ATP-Citrate Lyase-Dependent Epigenetic Control of Renal Collecting Duct Morphogenesis

 

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ATP-Citrate Lyase-Dependent Epigenetic Control of Renal Collecting Duct Morphogenesis

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Ziyi
Zhao
Ziyi Zhao nephox@sjtu.edu.cn Xin Hua Hospital of Shanghai Jiao Tong University School of Medicine Department of Internal Medicine Shanghai China *
Xuantong Dai xuantongdai@163.com Xin Hua Hospital of Shanghai Jiao Tong University School of Medicine Department of Internal Medicine Shanghai China -
Gengru Jiang jianggeng-ru@hotmail.com Xin Hua Hospital of Shanghai Jiao Tong University School of Medicine Department of Internal Medicine Shanghai China -
Fujun Lin linfujun@xinhuamed.com.cn Xin Hua Hospital of Shanghai Jiao Tong University School of Medicine Department of Internal Medicine Shanghai China -
 
 
 
 
 
 
 
 
 
 
 

Abnormal development of the renal collecting system contributes to congenital anomalies of the kidney and urinary tract (CAKUT), a major cause of pediatric end-stage renal disease. ATP-citrate lyase (ACLY) is an enzyme that transfers acetyl-CoA from the mitochondria to the nucleus, where it serves as an essential substrate for histone acetylation. Given its abundant expression in renal collecting duct cells, we hypothesized that ACLY plays a critical role in the epigenetic regulation of collecting duct morphogenesis.

To explore the role of ACLY in renal development, we generated Acly knockout mice and examined renal morphology and function. We further performed single-cell RNA sequencing (scRNA-seq) and CUT&Tag-seq analyses on collecting duct cells to characterize transcriptional and epigenetic alterations associated with ACLY deficiency.

Six-week-old Acly knockout mice displayed reduced kidney weight, nephron number, and structural abnormalities in the collecting system. Immunostaining showed decreased expression of aquaporin-2 (AQP2) and several ion channels, suggesting impaired collecting duct differentiation. Single-cell transcriptomic analysis revealed a significant downregulation of ribosomal protein genes in Acly-deficient collecting duct cells, while CUT&Tag-seq demonstrated reduced histone acetylation at ribosomal gene promoters. These findings indicate that ACLY is essential for maintaining ribosomal gene transcription and epigenetic homeostasis in collecting duct cells.

ACLY-mediated acetyl-CoA transport supports histone acetylation and ribosomal gene expression required for proper collecting duct development. Loss of ACLY disrupts ribosomal biogenesis and ion channel synthesis, leading to structural and functional defects that may underlie CAKUT. Our study identifies an epigenetic mechanism by which cellular metabolism regulates renal morphogenesis.

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