine (hOGG1) and alkyladenine DNA glycosylases (hAAG) are responsible for two major forms of oxidative and alkylative damage repair, and their aberrant activities may cause repair deficiencies that are associated with a variety of human diseases, including cancers. Due to their complicated catalytic pathways and hydrolysis mechanisms, simultaneous and accurate detection of multiple repair glycosylases has remained a great challenge. Herein, by taking advantage of unique features of T7-based transcription and the intrinsic superiorities of single-molecule imaging techniques, we demonstrate for the first time the development of a controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of hOGG1 and hAAG. The presence of hOGG1 and hAAG can remove damaged 8-oxoG and deoxyinosine, respectively, from the dumbbell substrate, resulting in breaking of the dumbbell substrate, unfolding of two loops, and exposure of two T7 promoters simultaneously. The T7 promoters can activate symmetric transcription amplifications with the unfolded loops as the templates, inducing efficient transcription to produce two different single-stranded RNA transcripts (i.e., reporter probes 1 and 2). Reporter probes 1 and 2 hybridize with signal probes 1 and 2, respectively, to initiate duplex-specific nuclease-directed cyclic digestion of the signal probes, liberating large amounts of Cy3 and Cy5 fluorescent molecules. The released Cy3 and Cy5 molecules can be simply measured by total internal reflection fluorescence-based single-molecule detection, with the Cy3 signal indicating the presence of hOGG1 and the Cy5 signal indicating the presence of hAAG. This method exhibits good specificity and high sensitivity with a detection limit of 3.52 × 10-8 U μL-1 for hOGG1 and 3.55 × 10-7 U μL-1 for hAAG, and it can even quantify repair glycosylases at the single-cell level. Moreover, it can be applied for the measurement of kinetic parameters, the screening of potential inhibitors, and the detection of repair glycosylases in human serum, providing a new paradigm for repair enzyme-related biomedical research, drug discovery, and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
- School of Chemistry and Chemical Engineering, Southeast University Nanjing 211189 China
| | - Le Liang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
| | - Bing-Jie Liu
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - BingHua Jiang
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
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32
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Advani D, Sharma S, Kumari S, Ambasta RK, Kumar P. Precision Oncology, Signaling and Anticancer Agents in Cancer Therapeutics. Anticancer Agents Med Chem 2021; 22:433-468. [PMID: 33687887 DOI: 10.2174/1871520621666210308101029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/05/2021] [Accepted: 01/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The global alliance for genomics and healthcare facilities provides innovational solutions to expedite research and clinical practices for complex and incurable health conditions. Precision oncology is an emerging field explicitly tailored to facilitate cancer diagnosis, prevention and treatment based on patients' genetic profile. Advancements in "omics" techniques, next-generation sequencing, artificial intelligence and clinical trial designs provide a platform for assessing the efficacy and safety of combination therapies and diagnostic procedures. METHOD Data were collected from Pubmed and Google scholar using keywords: "Precision medicine", "precision medicine and cancer", "anticancer agents in precision medicine" and reviewed comprehensively. RESULTS Personalized therapeutics including immunotherapy, cancer vaccines, serve as a groundbreaking solution for cancer treatment. Herein, we take a measurable view of precision therapies and novel diagnostic approaches targeting cancer treatment. The contemporary applications of precision medicine have also been described along with various hurdles identified in the successful establishment of precision therapeutics. CONCLUSION This review highlights the key breakthroughs related to immunotherapies, targeted anticancer agents, and target interventions related to cancer signaling mechanisms. The success story of this field in context to drug resistance, safety, patient survival and in improving quality of life is yet to be elucidated. We conclude that, in the near future, the field of individualized treatments may truly revolutionize the nature of cancer patient care.
