Age-Expanded Inflammatory HSC Subpopulation Found in Human Bone Marrow

As humans age, the blood system loses immune efficiency, oxygen-carrying capacity, and lymphocyte production. These changes originate partly in hematopoietic stem cells (HSCs), which accumulate mutations, expand clonally, and skew toward myeloid output over time. Despite multiple prior human studies, no consensus molecular map of HSC aging existed—partly due to technical variation between datasets.

To address this, the authors integrated six published and one unpublished single-cell or single-nucleus RNA sequencing datasets from 98 donors, annotating 28,989 HSCs using the BoneMarrowMap atlas. Differential gene expression between young (19–37 y.o., n=25) and aged (60–87 y.o., n=15) donors identified 68 upregulated and 29 downregulated genes in aged HSCs. Three AP-1 complex members—JUN, JUNB, and FOSB—were consistently elevated across all datasets in aged donors, implicating stress-activated MAPK signaling and quiescence regulation.

Gene set enrichment analysis (GSEA) confirmed two dominant biological themes in aged HSCs: upregulation of inflammatory pathways (TNF via NFκB, IFN-γ response, AP-1 signaling) and increased quiescence, contrasting with proliferative signatures enriched in young HSCs. Critically, these patterns were not uniformly distributed across all HSCs. Clustering and co-varying neighborhood analysis (CNA) revealed that clusters 0 and 3 harbored the strongest aging and TNF signatures and were significantly more abundant in aged donors, while a proliferative cluster (cluster 4) was enriched in young donors.

To capture heterogeneity beyond clustering, the team applied consensus non-negative matrix factorization (cNMF) to 22 samples with ≥100 HSCs, identifying four meta-gene expression programs (metaGEPs). metaGEP1 co-enriched aging signatures, TNF signaling, and quiescence within a single program—suggesting these are not independent phenomena but are mechanistically linked. SCENIC transcription factor analysis further confirmed AP-1 members as the top differentially active regulators in aged HSC populations.

These findings define an inflammatory-quiescent HSC subpopulation that expands with age, consistent with the 'inflammaging' concept at the stem cell level. The co-occurrence of inflammation and quiescence within one molecular program is notable: it may reflect a protective response that simultaneously limits proliferation-driven mutation accumulation while sustaining low-grade chronic inflammation. This dual state could impair immune and hematopoietic output in older adults. Targeting AP-1 or TNF/NFκB activity specifically in this subpopulation represents a plausible, though still experimental, avenue for longevity interventions.