Table 3_Genome-wide DNA methylation analysis identifies kidney epigenetic dysregulation in a cystinosis mouse model.xlsx

IntroductionNephropathic cystinosis is a rare genetic disorder characterized by cystine accumulation in lysosomes that causes early renal dysfunction and progressive chronic kidney disease. Although several metabolic pathways, including oxidative stress and inflammation, have been implicated in the progression of renal parenchyma damage, the precise mechanisms driving its progression are not fully understood. Recent studies suggest that epigenetic modifications, particularly DNA methylation (DNAm), play a critical role in the development of chronic kidney disease. We hypothesized that epigenetic dysregulation may contribute to the progression of kidney disease in cystinosis.
MethodsTo investigate this, we conducted genome-wide DNAm analyses on kidneys harvested from 6-month-old wild type (WT) and Ctns−/− mice, a well-established model of cystinosis.
ResultsOur analysis revealed extensive DNAm alterations in cystinotic kidneys, characterized by a significant hypermethylation profile. Interestingly, the majority of differentially methylated CpG sites were located within gene bodies and to a lesser extent in promoter and enhancer regions. Methylation changes were primarily found in genes and pathways crucial for kidney function, particularly those related to the physiology of the proximal tubules. Importantly, DNAm changes correlated with changes in gene expression, as validated by qPCR analyses of key genes. Furthermore, in vitro treatment of human proximal tubular epithelial cells with the demethylating agent decitabine resulted in the upregulation of critical transporter genes, suggesting a potential therapeutic approach.
ConclusionsThese findings underscore the role of epigenetic regulation in the progression of kidney damage in cystinosis and suggest that DNAm could serve as a promising target for novel therapeutic strategies.

引言
肾病性胱氨酸贮积症是一种罕见的遗传性疾病，以溶酶体内胱氨酸蓄积为特征，可导致早期肾功能不全及进行性慢性肾脏病。尽管已有多项代谢通路（包括氧化应激与炎症）被证实参与肾实质损伤的进展过程，但其确切的致病进展机制仍未完全阐明。近期研究表明，表观遗传修饰，尤其是DNA甲基化（DNA methylation, DNAm），在慢性肾脏病的发生发展中发挥关键作用。本研究提出假说：表观遗传失调可能参与肾病性胱氨酸贮积症患者肾脏疾病的进展过程。
方法
为探究该假说，本研究对6月龄野生型（wild type, WT）小鼠及成熟公认的肾病性胱氨酸贮积症模型Ctns−/−小鼠的肾脏组织开展全基因组DNA甲基化分析。
结果
本研究分析发现，胱氨酸贮积症小鼠肾脏组织存在广泛的DNA甲基化改变，以显著的高甲基化特征为主要表现。值得注意的是，绝大多数差异甲基化CpG位点位于基因本体区域，仅少量分布于启动子与增强子区域。甲基化改变主要富集于与肾功能密切相关的基因及通路，尤其是与近端小管生理功能相关的基因。重要的是，DNA甲基化变化与基因表达改变存在相关性，这一结论通过关键基因的实时定量PCR（qPCR）分析得到验证。此外，体外使用去甲基化药物地西他滨（decitabine）处理人近端肾小管上皮细胞后，关键转运蛋白基因的表达出现上调，提示该策略可能具有潜在治疗价值。
结论
本研究结果凸显了表观遗传调控在肾病性胱氨酸贮积症肾脏损伤进展过程中的作用，并表明DNA甲基化有望成为新型治疗策略的潜在靶点。