Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University (Naval Medical University), Shanghai, 200000, China; Department of Nephrology, 905th Hospital of PLA Navy, Shanghai, 200000, China.
Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University (Naval Medical University), Shanghai, 200000, China.
Biochem Biophys Res Commun. 2024 Nov 26;735:150848. doi: 10.1016/j.bbrc.2024.150848. Epub 2024 Oct 18.
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most prevalent genetic disorder affecting the kidneys. Understanding epigenetic regulatory mechanisms and the role of microRNAs (miRNAs) is crucial for developing therapeutic interventions. Two mRNA datasets (GSE7869 and GSE35831) and miRNA expression data (GSE133530) from ADPKD patients were used to find differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs), with a focus on genes regulated by hub transcription factors (TFs) and their target genes. The expression of hub TFs was validated in human kidneys and animal models through Western Blot (WB) and RT-PCR analysis. The location of the hub TF proteins in kidney cells was observed by a laser confocal microscope. A total of 2037 DEGs were identified. DEM analysis resulted in 59 up-regulated and 107 down-regulated miRNAs. Predicted target DEGs of DEMs indicated two top dysregulated TFs: hepatocyte nuclear factor 4 alpha (HNF4α) and Kruppel-like factor 4 (KLF4). RT-PCR, WB, and immunochemistry results showed that mRNA and protein levels of HNF4α were significantly decreased while KLF4 levels were significantly up-regulated in human ADPKD kidneys and Pkd1 conditional knockout mice compared with normal controls. Laser confocal microscopy revealed that KLF4 was mainly located in the cytoplasm while HNF4α was in the nucleus. Functional enrichment analysis indicated that genes regulated by HNF4α were mainly associated with metabolic pathways, while KLF4-regulated genes were linked to kidney development. Drug response prediction analysis revealed potential drug candidates for ADPKD treatment, including BI-2536, Sepantronium, and AZD5582. This integrated analysis provides new epigenetic insights into the complex miRNA-TF-mRNA network in ADPKD and identifies HNF4α and KLF4 as key TFs. These findings offer valuable resources for further research and potential drug development for ADPKD.
常染色体显性多囊肾病 (ADPKD) 是最常见的影响肾脏的遗传性疾病。了解表观遗传调控机制和 microRNAs (miRNAs) 的作用对于开发治疗干预措施至关重要。使用来自 ADPKD 患者的两个 mRNA 数据集 (GSE7869 和 GSE35831) 和 miRNA 表达数据 (GSE133530)，寻找差异表达基因 (DEGs) 和差异表达 miRNAs (DEMs)，重点关注受枢纽转录因子 (TFs) 及其靶基因调控的基因。通过 Western Blot (WB) 和 RT-PCR 分析验证了枢纽 TF 在人肾脏和动物模型中的表达。通过激光共聚焦显微镜观察枢纽 TF 蛋白在肾细胞中的位置。共鉴定出 2037 个 DEGs。DEM 分析导致 59 个上调和 107 个下调的 miRNAs。预测的 DEMs 的靶基因 DEGs 表明两个失调最严重的 TF：肝细胞核因子 4 阿尔法 (HNF4α) 和 Kruppel 样因子 4 (KLF4)。RT-PCR、WB 和免疫组织化学结果表明，与正常对照组相比，人 ADPKD 肾脏和 Pkd1 条件性敲除小鼠中 HNF4α 的 mRNA 和蛋白水平显著降低，而 KLF4 水平显著升高。激光共聚焦显微镜显示，KLF4 主要位于细胞质中，而 HNF4α 位于细胞核中。功能富集分析表明，HNF4α 调控的基因主要与代谢途径有关，而 KLF4 调控的基因与肾脏发育有关。药物反应预测分析揭示了用于 ADPKD 治疗的潜在药物候选物，包括 BI-2536、Sepantronium 和 AZD5582。这项综合分析为 ADPKD 中复杂的 miRNA-TF-mRNA 网络提供了新的表观遗传见解，并确定 HNF4α 和 KLF4 为关键 TF。这些发现为进一步研究和 ADPKD 的潜在药物开发提供了有价值的资源。
