National Clinical Research Center for Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China.
National Clinical Research Center for Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China.
Kidney Int. 2017 Nov;92(5):1119-1129. doi: 10.1016/j.kint.2017.04.022. Epub 2017 Jul 12.
Gene expression differs substantially among individual cells of the same type. We speculate 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.
同类型的细胞中，基因表达存在显著差异。我们推测，在给定类型的细胞中，只有一部分细胞表达的基因可能是必需的，对于细胞存活（管家）或细胞类型的独特结构和功能是必需的，使生物体能够存活。在这里，我们使用 Fluidigm C1 系统对 20 个小鼠足细胞进行了 RNA-seq 分析，鉴定出 335 个在所有细胞中都表达的基因。其中，239 个基因也在系膜细胞和内皮细胞中表达，作为管家基因参与能量代谢、蛋白质合成等。相比之下，92 个基因在足细胞中优先表达（相对于系膜细胞和内皮细胞表达高出五倍），因此是足细胞特有的必需候选基因。通过生物信息学评估、在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必要性。实际上，92 个基因中的 27 个已经被证明对足细胞的结构和功能是必需的。通过 siRNA 沉默对 37 个新基因进行了功能分析，我们发现 30 个基因的缺乏导致了细胞骨架损伤（FGFR1、AOX1、AIF1L、HAUS8、RAB3B、LPIN2、GOLIM4、CERS6、ARHGEF18、ARPC1A、SRGAP1、ITGB5、ILDR2、MPP5、TSC22D1、DNAJC11、SEPT10、MOCS2、FNBP1L 和 TMOD3）或 CD2AP 和 synaptopodin 的显著下调（IFT80、MYOM2、ANXA4、CYB5R4、GPC1、ZNF277、NSF、ITGAV、CRYAB 和 MTSS1）。因此，通过单细胞 RNA 测序扩展了足细胞细胞骨架必需基因的列表。似乎足细胞特有的必需基因主要与足细胞细胞骨架有关。
