Table_5_Gut Microbiota Composition Is Associated With the Global DNA Methylation Pattern in Obesity.xlsx

Objective: Obesity and obesity-related metabolic diseases are characterized by gut microbiota and epigenetic alterations. Recent insight has suggested the existence of a crosstalk between the gut microbiome and the epigenome. However, the possible link between alterations in gut microbiome composition and epigenetic marks in obesity has been not explored yet. The aim of this work is to establish a link between the gut microbiota and the global DNA methylation profile in a group of obese subjects and to report potential candidate genes that could be epigenetically regulated by gut microbiota in adipose tissue. Methods: Gut microbiota composition was analyzed in DNA stool samples from 45 obese subjects by 16S ribosomal RNA (rRNA) gene sequencing. Twenty patients were selected based on their Bacteroidetes-to-Firmicutes ratio (BFR): HighBFR group (BFR > 2.5, n = 10) and LowBFR group (BFR < 1.2, n = 10). Genome-wide analysis of DNA methylation pattern in both whole blood and visceral adipose tissue of these selected patients was performed with an Infinium EPIC BeadChip array-based platform. Gene expression analysis of candidate genes was done in adipose tissue by real-time quantitative PCR. Results: Genome-wide analysis of DNA methylation revealed a completely different DNA methylome pattern in both blood and adipose tissue in the low BFR group vs. the high BFR group. Two hundred fifty-eight genes were differentially methylated in both blood and adipose tissue, of which several potential candidates were selected for gene expression analysis. We found that in adipose tissue, both HDAC7 and IGF2BP2 were hypomethylated and overexpressed in the low BFR group compared with the high BFR group. β values of both genes significantly correlated with the BFR ratio and the relative abundance of Bacteroidetes and/or Firmicutes. Conclusions: In this study, we demonstrate that the DNA methylation status is associated with gut microbiota composition in obese subjects and that the expression levels of candidate genes implicated in glucose and energy homeostasis (e.g., HDAC7 and IGF2BP2) could be epigenetically regulated by gut bacterial populations in adipose tissue.研究目标：肥胖及肥胖相关代谢疾病以肠道菌群（gut microbiota）和表观遗传改变（epigenetic alterations）为特征。现有研究已证实肠道微生物组与表观基因组（epigenome）之间存在交互调控关系，但目前尚未明确肥胖状态下肠道微生物组组成改变与表观遗传标记之间的潜在关联。本研究旨在明确肥胖受试者群体中肠道菌群与全基因组DNA甲基化谱之间的关联，并筛选出可在脂肪组织（adipose tissue）中由肠道菌群进行表观遗传调控的潜在候选基因。 研究方法：本研究采用16S核糖体RNA（16S ribosomal RNA, rRNA）基因测序技术，对45名肥胖受试者的粪便DNA样本开展肠道菌群组成分析。研究人员基于拟杆菌门（Bacteroidetes）与厚壁菌门（Firmicutes）比值（Bacteroidetes-to-Firmicutes ratio, BFR）筛选出20名受试者，分为HighBFR组（BFR>2.5，n=10）与LowBFR组（BFR<1.2，n=10）。采用基于Infinium EPIC微珠芯片阵列（Infinium EPIC BeadChip array）的检测平台，对上述筛选受试者的全血及内脏脂肪组织进行全基因组DNA甲基化模式分析。通过实时定量PCR（real-time quantitative PCR）对脂肪组织中的候选基因进行表达分析。 研究结果：全基因组DNA甲基化分析结果显示，与HighBFR组相比，LowBFR组受试者的血液与脂肪组织中DNA甲基化组模式存在显著差异。共鉴定出258个在血液与脂肪组织中均存在差异甲基化的基因，从中选取若干潜在候选基因进行表达分析。研究发现，相较于HighBFR组，LowBFR组受试者脂肪组织中的HDAC7与IGF2BP2均呈低甲基化状态，且基因表达水平显著上调。上述两个基因的β值均与BFR比值以及拟杆菌门和/或厚壁菌门的相对丰度显著相关。 研究结论：本研究证实，肥胖受试者的DNA甲基化状态与肠道菌群组成密切相关，且参与葡萄糖与能量稳态调控的候选基因（如HDAC7和IGF2BP2）的表达水平可在脂肪组织中由肠道菌群通过表观遗传机制实现调控。