Faculty of Dentistry, Division of Health Sciences, Universidad Santo Tomás, Bucaramanga, Colombia.
Neurosciences Research Group, Faculty of Medicine and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia.
J Periodontal Res. 2021 Aug;56(4):710-725. doi: 10.1111/jre.12868. Epub 2021 Mar 4.
To investigate the differences in the epigenomic patterns of DNA methylation in peripheral leukocytes between patients with periodontitis and gingivally healthy controls evaluating its functional meaning by functional enrichment analysis.
The DNA methylation profiling of peripheral leukocytes as immune-related tissue potentially relevant as a source of biomarkers between periodontitis patients and gingivally healthy subjects has not been investigated.
A DNA methylation epigenome-wide study of peripheral leukocytes was conducted using the Illumina MethylationEPIC platform in sixteen subjects, eight diagnosed with periodontitis patients and eight age-matched and sex-matched periodontally healthy controls. A trained periodontist performed the clinical evaluation. Global DNA methylation was estimated using methylation-sensitive high-resolution melting in LINE1. Routine cell count cytometry and metabolic laboratory tests were also performed. The analysis of differentially methylated positions (DMPs) and differentially methylated regions (DMRs) was made using R/Bioconductor environment considering leukocyte populations assessed in both routine cell counts and using the FlowSorted.Blood.EPIC package. Finally, a DMP and DMR intersection analysis was performed. Functional enrichment analysis was carried out with the differentially methylated genes found in DMP.
DMP analysis identified 81 differentially hypermethylated genes and 21 differentially hypomethylated genes. Importantly, the intersection analysis showed that zinc finger protein 718 (ZNF718) and homeobox A4 (HOXA4) were differentially hypermethylated and zinc finger protein 57 (ZFP57) was differentially hypomethylated in periodontitis. The functional enrichment analysis found clearly immune-related ontologies such as "detection of bacterium" and "antigen processing and presentation."
The results of this study propose three new periodontitis-related genes: ZNF718, HOXA4, and ZFP57 but also evidence the suitability and relevance of studying leukocytes' DNA methylome for biological interpretation of systemic immune-related epigenetic patterns in periodontitis.
通过功能富集分析，研究牙周炎患者与牙龈健康对照者外周血白细胞 DNA 甲基化组在表观遗传学模式上的差异，评估其功能意义。
尚未研究过外周血白细胞的 DNA 甲基化谱作为潜在的与牙周炎患者和牙龈健康受试者相关的免疫相关组织的生物标志物来源。
使用 Illumina MethylationEPIC 平台，对 16 名受试者（8 名牙周炎患者和 8 名年龄和性别匹配的牙周健康对照者）的外周血白细胞进行了全基因组 DNA 甲基化组学研究。一名经过培训的牙周病学家进行了临床评估。使用 LINE1 甲基化敏感高分辨率熔解曲线法估计全基因组 DNA 甲基化。还进行了常规细胞计数流式细胞术和代谢实验室检测。使用 R/Bioconductor 环境进行差异甲基化位置（DMP）和差异甲基化区域（DMR）分析，同时考虑到在常规细胞计数中评估的白细胞群体，并使用 FlowSorted.Blood.EPIC 包进行分析。最后，进行了 DMP 和 DMR 的交集分析。使用在 DMP 中发现的差异甲基化基因进行了功能富集分析。
DMP 分析鉴定出 81 个差异高甲基化基因和 21 个差异低甲基化基因。重要的是，交集分析显示，锌指蛋白 718（ZNF718）和同源盒 A4（HOXA4）在牙周炎中呈差异高甲基化，锌指蛋白 57（ZFP57）呈差异低甲基化。功能富集分析发现了明显与免疫相关的本体论，如“细菌检测”和“抗原加工和呈递”。
本研究提出了三个新的牙周炎相关基因：ZNF718、HOXA4 和 ZFP57，但也证明了研究白细胞 DNA 甲基组对于牙周炎中系统性免疫相关表观遗传学模式的生物学解释的适用性和相关性。
