Comparison of PGC and Biphenyl stationary phases for the high throughput analysis of DNA epigenetic modifications by UHPLC-MS/MS

IF 2.8 3区医学 Q2 BIOCHEMICAL RESEARCH METHODS Journal of Chromatography B Pub Date : 2024-11-17 DOI:10.1016/j.jchromb.2024.124382

Quentin Vandoolaeghe , Valérie Bouchart , Yolaine Guérin , Stéphanie Lagadu , Claire Lopez-Piffet , Raphaël Delépée

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Abstract

Epigenetic alterations such as cytosine methylation, hydroxymethylation, formylation and carboxylation are well known modifications that are frequently associated with various disease such as cancer. These modifications are usually studied at the gene level to evaluate their impact on the expression of genes but there is a need for a whole genome quantification that can be more easily used as effect biomarkers. Here, we compare two high throughput methods for the UHPLC-MS/MS analysis of these four epigenetic markers in large cohort studies. The first method uses a porous graphitic carbon stationary phase modified by surface adsorption of triethylamine while the second method uses a biphenyl reversed phase. The two developed methods are then applied to 40 blood neutrophils DNA samples of former smokers and never-smokers from an agricultural occupational biobank. The results obtained shows no differences for the evaluation of 5-methylcytosine and 5-hydroxymethylcytosine with the two methods but highlight a diminution of both DNA methylation and hydroxymethylation in former smokers when compared to a never smoking population.

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比较 PGC 和联苯固定相在超高效液相色谱-质谱/质谱 DNA 表观遗传修饰高通量分析中的应用。

胞嘧啶甲基化、羟甲基化、甲酰化和羧基化等表观遗传学改变是众所周知的修饰，经常与癌症等各种疾病相关。这些修饰通常在基因水平上进行研究，以评估它们对基因表达的影响，但现在需要一种更容易用作效应生物标记的全基因组量化方法。在这里，我们比较了在大型队列研究中对这四种表观遗传标记进行超高效液相色谱-质谱/质谱分析的两种高通量方法。第一种方法使用的是经三乙胺表面吸附修饰的多孔石墨碳固定相，第二种方法使用的是联苯反相。然后将这两种方法应用于一个农业职业生物库中的 40 份曾吸烟者和从不吸烟者的血液中性粒细胞 DNA 样本。结果表明，这两种方法对 5-甲基胞嘧啶和 5-羟甲基胞嘧啶的评估没有差异，但与从不吸烟的人群相比，曾经吸烟者的 DNA 甲基化和羟甲基化程度都有所降低。

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来源期刊

Journal of Chromatography B 医学-分析化学

CiteScore

5.60

自引率

3.30%

发文量

306

审稿时长

44 days

期刊介绍： The Journal of Chromatography B publishes papers on developments in separation science relevant to biology and biomedical research including both fundamental advances and applications. Analytical techniques which may be considered include the various facets of chromatography, electrophoresis and related methods, affinity and immunoaffinity-based methodologies, hyphenated and other multi-dimensional techniques, and microanalytical approaches. The journal also considers articles reporting developments in sample preparation, detection techniques including mass spectrometry, and data handling and analysis. Developments related to preparative separations for the isolation and purification of components of biological systems may be published, including chromatographic and electrophoretic methods, affinity separations, field flow fractionation and other preparative approaches. Applications to the analysis of biological systems and samples will be considered when the analytical science contains a significant element of novelty, e.g. a new approach to the separation of a compound, novel combination of analytical techniques, or significantly improved analytical performance.