Inactivation of transcription factor HNF-1ß with CRISPR/Cas9 induces epithelial-mesenchymal transition

Hepatocyte nuclear factor-1ß (HNF-1ß) is a tissue-specific transcription factor that is essential for the development of the kidney. Mutations of HNF-1ß produce autosomal dominant tubulointerstitial kidney disease (ADTKD) characterized by tubular cysts, renal fibrosis, and progressive decline in kidney function. To understand the functions of HNF-1ß, we generated HNF-1ß-deficient mIMCD3 renal epithelial cells. Gene editing with CRISPR/Cas9 was used to delete exon 1 of HNF-1ß by non-homologous end joining (NHEJ). We performed RNA-seq on three independent HNF-1ß-deficient mIMCD3 cell lines and three paired control cell lines. Our RNA-seq of HNF-1ß-deficient cells showed upregulation of 1,135 genes and repression of 759 genes compared to control cells. Pathway analysis revealed that fibrosis and epithelial-mesenchymal transition (EMT) pathways were highly activated in HNF-1ß-deficient cells. We conclude that loss of HNF-1ß in renal epithelial cells leads to the activation of a transcriptional network that induces EMT and aberrant TGFß signaling. Targeting this network may inhibit fibrosis in ADTKD and other chronic kidney diseases. Overall design: RNA-seq of three independent HNF-1ß-deficient mIMCD3 cell lines and three paired control cell lines.