Background Single-cell genomics techniques are revolutionizing our ability to characterize complex tissues. By contrast, the techniques used to analyze renal biopsy specimens have changed little over several decades. We tested the hypothesis that single-cell RNA-sequencing can comprehensively describe cell types and states in a human kidney biopsy specimen.

Methods We generated 8746 single-cell transcriptomes from a healthy adult kidney and a single kidney transplant biopsy core by single-cell RNA-sequencing. Unsupervised clustering analysis of the biopsy specimen was performed to identify 16 distinct cell types, including all of the major immune cell types and most native kidney cell types, in this biopsy specimen, for which the histologic read was mixed rejection.

Results Monocytes formed two subclusters representing a nonclassical CD16+ group and a classic CD16− group expressing dendritic cell maturation markers. The presence of both monocyte cell subtypes was validated by staining of independent transplant biopsy specimens. Comparison of healthy kidney epithelial transcriptomes with biopsy specimen counterparts identified novel segment-specific proinflammatory responses in rejection. Endothelial cells formed three distinct subclusters: resting cells and two activated endothelial cell groups. One activated endothelial cell group expressed Fc receptor pathway activation and Ig internalization genes, consistent with the pathologic diagnosis of antibody-mediated rejection. We mapped previously defined genes that associate with rejection outcomes to single cell types and generated a searchable online gene expression database.

Conclusions We present the first step toward incorporation of single-cell transcriptomics into kidney biopsy specimen interpretation, describe a heterogeneous immune response in mixed rejection, and provide a searchable resource for the scientific community.

背景技术单细胞基因组学技术正在革新我们表征复杂组织的能力。相比之下，过去几十年来，用于分析肾脏活检标本的技术几乎没有改变。我们测试了单细胞RNA测序可以全面描述人类肾脏活检标本中细胞类型和状态的假说。

方法我们通过单细胞RNA测序从一个健康的成年肾脏和一个肾脏移植活检组织中生成了8746个单细胞转录组。对该活检标本进行了无监督的聚类分析，以确定该活检标本中16种不同的细胞类型，包括所有主要的免疫细胞类型和大多数天然肾细胞类型，其组织学读数混合排斥。

结果单核细胞形成两个亚群，分别代表非经典CD16 +组和经典CD16-组，它们表达树突状细胞成熟标记。两种单核细胞亚型的存在通过独立移植活检标本的染色进行验证。健康肾脏上皮转录组与活检标本同行的比较确定了排斥反应中新的段特异性促炎反应。内皮细胞形成三个不同的亚群：静息细胞和两个活化的内皮细胞群。一个激活的内皮细胞组表达了Fc受体途径激活和Ig内在化基因，与抗体介导的排斥反应的病理诊断一致。

结论我们提出了将单细胞转录组学纳入肾脏活检标本解释的第一步，描述了混合排斥反应中的异质免疫反应，并为科学界提供了可搜索的资源。