Our Preprint Watch turns one! To celebrate this first anniversary, we’re shaking things up a bit: from now on, the most exciting preprints in experimental hematology and stem cell biology will be organized by broad research areas, giving you a wider perspective on the field.

We hope this new structure will help both specialists deepen their focus and newcomers dive into specific topics of interest.

And don’t worry—there’s still plenty of room for community submissions! You can submit one using this brief online form.

This month we welcome Dr. Termini and her team, with a thought-provoking work on the haematopoietic niche and radiation! 
 

From the Simply Blood Community:

 

The bone marrow niche and hematopoietic system are distinctly remodeled by CD45-targeted astatine-211 radioimmunotherapy

https://www.biorxiv.org/content/10.1101/2025.04.04.645037v1

We show that CD45-targeted radioimmunotherapy severely depletes the hematopoietic system and delays hematopoietic stem and progenitor cell regeneration compared to IgG radioimmunotherapy or cesium total body irradiation. Further, CD45-targeted radioimmunotherapy causes bone marrow endothelial niche destruction and transcriptional reprogramming compared to IgG radioimmunotherapy, cesium total body irradiation and untreated mice.

Social media handles: @cterminiPhD

 

Developmental Haematology

 

Hematopoietic Single Cell Atlas Reveals a Diverse Repertoire of Lymphoid Cells in Larval Zebrafish

https://www.biorxiv.org/content/10.1101/2025.05.12.653589v1?rss=1

In this work, scientists looked at the origins of immune cells during zebrafish development using temporal lineage tracing and single-cell RNA sequencing. They uncovered a greater lymphoid diversity than previously known, identifying Runx1-dependent T cells and innate lymphoid-like cells (ILCs). Both required Il2rγ, though only T cells depended on Rag1. The larval ILC-like cells localized to lymphoid and mucosal organs and responded to immune stimulation, revealing functional early immunity.
 

Bona fide hematopoietic stem cells in zebrafish originate from the supra-intestinal artery

https://www.biorxiv.org/content/10.1101/2025.05.20.655066v2

Scientists looked at the developmental origins of hematopoietic stem cells (HSCs) in zebrafish using high-resolution, infrared-mediated lineage tracing. Contrary to the prevailing view that HSCs arise from the dorsal aorta (DA), they discovered that lifelong self-renewing HSCs emerge from the supra-intestinal artery (SIA). While the DA produces short-lived precursors from unipotent hemogenic endothelial cells, the SIA generates HSCs from both unipotent and bipotent vessel-resident hemangioblasts, a finding further supported by single-cell transcriptomics. 
 

Rapunzel5 is necessary for normal hematopoietic development in zebrafish

https://www.biorxiv.org/content/10.1101/2025.08.09.669486v1?rss=1

Here, scientists investigated the role of the zebrafish gene rapunzel5 (rpz5) in vertebrate hematopoiesis. Through transcriptomic screening and morpholino-based knockdown experiments, they found that loss of rpz5 led to a marked decrease in red blood cells, myeloid cells, thrombocytes, and hematopoietic stem and progenitor cells (HSPCs), while exogenous rpz5 restored normal blood cell production.

 

Angptl5 restricts primitive hematopoiesis by modulating retinoic acid signaling in zebrafish

https://www.biorxiv.org/content/10.1101/2025.08.18.670818v1?rss=1

Researchers identified Angptl5 as a key regulator of hematopoietic homeostasis using zebrafish models. Loss of Angptl5 led to myeloid hyperplasia and erythroid progenitor expansion, mimicking reduced retinoic acid (RA) signaling, which could be rescued by exogenous RA. Mechanistic studies revealed that Angptl5 promotes RA pathway activity by transcriptionally activating dhrs9 through interaction with Integrin α6lβ5. These findings uncover Angptl5 as an essential modulator of embryonic hematopoiesis and highlight a new mechanism maintaining hematopoietic balance.

 

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

https://www.biorxiv.org/content/10.1101/2025.07.31.667883v1?rss=1

Researchers explored how the actin-binding protein Tropomyosin 1 (Tpm1) influences blood traits and platelet biology. Conditional deletion of Tpm1 in endothelial or hematopoietic cells showed that, while embryonic Tpm1 loss enhances hemogenic endothelial specification, postnatal hematopoiesis remains unaffected. Genetic data linked reduced TPM1 expression to higher platelet counts, which mechanistic studies attributed to prolonged platelet lifespan and reduced adhesion to fibronectin and fibrinogen. These defects impaired clot contraction but increased vascular occlusion in a stroke model.
 

