Regulation of PKM2 expression and function by GLIS3 during metabolic reprogramming in polycystic kidneys

Deficiency in GLI-similar 3 (GLIS3) in humans and mice causes polycystic kidney disease (PKD). We previously reported that Glis3-knockout (KO) kidneys undergo metabolic reprogramming and remain more reliant on aerobic glycolysis. Here, to understand the mechanism by which GLIS3 controls this process, we analyzed its role in regulating glycolytic gene expression using transcriptomics and cistromics. Transcriptomic analysis revealed increased expression of key glycolytic genes and reduced expression of several gluconeogenic genes in Glis3-KO compared with wild-type kidneys. Chromatin immunoprecipitation followed by sequencing analysis showed that many of these genes were directly regulated by GLIS3 in coordination with the transcription factor, HNF-1B. Pkm emerged as a key upregulated glycolytic GLIS3 target gene, which via alternative splicing generates two protein isoforms, PKM1 and PKM2. Expression of Pkm and the dimeric form of PKM2, which promotes aerobic glycolysis, was elevated in Glis3-KO kidneys, whereas exogenous GLIS3 expression in primary Glis3-KO renal epithelial cells suppressed Pkm expression. Phosphorylation of PKM2 at Y105 and S37, which stimulate dimer formation, nuclear localization and aerobic glycolysis, is increased in Glis3-KO kidneys, consistent with a role for PKM2 in metabolic reprogramming and cyst formation. Consistent with this, siRNA-mediated knockdown of PKM2 in Glis3-KO renal epithelial cells suppressed spheroid growth and glycolytic activity. In addition, pharmacological inhibition of PKM2 with compound 3K in GLIS3-deficient spheroid cultures and Glis3-KO kidneys significantly reduced spheroid size, cyst number and cystic area. Our study identifies GLIS3 as a novel regulator of glycolysis and PKM2 function, whose dysregulation contributes to metabolic reprogramming and cystogenesis in Glis3-KO kidneys.