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Affiliation(s)
- Dia Advani
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Sudhanshu Sharma
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory Shahbad Daulatpur, Bawana Road, Delhi 110042. India
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33
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Gorenberg M, Agbarya A, Groshar D, Volovik I, Avitan O, Sukhotnik I. Novel nanotech antioxidant cocktail prevents medical diagnostic procedures ionizing radiation effects. Sci Rep 2021; 11:5315. [PMID: 33674660 PMCID: PMC7935885 DOI: 10.1038/s41598-021-84596-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/11/2021] [Indexed: 11/15/2022] Open
Abstract
Ionizing radiation (IR) exposure results in oxidative damage causing cytotoxic and genotoxic effects. Double-strand breaks (DSBs) are considered the most significant DNA lesions induced by ionizing radiation. The present study evaluates the radio protective effect of a novel antioxidant cocktail through quantification of DSB in peripheral blood lymphocytes (PBL) in vivo. The study included 16 consecutive patients who were divided into 2 groups, 6 patients received the novel antioxidant cocktail and 10 control patients. Blood samples were drawn from the patients undergoing bone scan, before the injection of the 99mTc MDP tracer and 2 h after the injection. Quantification of the IR damage was done by Immunofluorescence analysis of the phosphorylated histone, γ-H2AX, used to monitor DSB induction and repair in PBL. The radiation effect of the control group was measured by 2 variables, the average DBSs foci per nucleus and the percent of the DSB bearing cells in PBL. The findings showed a significant increase in the DSBs after isotope injection with an average increment of 0.29 ± 0.13 of foci/nucleus and 17.07% ± 7.68 more DSB bearing cells (p < 0.05). The cocktail treated group showed a lower difference average of − 2.79% ± 6.13 DSB bearing cells. A paired t-test revealed a significant difference between the groups (p < 0.005) confirming the cocktail’s protective effect. The novel anti-oxidant treatment decreases the oxidative stress-induced DNA damage and can be considered as a preventative treatment before radiation exposure.
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Affiliation(s)
- Miguel Gorenberg
- Department of Nuclear Medicine, Bnai-Zion Medical Center, Golomb 47, P.O.B 4940, Haifa, Israel. .,Technion-Israel Institute of Technology, The Ruth and Bruce Rappaport Faculty of Medicine, Haifa, Israel.
| | - Abed Agbarya
- Oncology Unit, Bnai-Zion Medical Center, Haifa, Israel
| | - David Groshar
- Department of Nuclear Medicine, Belinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Ilya Volovik
- Medical Imaging Department, Bnai-Zion Medical Center, Haifa, Israel
| | - Ofir Avitan
- Urology Department, Bnai-Zion Medical Center, Haifa, Israel
| | - Igor Sukhotnik
- Department of Pediatric Surgery, Dana-Dwek Children's Hospital, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
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McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM. Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance. Mutagenesis 2021; 35:27-38. [PMID: 31816044 DOI: 10.1093/mutage/gez046] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
DNA is susceptible to a range of chemical modifications, with one of the most frequent lesions being apurinic/apyrimidinic (AP) sites. AP sites arise due to damage-induced (e.g. alkylation) or spontaneous hydrolysis of the N-glycosidic bond that links the base to the sugar moiety of the phosphodiester backbone, or through the enzymatic activity of DNA glycosylases, which release inappropriate bases as part of the base excision repair (BER) response. Unrepaired AP sites, which lack instructional information, have the potential to cause mutagenesis or to arrest progressing DNA or RNA polymerases, potentially causing outcomes such as cellular transformation, senescence or death. The predominant enzyme in humans responsible for repairing AP lesions is AP endonuclease 1 (APE1). Besides being a powerful AP endonuclease, APE1 possesses additional DNA repair activities, such as 3'-5' exonuclease, 3'-phophodiesterase and nucleotide incision repair. In addition, APE1 has been shown to stimulate the DNA-binding activity of a number of transcription factors through its 'REF1' function, thereby regulating gene expression. In this article, we review the structural and biochemical features of this multifunctional protein, while reporting on new structures of the APE1 variants Cys65Ala and Lys98Ala. Using a functional complementation approach, we also describe the importance of the repair and REF1 activities in promoting cell survival, including the proposed passing-the-baton coordination in BER. Finally, results are presented indicating a critical role for APE1 nuclease activities in resistance to the genotoxins methyl methanesulphonate and bleomycin, supporting biologically important functions as an AP endonuclease and 3'-phosphodiesterase, respectively.
