Single-cell multiomics gene regulatory landscape reveals impaired spermatogonial stem cells and macrophage-driven inflammaging during testicular aging

Testicular aging is a key driver of declining male reproductive health, but a comprehensive understanding of its underlying epigenetic drivers is lacking. To address this, we construct a multiomics aging atlas by integrating single-cell RNA sequencing, single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), and spatial transcriptomics of young and aged mouse testes. Our analysis reveals that altered chromatin accessibility accompanies transcriptional dysregulation and identifies spermatogonial stem cells (SSCs) as the most epigenetically vulnerable population. We further pinpoint ZFX as a consistently downregulated transcription factor in early germ cells, linking its decline to compromised SSC maintenance. In the somatic niche, we define disrupted regulatory networks that underpin impaired blood-testis barrier integrity in Sertoli cells and steroidogenic dysfunction in Leydig cells. Notably, we uncover an aberrant expansion of CD206⁺H2-Eb1^- macrophages that propagates local inflammation via the secreted factor CXCL13, which we demonstrate is sufficient to disrupt the SSC niche. Cross-species analysis identifies conserved aging-associated regulons, including BRCA1 and E2F1. This work provides resources for understanding testicular senescence and nominates ZFX and CXCL13 as potential therapeutic targets for mitigating age-related reproductive decline.