A conserved upstream element in the mouse Csf1r locus contributes to transcription in hematopoietic and trophoblast cells

https://www.biorxiv.org/content/10.1101/2025.08.05.668600v1?rss=1

From the authors: A regulatory element (CUREA) in the mouse Csf1r locus has both promoter and enhancer activity. Germ-line deletion of CUREA impacts differentiation of marrow progenitors, microglia, osteoclasts and placental trophoblasts.
 

Restraint of TGFβ family signaling by SMAD7 is necessary for hematopoietic stem cell maturation in the embryo

https://www.biorxiv.org/content/10.1101/2025.08.23.671940v1?rss=1

Researchers uncovered a crucial role for SMAD7 in the maturation of hematopoietic stem cells (HSCs) from their embryonic precursors. Using endothelial-specific deletion models, they found that loss of Smad7 permits the formation of pre-HSCs from hemogenic endothelial cells but prevents their transition into fully functional HSCs. These findings reveal that while TGFβ and BMP signaling drive early hematopoietic specification, their suppression via SMAD7 is essential for pre-HSC maturation, refining the understanding of HSC development.

 

Resolving hematopoietic stem versus progenitor cell potential in the mouse dorsal aorta by differential Runx1 +110 enhancer activity

https://www.biorxiv.org/content/10.1101/2025.09.02.673630v1?rss=1

Scientists investigated how hematopoietic stem cells (HSCs) and progenitors (HPCs) diverge during embryonic development by analyzing Runx1 enhancer activity in mice. Using a Runx1 +110 enhancer-GFP reporter, they found that +110 enhancer activity specifically marks HPCs, not emerging HSCs. Transcriptomic comparisons identified a 17-gene signature linked to long-term HSC potential, with Jarid2 and PRC2 components enriched in pre-HSCs. Single-cell multiome analysis further revealed distinct enhancer usage, with the +3 enhancer active in pre-HSCs and +110 in HPCs. 

 

Single-cell lineage tracing identifies hemogenic endothelial cells in the adult mouse bone marrow

https://www.biorxiv.org/content/10.1101/2025.10.09.681472v1?rss=1

Researchers discovered a rare population of adult bone marrow Cdh5/VE-Cadherin+ endothelial cells (ECs) with hemogenic potential. Using lineage tracing, single-cell RNA sequencing, and transplantation assays, they showed these adult hemogenic ECs can generate hematopoietic progenitors and functional mature blood cells. Importantly, their progeny engraft peripheral tissues and contribute to inflammatory responses similarly to developmental EC-derived blood cells. This work reveals a previously unrecognized source of adult hematopoiesis.
 

WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm

https://www.biorxiv.org/content/10.1101/2025.06.06.657928v1?rss=1

Here, the researchers investigated how WNT signaling influences the differentiation of human pluripotent stem cells (hPSCs) into hematopoietic intermediates for lymphocyte production. They found that early WNT activation via CHIR99021 induces KDR⁺ ALDH1A2⁺ mesodermal progenitors and promotes T-cell formation through a retinoic acid–dependent mechanism. Integrated transcriptomic and chromatin analyses revealed that HDAC2 acts as a key regulator of this WNT–RA axis, with its loss impairing and its overexpression enhancing progenitor generation.
 

Pediatric Malignancies

 

A lipid metabolism defect is an underlying contributor to Diamond-Blackfan anemia syndrome

https://www.biorxiv.org/content/10.1101/2025.05.22.654334v1?rss=1

From the authors: The variable anemia in Rpl5Skax23-Jus/+mice is triggered by intrinsic/extrinsic stress. Rpl5 haploinsufficient murine and human erythroid progenitors exhibit a lipid metabolism signature with downregulation of Scd1/SCD.
 

