The Transcription Factor TCF21 is necessary for adoption of cell fates by Foxd1+ stromal progenitors during kidney development

Normal kidney development requires coordinated interactions between multiple progenitor cell lineages. The Foxd1+ stromal progenitors are critical for normal nephrogenesis and their heterogeneity is increasingly appreciated. However, the molecular mechanisms and trajectories that drive the differentiation of Foxd1+ cells toward the renal stroma, capsule, mesangial cells, renin cells, pericytes, and vascular smooth muscle cells (VSMCs) are poorly understood. Recent work has implicated Tcf21, a mesoderm-specific bHLH transcription factor critical for embryogenesis, in the development of the kidney stroma and perivascular cells. To investigate the role of Tcf21 in Foxd1+ cells, we performed single-cell RNA sequencing (scRNA-seq) on GFP+ cells from E14.5 Foxd1 ^Cre ;Rosa26 ^mTmG ;Tcf21 ^f/f kidneys ( Tcf21 -cKO) and Foxd1 ^Cre controls. Clustering of the entire dataset identified a large stromal population and a smaller representation of non-stromal lineages. Subclustering of stromal cells identified six populations associated with healthy kidney development: medullary/perivascular, proliferating, differentiating nephron, nephrogenic zone-associated, collecting duct-associated, and ureteric. Loss of Tcf21 resulted in a dramatic reduction in the medullary/perivascular, proliferating, nephrogenic zone-associated, and collecting duct-associated stromal subpopulations. Immunostaining confirmed that Tcf21 -cKO has a severe constriction of the medullary and collecting duct-associated stromal space. We identified and validated a cluster unique to Tcf21 -cKO kidneys exhibiting mosaic expression of genes from nephrogenic, proliferating, medullary, and perivascular stromal cells spanning across all pseudotime, suggesting cells halted in the midst of differentiation. These findings underscore a critical role for Tcf21 in the emergence of Foxd1+ derivatives, with loss of Tcf21 leading to a shift in stromal cell fates that results in abnormal kidney development.