Folliculin deletion in the mouse kidney results in cystogenesis of the loops of Henle via aberrant TFEB activation

The mammalian kidney contains numerous nephrons connected to the collecting ducts, and each nephron consists of a glomerulus, a proximal tubule, the loop of Henle (LoH), and a distal tubule. Folliculin (Flcn) is a causative gene for Birt-Hogg-Dube (BHD) syndrome, which is characterized by a variety of symptoms including renal cysts and cancers. Although deletion of Flcn in the mouse collecting duct has been reported to result in cyst formation, its precise role in the nephron remains unclear. We report here that nephron-specific Flcn knockout mice exhibit cystogenesis along the entire nephron segments, most prominent in the LoH, preceded by an irregularly shaped lumen lined by enlarged epithelia. Single-cell RNA sequencing revealed many upregulated genes, especially in the mutant LoH. These genes include those related to lysosomal activity and mTORC1 activation and are likely targets of TFE3/TFEB. While the double Flcn/Tfe3 knockout only ameliorates the glomerular cysts, the double Flcn/Tfeb knockout dramatically reverses most of the phenotypes along the entire nephron. Thus, Flcn deletion leads to cystogenesis via aberrant TFEB activation. Our findings reveal the essential role of the Flcn-TFEB-mTORC1 signaling pathway in nephron development, particularly in LoH, and shed light on the initial disease state of BHD syndrome. Overall design: To investigate the gene expression profiles upon Flcn deletion in all nephron lineages, scRNA-seq analysis were performed using Flcn heterozygous (Six2Cre; Flcn flox/+) and Flcn homozygous (Six2Cre; Flcn flox/flox) neonatal kidneys (P0).