Angelica Varesi, Murtaza S. Nagree, Isabella Di Biasio, Andy G.X. Zeng, Sayyam Shah, Michael Zhang, Hyerin Kim, Alex Murison, Rohail Badami, Olga Gan, Liqing Jin, Jessica McLeod, Sheela A. Abraham, Mark D. Minden, Andréa Arruda, Igor Novitzky-Basso, Jonas Mattsson, John E. Dick, Stephanie Z. Xie
Long-term hematopoietic stem cells (LT-HSC) maintain lifelong hematopoiesis while preserving the stem cell compartment through self-renewal. The human LT-HSC compartment is molecularly and functionally heterogeneous and also varies across ontogeny. Dissecting the molecular basis for this variation is impeded by the paucity of immunophenotypic markers to resolve LT-HSC heterogeneity. Here, we identified ATPase plasma membrane calcium transporting 1 (ATP2B1/PMCA1) as a cell surface marker that is heterogeneously expressed by CD49f + LT-HSC from fetal to adult hematopoiesis. ATP2B1 immunophenotypic expression stratified human CD49f + LT-HSC from fetal liver, neonatal cord blood, and adult mobilized peripheral blood sources into functionally distinct subpopulations in single-cell (sc) clonogenic assays. CD49f + ATP2B1 + LT-HSC exhibited superior long-term repopulation and self-renewal capacities in vivo compared to CD49f + ATP2B1 – LT-HSC. Molecular profiling by scMultiome and immunofluorescence microscopy point to enrichment of an HSC self-renewal program that includes the TFEB–endolysosomal axis in CD49f + ATP2B1 + LT-HSC. Our study provides a framework to dissect the heterogeneous molecular programs in LT-HSC.