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Affiliation(s)
- Daniel R McNeill
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Wesley J Stark
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Peter J McKinnon
- Department of Genetics and Tumor Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - David M Wilson
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
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Sicińska P, Mokra K, Wozniak K, Michałowicz J, Bukowska B. Genotoxic risk assessment and mechanism of DNA damage induced by phthalates and their metabolites in human peripheral blood mononuclear cells. Sci Rep 2021; 11:1658. [PMID: 33462290 PMCID: PMC7814068 DOI: 10.1038/s41598-020-79932-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 12/15/2020] [Indexed: 01/20/2023] Open
Abstract
The human genome is persistently exposed to damage caused by xenobiotics, therefore the assessment of genotoxicity of substances having a direct contact with humans is of importance. Phthalates are commonly used in industrial applications. Widespread exposure to phthalates has been evidenced by their presence in human body fluids. We have assessed the genotoxic potential of selected phthalates and mechanism of their action in human peripheral blood mononuclear cells (PBMCs). Studied cells were incubated with di-n-butyl phthalate (DBP), butylbenzyl phthalate (BBP) and their metabolites: mono-n-butylphthalate (MBP), mono-benzylphthalate (MBzP) in the concentrations range of 0.1-10 µg/mL for 24 h. Analyzed compounds induced DNA single and double strand-breaks (DBP and BBP ≥ 0.5 µg/mL, MBP and MBzP ≥ 1 µg/mL) and more strongly oxidized purines than pyrimidines. None of the compounds examined was capable of creating adducts with DNA. All studied phthalates caused an increase of total ROS level, while hydroxyl radical was generated mostly by DBP and BBP. PBMCs exposed to DBP and BBP could not completely repair DNA strand-breaks during 120 min of postincubation, in opposite to damage caused by their metabolites, MBP and MBzP. We have concluded that parent phthalates: DBP and BBP caused more pronounced DNA damage compared to their metabolites.
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Affiliation(s)
- Paulina Sicińska
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska Str. 141/143, 90-236, Lodz, Poland.
| | - Katarzyna Mokra
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska Str. 141/143, 90-236, Lodz, Poland
| | - Katarzyna Wozniak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska Str. 141/143, 90-236, Lodz, Poland
| | - Jaromir Michałowicz
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska Str. 141/143, 90-236, Lodz, Poland
| | - Bożena Bukowska
- Department of Biophysics of Environmental Pollution, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska Str. 141/143, 90-236, Lodz, Poland
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Mitochondrial Reactive Oxygen Species (ROS) Production Alters Sperm Quality. Antioxidants (Basel) 2021; 10:antiox10010092. [PMID: 33440836 PMCID: PMC7827812 DOI: 10.3390/antiox10010092] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Besides ATP production, mitochondria are key organelles in several cellular functions, such as steroid hormone biosynthesis, calcium homoeostasis, intrinsic apoptotic pathway, and the generation of reactive oxygen species (ROS). Despite the loss of the majority of the cytoplasm occurring during spermiogenesis, mammalian sperm preserves a number of mitochondria that rearrange in a tubular structure at the level of the sperm flagellum midpiece. Although sperm mitochondria are destroyed inside the zygote, the integrity and the functionality of these organelles seem to be critical for fertilization and embryo development. The aim of this review was to discuss the impact of mitochondria-produced ROS at multiple levels in sperm: the genome, proteome, lipidome, epigenome. How diet, aging and environmental pollution may affect sperm quality and offspring health—by exacerbating oxidative stress—will be also described.
