Genome-wide methylation patterns associated with chronic stress

Chronic social defeat stress (CSDS) is a validated animal model for depression that produces sustained behavioral and transcriptional changes in the brain, notably the nucleus accumbens (nAcc). We used genome-wide analysis of cytosine methylation patterns in mouse nAcc following CSDS to identify candidate epigenetic mechanisms. CSDS produced extensive differential methylation, increasing CG hypermethylation compared to control conditions; non-CG methylation showed the opposite trend. Highly differentially methylated (DM) regions included several genes implicated in behavioral effects of CSDS, including estrogen receptor alpha (Esr1). Analysis of DM sites within gene bodies revealed ß-catenin as a hub gene of a network including the ß-catenin-related WNT/frizzled signaling pathway. Analysis of DM sites upstream of transcription start sites revealed a gene network with the Tcf4 transcription factor as a hub. Genes DM within the gene body were enriched for synaptic function and primarily expressed in D1+ and D2+ medium spiny neurons, which, like the WNT/ß-catenin pathway, are estrogen sensitive and implicated in the behavioral effects of CSDS. We found significant overlap between DM genes associated with CSDS and those associated with major depressive disorder in genome-wide association studies, suggesting that effects on DNA methylation are implicated in the molecular pathways that link chronic stress to depression. Depression is a serious health problem affecting millions of people worldwide. One of the major risk factors for depression is long-term stress. To better understand how stress affects the brain and its links to depression, we studied mice exposed to chronic social defeat stress – a model which mimics features of depression in humans. The research focused on an area of the brain called the nucleus accumbens, which is well known to regulate motivational and emotional responses. DNA methylation is a modification to DNA that can turn genes “on” or “off” without altering the genetic code itself. In this study, we obtained data on methylation across the entire mouse genome at the resolution of single bases of DNA. It was found that stress caused widespread methylation changes throughout the genome. Some of the genes that contained the highest levels of methylation changes are known to be involved in stress and depression. Importantly, many of these genes overlapped with ones associated with depression in human studies. We identified networks of genes affected by stress, one centered on the gene which produces a protein called β-catenin, another on the transcription factor Tcf4. These genes are involved in communication between brain cells. Our results suggest that stress-induced methylation changes in the brain could be one of the ways that chronic stress increases the risk for depression. Further understanding of the mechanisms involved may eventually lead to new approaches for the prevention or treatment of depression.

慢性社交挫败应激（Chronic social defeat stress, CSDS）是一种经过验证的抑郁症动物模型，可在大脑中引发持久的行为学与转录组学改变，尤其累及伏隔核（nucleus accumbens, nAcc）。本研究针对慢性社交挫败应激暴露后小鼠伏隔核的胞嘧啶甲基化（cytosine methylation）模式开展全基因组分析，以筛选潜在的表观遗传调控机制。慢性社交挫败应激诱导了广泛的差异甲基化（differentially methylated, DM）现象：与对照组相比，CG位点呈现高甲基化趋势，而非CG位点则表现出相反的变化模式。高度差异甲基化区域涵盖了多个与慢性社交挫败应激行为效应相关的基因，包括雌激素受体α（estrogen receptor alpha, Esr1）。对基因体内差异甲基化位点的分析显示，β-连环蛋白（ß-catenin）是包含其相关WNT/卷曲蛋白信号通路（WNT/frizzled signaling pathway）在内的基因网络的枢纽基因；对转录起始位点（transcription start sites）上游差异甲基化位点的分析则揭示了以Tcf4转录因子（Tcf4 transcription factor）为枢纽的基因调控网络。基因体内存在差异甲基化的基因富集于突触功能通路，且主要在D1阳性与D2阳性中型多棘神经元（medium spiny neurons）中表达——这类神经元与WNT/β-连环蛋白通路一样，均对雌激素敏感，且与慢性社交挫败应激的行为效应密切相关。本研究发现，慢性社交挫败应激相关的差异甲基化基因与全基因组关联研究（genome-wide association studies）中鉴定的重度抑郁症（major depressive disorder）相关基因存在显著重叠，提示DNA甲基化改变参与了慢性应激指向抑郁症的分子通路。抑郁症是一类严重影响全球数百万人健康的公共卫生问题，长期应激是抑郁症的主要风险因素之一。为深入解析应激影响大脑的机制及其与抑郁症的关联，本研究以暴露于慢性社交挫败应激的小鼠为研究对象——该模型可模拟人类抑郁症的部分特征。研究聚焦于伏隔核这一已知可调控动机与情绪反应的脑区。DNA甲基化是一种不改变DNA序列即可调控基因“开启”或“关闭”的表观遗传修饰。本研究获取了单碱基分辨率下小鼠全基因组范围内的甲基化数据。研究发现，应激可引发全基因组范围内广泛的甲基化改变。部分甲基化改变最为显著的基因，已被证实与应激及抑郁症相关。值得注意的是，其中许多基因与人类研究中鉴定的抑郁症相关基因存在重叠。本研究还鉴定了受应激影响的基因调控网络：一个以编码β-连环蛋白的基因为枢纽，另一个则以Tcf4转录因子为核心。这类基因参与大脑神经元之间的信号通信。本研究结果表明，应激诱导的大脑DNA甲基化改变，可能是慢性应激增加抑郁症发病风险的重要途径之一。对相关机制的深入解析，有望最终为抑郁症的预防与治疗提供全新的策略。