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Zhao M, Guo J, Chen Z, Wang F. A disposable electrochemical magnetic immunosensor for the rapid and sensitive detection of 5-formylcytosine and 5-carboxylcytosine in DNA. Biosens Bioelectron 2024; 262:116547. [PMID: 38968775 DOI: 10.1016/j.bios.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
5-formylcytosine (5 fC) and 5-carboxylcytosine (5caC) serve as key intermediates in DNA demethylation process with significant implications for gene regulation and disease progression. In this study, we introduce a novel electrochemical sensing platform specifically designed for the sensitive and selective detection of 5 fC and 5caC in DNA. Protein A-modified magnetic beads (ProtA-MBs) coupled with specific antibodies facilitate the immunorecognition and enrichment of these modified bases. Signal amplification is achieved through several chemical reactions involving the interaction between N3-kethonaxl and guanine, copper-free click chemistry for the attachment of dibenzocyclooctyne (DBCO)-Biotin, and the subsequent recognition by streptavidin-conjugated horseradish peroxidase (SA-HRP). The assay's readout is performed on a disposable laser-induced graphene (LIG) electrode, modified with the bead-antibody-DNA complex in a magnetic field, and analyzed using differential pulse voltammetry in a system employing hydroquinone (HQ) as the redox mediator and H2O2 as the substrate. This immunosensor displayed excellent sensitivity, with detection limits of 14.8 fM for 5 fC across a 0.1-1000 pM linear range and 87.4 fM for 5caC across a 0.5-5000 pM linear range, and maintained high selectivity even in the presence of interferences from other DNA modifications. Successful application in quantifying 5 fC and 5caC in genomic DNA from cell extracts, with recovery rates between 97.7% to 102.9%, underscores its potential for clinical diagnostics. N3-kethoxal was used for the first time in an electrochemical sensor. This work not only broadens the toolkit for detecting DNA modifications but also provides a fresh impetus for the development of point-of-care testing (POCT) technologies.
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Affiliation(s)
- Mei Zhao
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Jingyi Guo
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Zilin Chen
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Fang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
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2
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Xu R, Zhang Y, Gao Y, Jia S, Choi S, Xu Y, Gong J. Development of a targeted method for DNA adductome and its application as sensitive biomarkers of ambient air pollution exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135018. [PMID: 38959829 DOI: 10.1016/j.jhazmat.2024.135018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/11/2024] [Accepted: 06/22/2024] [Indexed: 07/05/2024]
Abstract
DNA adducts are widely recognized as biomarkers of exposure to environmental carcinogens and associated health effects in toxicological and epidemiological studies. This study presents a targeted and sensitive method for comprehensive DNA adductome analysis using ultra-high-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QqQ-MS/MS). The method was developed using calf thymus DNA, with careful optimization of mass spectrometric parameters, chromatographic separation conditions, and pretreatment methods. Ultimately, a targeted method was established for 41 DNA adducts, which showed good linearity (R2 ≥0.992), recovery (80.1-119.4 %), accuracy (81.3-117.8 %), and precision (relative standard deviation <14.2 %). The established method was employed to analyze DNA adducts in peripheral blood cells from pregnant women in Shanxi and Beijing. Up to 23 DNA adducts were successfully detected in samples of varying sizes. From 2 μg of maternal DNA samples, seven specific adducts were identified: 5-methyl-2'-deoxycytidine (5-MedC), 5-hydroxymethyl-2'-deoxycytidine (5-HmdC), N6-methyl-2'-deoxyadenosine (N6-MedA), 8-hydroxy-2'-deoxyguanosine (8-OHdG), 5-hydroxy-2'-deoxycytidine (5-OHdC), 1,N6-etheno-2'-deoxyadenosine (1,N6-εdA), and N2-methyl-2'-deoxyguanosine (N2-MedG). This study reveals that exposure to higher concentrations of ambient air pollutants may elevate the levels of DNA methylation and oxidative damage at different base sites, highlighting the application potential of DNA adducts as sensitive biomarkers of air pollution exposure.
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Affiliation(s)
- Ruiwei Xu
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Yi Zhang
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Yingfeng Gao
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Shuyu Jia
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Seokho Choi
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Yifan Xu
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Jicheng Gong
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China.
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Marchante-Gayón JM, Nicolás Carcelén J, Potes Rodríguez H, Pineda-Cevallos D, Rodas Sánchez L, González-Gago A, Rodríguez-González P, García Alonso JI. Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:998-1018. [PMID: 37597182 DOI: 10.1002/mas.21865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/21/2023]
Abstract
Epigenetic modifications are closely related to certain disorders of the organism, including the development of tumors. One of the main epigenetic modifications is the methylation of DNA cytosines, 5-methyl-2'-deoxycycytidine. Furthermore, 5-mdC can be oxidized to form three new modifications, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxy-2'-deoxycytidine. The coupling of liquid chromatography with tandem mass spectrometry has been widely used for the total determination of methylated DNA cytosines in samples of biological and clinical interest. These methods are based on the measurement of the free compounds (e.g., urine) or after complete hydrolysis of the DNA (e.g., tissues) followed by a preconcentration, derivatization, and/or clean-up step. This review highlights the main advances in the quantification of modified nucleotides and nucleosides by isotope dilution using isotopically labeled analogs combined with liquid or gas chromatography coupled to mass spectrometry reported in the last 20 years. The different possible sources of labeled compounds are indicated. Special emphasis has been placed on the different types of chromatography commonly used (reverse phase and hydrophilic interaction liquid chromatography) and the derivatization methods developed to enhance chromatographic resolution and ionization efficiency. We have also revised the application of bidimensional chromatography and indicated significant biological and clinical applications of these determinations.
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Affiliation(s)
- Juan M Marchante-Gayón
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jesús Nicolás Carcelén
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Helí Potes Rodríguez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Daniela Pineda-Cevallos
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Laura Rodas Sánchez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Adriana González-Gago
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jose I García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
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Ploypetch S, Luo X, Zhao S, Roytrakul S, Li L, Suriyaphol G. Salivary metabolomic identification of biomarker candidates for oral melanoma and oral squamous cell carcinoma in dogs. J Vet Intern Med 2024; 38:2293-2304. [PMID: 38703129 PMCID: PMC11256132 DOI: 10.1111/jvim.17092] [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: 12/13/2023] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Oral melanoma (OM) and oral squamous cell carcinoma (OSCC) are frequently diagnosed in dogs, presenting a challenge in distinguishing them from benign oral tumors (BN). Salivary metabolomic biomarkers offer a practical solution because of saliva's direct contact with tumors and the noninvasive nature of collection. OBJECTIVE Assess the diversity and abundance of the salivary metabolome in dogs with BN, OM, and OSCC using amine/phenol submetabolome analysis and high-performance chemical isotope labeling liquid chromatography-mass spectrometry (CIL LC-MS). ANIMALS Study included 11 BN, 24 OM, 10 OSCC, and 20 healthy control dogs. METHODS Case-control cross-sectional study was conducted to assess salivary submetabolic profiles in dogs with BN, OM, and OSCC and healthy dogs. Samples were labeled with 12C-dansyl chloride and analyzed using CIL LC-MS targeted to amine- and phenol-containing metabolites for amine/phenol submetabolome analysis. RESULTS Distinct clusters and significant differences in metabolite concentrations were observed among the oral cancer, BN, and control groups. A total of 154 and 66 metabolites showed significantly altered concentrations, particularly in OM and OSCC, respectively, when compared with BN (Padj < .05). Potential metabolic biomarkers were identified for each cancer, including decreased concentrations of seryl-arginine and sarcosine in OSCC. Moreover, high-confidence putative metabolites were identified, including an increase in tryptophyl-threonine and a decrease in 1,2-dihydroxynapthalene-6-sulfonic acid and hydroxyprolyl-hydroxyproline for OM. CONCLUSIONS AND CLINICAL IMPORTANCE We identified high coverage of the amine/phenol submetabolome, including seryl-arginine, and sarcosine, in OSCC. Our findings emphasize the potential of these biomarkers for distinguishing between oral OSCC and BN in dogs.
