Proximal tubular cells (PTCs) are the most abundant cell type in the kidney. PTCs are central to normal kidney function and to regeneration versus organ fibrosis following injury. This study used single-nucleus RNA sequencing (snRNAseq) to describe the phenotype of PTCs in renal fibrosis.

Kidneys were harvested from naïve mice and from mice with renal fibrosis induced by chronic aristolochic acid administration. Nuclei were isolated using Nuclei EZ Lysis buffer. Libraries were prepared on the 10x platform, and snRNAseq was completed using the Illumina NextSeq 550 System. Genome mapping was carried out with high-performance computing.

A total of 23,885 nuclei were analyzed. PTCs were found in five abundant clusters, mapping to S1, S1–S2, S2, S2-cortical S3, and medullary S3 segments. Additional cell clusters ("new PTC clusters") were at low abundance in normal kidney and in increased number in kidneys undergoing regeneration/fibrosis following injury. These clusters exhibited clear molecular phenotypes, permitting labeling as proliferating, New-PT1, New-PT2, and (present only following injury) New-PT3. Each cluster exhibited a unique gene expression signature, including multiple genes previously associated with renal injury response and fibrosis progression. Comprehensive pathway analyses revealed metabolic reprogramming, enrichment of cellular communication and cell motility, and various immune activations in new PTC clusters. In ligand-receptor analysis, new PTC clusters promoted fibrotic signaling to fibroblasts and inflammatory activation to macrophages.

These data identify unrecognized PTC phenotype heterogeneity and reveal novel PTCs associated with kidney fibrosis.

近端肾小管细胞 (PTC) 是肾脏中最丰富的细胞类型。PTC 是正常肾功能和再生与损伤后器官纤维化的核心。本研究使用单核 RNA 测序 (snRNAseq) 来描述肾纤维化中 PTC 的表型。

从幼稚小鼠和慢性马兜铃酸诱导的肾纤维化小鼠中采集肾脏。使用 Nuclei EZ Lysis 缓冲液分离细胞核。在 10 x平台上制备文库，并使用 Illumina NextSeq 550 系统完成 snRNAseq。基因组作图是用高性能计算进行的。

总共分析了 23,885 个细胞核。在五个丰富的簇中发现了 PTC，映射到 S1、S1–S2、S2、S2-皮质 S3 和髓质 S3 节段。其他细胞簇（“新 PTC 簇”）在正常肾脏中丰度较低，而在受伤后经历再生/纤维化的肾脏中数量增加。这些簇表现出清晰的分子表型，允许标记为增殖、New-PT1、New-PT2 和（仅在受伤后出现）New-PT3。每个簇都表现出独特的基因表达特征，包括先前与肾损伤反应和纤维化进展相关的多个基因。综合通路分析揭示了新 PTC 簇中的代谢重编程、细胞通讯和细胞运动的丰富以及各种免疫激活。在配体-受体分析中，

这些数据确定了未被识别的 PTC 表型异质性，并揭示了与肾纤维化相关的新型 PTC。