Enhancer Rewiring Orchestrates Inflammation and Loss of Cell Identity During Muscle Stem Cell Aging
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. At baseline, young male MuSCs showed reduced expression of cell cycle-related mRNAs. In aged mice, particularly males, MuSCs exhibited early alterations (emerging during the transition from young to old age) including enhanced proinflammatory signaling, and loss of cell identity. Late alterations (emerging during the transition from old to geriatric age) included heightened inflammation, widespread enhancer activation, and extensive 3D genome rewiring. Proinflammatory pathways were enriched for interferon signaling and correlated with endogenous retroviral expression and NFκB activity. Late-stage epigenome and 3D genome rewiring reflected downstream degenerative changes in muscle organization, response to cytokines, and loss of myogenic identity. Thus, progressive molecular shifts may explain the aggravated proliferative deficit and functional impairment observed in MuSCs during aging.
Authors
- Na Yang (ORCID: https://orcid.org/0000-0002-3292-7156)
- Thomas A. Rando (ORCID: https://orcid.org/0000-0001-5843-8564)
- Changyou Shi
- Qiong Meng (ORCID: https://orcid.org/0000-0002-8378-9021)
- Chang‐Yi Cui (ORCID: https://orcid.org/0000-0002-9856-9427)
- Christopher Dunn (ORCID: https://orcid.org/0000-0001-7899-0110)
- James R. Occean (ORCID: https://orcid.org/0000-0002-6823-6381)
- Payel Sen (ORCID: https://orcid.org/0000-0003-2809-0901)
- Supriyo De (ORCID: https://orcid.org/0000-0002-2075-7655)
- Jianlin Jack Cheng (ORCID: https://orcid.org/0000-0003-0305-2853)
- Nirad Banskota (ORCID: https://orcid.org/0009-0000-5511-8346)
- Frimpong Boadu (ORCID: https://orcid.org/0000-0002-4464-6191)
- Vittorio Sartorelli (ORCID: https://orcid.org/0000-0002-9284-3675)
- Ling Liu (ORCID: https://orcid.org/0000-0002-0496-9551)
- Lin Wang (ORCID: https://orcid.org/0000-0002-2148-1929)
- Jinshui Fan
- Jen‐Hao Yang (ORCID: https://orcid.org/0009-0004-4320-0843)
- Evelyn Pizano
Institutions
- University of California, Los Angeles (US)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (US)
- Institute on Aging (US)
- National Institute on Aging (US)
- Broad Center (US)
- University of Missouri (US)
Publication Details
- Journal
- Aging Cell
- Published
- 2025-11-14
- DOI
- https://doi.org/10.1111/acel.70289
- Primary Topic
- Muscle Physiology and Disorders
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Science Foundation
- U.S. Department of Health and Human Services
- National Institutes of Health
- National Institute on Aging
- National Institute of Arthritis and Musculoskeletal and Skin Diseases