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Affiliation(s)
- Sekkarin Ploypetch
- Department of Clinical Sciences and Public Health, Faculty of Veterinary ScienceMahidol UniversityNakhon PathomThailand
| | - Xian Luo
- The Metabolomics Innovation CentreUniversity of AlbertaEdmontonAlbertaCanada
| | - Shuang Zhao
- The Metabolomics Innovation CentreUniversity of AlbertaEdmontonAlbertaCanada
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and BiotechnologyNational Science and Technology Development AgencyPathum ThaniThailand
| | - Liang Li
- The Metabolomics Innovation CentreUniversity of AlbertaEdmontonAlbertaCanada
- Department of ChemistryUniversity of AlbertaEdmontonAlbertaCanada
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary ScienceChulalongkorn UniversityBangkokThailand
- Center of Excellence for Companion Animal Cancer, Faculty of Veterinary ScienceChulalongkorn UniversityBangkokThailand
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5
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Chen S, Lai W, Wang H. Recent advances in high-performance liquid chromatography tandem mass spectrometry techniques for analysis of DNA damage and epigenetic modifications. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503755. [PMID: 38821674 DOI: 10.1016/j.mrgentox.2024.503755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 06/02/2024]
Abstract
Environmental exposure would cause DNA damage and epigenetic modification changes, potentially resulting in physiological dysfunction, thereby triggering diseases and even cancer. DNA damage and epigenetic modifications are thus promising biomarkers for environmental exposures and disease states. Benefiting from its high sensitivity and accuracy, high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) is considered the "gold standard technique" for investigating epigenetic DNA modifications. This review summarizes the recent advancements of UHPLC-MS/MS-based technologies for DNA damage and epigenetic modifications analysis, mainly focusing on the innovative methods developed for UHPLC-MS/MS-related pretreatment technologies containing efficient genomic DNA digestion and effective removal of the inorganic salt matrix, and the new strategies for improving detection sensitivity of liquid chromatography-mass spectrometry. Moreover, we also summarized the novel hyphenated techniques of the advanced UHPLC-MS/MS coupled with other separation and analysis methods for the measurement of DNA damage and epigenetic modification changes in special regions and fragments of chromosomes.
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Affiliation(s)
- Shaokun Chen
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyi Lai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Environment and Health, Institute for Advanced Study, UCAS, Hangzhou 310000, China
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6
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Shao Z, Chen J, Wang S, Wang W, Zhu L. Sulfonamide-induced DNA hypomethylation disturbed sugar metabolism in rice (Oryza sativa L.). ENVIRONMENT INTERNATIONAL 2024; 187:108737. [PMID: 38735075 DOI: 10.1016/j.envint.2024.108737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
DNA methylation is well-accepted as a bridge to unravel the complex interplay between genome and environmental exposures, and its alteration regulated the cellular metabolic responses towards pollutants. However, the mechanism underlying site-specific aberrant DNA methylation and metabolic disorders under pollutant stresses remained elusive. Herein, the multilevel omics interferences of sulfonamides (i.e., sulfadiazine and sulfamerazine), a group of antibiotics pervasive in farmland soils, towards rice in 14 days of 1 mg/L hydroponic exposure were systematically evaluated. Metabolome and transcriptome analyses showed that 57.1-71.4 % of mono- and disaccharides were accumulated, and the differentially expressed genes were involved in the promotion of sugar hydrolysis, as well as the detoxification of sulfonamides. Most differentially methylated regions (DMRs) were hypomethylated ones (accounting for 87-95 %), and 92 % of which were located in the CHH context (H = A, C, or T base). KEGG enrichment analysis revealed that CHH-DMRs in the promoter regions were enriched in sugar metabolism. To reveal the significant hypomethylation of CHH, multi-spectroscopic and thermodynamic approaches, combined with molecular simulation were conducted to investigate the molecular interaction between sulfonamides and DNA in different sequence contexts, and the result demonstrated that sulfonamides would insert into the minor grooves of DNA, and exhibited a stronger affinity with the CHH contexts of DNA compared to CG or CHG contexts. Computational modeling of DNA 3D structures further confirmed that the binding led to a pitch increase of 0.1 Å and a 3.8° decrease in the twist angle of DNA in the CHH context. This specific interaction and the downregulation of methyltransferase CMT2 (log2FC = -4.04) inhibited the DNA methylation. These results indicated that DNA methylation-based assessment was useful for metabolic toxicity prediction and health risk assessment.
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Affiliation(s)
- Zexi Shao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Jie Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Shuyuan Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Wei Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China.
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7
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Jiang T, Zhou Q, Yu KK, Chen SY, Li K. Identification and quantification of N6-methyladenosine by chemical derivatization coupled with 19F NMR spectroscopy. Org Biomol Chem 2024; 22:2566-2573. [PMID: 38465392 DOI: 10.1039/d4ob00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
N 6-Methyladenosine (6mA) is a well-known prokaryotic DNA modification that has been shown to play epigenetic roles in eukaryotic DNA. Accurate detection and quantification of 6mA are prerequisites for molecular understanding of the impact of 6mA modification on DNA. However, the existing methods have several problems, such as high false-positive rate, time-consuming and complex operating procedures. Chemical sensors for the selective detection of 6mA modification are rarely reported in the literature. Fluorinated phenylboronic acid combined with 19F NMR analysis is an effective method for determining DNA or RNA modification. In this study, we presented a simple and fast chemical method for labelling the 6th imino group of 6mA using a boric-acid-derived probe. Besides, the trifluoromethyl group of trifluoromethyl phenylboronic acid (2a) could detect 6mA modification through 19F NMR. Combined with this sensor system, 6mA modification could be detected well and quickly in 6 types of deoxynucleoside mixtures and DNA samples. Taken together, the method developed in the current study has potential for specific detection of 6mA in biological samples.
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Affiliation(s)
- Ting Jiang
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Qian Zhou
- Department of Chemistry, Xihua University, Chengdu 610039, P. R. China
| | - Kang-Kang Yu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Shan-Yong Chen
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
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8
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Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [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: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
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Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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9
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Erlitzki N, Kohli RM. An Overview of Global, Local, and Base-Resolution Methods for the Detection of 5-Hydroxymethylcytosine in Genomic DNA. Methods Mol Biol 2024; 2842:325-352. [PMID: 39012604 DOI: 10.1007/978-1-0716-4051-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The discovery of 5-hydroxymethylcytosine (5hmC) as a common DNA modification in mammalian genomes has ushered in new areas of inquiry regarding the dynamic epigenome. The balance between 5hmC and its precursor, 5-methylcytosine (5mC), has emerged as a determinant of key processes including cell fate specification, and alterations involving these bases have been implicated in the pathogenesis of various diseases. The identification of 5hmC separately from 5mC initially posed a challenge given that legacy epigenetic sequencing technologies could not discriminate between these two most abundant modifications, a significant blind spot considering their potentially functionally opposing roles. The growing interest in 5hmC, as well as in the Ten-Eleven Translocation (TET) family enzymes that catalyze its generation and further oxidation to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC), has spurred the development of versatile methods for 5hmC detection. These methods enable the quantification and localization of 5hmC in diverse biological samples and, in some cases, at the resolution of individual nucleotides. However, navigating this growing toolbox of methods for 5hmC detection can be challenging. Here, we detail existing and emerging methods for the detection, quantification, and localization of 5hmC at global, locus-specific, and base resolution levels. These methods are discussed in the context of their advantages and limitations, with the goal of providing a framework to help guide researchers in choosing the level of resolution and the associated method that could be most suitable for specific needs.
