Single cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis

Abstract

The kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. Defects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the “primed” and “self-renewing” sub-populations of nephron progenitors, with increased expression of the cell cycle related genes Birc5, Cdca3, Smc2 and Smc4 in “primed” nephron progenitors. Augmented Birc5 expression was also detected in immature distal tubules and a sub-set of ureteric bud cells, suggesting that Birc5 might be a novel key molecule required for early events of nephron patterning and tubular fusion between the distal nephron and the collecting duct epithelia.

Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development

“…In addition to the published enhancer of Eya1 (Park et al, 2012) ( Supplemental figure 4 ), a closing DAR in one of Eya1’s introns ( Figure 3A,B ) encompasses a region predicted to have enhancer activity on the Eya1 gene in mouse neural progenitor and granulocyte-monocyte progenitor cells (Gao and Qian, 2020). In line with a reduction in enhancer activity, we have previously observed that expression of Eya1 is decreased in differentiating nephron progenitors using E14.5 single-cell RNA sequencing (scRNA-seq; Figure 3E ) (Bais et al, 2020). This potential enhancer also contains transcription factor footprints for Homeobox D10 (Hoxd10) within its peak; Hoxd10 is a transcription factor that is essential for differentiation and integration of nephron progenitors during mesenchymal-to-epithelial transitions (MET) (Yallowitz et al, 2011) and whose overexpression has been associated with Wilms tumor in humans (Royer-Pokora et al, 2010).…”

“…Single-cell gene expression data was processed for a previous manuscript (BioRxiv https://www.biorxiv.org/content/10.1101/2020.09.16.300293v1) (Bais et al, 2020), and was retrieved from the Gene Expression Omnibus (GEO ID GSE158166). Processed data incorporated into ( Figure 3) include cell types, gene expression levels, low-dimensional (tSNE) embeddings, and pseudotime annotations relative to the trajectory established between clusters of proliferating and differentiating nephron progenitors.…”