Biology subjects

Hadland, B.

Publications and source records attributed to Hadland, B..

10 recordsLinked to original sources

bioRxiv2026

Single-Cell Behavioromics Enables Fate Prediction of Individual Hematopoietic Stem Cells

Achieving near-single-cell precision in the prospective identification of long-term engrafting hematopoietic stem cells (LT-HSCs) remains challenging, likely because current static, point-in-time single-cell phenotyping technologies do not capture the dynamic nature of cell fate decisions. Here, we overcome this barrier by longitudinally tracking individual hematopoietic stem and progenitor cells (HSPCs) in ex vivo niche cultures using live imaging, coupled with downstream immunophenotyping, single-cell transcriptomics, and transplant assays. Deep learning analysis of live imaging data achieved 98.5% average precision in predicting serially-engrafting LT-HSC (serial-LT-HSC) identity from the behaviorome (the totality of observed behaviors) of each cell, outperforming currently available technologies. Serial-LT-HSCs exhibited lower motility among HSPC populations, which was associated with reduced Activin signaling activity and elevated expression of cell adhesion genes. Correspondingly, antagonizing Activin signaling by Inhibin-A treatment in ex vivo niche cultures suppressed HSPC motility while increasing the frequency of post-expansion serial-LT-HSCs, revealing a novel role for Activin signaling in HSPC behavior and fate determination. Collectively, this study establishes a broadly applicable framework that connects behavioromic analysis and single-cell transcriptomics to enable near-single-cell precision in predicting stem cell fate and uncover molecular mechanisms governing behavior-fate relationships.

cell biology↗

bioRxiv2026

Developmental programming of hematopoietic stem cell dormancy by evasion of Notch signaling

Dormant hematopoietic stem cells (HSCs) are a rare subset of deeply quiescent, metabolically inactive cells that preserve lifelong hematopoietic regeneration. In mice, these cells were thought to arise exclusively after birth in the BM, while fetal liver HSCs were considered uniformly proliferative and rapidly expanding. Here, using H2B-GFP label-retention strategies, we identify a previously unrecognized population of low-dividing HSCs that is specified during embryogenesis and persists into adulthood. We show that this dormant state is established in specific fetal HSCs that evade the activation of Notch signaling within the fetal liver niche, rather than through global loss of pathway activity. Genetic and transient perturbation of Notch signaling reveals a narrow developmental window in during which reduced Notch exposure promotes entry into a durable dormancy program, whereas irreversible pathway disruption compromises long-term function. Notably, transient Notch during fetal development, but not in adult BM, induces HSC quiescence while enhancing long-term repopulation capacity. Together, these findings demonstrate that HSC dormancy is developmentally programmed before birth and identify evasion of Notch signaling as a key mechanism establishing this state, fundamentally revising current models of how long-term regenerative potential is specified.

developmental biology↗

bioRxiv2025

Depletion of microenvironmental syndecan-2 impairs hematopoietic stem cell self-renewal and cytokine responses

Syndecan-2 is a heparan sulfate proteoglycan highly enriched on murine bone marrow hematopoietic stem cells (HSCs) compared to terminally differentiated hematopoietic cells. Syndecan-2 binds growth factors via its heparan sulfate glycosaminoglycan chains to coordinate cell signaling. Knockdown of syndecan-2 reduces HSC self-renewal ability and promotes cell cycling via Cdkn1c. In this study, we analyzed the function of syndecan-2 expressed by bone marrow niche cells in hematopoiesis and HSC self-renewal. We determined that syndecan-2 is highly expressed by bone marrow mesenchymal stromal cells and moderately expressed by endothelial cells. To test the function of niche-expressed syndecan-2 in hematopoiesis, we generated transgenic mice depleted of Sdc2 in Lepr-targeted mesenchymal stromal cells (Sdc2{Delta}MSC mice) or Cdh5-targeted endothelial cells (Sdc2{Delta}EC mice). Loss of syndecan-2 from endothelial or mesenchymal stromal cells did not change bone marrow HSC frequencies or numbers. However, depletion of syndecan-2 from Lepr-targeted mesenchymal stromal cells, but not Cdh5-targeted endothelial cells, diminishes HSC self-renewal ability analyzed by competitive transplants into lethally irradiated mice. Ex vivo studies further show that HSCs co-cultured with HS-5 stromal cells depleted of SDC2 exhaust more rapidly than HSCs cultured with control HS-5 cells. Single-cell RNA sequencing analyses reveal that the depletion of Sdc2 from mesenchymal stromal cells significantly remodels the HSC transcriptome by enriching for pathways associated with excessive growth factor signaling. Together, our findings suggest that HSC self-renewal is supported by cell-extrinsic mechanisms enacted by syndecan-2 from the MSC niche, highlighting the importance of the niche proteoglycome in HSC functions. KEY POINTSO_LIThe heparan sulfate proteoglycan syndecan-2 expressed by mesenchymal stromal cells but not endothelial cells regulates HSC self-renewal C_LIO_LIDepletion of syndecan-2 from Lepr-targeted mesenchymal stromal cells remodels the hematopoietic stem cell transcriptional landscape C_LI

cell biology↗

bioRxiv2025

Cross-Species Morphology Learning Enables Nucleic Acid-Independent Detection of Live Mutant Blood Cells