Oncogenic PTPN11/SHP2 drives immune escape in juvenile myelomonocytic leukemia (JMML) through activation of ectonucleotidase/adenosine signaling

https://www.biorxiv.org/content/10.1101/2025.10.01.679664v1?rss=1

Here, researchers investigated mechanisms of immune escape in oncogenic PTPN11-driven JMML and found elevated expression of ectonucleotidases CD39 and CD73—key adenosine pathway mediators—on leukemic myeloid cells. GM-CSF stimulation increased, while MEK inhibition reduced, ectonucleotidase expression. Functionally, mutant myeloid cells suppressed T cell activation through adenosine signaling, an effect reversed by CD39 inhibition with POM-1. In vivo, POM-1 treatment in Ptpn11D61Y/+ mice alleviated myeloproliferation, restored immune responsiveness, and induced leukemic cell apoptosis. These findings highlight CD39 inhibition as a promising immunomodulatory strategy to counteract immune evasion and relapse in JMML.
 

Ribosomal protein L5 (RPL5/uL18) I60V mutation is associated to increased translation and modulates drug sensitivity in T-cell acute lymphoblastic leukemia cells

https://www.biorxiv.org/content/10.1101/2025.07.16.665036v1?rss=1

From the authors: RPL5 mutations have been reported in T-cell acute lymphoblastic leukemia (T-ALL). Ribosomes containing the RPL5 I60V mutation exhibit increased translational activity. Increased proliferation is observed in cells harboring the RPL5-I60V mutation, which confers a specific drug sensitivity profile

 

METTL13 Promotes Pre-Leukemic Transformation and the Development of Pediatric Leukemia

https://www.biorxiv.org/content/10.1101/2025.08.29.673071v1?rss=1

From the authors:  In this study we uncovered a novel regulatory link between ADAR1 and the METTL-family of RNA methyltransferases in hematopoietic stem cells. Overexpression of ADAR1 uniquely upregulated METTL13 while suppressing other METTL genes. Loss of orphan gene METTL13 affected proliferation, apoptosis and p53 signaling in hematopoietic stem cells. Furthermore, loss of METTL13 suppressed cell proliferation and survival in pediatric T-ALL. Our findings suggest a potential role for METTL13 in pre-leukemia transformation and oncogenic development.

 

Identifying potential therapeutic targets for T-cell acute lymphoblastic leukemia using malignant networks and topological analysis

https://www.biorxiv.org/content/10.1101/2025.10.08.681235v1?rss=1

Using network-based analysis of overexpressed genes in T-ALL, researchers applied topological metrics and persistent homology to evaluate gene importance. Simulating gene removal across subnetworks, they identified critical nodes, with NPM1 emerging as essential for maintaining network integrity, supporting proliferation, and promoting cell survival. These findings suggest NPM1 as a promising therapeutic target in T-ALL, demonstrating the value of topological approaches for prioritizing cancer vulnerabilities.
 

PAMD-Ch17, a Polymeric Analog of Plerixafor, Induces Mitochondrial Dysfunction in T-ALL Cells Independent of CXCR4

https://www.biorxiv.org/content/10.1101/2025.05.28.656643v1?rss=1

From the authors: PAMD-Ch17, a polymeric drug based on AMD3100/Plerixafor, has novel anti-leukemic activities against T-ALL that are independent of CXCR4 inhibition. PAMD-Ch17 induces increased mitochondrial superoxide and cell death in primary ALL cells, but not healthy bone marrow cells.
 

LCK-targeting molecular glues overcome resistance to inhibitor-based therapy in T-cell acute lymphoblastic leukemia

https://www.biorxiv.org/content/10.1101/2025.07.03.663042v1?rss=1

Here, scientists identified cereblon-recruiting molecular glue degraders (MGDs) that selectively target the oncogenic kinase LCK in T-ALL. These MGDs induce CRBN-dependent LCK degradation and potent cytotoxicity in vitro, acting through a non-canonical degron located in the LCK G-loop. Notably, their efficacy is maintained against gatekeeper mutations that confer resistance to ATP-competitive inhibitors. 

 

Combined multi-color immunofluorescence staining and spatial in situ mRNA expression analysis identifies potential fibrosis drivers in acute lymphoblastic leukemia

https://www.biorxiv.org/content/10.1101/2025.08.29.673047v1?rss=1

Researchers developed an advanced spatial analysis combining multicolor immunofluorescence and in situ RNA expression (RNAscope®) to investigate the mechanisms driving bone marrow (BM) fibrosis in pediatric ALL. Using patient BM biopsies, they mapped the expression of key fibrotic cytokines—TGFB1 and PDGFA1—within specific cellular niches. The study revealed that CD271⁺ mesenchymal stromal cells were enriched in ALL, correlating with fibrosis, and that megakaryocytes (MKs) exhibited markedly elevated TGFB1 and PDGFA1 expression compared to normal and primary myelofibrosis (PMF) samples. Expression levels in MKs correlated with fibrosis grade, while leukemic blasts also expressed these cytokines at lower levels. These findings identify MKs and blasts as potential sources of fibrosis-driving signals in ALL.

