Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA.
Department of Molecular, Cellular and Integrative Biological Sciences, The Pennsylvania State University, University Park, PA, USA.
Epigenetics. 2023 Dec;18(1):2230686. doi: 10.1080/15592294.2023.2230686.
Identifying factors that influence the stability of DNA methylation measurements across biological replicates is of critical importance in basic and clinical research. Using a within-person between-group experimental design ( = 31, number of observations = 192), we report the stability of biological replicates over a variety of unique temporal scenarios, both in the absence and presence of acute psychosocial stress, and between individuals who have experienced early life adversity (ELA) and non-exposed individuals. We found that varying time intervals, acute stress, and ELA exposure influenced the stability of repeated DNA methylation measurements. In the absence of acute stress, probes were less stable as time passed; however, stress exerted a stabilizing influence on probes over longer time intervals. Compared to non-exposed individuals, ELA-exposed individuals had significantly lower probe stability immediately following acute stress. Additionally, we found that across all scenarios, probes used in most epigenetic-based algorithms for estimating epigenetic age or immune cell proportions had average or below-average stability, except for the Principal Component and DunedinPACE epigenetic ageing clocks, which were enriched for more stable probes. Finally, using highly stable probes in the absence of stress, we identified multiple probes that were hypomethylated in the presence of acute stress, regardless of ELA status. Two hypomethylated probes are located near the transcription start site of the glutathione-disulfide reductase gene (), which has previously been shown to be an integral part of the stress response to environmental toxins. We discuss implications for future studies concerning the reliability and reproducibility of DNA methylation measurements. DNAm - DNA methylation, CpG - 5'-cytosine-phosphate-guanine-3,' ICC - Interclass correlation coefficient, ELA - Early-life adversity, PBMCs - Peripheral blood mononuclear cells, mQTL - Methylation quantitative trait loci, TSS - Transcription start site, GSR - Glutathione-disulfide reductase gene, TSST - Trier social stress test, PC - Principal component.
确定影响生物重复中 DNA 甲基化测量稳定性的因素，对于基础和临床研究至关重要。我们采用个体内组间实验设计（ = 31，观测数 = 192），报告了在各种独特的时间情景下，包括在没有和存在急性心理社会压力的情况下，以及在经历过早期生活逆境（ELA）和未暴露个体的个体之间，生物重复的稳定性。我们发现，不同的时间间隔、急性压力和 ELA 暴露会影响重复 DNA 甲基化测量的稳定性。在没有急性压力的情况下，随着时间的推移，探针的稳定性降低；然而，压力在较长的时间间隔内对探针产生稳定的影响。与未暴露个体相比，经历过 ELA 的个体在急性压力后立即进行探针稳定性测试时，其探针稳定性显著降低。此外，我们发现，在所有情况下，用于估计表观遗传年龄或免疫细胞比例的大多数基于表观遗传的算法中使用的探针的稳定性平均或低于平均水平，除了主要成分和 DunedinPACE 表观遗传年龄时钟，它们富集了更稳定的探针。最后，在没有压力的情况下使用高度稳定的探针，我们鉴定出多个探针在急性压力存在下呈低甲基化状态，无论 ELA 状态如何。两个低甲基化探针位于谷胱甘肽二硫还原酶基因（）的转录起始位点附近，该基因以前被证明是环境毒素应激反应的一个组成部分。我们讨论了对未来研究的影响，这些研究涉及 DNA 甲基化测量的可靠性和可重复性。DNAm - DNA 甲基化，CpG - 5'-胞嘧啶-磷酸-鸟嘌呤-3'，ICC - 组内相关系数，ELA - 早期生活逆境，PBMCs - 外周血单核细胞，mQTL - 甲基化数量性状基因座，TSS - 转录起始位点，GSR - 谷胱甘肽二硫还原酶基因，TSST - 特里尔社会应激测试，PC - 主成分。