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Affiliation(s)
- Noa Erlitzki
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Xie NB, Wang M, Chen W, Ji TT, Guo X, Gang FY, Wang YF, Feng YQ, Liang Y, Ci W, Yuan BF. Whole-Genome Sequencing of 5-Hydroxymethylcytosine at Base Resolution by Bisulfite-Free Single-Step Deamination with Engineered Cytosine Deaminase. ACS CENTRAL SCIENCE 2023; 9:2315-2325. [PMID: 38161361 PMCID: PMC10755730 DOI: 10.1021/acscentsci.3c01131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
The epigenetic modification 5-hydroxymethylcytosine (5hmC) plays a crucial role in the regulation of gene expression. Although some methods have been developed to detect 5hmC, direct genome-wide mapping of 5hmC at base resolution is still highly desirable. Herein, we proposed a single-step deamination sequencing (SSD-seq) method, designed to precisely map 5hmC across the genome at single-base resolution. SSD-seq takes advantage of a screened engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein, known as eA3A-v10, to selectively deaminate cytosine (C) and 5-methylcytosine (5mC) but not 5hmC. During sequencing, the deaminated C and 5mC are converted to uracil (U) and thymine (T), read as T in the sequencing data. However, 5hmC remains unaffected by eA3A-v10 and is read as C during sequencing. Consequently, the presence of C in the sequence reads indicates the original 5hmC. We applied SSD-seq to generate a base-resolution map of 5hmC in human lung tissue. Our findings revealed that 5hmC was predominantly localized to CpG dinucleotides. Furthermore, the base-resolution map of 5hmC generated by SSD-seq demonstrated a strong correlation with prior ACE-seq results. The advantages of SSD-seq are its single-step process, absence of bisulfite treatment or DNA glycosylation, cost effectiveness, and ability to detect and quantify 5hmC directly at single-base resolution.
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Affiliation(s)
- Neng-Bin Xie
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
- Research
Center of Public Health, Renmin Hospital
of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Min Wang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Wei Chen
- Department
of Laboratory Medicine, Zhongnan Hospital
of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tong-Tong Ji
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xia Guo
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Fang-Yin Gang
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Ya-Feng Wang
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yuan Liang
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute
of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Weimin Ci
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute
of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Bi-Feng Yuan
- Department
of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
- Research
Center of Public Health, Renmin Hospital
of Wuhan University, Wuhan University, Wuhan 430060, China
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
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11
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Thonghlueng J, Ngernpimai S, Chuaephon A, Phanchai W, Wiwasuku T, Wanna Y, Wiratchawa K, Intharah T, Thanan R, Sakonsinsiri C, Puangmali T. Dual-Responsive Carbon Quantum Dots for the Simultaneous Detection of Cytosine and 5-Methylcytosine Interpreted by a Machine Learning-Assisted Smartphone. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40141-40152. [PMID: 37585565 DOI: 10.1021/acsami.3c00785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
DNA methylation is an epigenetic alteration that results in 5-methylcytosine (5-mC) through the addition of a methyl group to the fifth carbon of a cytosine (C) residue. The methylation level, the ratio of 5-mC to C, in urine might be related to the whole-body epigenetic status and the occurrence of common cancers. To date, never before have any nanomaterials been developed to simultaneously determine C and 5-mC in urine samples. Herein, a dual-responsive fluorescent sensor for the urinary detection of C and 5-mC has been developed. This assay relied on changes in the optical properties of nitrogen-doped carbon quantum dots (CQDs) prepared by microwave-assisted pyrolysis. In the presence of C, the blue-shifted fluorescence intensity of the CQDs increased. However, fluorescence quenching was observed upon the addition of 5-mC. This was primarily due to photoinduced electron transfer as confirmed by the density functional theory calculation. In urine samples, our sensitive fluorescent sensor had detection limits for C and 5-mC of 43.4 and 74.4 μM, respectively, and achieved satisfactory recoveries ranging from 103.5 to 115.8%. The simultaneous detection of C and 5-mC leads to effective methylation level detection, achieving recoveries in the range of 104.6-109.5%. Besides, a machine learning-enabled smartphone was also developed, which can be effectively applied to the determination of methylation levels (0-100%). These results demonstrate a simple but very effective approach for detecting the methylation level in urine, which could have significant implications for predicting the clinical prognosis.
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Affiliation(s)
- Janpen Thonghlueng
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sawinee Ngernpimai
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Adulvit Chuaephon
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Theanchai Wiwasuku
- Functional Materials and Nanotechnology Center of Excellence, School of Science, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Yupaporn Wanna
- Department of Statistics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kannika Wiratchawa
- Department of Statistics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thanapong Intharah
- Department of Statistics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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12
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Oliveira JES, Araújo AP, Alves AS, Silva MWF, Almeida JPBD, Nascimento JAM, Dos Santos VB, Oliveira SCB. Simultaneous voltammetric determination of 7-methyl-guanine and 5-methyl-cytosine using a cathodically pre-treated boron-doped diamond electrode. Anal Biochem 2023; 671:115135. [PMID: 37019253 DOI: 10.1016/j.ab.2023.115135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/07/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023]
Abstract
Given the importance of identifying the presence of biomarkers of human diseases in DNA samples, the main objective of this work was to investigate, for the first time, the electro-catalytic oxidation of 7-methyl-guanine (7-mGua) and 5-methyl-cytosine (5-mCyt) on a boron doped diamond electrode pre-treated cathodically (red-BDDE), using differential pulse voltammetry (DPV) and cyclic voltammetry (CV). The anodic peak potentials of 7-mGua and 5-mCyt by DPV were at E = 1.04 V and E = 1.37 V at pH = 4.5, indicating excellent peak separation of approximately 330 mV between species. Using DPV, experimental conditions such as supporting electrolyte, pH and influence of interferents were also investigated to develop a sensitive and selective method for individual and simultaneous quantification of these biomarkers. The analytical curves for the simultaneous quantification of 7-mGua and 5-mCyt in the acid medium (pH = 4.5) were: concentration range of 0.50-5.00 μmol L-1 (r = 0.999), detection limit of 0.27 μmol L-1 for 7-mGua; from 3.00 to 25.00 μmol L-1 (r = 0.998), with a detection limit of 1.69 μmol L-1 for 5-mCyt. A new DP voltammetric method for the simultaneous detection and quantification of biomarkers 7-mGua and 5-mCyt using a red-BDDE is proposed.
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Affiliation(s)
| | - Alex P Araújo
- Department of Chemistry, Federal Rural University of Pernambuco, Recife, PE, Brazil
| | - Arthur S Alves
- Department of Chemistry, Federal Rural University of Pernambuco, Recife, PE, Brazil
| | - Maycom W F Silva
- Department of Chemistry, Federal Rural University of Pernambuco, Recife, PE, Brazil
| | | | | | - Vagner B Dos Santos
- Fundamental Chemistry Department, Federal University of Pernambuco, Recife, PE, Brazil
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13
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Chen YN, Shen XY, Yu Y, Xue CY, Zhou YL, Zhang XX. In-source fragmentation of nucleosides in electrospray ionization towards more sensitive and accurate nucleoside analysis. Analyst 2023; 148:1500-1506. [PMID: 36883656 DOI: 10.1039/d3an00047h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Nucleosides have been found to suffer in-source fragmentation (ISF) in electrospray ionization mass spectrometry, which leads to reduced sensitivity and ambiguous identification. In this work, a combination of theoretical calculations and nuclear magnetic resonance analysis revealed the key role of protonation at N3 near the glycosidic bond during ISF. Therefore, an ultrasensitive liquid chromatography-tandem mass spectrometry system for 5-formylcytosine detection was developed with 300 fold signal enhancement. Also, we established a MS1-only platform for nucleoside profiling and successfully identified sixteen nucleosides in the total RNA of MCF-7 cells. Taking ISF into account, we can realize analysis with higher sensitivity and less ambiguity, not only for nucleosides, but for other molecules with similar protonation and fragmentation behaviors.
