Hu Yuzhu, Su Dongmei, Zhang Yue, Fu Yanjiang, Li Sijia, Chen Xiaoya, Zhang Xiao, Zheng Shunfei, Ma Xu, Hu Shanshan
Mudanjiang Medical University, Mudanjiang, Heilongjiang, China.
Department of Genetics, Health Department, National Research Institute for Family Planning, Beijing, China.
PLoS One. 2025 Jan 30;20(1):e0316766. doi: 10.1371/journal.pone.0316766. eCollection 2025.
DNA methylation is known to be associated with cataracts. In this study, we used a mouse model and performed DNA methylation and transcriptome sequencing analyses to find epigenetic indicators for age-related cataracts (ARC). Anterior lens capsule membrane tissues from young and aged mice were analyzed by MethylRAD-seq to detect the genome-wide methylation of extracted DNA. The young and aged mice had 76,524 and 15,608 differentially methylated CCGG and CCWGG sites, respectively. The Pearson correlation analysis detected 109 and 33 differentially expressed genes (DEGs) with negative methylation at CCGG and CCWGG sites, respectively, in their promoter regions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses showed that DEGs with abnormal methylation at CCGG sites were primarily associated with protein kinase C signaling (Akap12, Capzb), protein threonine kinase activity (Dmpk, Mapkapk3), and calcium signaling pathway (Slc25a4, Cacna1f), whereas DEGs with abnormal methylation at CCWGG sites were associated with ribosomal protein S6 kinase activity (Rps6ka3). These genes were validated by pyrosequencing methylation analysis. The results showed that the ARC group (aged mice) had lower Dmpk and Slc25a4 methylation levels and a higher Rps6ka3 methylation than the control group (young mice), which is consistent with the results of the joint analysis of differentially methylated and differentially expressed genes. In conclusion, we confirmed the genome-wide DNA methylation pattern and gene expression profile of ARC based on the mouse cataract model with aged mice. The identified methylation molecular markers have great potential for application in the future diagnosis and treatment of ARC.
已知DNA甲基化与白内障有关。在本研究中，我们使用小鼠模型并进行了DNA甲基化和转录组测序分析，以寻找年龄相关性白内障（ARC）的表观遗传指标。通过MethylRAD-seq分析年轻和老年小鼠的晶状体前囊膜组织，以检测提取DNA的全基因组甲基化情况。年轻和老年小鼠分别有76,524个和15,608个差异甲基化的CCGG和CCWGG位点。Pearson相关性分析分别在CCGG和CCWGG位点的启动子区域检测到109个和33个甲基化呈负相关的差异表达基因（DEG）。基因本体论（GO）和京都基因与基因组百科全书（KEGG）功能富集分析表明，CCGG位点甲基化异常的DEG主要与蛋白激酶C信号传导（Akap12、Capzb）、蛋白苏氨酸激酶活性（Dmpk、Mapkapk3）和钙信号通路（Slc25a4、Cacna1f）有关，而CCWGG位点甲基化异常的DEG与核糖体蛋白S6激酶活性（Rps6ka3）有关。这些基因通过焦磷酸测序甲基化分析得到验证。结果显示，ARC组（老年小鼠）的Dmpk和Slc25a4甲基化水平低于对照组（年轻小鼠），而Rps6ka3甲基化水平高于对照组，这与差异甲基化和差异表达基因的联合分析结果一致。总之，我们基于老年小鼠白内障模型确定了ARC的全基因组DNA甲基化模式和基因表达谱。所鉴定的甲基化分子标志物在ARC未来的诊断和治疗中具有巨大的应用潜力。
