A cross-species single-cell kidney epigenome atlas reveals epithelial-dominant aging-like states in disease.

Epigenetic aging is a hallmark of chronic diseases. While such epigenetic changes can arise following tissue injury, the cell types most affected remain largely unknown. Here we built a cross-species single-cell multiomics atlas of DNA methylation, chromatin accessibility and transcription profiles from healthy, injured (human) and aged (mouse) kidneys. We found that tubular epithelial cells in diseased kidneys exhibit pronounced accelerated epigenetic aging and showed that this pathological state mirrors transcriptional trajectories observed during aging, driven by preferential dysregulation of lineage-specific genes lacking CpG islands. Spatially, these epigenetic changes mapped to pathological niches of unresolved repair. Co-profiling single-cell DNA methylation and 3D genome architecture revealed that epithelial repair states in disease undergo significant higher-order genome reorganizations, alongside activation of genes associated with renal decline. Together, our findings characterize a loss of epigenetic repression within coordinated three-dimensional chromatin structures and reduced local methylome integrity, which compromises epithelial cell identity during aging and impedes repair.