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Affiliation(s)
- Yu-Nan Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Xu-Yang Shen
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Yue Yu
- Institute of Biotechnology Development, Qilu Pharmaceutical, Jinan, China
| | - Chen-Yu Xue
- Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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14
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Song X, Song X, Lai W, Wang H. Hyperactive DNA Cutting for Unbiased UHPLC-MS/MS Quantification of Epigenetic DNA Marks by Engineering DNase I Mutants. Anal Chem 2022; 94:17670-17676. [PMID: 36490323 DOI: 10.1021/acs.analchem.2c04485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic DNA modifications, such as 5-methylcytosine, 5-hydroxymethylcytosine, and 5-formylcytosine, are associated with a variety of diseases and potential biomarkers for cancer diagnosis and therapy. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays are considered to be the gold standard for qualitative and quantitative detection of DNA modifications. DNA digestion for converting long DNA polymer into 2'-deoxynucleosides is an important preprocessing step to achieve sensitive and accurate LC-MS/MS quantification. Here, we showed that, as stimulated by divalent metal ions, Mg2+ and Mn2+, the engineered human DNase I Q9R:E13R:N74K mutant can efficiently digest DNA in the presence of monovalent metal ions at a high concentration (e.g., 1 M NaCl), showing hyperactivity on DNA cutting. We also found that the engineered DNase I mutants display exceptional DNA-cutting activity over a wider pH range (5.5-9.5). Due to their hyperactivity and high salt tolerance, the engineered DNase I mutants cut DNA 5mC and dC efficiently. Benefitting from this DNA-cutting hyperactivity, we demonstrated an LC-MS/MS assay for unbiased and accurate quantification of DNA 5mC.
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Affiliation(s)
- Xingrui Song
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xinyue Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Cui Y, Wang Y. Mass spectrometry-based DNA adductomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Hu Y, Hong X, Yuan Z, Mu J, Zhang X, Fang Z, Yuan Y, Zheng S, Guo C. Pan-cancer analysis of DNA epigenetic modifications by hydrophilic interaction liquid chromatography-tandem mass spectrometry. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Ultrasensitive Simultaneous Detection of Multiple Rare Modified Nucleosides as Promising Biomarkers in Low-Put Breast Cancer DNA Samples for Clinical Multi-Dimensional Diagnosis. Molecules 2022; 27:molecules27207041. [DOI: 10.3390/molecules27207041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Early cancer diagnosis is essential for successful treatment and prognosis, and modified nucleosides have attracted widespread attention as a promising group of cancer biomarkers. However, analyzing these modified nucleosides with an extremely low abundance is a great challenge, especially analyzing multiple modified nucleosides with a different abundance simultaneously. In this work, an ultrasensitive quantification method based on chemical labeling, coupled with LC-MS/MS analysis, was established for the simultaneous quantification of 5hmdC, 5fdC, 5hmdU and 5fdU. Additionally, the contents of 5mdC and canonical nucleosides could be obtained at the same time. Upon derivatization, the detection sensitivities of 5hmdC, 5fdC, 5hmdU and 5fdU were dramatically enhanced by several hundred times. The established method was further applied to the simultaneous detection of nine nucleosides with different abundances in about 2 μg genomic DNA of breast tissues from 20 breast cancer patients. The DNA consumption was less than other overall reported quantification methods, thereby providing an opportunity to monitor rare, modified nucleosides in precious samples and biology processes that could not be investigated before. The contents of 5hmdC, 5hmdU and 5fdU in tumor tissues and normal tissues adjacent to the tumor were significantly changed, indicating that these three modified nucleosides may play certain roles in the formation and development of tumors and be potential cancer biomarkers. While the detection rates of 5hmdC, 5hmdU and 5fdU alone as a biomarker for breast cancer samples were 95%, 75% and 85%, respectively, by detecting these three cancer biomarkers simultaneously, two of the three were 100% consistent with the overall trend. Therefore, simultaneous detection of multiple cancer biomarkers in clinical samples greatly improved the accuracy of cancer diagnosis, indicating that our method has great application potential in clinical multidimensional diagnosis.
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18
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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19
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Varma SJ, Calvani E, Grüning NM, Messner CB, Grayson N, Capuano F, Mülleder M, Ralser M. Global analysis of cytosine and adenine DNA modifications across the tree of life. eLife 2022; 11:81002. [PMID: 35900202 PMCID: PMC9333990 DOI: 10.7554/elife.81002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022] Open
Abstract
Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global quantification of DNA modifications have thus far been applied mostly to individual problems. We established a mass spectrometric method for the sensitive and accurate quantification of multiple enzymatic DNA modifications. Then, we isolated DNA from 124 archean, bacterial, fungal, plant, and mammalian species, and several tissues and created a resource of global DNA modification quantities. Our dataset provides insights into the general nature of enzymatic DNA modifications, reveals unique biological cases, and provides complementary quantitative information to normalize and assess the accuracy of sequencing-based detection of DNA modifications. We report that only three of the studied DNA modifications, methylcytosine (5mdC), methyladenine (N6mdA) and hydroxymethylcytosine (5hmdC), were detected above a picomolar detection limit across species, and dominated in higher eukaryotes (5mdC), in bacteria (N6mdA), or the vertebrate central nervous systems (5hmdC). All three modifications were detected simultaneously in only one of the tested species, Raphanus sativus. In contrast, these modifications were either absent or detected only at trace quantities, across all yeasts and insect genomes studied. Further, we reveal interesting biological cases. For instance, in Allium cepa, Helianthus annuus, or Andropogon gerardi, more than 35% of cytosines were methylated. Additionally, next to the mammlian CNS, 5hmdC was also detected in plants like Lepidium sativum and was found on 8% of cytosines in the Garra barreimiae brain samples. Thus, identifying unexpected levels of DNA modifications in several wild species, our resource underscores the need to address biological diversity for studying DNA modifications.