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Wang Y, Wu J, Wu J, Wang Y. DNA Polymerase II Supports the Replicative Bypass of N2-Alkyl-2'-deoxyguanosine Lesions in Escherichia coli Cells. Chem Res Toxicol 2021; 34:695-698. [PMID: 33417436 DOI: 10.1021/acs.chemrestox.0c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alkylation represents a main form of DNA damage. The N2 position of guanine is frequently alkylated in DNA. The SOS-induced polymerases have been shown to be capable of bypassing various DNA damage products in Escherichia coli. Herein, we explored the influences of four N2-alkyl-dG lesions (alkyl = ethyl, n-butyl, isobutyl, or sec-butyl) on DNA replication in AB1157 E. coli cells and the corresponding strains with polymerases (Pol) II, IV, and V being individually or simultaneously knocked out. We found that N2-Et-dG is slightly less blocking to DNA replication than the N2-Bu-dG lesions, which display very similar replication bypass efficiencies. Additionally, Pol II and, to a lesser degree, Pol IV and Pol V are required for the efficient bypass of the N2-alkyl-dG adducts, and none of these lesions was mutagenic. Together, our results support that the efficient replication across small N2-alkyl-dG DNA adducts in E. coli depends mainly on Pol II.
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Hans F, Senarisoy M, Bhaskar Naidu C, Timmins J. Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets. Int J Mol Sci 2020; 21:ijms21239226. [PMID: 33287345 PMCID: PMC7730500 DOI: 10.3390/ijms21239226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is the second leading cause of death with tens of millions of people diagnosed with cancer every year around the world. Most radio- and chemotherapies aim to eliminate cancer cells, notably by causing severe damage to the DNA. However, efficient repair of such damage represents a common mechanism of resistance to initially effective cytotoxic agents. Thus, development of new generation anticancer drugs that target DNA repair pathways, and more particularly the base excision repair (BER) pathway that is responsible for removal of damaged bases, is of growing interest. The BER pathway is initiated by a set of enzymes known as DNA glycosylases. Unlike several downstream BER enzymes, DNA glycosylases have so far received little attention and the development of specific inhibitors of these enzymes has been lagging. Yet, dysregulation of DNA glycosylases is also known to play a central role in numerous cancers and at different stages of the disease, and thus inhibiting DNA glycosylases is now considered a valid strategy to eliminate cancer cells. This review provides a detailed overview of the activities of DNA glycosylases in normal and cancer cells, their modes of regulation, and their potential as anticancer drug targets.
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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40
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Blázquez-Castro A, Fernández-Piqueras J, Santos J. Genetic Material Manipulation and Modification by Optical Trapping and Nanosurgery-A Perspective. Front Bioeng Biotechnol 2020; 8:580937. [PMID: 33072730 PMCID: PMC7530750 DOI: 10.3389/fbioe.2020.580937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
Light can be employed as a tool to alter and manipulate matter in many ways. An example has been the implementation of optical trapping, the so called optical tweezers, in which light can hold and move small objects with 3D control. Of interest for the Life Sciences and Biotechnology is the fact that biological objects in the size range from tens of nanometers to hundreds of microns can be precisely manipulated through this technology. In particular, it has been shown possible to optically trap and move genetic material (DNA and chromatin) using optical tweezers. Also, these biological entities can be severed, rearranged and reconstructed by the combined use of laser scissors and optical tweezers. In this review, the background, current state and future possibilities of optical tweezers and laser scissors to manipulate, rearrange and alter genetic material (DNA, chromatin and chromosomes) will be presented. Sources of undesirable effects by the optical procedure and measures to avoid them will be discussed. In addition, first tentative approaches at cellular-level genetic and organelle surgery, in which genetic material or DNA-carrying organelles are extracted out or introduced into cells, will be presented.
