ULK1, AS A KEY DETERMINANT OF RENAL TUBULE RECOVERY IN CHRONIC KIDNEY DISEASE REVEALED BY SINGLE-CELL ANALYSIS

Chronic kidney disease (CKD) is characterized by progressive kidney function decline, in which irreversible changes in tubular epithelial cells play a central role. We recently reported that dysfunction of AMP-activated protein kinase (AMPK) and associated lipid metabolism impairment are critical in CKD pathogenesis. However, it remains unclear which nephron segments are involved and what mechanisms are responsible for epithelial cell injury and repair driven by these pathways.

To evaluate the transition from tubular epithelial injury to CKD, we employed a folic acid nephropathy model. C57BL/6 mice were administered folic acid, and kidney function and pathology were assessed over time. Kidneys were harvested and analyzed alongside healthy controls using bulk renal RNA sequencing and single-cell RNA sequencing (scRNA-seq) to perform comprehensive single-cell transcriptome analysis. Clustering and pseudotime analyses were conducted to comprehensively elucidate the signaling pathways responsible for the progression from cellular injury to repair or failure.

Kidney function declined rapidly within two weeks after folic acid administration and partially recovered thereafter. By four weeks, injury had stabilized and CKD pathology was established. Bulk RNA-seq at four weeks revealed increased interferon (IFN) signaling and decreased LKB1-AMPK signaling. scRNA-seq identified a novel cell cluster exclusively present in CKD kidneys, exhibiting features of proximal tubules while expressing genes typical of thick ascending loop of Henle (TAL) and distal tubule segments (e.g., Umod, Slc12a3, Slc12a1). This cluster likely represents “naive” tubular epithelial cells that have dedifferentiated post-injury. Pseudotime analysis focusing on this cluster and proximal tubule cells demonstrated that AMPK signaling, particularly Unc-51-like kinase (ULK1) -AMPKγ signaling involved in energy sensing, is critical for determining the fate of dedifferentiated epithelial cells.

Following CKD-inducing injury, proximal tubular cells dedifferentiate into naive tubular cells exhibiting gene expression patterns reminiscent of TAL and distal tubules. The repair process of these naive tubular cells is regulated by IFN signaling and ULK1-AMPK signaling within tubular epithelium, highlighting potential therapeutic targets for enhancing tubular repair in CKD.