Filippov Valery, Jaceldo-Siegl Karen, Eroshkin Alexey, Loskutov Vasiliy, Chen Xin, Wang Charles, Duerksen-Hughes Penelope J
Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
Department of Nutrition, School of Public Health, Loma Linda University, Loma Linda, CA 92354, USA.
Epigenomes. 2020 Dec;4(4). doi: 10.3390/epigenomes4040028. Epub 2020 Dec 11.
Epigenetic studies in animal models have demonstrated that diet affects gene regulation by altering methylation patterns. We interrogated methylomes in humans who have different sources of protein in their diet. We compared methylation of DNA isolated from buffy coat in 38 vegans, 41 pescatarians and 68 nonvegetarians. Methylation data were obtained using Infinium HumanMethylation450 arrays and analyzed using the Partek Genomic software. Differences in differentially methylated sites were small, though with the use of relaxed statistical tests we did identify diet-associated differences. To further test the validity of these observations, we performed separate and independent comparisons of the methylation differences between vegans and nonvegetarians, and between vegans and pescatarians. The detected differences were then examined to determine if they were enriched in specific pathways. Pathway analysis revealed enrichment of several specific processes, including homeobox transcription and glutamate transport. The detected differences in DNA methylation patterns between vegans, pescatarians, and nonvegetarians enabled us to identify 77 CpG sites that may be sensitive to diet and/or lifestyle, though high levels of individual-specific differences were also noted.
动物模型中的表观遗传学研究表明，饮食通过改变甲基化模式来影响基因调控。我们对饮食中蛋白质来源不同的人群的甲基化组进行了研究。我们比较了38名纯素食者、41名鱼素者和68名非素食者从血沉棕黄层中分离出的DNA的甲基化情况。甲基化数据通过Infinium HumanMethylation450芯片获得，并使用Partek Genomic软件进行分析。尽管使用宽松的统计检验我们确实发现了与饮食相关的差异，但差异甲基化位点的差异很小。为了进一步检验这些观察结果的有效性，我们分别独立比较了纯素食者与非素食者之间以及纯素食者与鱼素者之间的甲基化差异。然后检查检测到的差异，以确定它们是否在特定途径中富集。通路分析显示了几个特定过程的富集，包括同源框转录和谷氨酸转运。纯素食者、鱼素者和非素食者之间检测到的DNA甲基化模式差异使我们能够识别出77个可能对饮食和/或生活方式敏感的CpG位点，不过也注意到了高水平的个体特异性差异。
