Hepatocyte nuclear factor-1β shapes the energetic homeostasis of kidney tubule cells

Energetic metabolism controls key steps of kidney development, homeostasis, and epithelial repair following acute kidney injury (AKI). Hepatocyte nuclear factor-1 beta (HNF-1 beta) is a master transcription factor that controls mitochondrial function in proximal tubule (PT) cells. Patients with HNF1B pathogenic variant display a wide range of kidney developmental abnormalities and progressive kidney fibrosis. Characterizing the metabolic changes in PT cells with HNF-1 beta deficiency may help to identify new targetable molecular hubs involved in HNF1B-related kidney phenotypes and AKI. Here, we combined H-1-NMR-based metabolomic analysis in a murine PT( )cell line with CrispR/Cas9-induced Hnf1b invalidation (Hnf1b(-/-)), clustering analysis, targeted metabolic assays, and data-mining of published RNA-seq and ChIP-seq dataset to identify the role of HNF-1 beta in metabolism. Hnf1b(-/-) cells grown in normoxic conditions display intracellular ATP depletion, increased cytosolic lactate concentration, increased lipid droplet content, failure to use pyruvate for energetic purposes, increased levels of tricar-boxylic acid (TCA) cycle intermediates and oxidized glutathione, and a reduction of TCA cycle byproducts, all features consistent with mitochondrial dysfunction and an irreversible switch toward glycolysis. Unsupervised clustering analysis showed that Hnf1b(-/-) cells mimic a hypoxic signature and that they cannot furthermore increase glycolysis-dependent energetic supply during hypoxic challenge. Metabolome analysis also showed alteration of phospholipid biosynthesis in Hnf1b(-/-) cells leading to the identification of Chka, the gene coding for choline kinase alpha, as a new putative target of HNF-1 beta. HNF-1 beta shapes the energetic metabolism of PT cells and HNF1B deficiency in patients could lead to a hypoxia-like metabolic state precluding further adaptation to ATP depletion following AKI.