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Affiliation(s)
| | - Enrica Calvani
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nana-Maria Grüning
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Grayson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
| | - Michael Mülleder
- Core Facility-High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany.,The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom
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20
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Zhang Z, He T, Qi Y, Dai Y, Lao K, Gou X. Rapid and highly specific detection of site-specific 5-hydroxymethylcytosine based on peroxotungstate oxidation and mismatch ligation-based LAMP. RSC Adv 2022; 12:19885-19889. [PMID: 35865199 PMCID: PMC9261916 DOI: 10.1039/d2ra03310k] [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: 05/26/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
We have developed a rapid and specific method for site-specific 5-hydroxymethylcytosine (5hmC) quantification at single-base resolution. This bisulfite-free method integrates the peroxotungstate oxidization with the mismatched probe-assisted ligation to guarantee the specificity. Moreover, the high-efficiency LAMP also makes the proposed method suitable for the detection of low-content samples. A facile and highly specific mismatch ligation-based amplification platform for quantification of site-specific 5hmC at single base resolution in low-content samples.![]()
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Affiliation(s)
- Zhenhao Zhang
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Tong He
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Yan Qi
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Yuxuan Dai
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Kejing Lao
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
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21
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Ličytė J, Kvederavičiūtė K, Rukšėnaitė A, Godliauskaitė E, Gibas P, Tomkutė V, Petraitytė G, Masevičius V, Klimašauskas S, Kriukienė E. Distribution and regulatory roles of oxidized 5-methylcytosines in DNA and RNA of the basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea. Open Biol 2022; 12:210302. [PMID: 35232254 PMCID: PMC8889193 DOI: 10.1098/rsob.210302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The formation of three oxidative DNA 5-methylcytosine (5mC) modifications (oxi-mCs)-5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)-by the TET/JBP family of dioxygenases prompted intensive studies of their functional roles in mammalian cells. However, the functional interplay of these less abundant modified nucleotides in other eukaryotic lineages remains poorly understood. We carried out a systematic study of the content and distribution of oxi-mCs in the DNA and RNA of the basidiomycetes Laccaria bicolor and Coprinopsis cinerea, which are established models to study DNA methylation and developmental and symbiotic processes. Quantitative liquid chromatography-tandem mass spectrometry revealed persistent but uneven occurrences of 5hmC, 5fC and 5caC in the DNA and RNA of the two organisms, which could be upregulated by vitamin C. 5caC in RNA (5carC) was predominantly found in non-ribosomal RNA, which potentially includes non-coding, messenger and small RNA species. Genome-wide mapping of 5hmC and 5fC using the single CG analysis techniques hmTOP-seq and foTOP-seq pointed at involvement of oxi-mCs in the regulation of gene expression and silencing of transposable elements. The implicated diverse roles of 5mC and oxi-mCs in the two fungi highlight the epigenetic importance of the latter modifications, which are often neglected in standard whole-genome bisulfite analyses.
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Affiliation(s)
- Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Audronė Rukšėnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Eglė Godliauskaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Vita Tomkutė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Gražina Petraitytė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Viktoras Masevičius
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
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22
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Zhang QF, Xiao HM, Zhan JT, Yuan BF, Feng YQ. Simultaneous determination of indole metabolites of tryptophan in rat feces by chemical labeling assisted liquid chromatography-tandem mass spectrometry. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Liu H, Wang Y, Zhou X. Labeling and sequencing nucleic acid modifications using bio-orthogonal tools. RSC Chem Biol 2022; 3:994-1007. [PMID: 35975003 PMCID: PMC9347354 DOI: 10.1039/d2cb00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/20/2022] [Indexed: 11/25/2022] Open
Abstract
The bio-orthogonal reaction is a type of reaction that can occur within a cell without interfering with the active components of the cell. Bio-orthogonal reaction techniques have been used to label and track the synthesis, metabolism, and interactions of distinct biomacromolecules in cells. Thus, it is a handy tool for analyzing biological macromolecules within cells. Nucleic acid modifications are widely distributed in DNA and RNA in cells and play a critical role in regulating physiological and pathological cellular activities. Utilizing bio-orthogonal tools to study modified bases is a critical and worthwhile research direction. The development of bio-orthogonal reactions focusing on nucleic acid modifications has enabled the mapping of nucleic acid modifications in DNA and RNA. This review discusses the recent advances in bio-orthogonal labeling and sequencing nucleic acid modifications in DNA and RNA. Labeling nucleic acid modifications using bio-orthogonal tools, then sequencing and imaging the labeled modifications in DNA and RNA.![]()
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Affiliation(s)
- Hui Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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24
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Site-specific quantification of 5-carboxylcytosine in DNA by chemical conversion coupled with ligation-based PCR. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.05.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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25
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Dai Y, Yuan BF, Feng YQ. Quantification and mapping of DNA modifications. RSC Chem Biol 2021; 2:1096-1114. [PMID: 34458826 PMCID: PMC8341653 DOI: 10.1039/d1cb00022e] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.
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Affiliation(s)
- Yi Dai
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
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26
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Wang Q, Yin H, Zhou Y, Wang J, Ai S. Investigation of the inhibited biotoxicity of heavy metals towards 5- formylcytosine in rice by hydrochar based on photoelectrochemical biosensor. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125293. [PMID: 33647617 DOI: 10.1016/j.jhazmat.2021.125293] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/30/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
A photoelectrochemical (PEC) biosensor was constructed for 5-formylcytosine (5fC) nucleotide detection based on Ag2S@WS2 photoactive material and FeVO4 catalytic signal quenching. After Ag2S@WS2 was modified onto the ITO substrate surface, 5fC recognition reagent of Au@4-amino3hydrazino5mercapto-1,2,4-triazol (Au@AHMT) was further modified through electrostatic adsorption. Afterwards, based on the specific chemical reaction between -NH2 and -CHO, 5fC can be selectively recognized and captured. Subsequently, the nanoenzyme of FeVO4 was recognized based on the specific reaction between the phosphate group of 5fC nucleotide and Fe3+. Under the catalysis of FeVO4, the 4-chloro-1-naphthol in the detection solution can be oxidized to generate a precipitate, which will be retained on the electrode surface to inhibit the PEC signal. The developed method presented a widely dynamic range from 0.1 to 400 nM. The detection limit was 0.062 nM (3σ). This method also showed good detection selectivity, reproducibility and stability. The applicability was verified by investigating 5fC content change in genomic DNA of rice tissues after incubated with heavy metals. Moreover, the inhibited influence of hydrochar towards heavy metals was also assessed.
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Affiliation(s)
- Qian Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China.
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
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27
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Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
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Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
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28
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Cao X, Lintelmann J, Padoan S, Bauer S, Huber A, Mudan A, Oeder S, Adam T, Di Bucchianico S, Zimmermann R. Adenine derivatization for LC-MS/MS epigenetic DNA modifications studies on monocytic THP-1 cells exposed to reference particulate matter. Anal Biochem 2021; 618:114127. [PMID: 33571488 DOI: 10.1016/j.ab.2021.114127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 11/18/2022]
Abstract
The aim of this study was to explore the impact of three different standard reference particulate matter (ERM-CZ100, SRM-1649, and SRM-2975) on epigenetic DNA modifications including cytosine methylation, cytosine hydroxymethylation, and adenine methylation. For the determination of low levels of adenine methylation, we developed and applied a novel DNA nucleobase chemical derivatization and combined it with liquid chromatography tandem mass spectrometry. The developed method was applied for the analysis of epigenetic modifications in monocytic THP-1 cells exposed to the three different reference particulate matter for 24 h and 48 h. The mass fraction of epigenetic active elements As, Cd, and Cr was analyzed by inductively coupled plasma mass spectrometry. The exposure to fine dust ERM-CZ100 and urban dust SRM-1649 decreased cytosine methylation after 24 h exposure, whereas all 3 p.m. increased cytosine hydoxymethylation following 24 h exposure, and the epigenetic effects induced by SRM-1649 and diesel SRM-2975 were persistent up to 48 h exposure. The road tunnel dust ERM-CZ100 significantly increased adenine methylation following the shorter exposure time. Two-dimensional scatters analysis between different epigenetic DNA modifications were used to depict a significantly negative correlation between cytosine methylation and cytosine hydroxymethylation supporting their possible functional relationship. Metals and polycyclic aromatic hydrocarbons differently shapes epigenetic DNA modifications.
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Affiliation(s)
- Xin Cao
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Jutta Lintelmann
- Research Unit of Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Sara Padoan
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Neubiberg, Germany
| | - Stefanie Bauer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany
| | - Anja Huber
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany
| | - Ajit Mudan
- University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Neubiberg, Germany
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Adam
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Neubiberg, Germany
| | - Sebastiano Di Bucchianico
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany.