 

Identification of Novel Fusion Genes in Pediatric B-ALL patients Using Whole Transcriptome Sequencing

https://www.biorxiv.org/content/10.1101/2025.09.23.677992v1?rss=1

Fusion genes (FGs) are pivotal diagnostic, prognostic, and therapeutic biomarkers in acute leukemia, as well as critical tools for measurable residual disease (MRD) monitoring. To characterize their distribution, researchers performed whole transcriptome sequencing (WTS) on samples from 12 newly diagnosed, treatment-naive pediatric B-ALL patients. The analysis identified 19 high-confidence in-frame fusion events involving 29 unique partner genes. Classical subtype-defining fusions such as ETV6-RUNX1, TCF3-PBX1, and BCR-ABL1 were each detected in 8.3% of patients. Additionally, rearrangements in PAX5, ABL1, and ATXN3 with novel partner genes—PAX5-ETV6, ABL1-SNX2, and CMC2-ATXN3—were uncovered. 

 

Intra-subtype heterogeneity shapes treatment response in KMT2A-rearranged ALL across all age groups

https://www.biorxiv.org/content/10.1101/2025.06.05.657589v2

Researchers analyzed 465 KMT2A-rearranged B-ALL cases to understand how developmental state, fusion partner, and age affect early treatment response. They found that younger patients and leukemias with lower B-cell maturity scores or AFF1 fusions had slower MRD clearance, while higher maturity correlated with better ex vivo drug responses. Gene expression signatures linked to chromatin, immune modulation, and proliferation further stratified drug sensitivity, highlighting Venetoclax as potentially effective in immature cases. This work establishes a developmental maturity score as a predictive tool for therapy response and precision treatment planning.

 

The 3D genome of pediatric B-cell precursor acute lymphoblastic leukemia

https://www.biorxiv.org/content/10.1101/2025.07.22.666073v1?rss=1

This work maps the three-dimensional chromatin architecture of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) using high-resolution Micro-C in 35 primary cases. The data reveal that genetic aberrations such as fusions, aneuploidies, and structural variants extensively reconfigure 3D genome organization, weakening TAD boundaries and altering gene regulation. Over 25,000 enhancer–promoter loops controlling more than 10,000 genes were identified, including regulatory circuits driving subtype-specific expression of key leukemia genes like HOXA9 and IKZF1. 

 

Comparative analysis of plasma and bone marrow nutrient levels in pediatric B-ALL patients

https://www.biorxiv.org/content/10.1101/2025.08.05.668707v1?rss=1

Researchers profiled nutrient availability in pediatric B-ALL to understand how metabolic environments shape disease progression and treatment response. By comparing plasma and bone marrow from patients across B-ALL subtypes and treatment phases, they uncovered distinct metabolic signatures, particularly in arginine and asymmetric dimethylarginine metabolism in hyperdiploid B-ALL. Bone marrow and circulating metabolite profiles were largely similar, even post-chemotherapy, suggesting metabolic equivalence between these compartments. Comparison with solid tumors revealed that B-ALL uniquely enriches tricarboxylic acid cycle intermediates in circulation. 

 

Integrated multi-omic analysis reveals novel subtype-specific regulatory interactions in pediatric B-cell acute lymphoblastic leukemia

https://www.biorxiv.org/content/10.1101/2025.08.13.670107v1?rss=1 

Here, researchers integrated transcriptomic, proteomic, and phosphoproteomic data to characterize two pediatric B-ALL subtypes—Ph-like (BCR::ABL1-like) and ETV6::RUNX1. This multi-omic approach not only confirmed known transcriptomic patterns but also uncovered novel subtype-specific proteomic and phosphoproteomic biomarkers. The analysis revealed an unexpected role for calcium-dependent signaling pathways in Ph-like B-ALL, suggesting potential therapeutic targets.

 

Inhibition of MLLT1 limits growth of MLL-AF4 leukaemias without killing healthy haematopoietic stem cells

https://www.biorxiv.org/content/10.1101/2025.04.30.651417v1?rss=1

Researchers tested the MLLT1 inhibitor SGC-iMLLT as a selective therapy for MLL-AF4-driven leukemia. The compound potently suppressed leukemia cell growth both in vitro and in vivo, while sparing healthy hematopoietic stem and progenitor cells, preserving their colony-forming and long-term functions. These findings suggest that SGC-iMLLT offers a promising therapeutic window for aggressive MLL-AF4 leukemias.