In both neonates and adults, the presence of malignancy-associated mutations in peripheral blood (PB) correlates with an elevated risk of future neoplastic transformation, with certain mutations, such as KMT2A rearrangements, exhibiting near-complete penetrance. If feasible, pre-malignant screening could enable early intervention and even disease prevention. However, nucleic acid sequencing- and hybridization-based mutation detection have limited cost-efficiency, constraining their use in screening. Here, we introduce a computer vision platform that can identify mutant cells in fresh PB samples that carry KMT2A-MLLT3 (a frequent mutation in pediatric and adult leukemias and detectable in newborn blood samples) or JAK2V617F (a frequent mutation in myeloproliferative neoplasms and clonal hematopoiesis). This is achieved by high-throughput single-cell imaging and mutation detection by machine learning (ML)-powered morphology recognition. The ML models were developed by cross-species learning of conserved features between mutant cells from mouse genetic models and from human samples, enabling a cost-effective approach for detecting mutations in live blood cells. This platform holds promise for pre-malignant screening in asymptomatic neonates and adults with KMT2A-MLLT3 or JAK2V617Fmutation and is potentially generalizable to the detection other malignancy-associate mutations. Our platform provides a novel single-cell morphological data modality that complements existing single-cell genomics.

pathology↗

bioRxiv2024

Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells

Hematopoietic stem cells (HSCs) arise in embryogenesis from a specialized hemogenic endothelium (HE). In this process, HE cells undergo a unique fate change termed endothelial-to-hematopoietic transition, or EHT. While induced pluripotent stem cells (iPSCs) give rise to HE with robust hemogenic potential, the generation of bona fide HSCs from iPSCs remains a challenge. Here, we map single cell dynamics of EHT during embryoid body differentiation from iPSCs and integrate it with human embryo datasets to identify key transcriptional differences between in vitro and in vivo cell states. We further map ligand-receptor interactions associated with differential expression of developmental programs in the iPSC system. We found that the expression of endothelial genes was incompletely repressed during iPSC EHT. Elevated FGF signaling by FGF23, an endothelial pathway ligand, was associated with differential gene expression between in vitro and in vivo EHT. Chemical inhibition of FGF signaling during EHT increased HSPC generation in the zebrafish, while an FGF agonist had the opposite effect. Consistently, chemical inhibition of FGF signaling increased hematopoietic output from iPSCs. In summary, we map the dynamics of EHT from iPSCs at single cell resolution and identify ligand-receptor interactions that can be modulated to improve iPSC differentiation protocols. We show, as proof of principle, that chemical inhibition of FGF signaling during EHT improves hematopoietic output in zebrafish and the iPSC system.

developmental biology↗

bioRxiv2024

Under pressure: altered endothelial flow response

Blood flow within the vasculature is a critical determinant of endothelial cell (EC) identity and functionality, yet the intricate interplay of various hemodynamic forces and their collective impact on endothelial and vascular responses are not fully understood. Specifically, the role of hydrostatic pressure in the EC flow response is understudied, despite its known significance in vascular development and disease. To address this gap, we developed in vitro models to investigate how pressure influences EC responses to flow. Our study demonstrates that elevated pressure conditions significantly modify shear-induced flow alignment and increase endothelial cell density. Bulk and single-cell RNA sequencing analyses revealed that, while shear stress remains the primary driver of flow-induced transcriptional changes, pressure modulates shear- induced signaling in a dose-dependent manner. These pressure-responsive transcriptional signatures identified in human ECs were conserved during the onset of circulation in early mouse embryonic vascular development, where pressure was notably associated with transcriptional programs essential to arterial and hemogenic EC fates. Our findings suggest that pressure plays a synergistic role with shear stress on ECs and emphasizes the need for an integrative approach to endothelial cell mechanotransduction, one that encompasses the effects induced by pressure alongside other hemodynamic forces.

bioengineering↗

bioRxiv2024

Multiplexed single cell transcriptomics optimizes mesodermal patterning and hemogenic endothelial output from murine embryonic stem cells

