Heterogeneity in hematopoietic stem cell enables adaptation to the aged microenvironment

Aging reshapes hematopoietic stem cell (HSC) behavior, yet how pre-existing heterogeneity forecasts clonal performance in aged microenvironments remains unclear. Using cellular barcoding and single cell-RNA-seq to longitudinally sample shared sister-clones across hetero- and homochronic transplants in mice, we quantify (i) intra- and inter-cellular transcriptional heterogeneity in young and old HSC, (ii) differential self-renewal and clonal fitness of HSC in reconstituted hematopoiesis, and (iii) clone-wise associations between pre-existing programs and fitness in aging contexts via predictive machine learning models. Old HSC exhibit greater heterogeneity and rates of generation of heterogeneity, driven by specific gene sets with known roles in HSC fitness. Old HSC exhibit higher self-renewal in old relative to young hosts, likely reflecting adaptation over life to the aged altered niche. Clones with higher fitness in aged mice are enriched for signatures of quiescence, genome integrity/DNA repair, and inflammaging when compared to lower-fitness clones before transplantation. Pre-existing heterogeneity predicts both higher clone fitness and higher self-renewal in the old hosts after transplantation, providing greater phenotypic variability for selection of adaptive clones. Together, these data argue that intrinsic aging encodes variable clonal ‘starting positions’ that interact with niche age to shape hematopoietic output. Our results contextualize recent clonal tracing studies in native hematopoiesis and aging—where lineage output is clonally restricted and age-expanded clones persist—and extend them by prospectively linking baseline HSC state variation to subsequent fitness under aged conditions. These findings nominate actionable, pre-transplant molecular predictors of clonal performance and suggest strategies to modulate aging programs to rebalance hematopoiesis.