Rhythmic nephron formation in the developing kidney [E17_NZC_scRNAseq]

The mammalian kidney achieves massive parallelization of function by exponentially duplicating nephron-forming niches during development. Each niche caps a tip of the ureteric bud epithelium (the future urinary collecting duct tree) as it undergoes branching morphogenesis, while nephron progenitors within niches balance self-renewal and differentiation to early nephron cells. Nephron formation rate approximately matches branching rate over a large fraction of mouse gestation, yet the nature of this apparent pace-maker is unknown. Here we correlate spatial transcriptomics data with branching 'life-cycle' to discover rhythmically alternating signatures of nephron progenitor differentiation and renewal across Wnt, Hippo/Yap, retinoic acid (RA), and other pathways. Our data bring temporal resolution to the renewal vs. differentiation balance in the nephrogenic niche and inform new strategies to achieve self-sustaining nephron formation in synthetic human kidney tissues. Overall design: single cell RNA-sequencing of isolated nephrogenic zone cells from pooled E17 wild-type CD1 kidneys.

哺乳动物肾脏在发育进程中通过指数级扩增肾单位形成微环境（niche），实现功能的大规模并行化。在分支形态发生过程中，每个微环境均覆盖于输尿管芽上皮（ureteric bud epithelium，即未来的泌尿收集管树状结构）的顶端；与此同时，微环境内的肾单位祖细胞需平衡自我更新与向早期肾单位细胞的分化进程。在小鼠妊娠的大部分阶段，肾单位形成速率与分支速率大致相当，但这一表观调控节律的本质目前仍不明晰。本研究将空间转录组学（spatial transcriptomics）数据与分支‘生命周期’进行关联分析，最终在Wnt、Hippo/Yap、视黄酸（retinoic acid, RA）等信号通路中，发现了肾单位祖细胞分化与更新的节律性交替特征。本研究的数据为肾生成微环境中的自我更新与分化平衡问题提供了时序分辨率层面的解析，并为在人工合成人类肾脏组织中实现可持续的肾单位形成提供了新的策略思路。实验整体设计：对混合的胚胎第17天（embryonic day 17, E17）野生型CD1小鼠肾脏的分离肾生成区细胞进行单细胞RNA测序（single cell RNA-sequencing）。