Global hypomethylation pattern in systemic sclerosis: An application for absolute quantification of epigenetic DNA modification products by 2D-UPLC-MS/MS

Dal-Bekar, Nazlı Ecem; Siomek-Górecka, Agnieszka; Gackowski, Daniel; Köken-Avşar, Aydan; Yarkan-Tuğsal, Handan; Bırlık, Merih; İşlekel, Hüray

doi:10.1016/j.clim.2022.108997

Cited by 6 publications

(6 citation statements)

References 12 publications

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“…The following supporting information can be downloaded at https: //www.mdpi.com/article/10.3390/diagnostics14060652/s1, Supplementary Table S1: Characteristics of the studies analyzing DNA methylation aberrancies in SSc. References [64][65][66] are cited only in Supplementary Table S1. References [19,29,61,[64][65][66] are cited in the main text and in Supplementary Table S1.…”

Section: Supplementary Materialsmentioning

confidence: 99%

“…References [ 64 , 65 , 66 ] are cited only in Supplementary Table S1. References [ 19 , 29 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 61 , 64 , 65 , 66 ] are cited in the main text and in Supplementary Table S1.…”

mentioning

confidence: 99%

“…The following supporting information can be downloaded at , Supplementary Table S1: Characteristics of the studies analyzing DNA methylation aberrancies in SSc. References [ 64 , 65 , 66 ] are cited only in Supplementary Table S1. References [ 19 , 29 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 61 , 64 , 65 , 66 ] are cited in the main text and in Supplementary Table S1.…”

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confidence: 99%

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Recent Insights into the Role of DNA Methylation and Histone Modifications in Systemic Sclerosis: A Scoping Review

Kostova,

Karalilova,

Batalov

et al. 2024

Diagnostics

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Systemic sclerosis is a complex idiopathic disease originating from an intricate interplay between genetic susceptibility, environmental factors, and epigenetic modifications. This scoping review aims to map the advancements made regarding DNA methylation abnormalities and histone modifications in systemic sclerosis in the past decade. A literature search was conducted using three electronic databases (Scopus, Web of Science and PubMed) to identify relevant articles. A total of 44 studies were selected for this review, demonstrating the critical contribution of epigenetic perturbations in multiple cell types to disease pathogenesis. In conclusion, this scoping review has elucidated the significant discoveries made in the past decade regarding the role of DNA methylation and histone modifications in systemic sclerosis. Further progress in the field could lead to the development of novel treatment possibilities targeting epigenetic marks.

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Section: Supplementary Materialsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Recent Insights into the Role of DNA Methylation and Histone Modifications in Systemic Sclerosis: A Scoping Review

Kostova,

Karalilova,

Batalov

et al. 2024

Diagnostics

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“…The traditional techniques for 5hmU assay mainly include antibody-based methods, 17,18 gas chromatography negative ion chemical ionization mass spectrometry (GC/NICI/MS), 19 and isotope-dilution automated online two-dimensional ultraperformance liquid chromatography with tandem mass spectrometry (2D-UPLC-MS/MS). 10,20 Specific antibodybased immunoblotting and immunoprecipitation have been applied for 5hmU assay. 17,21 However, antibodies are relatively expensive and difficult to generate from cells/animals, with poor stability under harsh detection conditions.…”

mentioning

confidence: 99%

“…The traditional techniques for 5hmU assay mainly include antibody-based methods, , gas chromatography negative ion chemical ionization mass spectrometry (GC/NICI/MS), and isotope-dilution automated online two-dimensional ultraperformance liquid chromatography with tandem mass spectrometry (2D-UPLC-MS/MS). , Specific antibody-based immunoblotting and immunoprecipitation have been applied for 5hmU assay. , However, antibodies are relatively expensive and difficult to generate from cells/animals, with poor stability under harsh detection conditions . Although stable isotope-based GC/NICI/MS and 2D-UPLC-MS/MS may provide more structural information about 5hmU, these methods usually involve laborious procedures, long assay time, and poor sensitivity. ,, Alternatively, several novel approaches have been developed for 5hmU assay on the basis of either chemical oxidation of 5hmU or the β-glycosyltransferase (β-GT)-mediated glucosylation reaction.…”

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confidence: 99%

Bioorthogonal Reaction-Mediated Enzymatic Elongation-Driven Dendritic Nanoassembly for Genome-Wide Analysis of 5-Hydroxymethyluracil in Breast Tissues

Jiang,

Cai,

Zhang

et al. 2023

Nano Lett.

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Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry

Marchante‐Gayón,

Nicolás Carcelén,

Potes Rodríguez

et al. 2023

Mass Spectrometry Reviews

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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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Global hypomethylation pattern in systemic sclerosis: An application for absolute quantification of epigenetic DNA modification products by 2D-UPLC-MS/MS

Cited by 6 publications

References 12 publications

Recent Insights into the Role of DNA Methylation and Histone Modifications in Systemic Sclerosis: A Scoping Review

Recent Insights into the Role of DNA Methylation and Histone Modifications in Systemic Sclerosis: A Scoping Review

Bioorthogonal Reaction-Mediated Enzymatic Elongation-Driven Dendritic Nanoassembly for Genome-Wide Analysis of 5-Hydroxymethyluracil in Breast Tissues

Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry

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