Epigenetic Age Estimation by Detecting DNA Methylation Status in Buccal Swabs.

IF 3 3区生物学 Q2 BIOCHEMICAL RESEARCH METHODS ELECTROPHORESIS Pub Date : 2024-10-14 DOI:10.1002/elps.202400075

Zimeng Guan, Jiaqi Wang, Zidong Liu, Chengwen Yang, Xin Xu, Xinjie Wang, Gengqian Zhang

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Abstract

The analysis of DNA methylation (DNAm) levels at specific CpG sites represents one of the most promising molecular techniques for estimating an individual's age. To date, a considerable number of studies have reported the development of age prediction models on the basis of DNAm in body fluids, with only a few utilizing buccal swabs. The objective of this study was to identify age-dependent methylation CpG sites in three different genes (HOXC4, TRIM59, and ELOVL2) in buccal swab samples from the Chinese Han population. A total of 461 buccal swabs, with an age range of 0.4-80.8 years, were divided into a training set (n = 325) and a validation set (n = 136). Samples were analyzed by pyrosequencing in order to identify age-related genes with correlation coefficient. A random forest regression model was ultimately proposed, including eight CpGs in three genes, with a mean absolute error (MAE) of 2.119 years. The model performs independent validation set with an MAE of 4.391 years. Our findings illustrate that buccal swabs present a suitable alternative to biological traces for age prediction based on DNAm pattern using pyrosequencing and random forest regression, offering the additional advantage of being collected noninvasively.

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通过检测口腔拭子中的 DNA 甲基化状态估算表观遗传学年龄

对特定 CpG 位点的 DNA 甲基化（DNAm）水平进行分析，是估算个人年龄最有前途的分子技术之一。迄今为止，已有相当多的研究报告根据体液中的 DNAm 建立了年龄预测模型，只有少数研究利用了颊拭子。本研究的目的是鉴定中国汉族人群颊拭子样本中三个不同基因（HOXC4、TRIM59 和 ELOVL2）中与年龄相关的甲基化 CpG 位点。461 份年龄在 0.4-80.8 岁之间的颊拭子样本被分为训练集（325 份）和验证集（136 份）。对样本进行了热测序分析，以确定与年龄相关的相关系数基因。最终提出了一个随机森林回归模型，包括三个基因中的八个 CpGs，平均绝对误差（MAE）为 2.119 岁。该模型在独立验证集上的平均绝对误差为 4.391 岁。我们的研究结果表明，使用热测序和随机森林回归法根据 DNAm 模式预测年龄时，颊拭子是生物痕迹的合适替代品，而且还具有无创采集的额外优势。

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来源期刊

ELECTROPHORESIS 生物-分析化学

CiteScore

6.30

自引率

13.80%

发文量

244

审稿时长

1.9 months

期刊介绍： ELECTROPHORESIS is an international journal that publishes original manuscripts on all aspects of electrophoresis, and liquid phase separations (e.g., HPLC, micro- and nano-LC, UHPLC, micro- and nano-fluidics, liquid-phase micro-extractions, etc.). Topics include new or improved analytical and preparative methods, sample preparation, development of theory, and innovative applications of electrophoretic and liquid phase separations methods in the study of nucleic acids, proteins, carbohydrates natural products, pharmaceuticals, food analysis, environmental species and other compounds of importance to the life sciences. Papers in the areas of microfluidics and proteomics, which are not limited to electrophoresis-based methods, will also be accepted for publication. Contributions focused on hyphenated and omics techniques are also of interest. Proteomics is within the scope, if related to its fundamentals and new technical approaches. Proteomics applications are only considered in particular cases. Papers describing the application of standard electrophoretic methods will not be considered. Papers on nanoanalysis intended for publication in ELECTROPHORESIS should focus on one or more of the following topics: • Nanoscale electrokinetics and phenomena related to electric double layer and/or confinement in nano-sized geometry • Single cell and subcellular analysis • Nanosensors and ultrasensitive detection aspects (e.g., involving quantum dots, "nanoelectrodes" or nanospray MS) • Nanoscale/nanopore DNA sequencing (next generation sequencing) • Micro- and nanoscale sample preparation • Nanoparticles and cells analyses by dielectrophoresis • Separation-based analysis using nanoparticles, nanotubes and nanowires.