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
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29
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Liu B, Wang H. Detection of N 6-Methyladenine in Eukaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:83-95. [PMID: 33791976 DOI: 10.1007/978-3-030-51652-9_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DNA N6-methyladenine (6mA) is a chemical modification at the N6-positon of adenine. In the last decades, 6mA had been found in genome from numerous prokaryotic species, but only existed in a few lower eukaryotes. In prokaryotes, 6mA plays an important role in restriction-modification, DNA replication, and DNA mismatch repair. Because of the too low abundance of 6mA, it was long-stalled whether 6mA existed in multicellular eukaryotes and playing any functions, particularly in mammals. In recent years, partially benefitting from the advances in analytical methods, 6mA was found in the genomes from Drosophila melanogaster, Chlamydomonas algae, Caenorhabditis elegans, zebrafish, Xenopus laevis and mouse embryonic stem cells and even in the human genome. The 6mA was dynamic changed in early embryonic development of fly and zebrafish and much more enriched in gene body of transposons in fly, repetitive regions in zebrafish, around the transcription start sites in Chlamydomonas, and widespread distribution in C. elegans, indicating 6mA probably playing different functions in different species. Meanwhile, 6mA methylases and demethylases were found in fly, worm, and Chlamydomonas. In this chapter, we will briefly review the distribution, regulation, and function of 6mA in eukaryotes and focus on the advances of 6mA analysis methods, especially LC-MS/MS, immunoprecipitation, next-generation sequencing, and single-molecule real-time sequencing technology.
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Affiliation(s)
- Baodong Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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30
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Wang X, Lai F, Xiong J, Zhu W, Yuan B, Cheng H, Zhou R. DNA methylation modification is associated with gonadal differentiation in Monopterus albus. Cell Biosci 2020; 10:129. [PMID: 33292595 PMCID: PMC7654577 DOI: 10.1186/s13578-020-00490-4] [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: 08/30/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background Both testis and ovary can be produced sequentially in an individual with the same genome when sex reversal occurs in the teleost Monopterus albus, and epigenetic modification is supposed to be involved in gonadal differentiation. However, DNA methylation regulation mechanism underlying the gonadal differentiation remains unclear. Results Here, we used liquid chromatography-electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) to simultaneously determine endogenous levels of both 5-methyl-2′-deoxycytidine (m5dC) and 5-hydroxymethyl-2′-deoxycytidine (hm5dC) during gonadal differentiation. Overall DNA methylation level was upregulated from ovary to testis via ovotestis. As a de novo methylase, dnmt3aa expression was also upregulated in the process. Notably, we determined transcription factor Foxa1 for dnmt3aa gene expression. Site-specific mutations and chromatin immunoprecipitation showed that Foxa1 can bind to and activate the dnmt3aa promoter. Furthermore, DNA methylation levels of key genes foxl2 (forkhead box L2) and cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a) in regulation of female hormone synthesis were consistently upregulated during gonadal differentiation. Conclusions These data suggested that dynamic change of DNA methylation modification is associated with gonadal differentiation.
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Affiliation(s)
- Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fengling Lai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Wang Zhu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bifeng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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31
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Huang X, Zhang L, Wei L, Wang M, Li B, Guo B, Ma M. One-Pot Derivatization for Wide-Scope Detection of Nucleobases and Deoxyribosides in Natural Medicinal Foods with Liquid Chromatography-Tandem Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10200-10212. [PMID: 32853523 DOI: 10.1021/acs.jafc.0c03328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A new chemical labeling-based LC-MS/MS approach was developed for quantitative profiling of nine canonical bases and deoxynucleosides (dNs) in natural products. Using 2-bromo-1-(4-dimethylamino-phenyl)-ethaone (BrDPE) as the tagging reagent, a previously unexploited N-alkylpyrimidine derivative (Nad) was created for one-pot labeling of widescope nucleobases via a flexible bromophilic substitution under mild conditions. The derivatization notably improved the LC-MS detection sensitivity by 31-107 fold, enabling a fast dilute-and-shoot analysis of highly diluted samples. The optimized and validated method demonstrated satisfactory accuracy (87-107%), precision (RSDs < 7.5%), and recovery (89-105%) for matrix-matched standard addition. The method was applied to simultaneously determine all target analytes and four uncanonical analogues and base-modified species in seven traditional health foods, which differ in contents by up to 600-fold for discrimination among samples. Further, the base-labeled Nads exhibit a unique fragmentation signature that could be used for untargeted screening of nucleobase-containing metabolites by simplified LC-MS/MS workflow to improve quality evaluation of natural medicinal products.
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Affiliation(s)
- Xingrong Huang
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Lu Zhang
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Lijuan Wei
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Meiling Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Bowen Li
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Bin Guo
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
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32
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Mass Spectrometry to Study Chromatin Compaction. BIOLOGY 2020; 9:biology9060140. [PMID: 32604817 PMCID: PMC7345930 DOI: 10.3390/biology9060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.
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33
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Zheng X, Duan H, Lin F, Li X, Shen J, Han F, Huang F, Li S, Chang L, Xu H, Wang K, Liu J. Quantification of microbiota-related phenols and aromatic acids in mouse feces of a diabetic nephropathy model by simultaneous BDAPE derivatization using ultra-performance liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 2020; 412:3241-3252. [PMID: 32342129 DOI: 10.1007/s00216-020-02585-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/24/2020] [Accepted: 03/09/2020] [Indexed: 01/06/2023]
Abstract
In the intestine, several phenols and aromatic acids are generated by microbiota and are highly related to the formation of uremic toxins. Herein, we developed a new derivatization reagent, 2-bromo-1-[4-(dimethylamino)phenyl] ethyl ketone (BDAPE), that reacted simultaneously with phenols and aromatic acids. Following a reaction within 2 h at 60 °C in the presence of 200 mM potassium carbonate (K2CO3), the obtained BDAPE derivatives were separated on a reversed-phase C18 column and quantified by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) in positive electrospray ionization mode. This method allowed a lower limit of quantification (LLOQ) of 0.090 μΜ for 3-indolepropionic acid (3IPA), indole-3-acetic acid (3IAA), p-cresol (PC), benzoic acid (BA), and phenol (PN); 0.30 μΜ for phenylacetic acid (PAA); 0.45 μΜ for 4-hydroxyphenylacetic acid (4HPAA); and 0.60 μΜ for 3-phenylpropionic acid (PPA). Methodological validation further demonstrated acceptable accuracy (%RE < 16.1) and precision (%RSD < 16.2), suggesting that this is a sensitive and robust method for simultaneous quantification of phenols and aromatic acids. The method was successfully applied to analyze these microbiota-related analytes in mouse feces of a diabetic nephropathy model. Graphical abstract.
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Affiliation(s)
- Xiaoli Zheng
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in University of Shandong, Yantai University, Yantai, 264005, People's Republic of China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China
| | - Haonan Duan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Feifei Lin
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China
| | - Xiaomei Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jianhua Shen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Fanghui Han
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Fubao Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shilin Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China
| | - Lu Chang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China
| | - Hui Xu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in University of Shandong, Yantai University, Yantai, 264005, People's Republic of China.
| | - Kai Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China. .,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, People's Republic of China.