 

The HOTAIRM1-miR-222 Axis Regulates Venetoclax Resistance and Defines a High-Risk Subset in Pediatric t(8;21) Acute Myeloid Leukemia

https://www.biorxiv.org/content/10.1101/2025.07.12.663834v1?rss=1

From the authors: Loss of myeloid lineage-specific isoform of lncRNA HOTAIRM1 - HOTAIRM1 variant 2, results in de-repression of microRNA miR-222, and contributes to venetoclax resistance in pediatric Acute Myeloid Leukemia (AML) patients harbouring the t(8;21)(q22;q22.1)/RUNX1::RUNX1T1 fusion. MicroRNA miR-222 shows potential as a single marker predictor that complements current risk stratification by identifying a subset of pediatric t(8;21) AML patients with poor prognosis.

 

A 3-genes interferon signature predicts sustained complete remission in pediatric AML patients

https://www.biorxiv.org/content/10.1101/2025.07.17.664572v1?rss=1

From the authors: We identified a novel three-gene IFN-related signature that distinguished pediatric AML patients by chemosensitivity and remission outcomes. It stratified patients across all risk groups, including the “standard-risk” group, with high expression linked to a T-cell-enriched microenvironment and longer survival. This signature may enhance risk stratification and guide targeted immunotherapy.

 

Integrated in silico and in vitro approaches identify SNX.2112 as a drug vulnerability in t(7;12) AML stem-like cells

https://www.biorxiv.org/content/10.1101/2025.09.06.674620v1?rss=1

In this work, scientists investigated therapeutic vulnerabilities in t(7;12) AML, an infant leukemia driven by MNX1 overexpression that originates during fetal hematopoiesis. Leveraging a transcriptional signature derived from a 3D gastruloid model of blood development, they screened hundreds of human cell lines in the GDSC drug sensitivity database and pinpointed 12 candidate compounds. Functional assays in engineered t(7;12) cell lines identified the HSP90 inhibitor SNX.2112 as a selective agent that eliminated leukemic progenitors, reduced MNX1 expression, and suppressed colony formation. These effects were recapitulated in the gastruloid model and validated in single-cell RNA-seq datasets from patient samples. Moreover, SNX.2112 synergized with cytarabine and mitoxantrone, highlighting its promise as a targeted and less toxic therapeutic option for t(7;12)-AML.
 

The activation of TP53 pathway is a therapeutic vulnerability in NUP98::KDM5A+ pediatric AML

https://www.biorxiv.org/content/10.1101/2025.09.11.675580v3

Researchers explored why NUP98::KDM5A-driven pediatric AML, an aggressive form of infant leukemia, shows such poor outcomes. By comparing fetal and adult hematopoietic stem and progenitor cell models, they found that leukemias arising in a fetal context maintain fetal-specific transcriptional programs that enhance malignancy. Multi-omic analyses uncovered a key dependency on the ATPase TRIP13, which partners with the phosphatase PPM1D to suppress TP53 activation. Targeting TRIP13—alone or combined with idasanutlin, navitoclax, and 5-azacytidine—reactivated TP53 signaling and triggered synergistic apoptosis. 
 

Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Prediction in Pediatric AML

https://www.biorxiv.org/content/10.1101/2025.09.25.678688v2

Most pediatric pAML patients achieve remission after chemotherapy, but relapse remains a major cause of mortality, emphasizing the need for improved early risk prediction. Here, scientists analyzed paired diagnosis–relapse samples from 33 pAML patients at single-cell resolution to identify chemoresistant populations that persist despite treatment. Incorporating these populations into a refined prognostic model revealed a previously unrecognized high-risk subgroup representing 20% of cases, responsible for half of the deaths among patients not receiving stem cell transplantation in first remission, and showing a 5-year event-free survival below 40%.

 

Blog post contributed by Alessandro Donada, PhD (Bluesky: @alessandrodonada.bsky.social) of the ISEH Publications Committee. 

 

Please note that the statements made by Simply Blood authors are their own views and not necessarily the views of ISEH. ISEH disclaims any or all liability arising from any author's statements or materials.