BackgroundEarly patterning of mesodermal precursor populations is a key step of hematopoietic development in the embryo. To better understand this process, we employed sci-Plex, a high-throughput method of measuring multiplexed perturbations at the single-cell level, to evaluate the transcriptional response of mouse embryonic stem cells subjected to a gradient of two key morphogens in early mesoderm/hematopoietic development, Activin and BMP4. Resultssci-Plex revealed varying combinations of Activin and BMP4 temporally influenced mesoderm patterning in vitro and subsequent production of cell types reflecting their in vivo counterparts. We leveraged sci-Plex data to further optimize the generation of intraembryonic-like hemogenic endothelial cells that serve as the precursors of definitive hematopoietic lineages, including hematopoietic stem cells. ConclusionsThis study highlights the utility of sci-Plex to dissect how dose and temporal integration of interacting signal pathways determines cell fates and serves as a resource to analyze cell fate choices in early mesoderm patterning at single cell resolution.

developmental biology↗

bioRxiv2023

Differentiation latency and dormancy signatures define fetal liver HSCs at single cell resolution

Decoding the gene regulatory mechanisms and signaling interactions that orchestrate the self-renewal of hematopoietic stem cells (HSCs) during their expansion in the fetal liver (FL) could unlock novel therapeutic strategies to expand transplantable HSCs, a long-standing challenge. Here, to explore intrinsic and extrinsic regulation of FL-HSC self-renewal at the single cell level, we engineered a culture platform designed to recapitulate the FL endothelial niche, which supports the ex vivo amplification of serially engraftable HSCs. Leveraging this platform in combination with single cell index flow cytometry, live imaging, serial transplantation assays, and single cell RNA-sequencing, we uncovered previously unrecognized heterogeneity within immunophenotypically defined FL-HSCs. Specifically, we demonstrated that differentiation latency, symmetric cell divisions, and transcriptional signatures of biosynthetic dormancy and lipid metabolism are distinguishing properties of rare FL-HSCs capable of serial, long-term multilineage hematopoietic reconstitution. Our findings support a paradigm in which intrinsic programs and extrinsic signals combinatorially facilitate the symmetric self-renewal and expansion of nascent HSCs in the FL niche while delaying their active participation in hematopoiesis. Additionally, our study provides a valuable resource for future investigations into the intrinsic and niche-derived signaling pathways that govern FL-HSC self-renewal.

developmental biology↗

bioRxiv2023

Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing

Transition between activation and quiescence programs in hematopoietic stem and progenitor cells (HSC/HSPCs) is perceived to be governed intrinsically and by microenvironmental co-adaptation. However, HSC programs dictating both transition and adaptability, remain poorly defined. Single cell multiome analysis divulging differential transcriptional activity between distinct HSPC states, indicated for the exclusive absence of Fli-1 motif from quiescent HSCs. We reveal that Fli-1 activity is essential for HSCs during regenerative hematopoiesis. Fli-1 directs activation programs while manipulating cellular sensory and output machineries, enabling HSPCs co-adoptability with a stimulated vascular niche. During regenerative conditions, Fli-1 presets and enables propagation of niche-derived Notch1 signaling. Constitutively induced Notch1 signaling is sufficient to recuperate functional HSC impairments in the absence of Fli-1. Applying FLI-1 modified-mRNA transduction into lethargic adult human mobilized HSPCs, enables their vigorous niche-mediated expansion along with superior engraftment capacities. Thus, decryption of stem cell activation programs offers valuable insights for immune regenerative medicine.

cell biology↗

bioRxiv2021

Engineering a niche supporting haematopoietic stem cell development using integrated single cell transcriptomics

Haematopoietic stem cells (HSCs) develop from haemogenic endothelium (HE) within embryonic arterial vessels such as the aorta of the aorta-gonad-mesonephros region (AGM). To identify the signals responsible for HSC formation, we used single cell RNA-sequencing to simultaneously analyze the transcriptional profiles of AGM-derived cells transitioning from HE to HSC, and AGM-derived endothelial cells which provide signals sufficient to support HSC maturation and self-renewal. Pseudotemporal ordering revealed dynamics of gene expression during the HE to HSC transition, identifying surface receptors specifically expressed on developing HSCs. Transcriptional profiles of niche endothelial cells enabled identification of corresponding ligands, including those signaling to Notch receptors, VLA-4 integrin, and CXCR4, which, when integrated in an engineered platform, were sufficient to support the generation of engrafting HSCs. These studies provide a transcriptional map of the signaling interactions necessary for the development of HSCs and advance the goal of engineering HSC for therapeutic applications.

developmental biology↗