Modeling Cell Population Dynamics in Early Hematopoiesis Reveals Mechanisms of Myeloid Bias Mediated By NFκB-Dysregulation

Alterations in hematopoiesis are associated with immune dysregulation and perturbations in NFκB signaling. Aging, for example, is correlated with increased myeloid and decreased lymphoid cell output, as well as elevated levels of NFκB activity in hematopoietic stem and progenitor cells (HSPC) and inflammatory cytokines in the bone marrow. Further, patients with myelodysplastic syndrome (MDS) show increased expression of components of the NFκB signaling pathway in HSPC and mesenchymal cells, in addition to increased production of inflammatory cytokines. Despite being implicated in these contexts, it remains unknown how elevated NFκB signaling might affect the production and abundance of certain HSPC subsets. Here we interrogate how increased NFκB activity may alter the developmental dynamics within the HSPC compartment to give rise to a biased progenitor population.

To investigate how myeloid cell overproduction arises in the bone marrow, we developed mathematical models to recapitulate HSPC population dynamics. To address the role of NFκB in the process, we leveraged data from the IκB^– mouse model (Nfkbia^+/- Nfkbib^-/- Nfkbie^-/-), which has constitutively elevated NFκB activity. Cell counts of HSPC subpopulations demonstrated a myeloid biased alteration in multipotent progenitor (MPP) abundances in the IκB^– mouse, reminiscent of what occurs with aging. Fitting the cell population dynamics model to these data suggested that accelerated differentiation of Short-Term HSC (STHSC) with skewing in their fate commitment is insufficient to account for the increase in MPP2 and MPP3 cells. To explore additional mechanisms contributing to myeloid bias, we utilized single-cell RNA sequencing (scRNAseq) data from IκB^– versus control HSPC. We first used pseudotime reconstruction to position cells along a continuous differentiation trajectory from HSCs to erythrocyte-megakaryocyte- (MPP2), myeloid- (MPP3), and lymphoid- (MPP4) primed progenitors and then fit these data to a partial differential equation (PDE) model of population dynamics. This analysis suggested not only a loss of lymphoid fate specification amongst HSC but also an increase in the expansion of early myeloid primed cells to produce more MPP3 cells. Transplantation of wildtype HSPC into a lethally irradiated IκB^– mouse additionally showed that an inflamed microenvironment is sufficient to drive myeloid bias. Utilizing the same mathematical models to describe these data revealed similar perturbations in population dynamics of the transplanted HSPC. Finally, the scRNAseq pseudotime analysis identified differentially expressed genes along the differentiating lineages that indicated decreased HSC commitment towards the lymphoid fate and increased proliferation of early myeloid primed cells, supporting the model predictions.

We next leveraged scRNAseq datasets from HSPC isolated from MDS patients and healthy aged-matched controls to explore if these features of NFκB-mediated immune dysregulation are clinically relevant. These data demonstrated myeloid bias in progenitors at the transcriptional level and suggested elevated NFκB signaling amongst the HSPC from MDS patients. Finally, applying the same mathematical modeling and gene expression analyses developed for the murine datasets revealed common perturbations in developmental dynamics of MDS HPSC as the IκB^– mouse models. These analyses motivate further study of the downstream consequences of immune dysregulation on hematopoiesis and the identification of perturbations in NFκB signaling in pathological contexts.