Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
Nephrology Clinic, National Cancer Center, Goyang, South Korea.
Kidney Int. 2019 Apr;95(4):787-796. doi: 10.1016/j.kint.2018.11.028. Epub 2019 Feb 27.
Bulk-tissue RNA-Seq is increasingly being used in the study of physiological and pathophysiological processes in the kidney; however, the presence of multiple cell types in kidney tissue complicates data interpretation. We addressed the question of which cell types are represented in whole-kidney RNA-Seq data in order to identify circumstances in which bulk-kidney RNA-Seq can be successfully interpreted. We carried out RNA-Seq in mouse whole kidneys and in microdissected renal tubule segments. To aid in the interpretation of the data, we compiled a database of cell-type selective protein markers for 43 cell types believed to be present in kidney tissue. The whole-kidney RNA-Seq analysis identified transcripts corresponding to 17,742 genes, distributed over 5 orders of magnitude of expression level. Markers for all 43 curated cell types were detectable. Analysis of the cellular makeup of mouse and rat kidney, calculated from published literature, suggests that proximal tubule cells account for more than half of the mRNA in a kidney. Comparison of RNA-Seq data from microdissected proximal tubules with data from whole kidney supports this view. RNA-Seq data for cell-type selective markers in bulk-kidney samples provide a valid means to identify changes in minority-cell abundances in kidney tissue. Because proximal tubules make up a substantial fraction of whole-kidney samples, changes in proximal tubule gene expression can be assessed presumptively by bulk-kidney RNA-Seq, although results could potentially be complicated by the presence of mRNA from other cell types.
组织块 RNA-Seq 越来越多地被用于研究肾脏的生理和病理生理过程；然而，肾脏组织中存在多种细胞类型使得数据解释变得复杂。我们提出了一个问题，即哪些细胞类型代表了整个肾脏的 RNA-Seq 数据，以便确定在何种情况下可以成功地解释批量肾脏 RNA-Seq。我们对小鼠整个肾脏和微分离的肾小管段进行了 RNA-Seq。为了帮助解释数据，我们为 43 种被认为存在于肾脏组织中的细胞类型编制了一个细胞类型选择性蛋白标记数据库。整个肾脏的 RNA-Seq 分析鉴定出了 17742 个基因的转录本，这些基因的表达水平跨越了 5 个数量级。所有 43 种经过精心挑选的细胞类型的标记物都可以检测到。根据已发表文献计算的小鼠和大鼠肾脏的细胞组成分析表明，近端肾小管细胞占肾脏 mRNA 的一半以上。从微分离的近端小管获得的 RNA-Seq 数据与整个肾脏的数据的比较支持了这一观点。批量肾脏样本中细胞类型选择性标记物的 RNA-Seq 数据为识别肾脏组织中少数细胞丰度的变化提供了一种有效的方法。由于近端小管构成了大量的整个肾脏样本，因此可以通过批量肾脏 RNA-Seq 来评估近端小管基因表达的变化，尽管由于其他细胞类型的 mRNA 的存在，结果可能会变得复杂。