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Affiliation(s)
- Alfonso Blázquez-Castro
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain.,Genome Dynamics and Function Program, Genome Decoding Unit, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Autonomous University of Madrid, Madrid, Spain
| | - José Fernández-Piqueras
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain.,Genome Dynamics and Function Program, Genome Decoding Unit, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Autonomous University of Madrid, Madrid, Spain.,Institute of Health Research Jiménez Diaz Foundation, Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBERER), Carlos III Institute of Health, Madrid, Spain
| | - Javier Santos
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain.,Genome Dynamics and Function Program, Genome Decoding Unit, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Autonomous University of Madrid, Madrid, Spain.,Institute of Health Research Jiménez Diaz Foundation, Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBERER), Carlos III Institute of Health, Madrid, Spain
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41
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Kciuk M, Marciniak B, Mojzych M, Kontek R. Focus on UV-Induced DNA Damage and Repair-Disease Relevance and Protective Strategies. Int J Mol Sci 2020; 21:ijms21197264. [PMID: 33019598 PMCID: PMC7582305 DOI: 10.3390/ijms21197264] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
The protective ozone layer is continually depleting due to the release of deteriorating environmental pollutants. The diminished ozone layer contributes to excessive exposure of cells to ultraviolet (UV) radiation. This leads to various cellular responses utilized to restore the homeostasis of exposed cells. DNA is the primary chromophore of the cells that absorbs sunlight energy. Exposure of genomic DNA to UV light leads to the formation of multitude of types of damage (depending on wavelength and exposure time) that are removed by effectively working repair pathways. The aim of this review is to summarize current knowledge considering cellular response to UV radiation with special focus on DNA damage and repair and to give a comprehensive insight for new researchers in this field. We also highlight most important future prospects considering application of the progressing knowledge of UV response for the clinical control of diverse pathologies.
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Affiliation(s)
- Mateusz Kciuk
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
- Correspondence:
| | - Beata Marciniak
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland;
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
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42
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Agarwal A, Majzoub A, Baskaran S, Panner Selvam MK, Cho CL, Henkel R, Finelli R, Leisegang K, Sengupta P, Barbarosie C, Parekh N, Alves MG, Ko E, Arafa M, Tadros N, Ramasamy R, Kavoussi P, Ambar R, Kuchakulla M, Robert KA, Iovine C, Durairajanayagam D, Jindal S, Shah R. Sperm DNA Fragmentation: A New Guideline for Clinicians. World J Mens Health 2020; 38:412-471. [PMID: 32777871 PMCID: PMC7502318 DOI: 10.5534/wjmh.200128] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Sperm DNA integrity is crucial for fertilization and development of healthy offspring. The spermatozoon undergoes extensive molecular remodeling of its nucleus during later phases of spermatogenesis, which imparts compaction and protects the genetic content. Testicular (defective maturation and abortive apoptosis) and post-testicular (oxidative stress) mechanisms are implicated in the etiology of sperm DNA fragmentation (SDF), which affects both natural and assisted reproduction. Several clinical and environmental factors are known to negatively impact sperm DNA integrity. An increasing number of reports emphasizes the direct relationship between sperm DNA damage and male infertility. Currently, several assays are available to assess sperm DNA damage, however, routine assessment of SDF in clinical practice is not recommended by professional organizations. This article provides an overview of SDF types, origin and comparative analysis of various SDF assays while primarily focusing on the clinical indications of SDF testing. Importantly, we report four clinical cases where SDF testing had played a significant role in improving fertility outcome. In light of these clinical case reports and recent scientific evidence, this review provides expert recommendations on SDF testing and examines the advantages and drawbacks of the clinical utility of SDF testing using Strength-Weaknesses-Opportunities-Threats (SWOT) analysis.
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Affiliation(s)
- Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA.
