A semen-specific deoxyribonucleic acid methylation model for epigenetic age estimation and its robustness under environmental challenges

IF 3 3区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

ELECTROPHORESIS Pub Date : 2024-08-20 DOI:10.1002/elps.202400054

Sena Er, Zehra Abik, Gokhan Ersoy, Gonul Filoglu, Hamdi Ozkara, Ozlem Bulbul

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引用次数: 0

Abstract

In forensic investigations, semen samples are a common form of biological evidence, especially in cases involving sexual assault. Therefore, accurately estimating the age of an individual is crucial in criminal cases. This study presents a novel age estimation model based on semen-specific CpG methylation patterns. A multiplex panel was developed, consisting of 12 CpG sites (PARP14, C5orf25, cg23488376, MXRA5, PFKFB3, DLL1, NOX4, cg12837463, TTC7B, KCNA7, NKX2-1, and SYNE4), which exhibit strong correlations with age. Additionally, this study investigates the resilience of these methylation markers under simulated environmental challenges. We collected ejaculate samples from a diverse cohort of 115 male individuals, aged 20–71 years, who underwent deoxyribonucleic acid extraction and bisulfite conversion. Methylation levels of the selected CpG sites were assessed using a SNaPshot assay, which revealed significant correlations with chronological age. We developed and validated two robust age estimation models through stepwise and enter regression analyses, achieving reliable accuracy with mean absolute errors ranging from 3.81 to 4.1 years. Additionally, the study also investigated the robustness of semen stains under diverse environmental conditions, including fabric type, washing, hematin exposure, and UV-C light. The selected methylation markers demonstrated remarkable resilience despite the challenges posed by washing procedures and environmental exposure, confirming their potential for age estimation in forensic genetics. This research presents successful age estimation models, emphasizing the strong correlations between methylation levels and chronological age. The proposed methodology's accuracy is affirmed through model validation on an independent test set, while also highlighting the resilience of semen stains on fabrics under varying storage and washing conditions.

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用于表观遗传年龄估计的精液特异性脱氧核糖核酸甲基化模型及其在环境挑战下的稳健性。

在法医调查中，精液样本是一种常见的生物证据，尤其是在涉及性侵犯的案件中。因此，准确估计一个人的年龄在刑事案件中至关重要。本研究提出了一种基于精液特异性 CpG 甲基化模式的新型年龄估计模型。该模型由 12 个 CpG 位点（PARP14、C5orf25、cg23488376、MXRA5、PFKFB3、DLL1、NOX4、cg12837463、TTC7B、KCNA7、NKX2-1 和 SYNE4）组成。此外，本研究还调查了这些甲基化标记物在模拟环境挑战下的恢复能力。我们收集了 115 名年龄在 20-71 岁之间的男性的射精样本，对其进行了脱氧核糖核酸提取和亚硫酸氢盐转换。我们使用 SNaPshot 检测法对所选 CpG 位点的甲基化水平进行了评估，结果显示其与年龄有显著相关性。通过逐步回归分析和进入回归分析，我们建立并验证了两个稳健的年龄估计模型，其准确性可靠，平均绝对误差在 3.81 到 4.1 岁之间。此外，该研究还调查了精液染色在不同环境条件下的稳健性，包括织物类型、洗涤、赤藓素暴露和紫外线照射。尽管洗涤程序和环境暴露带来了挑战，但所选的甲基化标记仍表现出了显著的适应性，证实了它们在法医遗传学年龄估计方面的潜力。这项研究提出了成功的年龄估计模型，强调了甲基化水平与年代年龄之间的强相关性。通过在独立测试集上进行模型验证，证实了所提出方法的准确性，同时还强调了织物上的精液污渍在不同储存和洗涤条件下的复原能力。

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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.