Preprint Watch: August
Welcome to another episode of our long-running Preprint Watch series! If you are preparing your return to the lab, these preprints will definitely help you out, catching some of the most exciting research in the field of experimental hematology! This month, we have two submissions from our community - one from the Erasmus Medical Center in the Netherlands and another from the University of Cambridge, UK, in which we were able to have a lovely chat with one of the first authors, Dr. Zarocsinceva.
If you want to see your research featured here, please send it through this form: https://www.iseh.org/page/Preprints.
From the Simply Blood Community:
Targeting mitochondria mitigates chemotherapy-induced bone marrow dysfunction
https://www.biorxiv.org/content/10.1101/2025.07.18.665515v1?rss=1
Herein, the authors have shown that 5-FU chemotherapy induces long-term damage to HSCs that resembles premature ageing and is driven by persistently altered mitochondrial metabolism. Treatment with mitochondrial-targeted antioxidant rescued blood parameters and enhanced HSC function of 5-FU treated mice.
Contact address: s.mansell@erasmusmc.nl
X: @ElsyDutchy, Bluesky: @elsydutchy.bsky.social, @tvantienhoven.bsky.social
A Step-wise, Deterministic and Fatal Mouse Model of Myeloid Neoplasm with Spontaneous Acquisition of Patient-relevant RTK–RAS Mutations
https://www.biorxiv.org/content/10.1101/2025.07.18.665518v1?rss=1
In this work, scientists recreated the hidden early stage of leukaemia by introducing a patient-derived CEBPA mutation into mouse blood progenitors. The altered cells produced a symptom-free phase before progressing to disease in all animals, each acquiring secondary RTK–RAS mutations, the same found in patients. Single-cell profiling showed a shift toward a plasmacytoid dendritic progenitor–like state. This model captures key features of juvenile myelomonocytic leukaemia (JMML) and provides a tractable system for studying mechanisms and testing therapies.
STEM AND PROGENITOR CELLS BIOLOGY
Aging changes the underlying mechanism of JAK2 modulation in neutrophil function
https://www.biorxiv.org/content/10.1101/2025.04.21.649782v1?rss=1
This study uncovers how JAK2 regulates neutrophil functions and highlights age- and sex-dependent differences. In young neutrophils, JAK2 promotes migration via actin and membrane remodeling, primes ROS production through NADPH oxidase components, enhances degranulation, and stimulates the pentose phosphate pathway. In aged neutrophils, JAK2-mediated effects are altered: granule release is impaired, ROS production is modified, and glycogen breakdown decreases. JAK2 also indirectly regulates NETosis through IL-1 signaling and ROS. These findings elucidate the intracellular pathways by which JAK2 controls neutrophil effector functions and point to age-specific therapeutic strategies for inflammatory diseases.
Dystrophin Dp71 is essential for the development and function of macrophages
https://www.biorxiv.org/content/10.1101/2025.04.24.650386v1?rss=1
Here, the researchers uncover an unexpected role for the DMD gene, long known for its involvement in muscular dystrophy, within the immune system. They show that hematopoietic stem cells express the Dp71 form of dystrophin, which diminishes as cells mature into macrophages. In mice lacking dystrophin, macrophages displayed defective development, with impaired migration and phagocytosis but heightened inflammatory activity. These findings reveal a previously unrecognized immune function for dystrophin.
Septin7 is essential in early hematopoiesis, but redundant at later stages
https://www.biorxiv.org/content/10.1101/2025.04.22.649981v4
In this study, scientists investigated the role of the cytoskeletal protein Septin7, long thought essential for cell division. While its complete loss in mice causes embryonic lethality and fibroblasts lacking it cannot divide properly, blood cell development seemed unaffected when Septin7 was deleted in specific immune lineages. The researchers found that this paradox arises because early hematopoietic cells strongly select against Septin7 loss, whereas later progenitors and immortalized precursors can tolerate its absence without defects. The work shows that Septin7 is crucial during early hematopoiesis but dispensable in mature blood lineages, refining our understanding of its role in cell division.
Targeting RhoA activity rejuvenates aged hematopoietic stem cells
https://www.biorxiv.org/content/10.1101/2025.04.23.647902v1?rss=1
Here, the researchers uncover a mechanical signaling pathway that drives the decline of blood stem cells with age. They show that aged HSCs experience higher nuclear envelope tension, which activates P-cPLA2 and RhoA, altering chromatin structure and gene activity. Inhibiting RhoA reduced nuclear tension, restored youthful chromatin features, and boosted the regenerative and balanced output of aged HSCs. These findings highlight RhoA-dependent mechanotransduction as a promising target to rejuvenate blood stem cell function in aging.
Niche Macrophages Recycle Iron to Tumor Cells and Foster Erythroblast Mimicry to Promote Bone Metastasis and Anemia
https://www.biorxiv.org/content/10.1101/2025.04.23.650120v1?rss=1
In this work, scientists reveal how breast cancer cells exploit the bone marrow niche to fuel metastasis while disrupting blood production. They identified a population of iron-regulating macrophages that normally support red blood cell formation but are hijacked by tumor cells to secure iron for their own growth. This diversion starves developing erythroblasts, leading to anemia, while cancer cells further adapt by mimicking red blood cell precursors and producing hemoglobin under hypoxic stress. The study highlights iron-recycling macrophages as central players in metastatic progression and anemia, offering new therapeutic angles in cancer.
