Loss of FERM domain-containing protein 3 (FRMD3) is associated with severity of chronic kidney disease

Purpose: Transcriptiome profiling of chronic kidney disease Methods: Transcriptome profiling was performed in human renal biopsy tissue and correlated with parameters of kidney function, including estimated glomerular filtration rate (eGFR), degree of renal tubulointerstitial fibrosis (%TIF), as well as CKD progression over a median follow-up period of 60 months. Results: Transcriptome analysis performed in two independent cohorts of patients with CKD (n=24 and n=17, respectively) identified a cluster of genes (n=93) significantly correlated (FDR P<0.05) with eGFR and %TIF, and associated with CKD progression, with enrichment for pathways associated with inflammation and immune-cell mediated infiltration. Expression of FRMD3, a previously reported candidate gene from human genetics studies in CKD, was negatively correlated with indices of CKD severity and progression. Knockdown of FRMD3 in human kidney epithelial cells enhanced fibrotic responses to the cytokine transforming growth factor-beta (TGF-β1). Analysis of FRMD3 binding partners indicated enrichment of proteins implicated in mitochondrial function and remodeling of epithelial adherens junctions. Lentivirus-mediated knockdown of FRMD3 in renal tubule epithelial cells yielded a significant reduction (>35%) in NAD(P)H-dependent oxidoreductase activity, and a corresponding increase in caspase activity (50%). Conclusions: Using global transcriptome profiling we define a cluster of transcripts associated with severity of CKD and identify loss of FRMD3 expression as a potential molecular driver. Loss of FRMD3 expression may contribute to mitochondrial function and TIF. We examined the transcriptional profile of human kidney biopsies, aiming to provide insight into the mechanisms of progressive CKD. This approach led to the identification of FERM domain protein 3, (FRMD3) as a molecular driver of disease.

研究目的：慢性肾脏病（chronic kidney disease, CKD）的转录组谱分析。
研究方法：对人类肾活检组织开展转录组谱分析（transcriptome profiling），并与多项肾功能参数进行关联分析，包括估算肾小球滤过率（estimated glomerular filtration rate, eGFR）、肾肾小管间质纤维化程度（%TIF），以及中位随访时长60个月期间的CKD进展情况。
研究结果：在两个独立的CKD患者队列（分别含24例和17例患者）中进行的转录组谱分析，鉴定出包含93个基因的基因簇，该基因簇与eGFR和%TIF显著相关（错误发现率（false discovery rate, FDR）P<0.05），且与CKD进展密切相关，同时富集于炎症及免疫细胞介导的浸润相关通路。此前在人类遗传学CKD研究中报道的候选基因FERM结构域蛋白3（FERM domain protein 3, FRMD3），其表达水平与CKD严重程度及进展指标呈负相关。在人类肾上皮细胞中敲低FRMD3，可增强细胞对细胞因子转化生长因子-β1（transforming growth factor-beta, TGF-β1）的纤维化应答。对FRMD3结合蛋白的分析显示，其富集的蛋白参与线粒体功能调控及上皮黏附连接重塑过程。在肾小管上皮细胞中通过慢病毒介导敲低FRMD3，可使NAD(P)H依赖性氧化还原酶活性显著降低（降幅>35%），同时半胱天冬酶（caspase）活性相应升高（增幅50%）。
研究结论：本研究通过全局转录组谱分析，确定了一组与CKD严重程度相关的转录本，并鉴定出FRMD3表达缺失作为潜在的分子驱动因素。FRMD3表达缺失可能参与线粒体功能异常及肾小管间质纤维化进程。本研究对人类肾活检组织的转录谱进行了分析，旨在为进展性CKD的发病机制提供新的见解。通过该研究策略，最终鉴定出FERM结构域蛋白3（FERM domain protein 3, FRMD3）作为疾病的分子驱动因子。