Genome-wide identification of genes essential for podocyte cytoskeletons based on single-cell RNA sequencing
Genome-wide identification of genes essential for podocyte cytoskeletons based on single-cell RNA sequencing
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基于单细胞 RNA 测序的足细胞骨架必需基因的全基因组鉴定
DOI：
10.1016/j.kint.2017.04.022
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发表时间：
2017-11-01
影响因子：
19.6
通讯作者：
Shi, Shaolin
中科院分区：
文献类型：
--
作者：
Lu, Yuqiu;Ye, Yuting;Shi, Shaolin
基因表达在同一类型的单个细胞中有很大差异。我们推测，除了一部分细胞外，在给定细胞类型的所有细胞中表达的基因可能是细胞生存（管家）或细胞类型独特结构和功能所必需的，使生物体能够生存。在这里，我们使用Fluidigm C1系统对20个小鼠足细胞进行了RNA-seq，并鉴定了335个在所有这些细胞中表达的基因。其中，239个基因也在系膜和内皮细胞中表达，并参与能量代谢、蛋白质合成等，管家基因。相比之下，92个基因优先在足细胞中表达（与在系膜和内皮细胞中的表达相比超过5倍），因此是足细胞特异性的必需候选基因。生物信息学评估、人足细胞中的保守表达以及与损伤/疾病的关联都支持这些基因对足细胞的重要性。事实上，92个基因中的27个已经被认为是足细胞结构和功能所必需的。通过siRNA沉默对37个新基因进行了功能分析，我们发现30个基因的缺失导致细胞骨架损伤，（FGFR1、AOX1、AIF1L、HAUS8、RAB3B、LPIN 2、GOLIM4、CERS6、ARHGEF18、ARPC1A、SRGAP1、ITGB5、ILDR2、MPP5、TSC22D1、DNAJC 11、SEPT 10、MOCS2、FNBP1L、和TMOD 3）或显著下调CD 2AP和突触足蛋白（IFFT 80、MYOM 2、ANXA 4、CYB 5 R4、GPC 1、ZNF 277、NSF、ITGAV、CD 2AB和MTSS 1）。因此，足细胞细胞骨架所必需的基因列表通过单细胞RNA测序而扩展。足细胞特异性必需基因主要与足细胞骨架相关。
Gene expression differs substantially among individual cells of the same type. Wespeculate that genes that are expressed in all but a portion of cells of a given cell type would be likely essential and required for either the cell survival ( housekeeping) or for the cell type's unique structure and function, enabling the organism to survive. Here, we performed RNA-seq of 20 mouse podocytes using the Fluidigm C1 system and identified 335 genes that were expressed in all of them. Among them, 239 genes were also expressed in mesangial and endothelial cells and were involved in energy metabolism, protein synthesis, etc., as housekeeping genes. In contrast, 92 genes were preferentially expressed in podocytes (over five-fold versus expression in mesangial and endothelial cells) and are, therefore, the essential candidate genes specific for podocytes. Assessments by bioinformatics, conserved expression in human podocytes, and association with injury/disease all support the essentiality of these genes for podocytes. Factually, 27 of the 92 genes are already known to be essential for podocyte structure and function. Thirty-seven novel genes were functionally analyzed by siRNA silencing, and we found that a deficiency of 30 genes led to either cytoskeletal injury (FGFR1, AOX1, AIF1L, HAUS8, RAB3B, LPIN2, GOLIM4, CERS6, ARHGEF18, ARPC1A, SRGAP1, ITGB5, ILDR2, MPP5, TSC22D1, DNAJC11, SEPT10, MOCS2, FNBP1L, and TMOD3) or significant downregulation of CD2AP and synaptopodin (IFT80, MYOM2, ANXA4, CYB5R4, GPC1, ZNF277, NSF, ITGAV, CRYAB, and MTSS1). Thus, the list of genes essential for podocyte cytoskeletons is expanded by single-cell RNA sequencing. It appears that podocyte-specific essential genes are mainly associated with podocyte cytoskeletons.