Architectural fragility of gene regulatory networks underlies hematopoietic stem cell aging

Abstract

Hematopoietic stem and progenitor cell (HSPC) aging contributes to immune dysfunction and age-associated disease, but its regulatory mechanisms remain unclear. Here, we present the largest single-cell multiome atlas of human circulating HSPCs to date, with >380,000 paired RNA and ATAC profiles across 77 donors. Beyond recapitulating established hallmarks of HSPC aging, we reconstructed a high-resolution gene regulatory network and identified a global rewiring in which stress-response and myeloid transcription factor (TF) programs expand, while self-renewal and lymphoid lineage-defining circuitry collapses. We associate these phenotypes with increased cis-regulatory entropy, including elevated transcriptomic noise, weakened peak-to-gene coupling, and chromatin peak broadening. This rewiring is selective, where TFs with GC-rich, promoter-proximal architectures are preserved or amplified, and complex, distal enhancer-dependent identity networks are eroded. Thus, these findings suggest that progressive entropic destabilization of gene regulatory architecture simultaneously drives stress hyperactivation, myeloid bias, and identity loss in aging HSPCs.