Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [Hi-C]

Loss of regeneration is a key feature of aging organs, often linked to stem cell exhaustion. Skeletal muscle stem cells (MuSCs) undergo age-related numerical and functional decline, contributing to reduced regenerative potential. Using low-input multi-omics, we systematically profiled the epigenome, transcriptome, and 3D genome of MuSCs from individual mice across 3 age groups (young, old, and geriatric) and both sexes. MuSCs from aged mice, particularly males, exhibited early alterations (evident in old), including enhanced proinflammatory signaling with loss of cell identity. Late alterations (evident in geriatric) included heightened inflammation, widespread enhancer activation, and 3D genome rewiring. Proinflammatory pathways were enriched for interferon signaling and correlated with endogenous retroviral expression and NF?B activity. Late-stage epigenome and 3D genome rewiring reflected downstream degenerative changes in muscle organization, response to cytokines, and loss of myogenic identity. These progressive molecular shifts may explain the aggravated proliferative deficit observed in MuSCs during aging. Overall design: Hi-C of sorted MuSCs was performed with a modified low cell number protocol using the Arima-HiC kit (Arima Genomics). ~800,000 MuSCs from 3-4 male mice was used per replicate ((young (n=2), old (n=2), and geriatric (n=4) replicates).