Long-term clonal analysis using stochastic models reveals heterogeneity and quiescence of hematopoietic stem cells

Hematopoietic stem cells (HSCs) maintain lifelong production of blood by balancing self-renewal and differentiation. However, certain aspects of their divisional dynamics, namely the role of quiescence and the intrinsic heterogeneity of the HSC pool, are not completely understood. High-resolution clonal tracking provides a powerful resource to investigate such dynamics as the data captures patterns of clonal persistence, dilution and late clonal emergence. Here, we apply mechanistic mathematical modeling to longitudinal clonal data from non-human primates to explore structural requirements that underlie the observed dynamical patterns. We show that models treating HSCs as a single, homogeneous population can explain the gradual loss of clonal diversity, but fail to reproduce clone size distributions and the long-term persistence of small and late-appearing clones. To address this, we propose a stochastic, two-compartment model in which HSCs transition reversibly between an actively cycling state and a quiescent, potentially niche-bound state. Compared to the simpler one-compartment model, this advanced framework provides a substantially improved fit for different metrics, consistently captures clone size distributions and explains the delayed activation and sustained coexistence of small and large clones. These results provide quantitative evidence that heterogeneity within the HSC pool, particularly the existence of a reversible quiescent state, is critical to account for clonal aspects of long-term hematopoiesis. Our findings highlight how clonal data can uncover underlying regulatory mechanisms and supports a central role for niche-mediated HSC quiescence in maintaining stable and diverse blood production over time. • Clonal data offers a robust approach to explore hematopoietic stem cell dynamics. • Homogeneous HSC population cannot reproduce observed long-term clonal patterns. • Niche-mediated quiescence improves model fit across different clonality metrics. • Model results suggest reversible transition between HSC quiescence and activation.