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Li F, Wang S, Yin H, Chen Y, Zhou Y, Huang J, Ai S. Photoelectrochemical Biosensor for DNA Formylation Detection in Genomic DNA of Maize Seedlings Based on Black Tio 2-Enhanced Photoactivity of MoS 2/WS 2 Heterojunction. ACS Sens 2020; 5:1092-1101. [PMID: 32159349 DOI: 10.1021/acssensors.0c00036] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
5-Formylcytosine (5fC) is a rare base found in mammalian DNA, which is thought to be involved in the demethylation of DNA. As a stable epigenetic modification, 5fC participates in gene regulation and cell differentiation, and plays an important role in the growth and development of plants. However, the abundance of 5fC is only as low as 0.002-0.02% of cytosine. Therefore, to further understand the functions of 5fC, a rapid, highly sensitive, and efficient method is needed for detecting 5fC. Herein, a novel photoelectrochemical (PEC) biosensor was constructed for 5fC detection, where a MoS2/WS2 nanosheet heterojunction was employed as a photoactive material, amino-functionalized Fe3O4 and SMCC were used as a linker, 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole was adopted as 5fC recognition reagent, and black TiO2 (B-TiO2) was used as a signal amplification unit. Under the optimal experimental conditions, this PEC biosensor showed a wide linear range of 0.01-200 nM and a low detection limit of 2.7 pM (S/N = 3). Due to the specific covalent reaction between -NH2 and -CHO, the biosensor presented high detection sensitivity, even discriminating 5fC with 5-methylcytosine and 5-hydroxymethylcytosine. The biosensor was then applied to investigate the effect of heavy metal Cd2+ on 5fC content in the root, stem, and leaves of maize seedlings.
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Affiliation(s)
- Fei Li
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Siyu Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Yan Chen
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Jing Huang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
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35
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Zhang Z, Yan J, Li Z. Peroxotungstate oxidation-mediated two-phase amplification system (POM-TPAS) for bisulfite-free quantification of locus-specific 5-hydroxymethylcytosine. Chem Commun (Camb) 2020; 56:3111-3114. [PMID: 32090228 DOI: 10.1039/d0cc00167h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The peroxotungstate oxidation-mediated two-phase amplification system (POM-TPAS) is applied for the first time to the sensitive detection of locus-specific 5-hydroxymethylcytosine (5hmC) in DNA with low non-specific amplification. This strategy greatly shortens reaction time, improves sensitivity, and reduces non-specific amplification.
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Affiliation(s)
- Zhenhao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Jingli Yan
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
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36
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Li F, Yin H, Chen Y, Wang S, Li J, Zhang Y, Li C, Ai S. Preparation of P-g-C3N4-WS2 nanocomposite and its application in photoelectrochemical detection of 5-formylcytosine. J Colloid Interface Sci 2020; 561:348-357. [DOI: 10.1016/j.jcis.2019.10.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
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37
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Chemical labeling – Assisted mass spectrometry analysis for sensitive detection of cytidine dual modifications in RNA of mammals. Anal Chim Acta 2020; 1098:56-65. [DOI: 10.1016/j.aca.2019.11.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/13/2019] [Accepted: 11/10/2019] [Indexed: 12/15/2022]
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38
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Zhang Z, Yang D, Tian W, Qi Y, Ren W, Li Z, Liu C. Facile Clamp-Assisted Ligation Strategy for Direct Discrimination and Background-Free Quantification of Site-Specific 5-Formylcytosine. Anal Chem 2020; 92:3477-3482. [PMID: 31970980 DOI: 10.1021/acs.analchem.9b05715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantification of site-specific 5-formylcytosine (5fC) in DNA is highly significant to better understand its biological functions. However, it is still a big challenge to precisely discriminate 5fC from cytosine (C), 5-hydroxymethylcytosine (5hmC), 5-methylcytosine (5mC), and 5-carboxycytosine (5caC) owing to their similar structures that will interfere the quantification of 5fC. To solve this issue, a novel peptide nucleic acid (PNA) clamp-assisted ligation amplification strategy coupled with a 5fC-selective chemical conversion route is employed, through which 5fC can be precisely quantified with other interfering signals completely suppressed. As a result, as low as 200 aM of site-specific 5fC-containing DNA target can be accurately determined at single-base resolution in a background-free manner.
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Affiliation(s)
- Zhenhao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Dandan Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Weimin Tian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Yan Qi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
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39
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Francés-Monerris A, Lineros-Rosa M, Miranda MA, Lhiaubet-Vallet V, Monari A. Photoinduced intersystem crossing in DNA oxidative lesions and epigenetic intermediates. Chem Commun (Camb) 2020; 56:4404-4407. [DOI: 10.1039/d0cc01132k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The propensity of 5-formyluracil and 5-formylcytosine, i.e. oxidative lesions and epigenetic intermediates, in acting as intrinsic DNA photosensitizers is unraveled by using a combination of molecular modeling, simulation and spectroscopy.
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Affiliation(s)
| | - Mauricio Lineros-Rosa
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Miguel Angel Miranda
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Antonio Monari
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
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40
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Yuan F, Yu Y, Zhou YL, Zhang XX. 5hmC-MIQuant: Ultrasensitive Quantitative Detection of 5-Hydroxymethylcytosine in Low-Input Cell-Free DNA Samples. Anal Chem 2019; 92:1605-1610. [DOI: 10.1021/acs.analchem.9b04920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Fang Yuan
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yue Yu
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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41
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Affiliation(s)
- Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry and Sauvage Center for Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
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42
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Liquid chromatography- mass spectrometry for analysis of DNA damages induced by environmental exposure. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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43
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Tang Y, Zhang JL. Recent developments in DNA adduct analysis using liquid chromatography coupled with mass spectrometry. J Sep Sci 2019; 43:31-55. [PMID: 31573133 DOI: 10.1002/jssc.201900737] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
Abstract
The formation of DNA adducts by genotoxic agents is an early event in cancer development, and it may lead to gene mutations, thereby initiating tumor development. The measurement of DNA adducts can provide critical information about the genotoxic potential of a chemical and its mechanism of carcinogenesis. In recent decades, liquid chromatography coupled with mass spectrometry has become the most important technique for analyzing DNA adducts. The improvements in resolution achievable with new chromatographic separation techniques coupled with the high specificity and sensitivity and wide dynamic range of new mass spectrometry systems have been used for both qualitative and quantitative analyses of DNA adducts. This review discusses the challenges in qualitative and quantitative analyses of DNA adducts by liquid chromatography coupled with mass spectrometry and highlights recent developments towards overcoming the limitations of liquid chromatography coupled with mass spectrometry methods. The key steps and new solutions, such as sample preparation, mass spectrometry fragmentation, and method validation, are summarized. In addition, the fundamental principles and latest advances in DNA adductomic approaches are reviewed.
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Affiliation(s)
- Yu Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
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44
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Yu Y, Yuan F, Zhang XH, Zhao MZ, Zhou YL, Zhang XX. Ultrasensitive Determination of Rare Modified Cytosines Based on Novel Hydrazine Labeling Reagents. Anal Chem 2019; 91:13047-13053. [DOI: 10.1021/acs.analchem.9b03227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yue Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao-Hui Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Ming-Zhe Zhao
- Capital Normal University High School, No. 33 Beiwa Road, Haidian District, Beijing, 100048, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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45
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Qi C, Ding J, Yuan B, Feng Y. Analytical methods for locating modifications in nucleic acids. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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You XJ, Liu T, Ma CJ, Qi CB, Tong Y, Zhao X, Yuan BF, Feng YQ. Determination of RNA Hydroxylmethylation in Mammals by Mass Spectrometry Analysis. Anal Chem 2019; 91:10477-10483. [PMID: 31318193 DOI: 10.1021/acs.analchem.9b01318] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA molecules harbor diverse chemical modifications that play important regulatory roles in a variety of biological processes. Up to date, more than 150 modifications have been identified in various RNA species. Most of these modifications occurring in nucleic acids are the methylation of nucleic acids. It has been demonstrated that many of these methylation are reversible and undergo dynamic demethylation. Previous studies established that the demethylation of the two most important and prevalent modifications of 5-methylcytidine (m5C) and N6-methyladenosine (m6A) in nucleic acids is through the hydroxylation of m5C and m6A, forming 5-hydroxymethylcytidine (hm5C) and N6-hydroxymethyladenosine (hm6A), respectively. This indicates the hydroxylation of the methylated nucleosides may be a general pathway for the demethylation of nucleic acid methylation. However, few other hydroxylmethylation modifications have yet to be reported in existence in mammals. In the current study, we developed a neutral enzymatic digestion method for the mild digestion of nucleic acids, followed by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. With the established method, we reported the existence of a new hydroxylmethylated nucleosides, N2-hydroxymethylguanosine (hm2G), in mammalian RNA. In addition, we found that the contents of hm2G, as well as N2-methylguanosine (m2G), showed significant differences between thyroid carcinoma tissues and tumor-adjacent normal tissues, indicating that m2G and hm2G in RNA may play certain roles in the carcinogenesis of thyroid carcinoma. Collectively, our study suggests that RNA hydroxylmethylation may be a new prevalent group of modifications existing in RNA, which expands the diversity of nucleic acid modifications and should exert regulatory functions in living organisms.
