Biology subjects

Shalaby, C.

Publications and source records attributed to Shalaby, C..

4 recordsLinked to original sources

bioRxiv2026

A single cell atlas defines perinatal factors that drive murine bone marrow development

Processes that direct initial colonization and maturation of the bone marrow remain elusive, despite lifelong importance to hematopoiesis. Bone marrow mesenchymal and stromal cell (BMSC) maturation establishes supportive niches prior to hematopoietic stem cell (HSC) recruitment. We define mouse BMSC progenitor identities and temporal emergence in a developmental single cell atlas spanning fetal life through 18 months of age. We clarify Cxcl12-abundant reticular (CAR) cell and osteoblast development, including temporal emergence of signaling modalities that direct HSC quiescence and regenerative capacity. CAR cells are absent until birth, with a developmental block during fetal maturation related to transcriptional changes during perinatal life. Temporal changes in Early B Cell Factor (Ebf) 1-3 expression and activity correlate with CAR formation and niche establishment, including Ebf2 repression and induction of Ebf3 activities that direct metabolic changes. Changes in systemic physiology underlie these transcriptional changes, including perinatal induction of lipid metabolism, inflammation, and hypoxic signaling. These systemic factors direct CAR cell emergence after birth, providing temporal and developmental resolution underlying the colonization and maturation of the bone marrow environment.

developmental biology↗

bioRxiv2025

Tropomyosin 1 promotes platelet adhesion and clot contraction separate from its roles in developmental hematopoiesis

Genome-wide associations studies (GWAS) have linked the Tropomyosin 1 (Tpm1) gene locus to quantitative blood trait variation, but related mechanisms are unclear. Tpm1 encodes an actin-binding protein that stabilizes actin filaments and influences cell adhesion, signaling, and actomyosin contractility. Murine Tpm1 deficiency enhances embryonic hemogenic endothelial cell specification, but it was unclear if these effects extended to postnatal hematopoiesis. We used Cdh5Cre or VavCre models to conditionally ablate Tpm1 in endothelium or hematopoietic cells. Both models produced knockout mice in normal Mendelian ratios with complete Tpm1 ablation in postnatal blood. Endothelial Tpm1 deletion increased hemogenic endothelial cell specification, but did not change hematopoietic progenitor cell production nor adult blood counts. This suggested separate roles for Tpm1 in the embryonic and adult blood systems. GWAS suggested genetic architecture specifically linking decreased TPM1 expression to increased platelet count. We examined platelet lifespan and function to explain these findings. Tpm1KO increased platelet lifespan and diminished adhesion to fibronectin and fibrinogen. Decreased platelet clearance could explain increased platelet count in GWAS. Platelet fibrin binding is necessary for blood clot contraction, which reduces vascular occlusion following initial hemostasis. Tpm1KO reduced clot contraction and enhanced clot formation with worsened vascular occlusion in a ferric chloride-induced stroke model. These findings reveal a new role for Tpm1 in platelet function, offering insight into how cytoskeletal regulation impacts human platelet traits and pointing to novel targets to modify stroke risk and thrombotic disease.

cell biology↗

bioRxiv2025

Multimodal analysis of in vitro hematopoiesis reveals blood cell-specific genetic impacts on complex disease traits

In vitro hematopoiesis systems can be used to define mechanisms for blood cell formation and function, produce cell therapeutics, and model blood cell contributions to systemic disease. Hematopoietic progenitor cell (HPC) production remains inefficient, precluded by knowledge gaps related to specification and morphogenesis of specialized hemogenic endothelial cells, which undergo an endothelial-to-hematopoietic transition (EHT) to form HPCs. We elected to define changes in gene expression and chromatin organization during HPC formation to reveal regulatory mechanisms. Using paired single cell RNA/ATAC sequencing together with Hi-C, we profiled cells before and after EHT. Pathway analysis and pseudotime inferences confirmed a continuum of stromal and endothelial cells undergoing development into HE cells and lineage-based HPCs in vitro. In these cell types, we characterize cis-regulatory elements and transcriptional regulatory activities that facilitate EHT and HPC homeostasis, including for SNAI1, SOX17, TGF{beta}, STAT4, as well as for GFI1b and KLF1 in megakaryocyte- and erythroid-biased progenitors, respectively. We then leveraged our insights into chromatin organization among in vitro-derived cells to assess enrichments corresponding to human trait variation reported in human genome wide association studies. HPCs revealed locus enrichment for quantitative blood traits and autoimmune disease predisposition, which were particularly enriched in myeloid- and lymphoid-biased populations. Stromal and endothelial cells from our in vitro cultures were specifically enriched for accessible chromatin at blood pressure loci. Our findings reveal genes and mechanisms governing in vitro hematopoietic development and blood cell-related disease pathology.

genetics↗

bioRxiv2024

Integrated local and systemic communication factors regulate nascent hematopoietic progenitor escape during developmental hematopoiesis

Mammalian blood cells originate from specialized hemogenic endothelial (HE) cells in major arteries. During the endothelial-to-hematopoietic transition (EHT), nascent hematopoietic stem cells (HSCs) bud from the arterial endothelial wall and enter circulation, destined to colonize the fetal liver before ultimately migrating to the bone marrow. Mechanisms and processes that facilitate EHT and the release of nascent HSCs are incompletely understood, but may involve signaling from neighboring vascular endothelial cells, stromal support cells, circulating preformed hematopoietic cells, and/or systemic factors secreted by distal organs. In this study, we used single cell RNA sequencing analysis from human embryonic cells to identify relevant signaling pathways that support nascent HSC release. In addition to intercellular and secreted signaling modalities that have been previously functionally validated to support EHT and/or developmental hematopoiesis in model systems, we identify several novel modalities with plausible mechanisms to support EHT and HSC release. Our findings paint a portrait of the complex interregulated signals from the local niche, circulating hematopoietic/inflammatory cells, and distal fetal liver that support hematopoiesis.

developmental biology↗