Integrative transcriptome analysis reveals TEKT2 and PIAS2 involvement in diabetic nephropathy
Integrative transcriptome analysis reveals TEKT2 and PIAS2 involvement in diabetic nephropathy
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综合转录组分析揭示 TEKT2 和 PIAS2 参与糖尿病肾病
DOI：
10.1096/fj.202200740rr
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发表时间：
2022-11-01
期刊：
影响因子：
4.8
通讯作者：
Peng，Hui
中科院分区：
文献类型：
--
作者：
Li，Yuanqing;Lin，Hongchun;Peng，Hui
细胞异质性阻碍了对糖尿病肾病（DN）患者大量转录组数据的准确解释。我们通过整合大量和单细胞转录组数据集进行了分析，以揭示导致DN的新机制，特别是在足细胞中。微解剖肾小球和小管转录组数据来自基因表达Omnibus （GEO）。然后评估数据集之间的一致性。整合了大量数据集和单核RNA数据集的分析，以揭示细胞类型特异性对DN的反应。候选基因在DN患者和糖尿病小鼠的肾组织中得到验证。我们比较了4个肾小球和4个肾小管的数据集，发现在不同的数据集中，关于递质表达基因（DEGs）、相关信号通路和标记富集谱存在相当大的差异。大量数据的反褶积显示，细胞类型比例的变化对这种差异有很大贡献。综合分析发现，包括tekt2和pias2在内的精子发生相关基因的失调参与了DN的发展。重要的是，TEKT2的mRNA水平与糖尿病肾小球中NPHS1 （r= - 0.66,p < 0.0001）和NPHS2 （r= - 0.85,p < 0.0001）的mRNA水平呈负相关。免疫染色证实，TEKT2和PIAS2在DN患者和糖尿病小鼠足细胞中表达上调。敲低tekt2可抵抗高糖诱导的细胞骨架重塑和培养足细胞中NPHS1蛋白的下调。综上所述，整合策略可以帮助我们有效地利用公开可用的转录组学资源。利用这一方法并结合经典研究方法，我们鉴定出了tekt2和pias2这两个与DN发病有关的精子发生相关基因。此外，tekt2i通过调节足细胞骨架参与了这一发病机制。
Cell heterogeneity has impeded the accurate interpretation of the bulk transcriptome data from patients with diabetic nephropathy (DN). We performed an analysis by integrating bulk and single‐cell transcriptome datasets to uncover novel mechanisms leading to DN, especially in the podocytes. Microdissected glomeruli and tubules transcriptome datasets were selected from Gene Expression Omnibus (GEO). Then the consistency between datasets was evaluated. The analysis of the bulk dataset and single‐nucleus RNA dataset was integrated to reveal the cell type‐specific responses to DN. The candidate genes were validated in kidney tissues from DN patients and diabetic mice. We compared 4 glomerular and 4 tubular datasets and found considerable discrepancies among datasets regarding the deferentially expressed genes (DEGs), involved signaling pathways, and the hallmark enrichment profiles. Deconvolution of the bulk data revealed that the variations in cell‐type proportion contributed greatly to this discrepancy. The integrative analysis uncovered that the dysregulation of spermatogenesis‐related genes, includingTEKT2andPIAS2, was involved in the development of DN. Importantly, the mRNA level of TEKT2 was negatively correlated with the mRNA levels of NPHS1 (r= −.66,p <.0001) and NPHS2 (r= −.85,p <.0001) in human diabetic glomeruli. Immunostaining confirmed that the expression of TEKT2 and PIAS2 were up‐regulated in podocytes of DN patients and diabetic mice. Knocking downTEKT2resisted high glucose‐induced cytoskeletal remodeling and down‐regulation of NPHS1 protein in the cultured podocyte. In conclusion, the integrative strategy can help us efficiently use the publicly available transcriptomics resources. Using this approach and combining it with classical research methods, we identifiedTEKT2andPIAS2, two spermatogenesis‐related genes involved in the pathogenesis of DN. Furthermore,TEKT2is involved in this pathogenesis by regulating the podocyte cytoskeleton.