| | - Ahmad Majzoub
- Department of Urology, Hamad Medical Corporation, Doha, Qatar
- Department of Urology, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Saradha Baskaran
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | | | - Chak Lam Cho
- Department of Surgery, Union Hospital, Hong Kong
- S. H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Ralf Henkel
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa
| | - Renata Finelli
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Kristian Leisegang
- School of Natural Medicine, Faculty of Community and Health Sciences, University of the Western Cape, Bellville, South Africa
| | - Pallav Sengupta
- Department of Physiology, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Malaysia
| | - Catalina Barbarosie
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Neel Parekh
- Department of Urology, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Marco G Alves
- Department of Microscopy, Laboratory of Cell Biology & Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Edmund Ko
- Department of Urology, Loma Linda University, Loma Linda, CA, USA
| | - Mohamed Arafa
- Department of Urology, Hamad Medical Corporation, Doha, Qatar
- Andrology Department, Cairo University, Giza, Egypt
| | - Nicholas Tadros
- Division of Urology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | | | - Parviz Kavoussi
- Austin Fertility & Reproductive Medicine/Westlake IVF, Austin, TX, USA
| | - Rafael Ambar
- Urology Department of Centro Universitario em Saude do ABC, Santo André, Brazil
| | | | - Kathy Amy Robert
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Concetta Iovine
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | | | - Sunil Jindal
- Department of Andrology and Reproductive Medicine, Jindal Hospital, Meerut, India
| | - Rupin Shah
- Department of Urology, Lilavati Hospital and Research Centre, Mumbai, India
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A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice: Impact of Sex and Age. Int J Mol Sci 2020; 21:ijms21186600. [PMID: 32917005 PMCID: PMC7555950 DOI: 10.3390/ijms21186600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023] Open
Abstract
Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2’-deoxyguanosine (8-oxodG), 5-hydroxy-2’-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
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Li W, Sancar A. Methodologies for detecting environmentally induced DNA damage and repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:664-679. [PMID: 32083352 PMCID: PMC7442611 DOI: 10.1002/em.22365] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/08/2020] [Accepted: 02/16/2020] [Indexed: 05/07/2023]
Abstract
Environmental DNA damaging agents continuously challenge the integrity of the genome by introducing a variety of DNA lesions. The DNA damage caused by environmental factors will lead to mutagenesis and subsequent carcinogenesis if they are not removed efficiently by repair pathways. Methods for detection of DNA damage and repair can be applied to identify, visualize, and quantify the DNA damage formation and repair events, and they enable us to illustrate the molecular mechanisms of DNA damage formation, DNA repair pathways, mutagenesis, and carcinogenesis. Ever since the discovery of the double helical structure of DNA in 1953, a great number of methods have been developed to detect various types of DNA damage and repair. Rapid advances in sequencing technologies have facilitated the emergence of a variety of novel methods for detecting environmentally induced DNA damage and repair at the genome-wide scale during the last decade. In this review, we provide a historical overview of the development of various damage detection methods. We also highlight the current methodologies to detect DNA damage and repair, especially some next generation sequencing-based methods.
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Affiliation(s)
- Wentao Li
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
| | - Aziz Sancar
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
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45
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Reuvers TGA, Kanaar R, Nonnekens J. DNA Damage-Inducing Anticancer Therapies: From Global to Precision Damage. Cancers (Basel) 2020; 12:E2098. [PMID: 32731592 PMCID: PMC7463878 DOI: 10.3390/cancers12082098] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 12/11/2022] Open
Abstract
DNA damage-inducing therapies are of tremendous value for cancer treatment and function by the direct or indirect formation of DNA lesions and subsequent inhibition of cellular proliferation. Of central importance in the cellular response to therapy-induced DNA damage is the DNA damage response (DDR), a protein network guiding both DNA damage repair and the induction of cancer-eradicating mechanisms such as apoptosis. A detailed understanding of DNA damage induction and the DDR has greatly improved our knowledge of the classical DNA damage-inducing therapies, radiotherapy and cytotoxic chemotherapy, and has paved the way for rational improvement of these treatments. Moreover, compounds targeting specific DDR proteins, selectively impairing DNA damage repair in cancer cells, form a promising novel therapy class that is now entering the clinic. In this review, we give an overview of the current state and ongoing developments, and discuss potential avenues for improvement for DNA damage-inducing therapies, with a central focus on the role of the DDR in therapy response, toxicity and resistance. Furthermore, we describe the relevance of using combination regimens containing DNA damage-inducing therapies and how they can be utilized to potentiate other anticancer strategies such as immunotherapy.
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Affiliation(s)
- Thom G. A. Reuvers
- Department of Molecular Genetics, Erasmus MC, Dr. Molenwaterplein 40, 3015 GD Rotterdam, The Netherlands; (T.G.A.R.); (R.K.)
