Background & Aims

Epigenetic mechanisms might be involved in the regulation of liver enzyme level. We aimed to identify CpG sites at which DNA methylation levels are associated with blood levels of liver enzymes and hepatic steatosis.

Methods

We conducted an epigenome-wide association study in whole blood for liver enzyme levels, including gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST), among a discovery set of 731 participants of the Rotterdam Study and sought replication in a non-overlapping sample of 719 individuals. Significant DNA methylation changes were further analyzed to evaluate their relation with hepatic steatosis. Expression levels of the top identified gene were measured in 9 human liver cell lines and compared with expression profiles of its potential targets associated with lipid traits. The candidate gene was subsequently knocked down in human hepatoma cells using lentiviral vectors expressing small hairpin RNAs.

Results

Eight probes annotated to SLC7A11, SLC1A5, SLC43A1, PHGDH, PSORS1C1, SREBF1, ANKS3 were associated with GGT and 1 probe annotated to SLC7A11 was associated with ALT after Bonferroni correction (1.0 × 10^-7). No probe was identified for AST levels. Four probes for GGT levels including cg06690548 (SLC7A11), cg11376147 (SLC43A1), cg22304262 (SLC1A5), and cg14476101 (PHGDH), and 1 for ALT cg06690548 (SLC7A11) were replicated. DNA methylation at SLC7A11 was associated with reduced risk of hepatic steatosis in participants (odds ratio, 0.69; 95% CI= 0.55–0.93; P value: 2.7 × 10^-3). In functional experiments, SLC7A11 was highly expressed in human liver cells; its expression is positively correlated with expression of a panel of lipid-associated genes, indicating a role of SLC7A11 in lipid metabolism.

Conclusions

Our results provide new insights into epigenetic mechanisms associated with markers of liver function and hepatic steatosis, laying the groundwork for future diagnostic and therapeutic applications.

中文翻译：

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广泛的表观基因组关联研究确定了与肝酶和肝脂肪变性相关的甲基化位点

背景与目标

表观遗传机制可能参与肝酶水平的调节。我们旨在鉴定DNA甲基化水平与肝酶和肝脂肪变性的血液水平相关的CpG位点。

方法

我们在全血中进行了表观基因组关联研究，研究了731个参与者的鹿特丹研究发现肝酶水平，包括γ-谷氨酰转移酶（GGT），丙氨酸氨基转移酶（ALT）和天冬氨酸氨基转移酶（AST）。在719个人的非重叠样本中寻求复制。进一步分析了重要的DNA甲基化变化，以评估其与肝脂肪变性的关系。在9个人类肝细胞系中测量了最先鉴定的基因的表达水平，并与与脂质性状相关的潜在靶标的表达谱进行了比较。随后使用表达小发夹RNA的慢病毒载体在人肝癌细胞中敲除候选基因。

结果

在Bonferroni校正后（1.0×10 ^-7），标注SLC7A11，SLC1A5，SLC43A1，PHGDH，PSORS1C1，SREBF1，ANKS3的8个探针与GGT相关，注释SLC7A11的1个探针与ALT相关。AST水平未发现任何探针。复制了四个用于gGT水平的探针，包括cg06690548（SLC7A11），cg11376147（SLC43A1），cg22304262（SLC1A5）和cg14476101（PHGDH），以及用于ALT cg06690548（SLC7A11）的探针。SLC7A11的DNA甲基化与参与者发生肝脂肪变性的风险降低相关（赔率，0.69； 95％CI = 0.55-0.93；P值：2.7×10 ^-3）。在功能性实验中，SLC7A11在人肝细胞中高表达。它的表达与一组脂质相关基因的表达呈正相关，表明SLC7A11在脂质代谢中的作用。

结论

我们的结果为与肝功能和肝脂肪变性标志物相关的表观遗传机制提供了新见解，为将来的诊断和治疗应用奠定了基础。