Department of Organ Transplant, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
Front Endocrinol (Lausanne). 2022 Apr 8;13:834187. doi: 10.3389/fendo.2022.834187. eCollection 2022.
This study aimed to explore the molecular mechanism of cytoplasmic vacuolation caused by BK polyomavirus (BKPyV) and thus search for potential target for drug repurposing.
Morphological features of BK polyomavirus-associated nephropathy (BKPyVAN) were studied under light and electron microscopes. Microarray datasets GSE75693, GSE47199, and GSE72925 were integrated by ComBat, and differentially expressed genes (DEGs) were analyzed using limma. Furthermore, the endoplasmic reticulum (ER)-related genes obtained from GenCLiP 2.0 were intersected with DEGs. GO and KEGG enrichment pathways were performed with intersection genes by R package clusterProfiler. The single-cell RNA sequencing (scRNA-seq) from a BKPyVAN recipient was analyzed with a dataset (GSE140989) downloaded from Gene Expression Omnibus (GEO) as control for gene set variation analysis (GSVA). Immunohistochemistry and electron microscopy of kidney sections from drug-induced ERS mouse models were performed to explore the association of ERS and renal tubular vacuolation. Protein-protein interaction (PPI) network of the intersection genes was constructed to identify hub target. AutoDock was used to screen Food and Drug Administration (FDA)-approved drugs that potentially targeted hub gene.
Light and electron microscopes exhibited obvious intranuclear inclusions, vacuoles, and virus particles in BKPyV-infected renal tubular cells. Transcriptome analysis revealed 629 DEGs between samples of BKPyVAN and stable transplanted kidneys, of which 16 were ER-associated genes. GO analysis with the intersection genes illustrated that ERS-related pathways were significantly involved, and KEGG analysis showed a prominent enrichment of MAPK, Toll-like receptor, and chemokine signaling pathways. GSVA analysis of the proximal tubule revealed similar pathways enrichment. An electron microscope image of the kidney from ERS mouse models showed an obvious renal tubular vacuolation with prominent activation of ERS markers verified by immunohistochemistry. Furthermore, DDIT3 was identified as the hub gene based on PPI analysis, and ZINCOOOOO1531009 (Risedronate) was indicated to be a potential drug for DDIT3.
ERS was involved in renal tubular cytoplasmic vacuolation in BKPyVAN recipients. Risedronate was screened as a potential drug for BKPyVAN by targeting DDIT3.
本研究旨在探索 BK 多瘤病毒（BKPyV）引起细胞质空泡化的分子机制，从而寻找潜在的药物再利用靶点。
通过光镜和电镜观察 BK 多瘤病毒相关性肾病（BKPyVAN）的形态特征。通过 ComBat 整合微阵列数据集 GSE75693、GSE47199 和 GSE72925，使用 limma 分析差异表达基因（DEGs）。此外，通过 GenCLiP 2.0 获取内质网（ER）相关基因，并与 DEGs 进行交集。使用 R 包 clusterProfiler 对交集基因进行 GO 和 KEGG 富集通路分析。使用从基因表达综合数据库（GEO）下载的数据集（GSE140989）分析 BKPyVAN 受者的单细胞 RNA 测序（scRNA-seq），并进行基因集变异分析（GSVA）。对药物诱导的 ERS 小鼠模型的肾组织切片进行免疫组织化学和电子显微镜检查，以探讨 ERS 与肾小管空泡化的关系。构建交集基因的蛋白质-蛋白质相互作用（PPI）网络，以识别关键靶点。使用 AutoDock 筛选可能靶向关键基因的 FDA 批准药物。
光镜和电镜显示 BKPyV 感染的肾小管细胞中存在明显的核内包涵体、空泡和病毒颗粒。转录组分析显示，BKPyVAN 样本与稳定移植肾脏样本之间有 629 个 DEGs，其中 16 个是 ER 相关基因。交集基因的 GO 分析表明，ERS 相关途径显著参与，KEGG 分析表明 MAPK、Toll 样受体和趋化因子信号通路明显富集。近端肾小管的 GSVA 分析显示出相似的通路富集。ERS 小鼠模型肾脏的电镜图像显示明显的肾小管空泡化，免疫组织化学证实 ERS 标志物明显激活。此外，基于 PPI 分析，确定 DDIT3 为关键基因，并且表明 ZINCOOOOO1531009（利塞膦酸钠）是针对 DDIT3 的潜在药物。
ERS 参与了 BKPyVAN 受者的肾小管细胞质空泡化。通过靶向 DDIT3，筛选出利塞膦酸钠可能是治疗 BKPyVAN 的潜在药物。