- Department of Radiology and Nuclear Medicine, Erasmus MC, Dr. Molenwaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC, Dr. Molenwaterplein 40, 3015 GD Rotterdam, The Netherlands; (T.G.A.R.); (R.K.)
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Jaarbeursplein 6, 3561 AL Utrecht, The Netherlands
| | - Julie Nonnekens
- Department of Molecular Genetics, Erasmus MC, Dr. Molenwaterplein 40, 3015 GD Rotterdam, The Netherlands; (T.G.A.R.); (R.K.)
- Department of Radiology and Nuclear Medicine, Erasmus MC, Dr. Molenwaterplein 40, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Jaarbeursplein 6, 3561 AL Utrecht, The Netherlands
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46
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Sobek J, Schmidt M, Grossmann J, Rehrauer H, Schmidt L, Schlapbach R. Single-molecule chemistry. Part I: monitoring oxidation of G in oligonucleotides using CY3 fluorescence. Methods Appl Fluoresc 2020; 8:035010. [PMID: 32428873 DOI: 10.1088/2050-6120/ab947d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial hybridisation fluorescence pulse pattern which we attribute to products created by chemical reactions at the nucleobases. The origin is a charge separated state created by a photoinduced electron transfer from nucleobases to the dye followed by secondary reactions with oxygen and water, respectively. The positive charge can migrate through the hybrid resulting in base modifications at distant sites. Static fluorescence spectra were recorded in order to determine the properties of CY3 stacking to different base pairs, and compared to pulse intensities. A characteristic pulse pattern change was assigned to the oxidation of G to 8-oG besides the formation of a number of secondary products that are not yet identified. Further, we present a method to visualise the degree of chemical reactions to gain an overview of ongoing processes. Our study demonstrates that CY3 is able to oxidise nucleobases in ds DNA, and also in ss overhangs. An important finding is the correlation between nucleobase oxidation potential and fluorescence quenching which explains the intensity changes observed in single molecule measurements. The analysis of fluorescence traces provides the opportunity to track complete and coherent reaction sequences enabling to follow the fate of a single molecule over a long period of time, and to observe chemical reactions in real-time. This opens up the opportunity to analyse reaction pathways, to detect new products and short-lived intermediates, and to investigate rare events due to the large number of single molecules observed in parallel.
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Affiliation(s)
- Jens Sobek
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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47
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Fijen C, Mahmoud MM, Kronenberg M, Kaup R, Fontana M, Towle-Weicksel JB, Sweasy JB, Hohlbein J. Using single-molecule FRET to probe the nucleotide-dependent conformational landscape of polymerase β-DNA complexes. J Biol Chem 2020; 295:9012-9020. [PMID: 32385112 PMCID: PMC7335799 DOI: 10.1074/jbc.ra120.013049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/07/2020] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic DNA polymerase β (Pol β) plays an important role in cellular DNA repair, as it fills short gaps in dsDNA that result from removal of damaged bases. Since defects in DNA repair may lead to cancer and genetic instabilities, Pol β has been extensively studied, especially its mechanisms for substrate binding and a fidelity-related conformational change referred to as "fingers closing." Here, we applied single-molecule FRET to measure distance changes associated with DNA binding and prechemistry fingers movement of human Pol β. First, using a doubly labeled DNA construct, we show that Pol β bends the gapped DNA substrate less than indicated by previously reported crystal structures. Second, using acceptor-labeled Pol β and donor-labeled DNA, we visualized dynamic fingers closing in single Pol β-DNA complexes upon addition of complementary nucleotides and derived rates of conformational changes. We further found that, while incorrect nucleotides are quickly rejected, they nonetheless stabilize the polymerase-DNA complex, suggesting that Pol β, when bound to a lesion, has a strong commitment to nucleotide incorporation and thus repair. In summary, the observation and quantification of fingers movement in human Pol β reported here provide new insights into the delicate mechanisms of prechemistry nucleotide selection.
