Prdm15 deficiency perturbs hematopoietic stem and progenitor cell homeostasis.

Single‐Cell Analyses Reveal Dysregulation of Ribosomal Protein Genes During Hematopoietic Stem and Progenitor Cell Aging

Hematopoietic stem and progenitor cells (HSPCs) sustain lifelong blood production, yet the molecular mechanisms underlying their functional decline with age remain incompletely understood. Understanding how aging alters the transcriptomic landscape of HSPCs is critical to uncovering the origins of immune system aging. We performed a comprehensive single‐cell RNA sequencing analysis integrating over 300,000 bone marrow‐derived HSPCs from 50 healthy individuals spanning 19 to 84 years of age. Aging was associated with immune lineage skewing, marked by increased myeloid and decreased lymphoid output in both bone marrow and peripheral blood. Subtle increases in HSCs, MEPs, and myeloid progenitors alongside reductions in lymphoid progenitors were already evident in aged bone marrow, suggesting that lineage bias is encoded at the progenitor level. Age‐associated transcriptional changes included extensive upregulation of ribosomal genes encoding small (RPS11, RPS12, RPS23) and large (RPL9, RPL19, RPL24) cytoplasmic ribosomal subunit proteins, as well as pro‐inflammatory mediators (IL1B, IL18, TGFB1, S100A8). Enrichment analysis identified mitochondrial function, ribosome biogenesis, chromatin remodeling, and inflammatory signaling as key ontologies disrupted during HSPC aging. Our study identifies molecular signatures of systemic aging rooted in bone marrow HSPCs and suggests that dysregulated ribosomal protein gene expression is an under‐appreciated hallmark of hematopoietic stem cell aging.

[CHAF1A sustains hematopoietic stem cell stemness by enhancing the activity of the NF-Y transcription factor family].

Abstract A005: Investigating the role of stabilin-2 in hematopoietic stem and progenitor cell emergence and migration in zebrafish

Hematopoietic stem cell transplantation is a critical yet high risk therapeutic treatment for patients with blood and immune disorders, including those with cancer where the bone marrow can be severely compromised due to malignancy, intensive chemotherapy and radiation. Despite its potential to restore hematopoietic function and immune health, the procedure leaves patients immunocompromised and vulnerable to dangerous infections until the donor hematopoietic stem and progenitor cells (HSPCs) engraft in the recipient’s bone marrow niche and regenerate their blood and immune system. Recently, we identified a conserved gene expression signature unique to sinusoidal endothelial cells of HSPC niches in fish and mammals, which includes specific membrane trafficking machinery and the scavenger receptor, Stabilin-2 (stab2). In other cellular contexts, stab2 is known to engage in both cell adhesion and endocytic functions. To determine the function of stab2 in the niche, we used CRISPR/Cas9 to knock out stab2 in zebrafish embryos and observed fewer HSPCs in the niche of stab2 mutants compared to sibling controls. To determine whether this reduction results from a defect in HSPC formation we used live, high resolution confocal microscopy to quantify the number of HSPCs forming in their site of birth in the Aorta Gonad Mesenpheros. We found no difference in the number of HSPCs that formed in stab2 mutants compared to their sibling controls. This data suggests that other mechanisms (e.g. defects in proliferation or niche migration) lead to fewer HSPCs in the niche in stab2 mutants. Collectively, these observations advance our basic understanding of the HSPC niche and could allow us to inform future clinical strategies to improve HSPC expansion ex vivo. Reema A . Elrefaie, Gwendolyn M. Beacham, Zewde Q . Ingram, Elliott J. Hagedorn. Investigating the role of stabilin-2 in hematopoietic stem and progenitor cell emergence and migration in zebrafish [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Breaking Barriers in the Fight against Rare Cancers; 2026 Jul 18-20; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(14_Suppl):Abstract nr A005.

Geneformer-guided multiomics integration identifies Pbx1 as a network hub of hematopoietic stem cell aging

Hematopoietic stem cells (HSCs) constitute an organized hematopoietic system that undergoes age-related alterations, including increased platelet production and decreased erythropoiesis. The fundamental mechanisms driving these shifts remain incompletely understood. We used single-cell RNA sequencing data to show that old HSCs contain two distinct transcriptional programs: one shared with megakaryocytes and the other reflecting the most primitive HSC state. Developmental time-series profiling further suggests that the acquisition of these programs begins early in life, with the primitive module rising prenatally and megakaryocytic priming emerging after birth. Using a fine-tuned Geneformer (transformer-based deep learning model) to capture higher-order differences between young and old HSCs, coupled with transcriptomic and epigenetic profiling, as well as transcription factor screens, we identified Pbx1 as a key regulator of these age-related transcriptional and differentiation changes. Specifically, Pbx1 suppresses erythroid differentiation by repressing Gata1 expression. These findings provide insight into HSC aging and may inform approaches to modulate age-associated HSC dysfunction.

Perturb-seq identifies co-regulated gene programs shaping hematopoietic stem and progenitor cell function

To sustain blood formation, hematopoietic stem and progenitor cells (HSPCs) coordinate a multitude of cell biological processes, from cell cycle control and stress responses to lineage priming. While many genetic regulators of high-level HSPC function have been identified, how HSPCs coordinate more basal cell biological programs, and how such programs relate to stem cell function, remains incompletely understood. Here we use Perturb-seq to profile the transcriptional consequences of targeting 520 genes by CRISPRi in primary mouse HSPC cultures. We developed an analytical strategy to separate perturbation-induced changes in cell-state abundance and clonal heterogeneity from cell-state-local transcriptional effects. From these local perturbation signatures, we identified 19 gene regulatory programs (GRPs) that are defined by co-regulation in response to genetic perturbation, in contrast to co-expression or human curation, and align well with cell biological processes. By decomposing gene expression data from functional and clinical studies into program activity, we show that GRP activities associate with, and predict, phenotypes such as clonal output after transplantation, as well as survival and drug response in retrospective acute myeloid leukemia (AML) cohorts. Together, our study establishes perturbation-derived co-regulation programs as an interpretable framework for linking genetic regulators, cell-biological processes and stem-cell-associated phenotypes.

RACK1 maintains mouse hematopoietic stem cells by directly binding to and stabilizing LDB1

Single-cell RNA sequencing indicates that adulthood Rack1 deletion in type I interferon-I-responsive cells leads to aberrant lineage-geneset-scores of transcriptional HSCs and the emergence of stressed HSCs, and Mechanistically, RACK1 prevents HSC loss through maintaining the protein level of LDB1.