Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
Genomic Imprinting Cancer Group, Institut d'Investigació Biomedica de Bellvitge, E-08908, Barcelona, Spain.
Clin Epigenetics. 2020 Feb 3;12(1):20. doi: 10.1186/s13148-020-0814-y.
Alzheimer's disease (AD) is a complex disorder caused by a combination of genetic and non-genetic risk factors. In addition, an increasing evidence suggests that epigenetic mechanisms also accompany AD. Genetic and epigenetic factors are not independent, but multiple loci show genetic-epigenetic interactions, the so-called quantitative trait loci (QTLs). Recently, we identified the first QTL association with AD, namely Peptidase M20 Domain Containing 1 (PM20D1). We observed that PM20D1 DNA methylation, RNA expression, and genetic background are correlated and, in turn, associated with AD. We provided mechanistic insights for these correlations and had shown that by genetically increasing and decreasing PM20D1 levels, AD-related pathologies were decreased and accelerated, respectively. However, since the PM20D1 QTL region encompasses also other genes, namely Nuclear Casein Kinase and Cyclin Dependent Kinase Substrate 1 (NUCKS1); RAB7, member RAS oncogene family-like 1 (RAB7L1); and Solute Carrier Family 41 Member 1 (SLC41A1), we investigated whether these genes might also contribute to the described AD association.
Here, we report a comprehensive analysis of these QTL genes using a repertoire of in silico methods as well as in vivo and in vitro experimental approaches. First, we analyzed publicly available databases to pinpoint the major QTL correlations. Then, we validated these correlations using a well-characterized set of samples and locus-specific approaches-i.e., Sanger sequencing for the genotype, cloning/sequencing and pyrosequencing for the DNA methylation, and allele-specific and real-time PCR for the RNA expression. Finally, we defined the functional relevance of the observed alterations in the context of AD in vitro. Using this approach, we show that only PM20D1 DNA methylation and expression are significantly correlated with the AD-risk associated background. We find that the expression of SLC41A1 and PM20D1-but not NUCKS1 and RAB7L1-is increased in mouse models and human samples of AD, respectively. However, SLC41A1 and PM20D1 are differentially regulated by AD-related stressors, with only PM20D1 being upregulated by amyloid-β and reactive oxygen species, and with only PM20D1 being neuroprotective when overexpressed in cell and primary cultures.
Our findings reinforce PM20D1 as the most likely gene responsible of the previously reported PM20D1 QTL association with AD.
阿尔茨海默病（AD）是一种由遗传和非遗传风险因素共同引起的复杂疾病。此外，越来越多的证据表明，表观遗传机制也伴随着 AD 的发生。遗传和表观遗传因素并不是独立的，而是多个基因座表现出遗传-表观遗传相互作用，即所谓的数量性状基因座（QTLs）。最近，我们发现了与 AD 相关的第一个 QTL 关联，即肽酶 M20 结构域包含蛋白 1（PM20D1）。我们观察到 PM20D1 的 DNA 甲基化、RNA 表达和遗传背景相互关联，并与 AD 相关。我们为这些相关性提供了机制上的见解，并表明通过遗传上增加和减少 PM20D1 的水平，AD 相关的病理分别减少和加速。然而，由于 PM20D1 QTL 区域还包含其他基因，即核结合激酶和细胞周期蛋白依赖性激酶底物 1（NUCKS1）；RAB7，RAS 癌基因家族样 1（RAB7L1）；和溶质载体家族 41 成员 1（SLC41A1），我们研究了这些基因是否也可能导致描述的 AD 关联。
在这里，我们使用一系列计算机方法以及体内和体外实验方法，对这些 QTL 基因进行了全面分析。首先，我们分析了公开可用的数据库，以确定主要的 QTL 相关性。然后，我们使用一组经过良好特征描述的样本和基因座特异性方法来验证这些相关性，即基因型的 Sanger 测序、DNA 甲基化的克隆/测序和焦磷酸测序，以及 RNA 表达的等位基因特异性和实时 PCR。最后，我们在体外环境中定义了观察到的改变与 AD 的功能相关性。使用这种方法，我们表明只有 PM20D1 的 DNA 甲基化和表达与 AD 风险相关的背景显著相关。我们发现 SLC41A1 和 PM20D1 的表达分别在 AD 小鼠模型和人类样本中增加，但 NUCKS1 和 RAB7L1 的表达没有增加。然而，SLC41A1 和 PM20D1 的表达受到 AD 相关应激的差异调节，只有 PM20D1 被淀粉样蛋白-β和活性氧上调，并且只有 PM20D1 在细胞和原代培养物中过表达时具有神经保护作用。
我们的发现进一步证实 PM20D1 是与 AD 相关的 PM20D1 QTL 关联最有可能的基因。
