Epigenetically silencing gluconeogenic enzyme PCK1 by EZH2 promotes renal tubulointerstitial fibrosis

Abstract Chronic kidney disease (CKD) is a leading cause of global morbidity. The kidney is a major gluconeogenic organ, and impaired renal gluconeogenesis contributes to CKD, yet the regulatory mechanisms remain poorly understood. Here we show that enhancer of zeste homolog 2 (EZH2), a histone H3K27 trimethyltransferase, epigenetically suppresses renal gluconeogenesis and drives tubulointerstitial fibrosis. Through integrative multi-omics profiling (RNA-seq, CUT&Tag, and single-nucleus RNA-seq), we show that EZH2 directly binds to and deposits H3K27 trimethylation at promoters of gluconeogenic genes in proximal tubular cells, with the most prominent repression observed at phosphoenolpyruvate carboxykinase ( Pck1 ) gene. In fibrotic kidneys, Ezh2 is markedly upregulated in proximal tubules and inversely correlates with Pck1 expression across injury and maladaptive repair states. Genetic ablation or pharmacological inhibition of EZH2 restores PCK1 expression, enhances lactate-to-glucose conversion, and attenuates extracellular matrix deposition and fibrotic marker expression in both cultured tubular cells and mouse models of kidney fibrosis. Stable isotope 13 C-lactate tracing shows that tubular Ezh2 deletion increases the labelling fractions of gluconeogenic intermediates while reducing the labelling fraction of acetyl-CoA, indicating preferential partitioning of lactate-derived carbon towards gluconeogenesis rather than oxidative entry into the tricarboxylic acid (TCA) cycle in vivo. Mechanistically, Pck1 gain- and loss-of-function experiments establish PCK1 as a non-redundant downstream effector of EZH2’s pro-fibrotic action. Collectively, our findings uncover an EZH2–PCK1 epigenetic–metabolic axis that couples histone methylation to gluconeogenic reprogramming and fibrogenesis. This axis may offer a dual therapeutic opportunity for CKD by concurrently restoring metabolic homeostasis and limiting fibrotic progression.