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Affiliation(s)
- Xue-Jiao You
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China.,Sauvage Center for Molecular Sciences , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Ting Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Cheng-Jie Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Chu-Bo Qi
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China.,Hubei Cancer Hospital, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430079 , People's Republic of China
| | - Yongjia Tong
- Hubei Key Laboratory of Cell Homeostasis , College of Life Sciences, Wuhan University , Wuhan 430072 , People's Republic of China
| | - Xiaolu Zhao
- Hubei Key Laboratory of Cell Homeostasis , College of Life Sciences, Wuhan University , Wuhan 430072 , People's Republic of China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China.,Sauvage Center for Molecular Sciences , Wuhan University , Wuhan 430072 , People's Republic of China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , People's Republic of China
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47
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Cao LL, Liu H, Yue Z, Pei L, Wang H, Jia M. The clinical values of dysregulated DNA methylation and demethylation intermediates in acute lymphoblastic leukemia. Hematology 2019; 24:567-576. [PMID: 31315520 DOI: 10.1080/16078454.2019.1642563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Lin-Lin Cao
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Hangqi Liu
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Zhihong Yue
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Lin Pei
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Mei Jia
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
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48
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Abstract
5-Formyl-2'-deoxycytidine (5fdC) is a naturally occurring nucleobase that is broadly distributed in genomic DNA. 5fdC is produced via the oxidation of 5-methylcytosine (5mdC) by ten-eleven translocation enzyme (TET) and can be further converted to 5-carboxylcytosine (5cadC) by TET. Both 5fdC and 5cadC can be restored to dC by TDG-mediated base excision repair and direct deformylation/decarboxylation. Thus, 5fdC is considered an intermediate in the TET-mediated DNA demethylation pathway. 5fdC also alters the structure and stability of genomic DNA and affects genetic expression. This review summarizes the recent research on 5fdC, detailing its formation, detection and distribution, biological functions and transformation in cells. The challenges and future prospects to further explore the function and metabolism of 5fdC are briefly discussed at the end.
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Affiliation(s)
- Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.
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49
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Zhang YF, Qi CB, Yuan BF, Feng YQ. Determination of cytidine modifications in human urine by liquid chromatography - Mass spectrometry analysis. Anal Chim Acta 2019; 1081:103-111. [PMID: 31446947 DOI: 10.1016/j.aca.2019.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/14/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
Both DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC) and RNA cytosine methylation (5-methylcytidine, m5rC) are important epigenetic marks that play regulatory roles in diverse biological processes. m5dC and m5rC can be further oxidized by the ten-eleven translocation (TET) proteins to form 5-hydroxymethyl-2'-deoxycytidine (hm5dC) and 5-hydroxymethylcytidine (hm5rC), respectively. 2'-O-methyl-5-hydroxymethylcytidine (hm5rCm) was recently also identified as a second oxidative metabolite of m5rC in RNA. Previous studies showed that the dysregulation of cytidine modifications in both DNA and RNA are closely related to a variety of human diseases. These cytidine modifications are generally excreted from cell into urine. If these cytidine modifications exhibit specific features related to certain diseases, determination of the cytidine modifications in urine could be utilized as non-invasive diagnostic of diseases. Here, we established a solid-phase extraction in combination with liquid chromatography-mass spectrometry (LC-MS/MS) analysis for simultaneous detection of these cytidine modifications in human urine samples. The developed method enabled the distinct detection of these cytidine modifications. We reported, for the first time, the presence of hm5rCm in human urine. Furthermore, we found that compared to the healthy controls, the contents of hm5dC, hm5rC, and hm5rCm showed significant increases in urine samples of cancer patients, including lymphoma patients, gastric cancer patients, and esophageal cancer patients. This study indicates that the urinary hydroxylmethylation modifications of hm5dC, hm5rC, and hm5rCm may serve as potential indicator of cancers.
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Affiliation(s)
- Yu-Fan Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Sauvage Center for Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Chu-Bo Qi
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, PR China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Sauvage Center for Molecular Sciences, Wuhan University, Wuhan, 430072, PR China.
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
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50
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Wang Y, Zhang X, Zou G, Peng S, Liu C, Zhou X. Detection and Application of 5-Formylcytosine and 5-Formyluracil in DNA. Acc Chem Res 2019; 52:1016-1024. [PMID: 30666870 DOI: 10.1021/acs.accounts.8b00543] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nucleic acids contain a variety of different base modifications, such as decoration at the fifth position of cytosine, which is one of the most important epigenetic modifications. Nucleic acid epigenetics mediate a wide variety of biological processes, including embryonic development and gene regulation, genomic imprinting, differentiation, and X-chromosome inactivation. Furthermore, the modification level can be aberrantly expressed in distinct sets of tissue that can indicate different tumor onsets and canceration. Thus, the analysis of modified nucleobases may contribute to the understanding of epigenetic modification-related biological processes and the correlation of modified nucleobase patterns with disease states for clinical diagnosis and treatment. In addition to 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine are found in organisms at a low content but are nevertheless extremely important chemical modifications, and 5-hydroxyuracil and 5-formyluracil compounds are also present. 5-Formyluracil is found in bacteriophages, prokaryotes, and mammalian cells. The 5-formyluracil content is higher in certain cancer tissues than in the normal tissues adjacent to the tumor. The content of 5-formyluracil in different cell tissues may have cell type specificity. With the continuous use of chemical tools, new detection technologies have greatly advanced the research on natural pyrimidine modifications. These modifications dynamically regulate the gene expression in eukaryotes and prokaryotes and provide mechanistic insights into the occurrence of diseases. Natural pyrimidine modifications act not only as intermediates for DNA demethylation or oxidative damage products but also as modulators of gene expression. Therefore, the development of more effective chemical tools will help us better understand the dynamic changes of natural pyrimidine modifications in vivo. In this Account, we summarize the recent advanced techniques for the detection of 5-formylpyrimidine (5-formylcytosine and 5-formyluracil) and highlight their great potential as biomarkers in biomedical applications. Focusing on the great urgency for the detection of epigenetic modifications, our group developed a series of methods for the qualitative and quantitative analysis of 5-formylpyrimidine in the past few years, aiming at facilitating the accurate detection and mapping of these epigenetic modifications. By the construction of probes, 5-formylpyrimidine can be selectively labeled. Using mass spectrometry, the epigenetic modifications can be quantified. Upon treatment under specific conditions, 5-formylcytosine can be recognized at single-base resolution. With this Account, we anticipate providing chemical and biological researchers with some insight to unlock the complex mechanism involved in 5-formylpyrimidine-related biological processes and stimulate more collaborative research interests from the different fields of materials, biological, medicine, and chemistry to promote the translational research of epigenetics in tumor diagnosis and treatment.
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Chaoxing Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
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