Transcriptomes of Major Proximal Tubule Cell Culture Models
Transcriptomes of Major Proximal Tubule Cell Culture Models
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DOI：
10.1681/asn.2020010009
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发表时间：
2021-01-01
影响因子：
13.6
通讯作者：
Knepper, Mark A.
中科院分区：
文献类型：
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作者：
Khundmiri, Syed J.;Chen, Lihe;Knepper, Mark A.
背景培养细胞系广泛用于肾近端小管的生理学、病理生理学、毒理学和药理学研究。最适合特定用途的品系取决于所表达的基因。使用RNA测序（RNASeq）的转录组学分析的新工具，使它有可能目录中表达的基因在每个cellline.Methods的14个不同的近端小管细胞系，代表6个物种，生长在可渗透的支持条件下，具体为各自的线。结果在细胞系中表达的转录本与在天然近曲小管中选择性表达的转录本相匹配。负鼠肾（OK）细胞显示出最高的匹配百分比（45%的近端标记基因[TPM阈值515]），猪肾细胞（LLC-PK 1）紧随其后（39%）。对于各种人类系，包括HK-2（26%）和来自啮齿动物肾脏的系，如NRK-52 E（23%），观察到较低的匹配百分比。名义上，来自不同来源的相同OK细胞在近曲小管标记物的表达上存在实质性差异。将细胞系转录组映射到各种近端小管功能（钠和水转运，蛋白质转运，代谢功能，内分泌功能）的基因集表明，不同的细胞系可能是实验建模每种功能的最佳选择。已创建在线资源（https：//esbl.nhlbi.nih.gov/JBrowse/KCT/）以查询细胞系转录组数据。NRK-52 E细胞的蛋白质组学分析证实了许多近曲小管标记蛋白的低表达。然而，一些测试的线是适合于在近端小管中看到的特殊的代谢和运输过程的研究。
Background Cultured cell lines are widely used for research in the physiology, pathophysiology, toxicology, and pharmacology of the renal proximal tubule. The lines that are most appropriate for a given use depend upon the genes expressed. New tools for transcriptomic profiling using RNA sequencing (RNASeq) make it possible to catalog expressed genes in each cell line.Methods Fourteen different proximal tubule cell lines, representing six species, were grown on permeable supports under conditions specific for the respective lines. RNA-Seq followed standard procedures.Results Transcripts expressed in cell lines variably matched transcripts selectively expressed in native proximal tubule. Opossum kidney (OK) cells displayed the highest percentage match (45% of proximal marker genes [TPMthreshold515]), with pig kidney cells (LLC-PK1) close behind (39%). Lower-percentage matches were seen for various human lines, including HK-2 (26%), and lines from rodent kidneys, such as NRK-52E (23%). Nominally, identical OK cells fromdifferent sources differed substantially in expression of proximal tubule markers. Mapping cell line transcriptomes to gene sets for various proximal tubule functions (sodium and water transport, protein transport, metabolic functions, endocrine functions) showed that different lines may be optimal for experimentallymodeling each function. An online resource (https:// esbl.nhlbi.nih.gov/JBrowse/KCT/) has been created to interrogate cell line transcriptome data. Proteomic analysis of NRK-52E cells confirmed low expression of many proximal tubule marker proteins.Conclusions No cell line fullymatched the transcriptome of native proximal tubule cells. However, some of the lines tested are suitable for the study of particularmetabolic andtransport processes seen in theproximal tubule.