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Affiliation(s)
- Carel Fijen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Mariam M Mahmoud
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Meike Kronenberg
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Rebecca Kaup
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mattia Fontana
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Jamie B Towle-Weicksel
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joann B Sweasy
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands; Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, The Netherlands.
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48
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Lee HT, Sanford S, Paul T, Choe J, Bose A, Opresko PL, Myong S. Position-Dependent Effect of Guanine Base Damage and Mutations on Telomeric G-Quadruplex and Telomerase Extension. Biochemistry 2020; 59:2627-2639. [PMID: 32578995 DOI: 10.1021/acs.biochem.0c00434] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Telomeres are hot spots for mutagenic oxidative and methylation base damage due to their high guanine content. We used single-molecule fluorescence resonance energy transfer detection and biochemical assays to determine how different positions and types of guanine damage and mutations alter telomeric G-quadruplex structure and telomerase activity. We compared 15 modifications, including 8-oxoguanine (8oxoG), O-6-methylguanine (O6mG), and all three possible point mutations (G to A, T, and C) at the 3' three terminal guanine positions of a telomeric G-quadruplex, which is the critical access point for telomerase. We found that G-quadruplex structural instability was induced in the order C < T < A ≤ 8oxoG < O6mG, with the perturbation caused by O6mG far exceeding the perturbation caused by other base alterations. For all base modifications, the central G position was the most destabilizing among the three terminal guanines. While the structural disruption by 8oxoG and O6mG led to concomitant increases in telomerase binding and extension activity, the structural perturbation by point mutations (A, T, and C) did not, due to disrupted annealing between the telomeric overhang and the telomerase RNA template. Repositioning the same mutations away from the terminal guanines caused both G-quadruplex structural instability and elevated telomerase activity. Our findings demonstrate how a single-base modification drives structural alterations and telomere lengthening in a position-dependent manner. Furthermore, our results suggest a long-term and inheritable effect of telomeric DNA damage that can lead to telomere lengthening, which potentially contributes to oncogenesis.
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Affiliation(s)
- Hui-Ting Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Samantha Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania 15261, United States
| | - Tapas Paul
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joshua Choe
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania 15261, United States
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania 15261, United States
| | - Sua Myong
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
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49
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Modulation of DNA Damage Response by Sphingolipid Signaling: An Interplay that Shapes Cell Fate. Int J Mol Sci 2020; 21:ijms21124481. [PMID: 32599736 PMCID: PMC7349968 DOI: 10.3390/ijms21124481] [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: 04/16/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/11/2022] Open
Abstract
Although once considered as structural components of eukaryotic biological membranes, research in the past few decades hints at a major role of bioactive sphingolipids in mediating an array of physiological processes including cell survival, proliferation, inflammation, senescence, and death. A large body of evidence points to a fundamental role for the sphingolipid metabolic pathway in modulating the DNA damage response (DDR). The interplay between these two elements of cell signaling determines cell fate when cells are exposed to metabolic stress or ionizing radiation among other genotoxic agents. In this review, we aim to dissect the mediators of the DDR and how these interact with the different sphingolipid metabolites to mount various cellular responses.
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50
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Richer AL, Riemondy KA, Hardie L, Hesselberth JR. Simultaneous measurement of biochemical phenotypes and gene expression in single cells. Nucleic Acids Res 2020; 48:e59. [PMID: 32286626 PMCID: PMC7261187 DOI: 10.1093/nar/gkaa240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/16/2020] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
Methods to measure heterogeneity among cells are rapidly transforming our understanding of biology but are currently limited to molecular abundance measurements. We developed an approach to simultaneously measure biochemical activities and mRNA abundance in single cells to understand the heterogeneity of DNA repair activities across thousands of human lymphocytes, identifying known and novel cell-type-specific DNA repair phenotypes.
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Affiliation(s)
- Amanda L Richer
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
- Molecular Biology Program
| | - Kent A Riemondy
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Lakotah Hardie
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
- Molecular Biology Program
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
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