GABA produced by multiple bone marrow cell types regulates hematopoietic stem and progenitor cells
https://www.biorxiv.org/content/10.1101/2025.04.30.651482v2
From the authors: we functionally test production of GABA metabolite in the bone marrow microenvironment as a regulator of hematopoietic stem and progenitor cells. Conditional deletion of GAD enzymes in B cells and endothelial cells demonstrated both are sources of GABA. Lower GABA level primed HSPCs to reduce proliferation and upregulate B cell differentiation programs.
Ischemic Injury Drives Tumor Growth via Accelerated Hematopoietic Aging
https://www.biorxiv.org/content/10.1101/2025.05.03.652034v1?rss=1
Here, the researchers link peripheral artery disease to faster cancer progression through changes in blood stem cells. In a mouse model, peripheral ischemia reprogrammed hematopoietic stem cells toward myeloid-biased output, boosting monocytes and neutrophils at the cost of lymphocytes. This shift fueled breast tumor growth, accompanied by more immunosuppressive cells in the tumor microenvironment. Multiomic analyses revealed lasting inflammatory and aging-like signatures in progenitors, changes that were transmissible by bone marrow transplantation. The study shows how vascular injury drives stem cell inflammaging and weakens anti-tumor immunity.
PATHOLOGICAL HEMATOPOIESIS
PATHOLOGICAL HEMATOPOIESIS
Understanding the Role of Toggle Genes in Chronic Lymphocytic Leukemia Proliferation
https://www.biorxiv.org/content/10.1101/2025.03.31.646494v1?rss=1
In this work, scientists explore how gene expression noise influences the plasticity of chronic lymphocytic leukemia (CLL) cells. By analyzing RNA-Seq data over 96 hours, they identified thousands of differentially expressed and toggle genes—genes that randomly switch ON or OFF at the single-cell level. Despite being fewer in number, toggle genes contributed strongly to variability and were enriched in pathways linked to proliferation and immune signaling. The findings suggest that such toggle dynamics drive cell-state transitions and heterogeneity, helping leukemia populations adapt and persist.
Single-Cell Multiomics Reveals Regulatory Mechanisms of CAR T Cell Persistence and Dysfunction in Multiple Myeloma
https://www.biorxiv.org/content/10.1101/2025.04.01.646378v1?rss=1
Here, the researchers dissect the fate of CAR T cells in multiple myeloma using single-cell multiomics and gene regulatory network analysis. They found that CAR T cells in the bone marrow showed stronger activation and exhaustion than those in blood, with disrupted transitions from effector to memory states leading to poor persistence. In one patient, a hyperexpanded CAR T clone produced high levels of IL-10, a signal that impaired proliferation and survival. The study uncovers regulatory mechanisms behind CAR T cell exhaustion and highlights molecular targets to boost persistence and efficacy in multiple myeloma therapy.
TTLL4 glutamyltransferase is a therapeutic target for NPM1-mutated acute myeloid leukemia
https://www.biorxiv.org/content/10.1101/2025.04.07.647605v1?rss=1
In this study, scientists uncover a novel vulnerability in NPM1-mutated acute myeloid leukemia (AML) linked to the enzyme TTLL4. TTLL4 adds glutamate modifications to the mutant NPM1c protein, stabilizing its cytoplasmic localization and blocking differentiation of leukemic cells. Genetic or pharmacological inhibition of TTLL4 reduced NPM1c glutamylation, restored myeloid differentiation, and impaired leukemia cell proliferation, improving survival in a mouse AML model. The work identifies glutamylation as a key regulatory axis and positions TTLL4 as a promising therapeutic target in NPM1c AML.
Novel Strategy against AML by Rescuing Loss of Phase Separation of Pathogenic NPM1c
https://www.biorxiv.org/content/10.1101/2025.04.08.646961v1?rss=1
Here, researchers reveal a new therapeutic strategy for NPM1-mutated AML by targeting the phase separation of the mutant NPM1c protein. They show that loss of RNA-mediated phase separation drives NPM1c mislocalization, a key factor in leukemia development. Using high-throughput screening, they identified a small molecule that restores NPM1c phase separation and nucleolar localization, suppressing leukemia cell growth in both cell lines and patient-derived blasts. The study highlights phase separation rescue as a promising avenue for AML treatment.
SKIDA1 transiently sustains MLL::ENL-Expressing hematopoietic progenitors during neonatal stages and promotes B-lineage priming
https://www.biorxiv.org/content/10.1101/2025.04.12.648529v1?rss=1
In this study, scientists explore why infant leukemias differ from adult forms by focusing on the fetal context of MLL-rearranged (MLLr) leukemia. Using a mouse model, they identify Skida1 as a gene preferentially activated in fetal and neonatal progenitors, which supports B-cell priming and maintenance of MLL::ENL–expressing stem and progenitor cells. While dispensable for normal blood formation, Skida1 deletion selectively impairs B-cell development in neonatal MLLr leukemia, revealing how age-specific gene targets shape leukemia cell fate.
A small molecule inhibitor of RNA-binding protein IGF2BP3 shows anti-leukemic activity
https://www.biorxiv.org/content/10.1101/2025.04.14.648780v2
Here, researchers report the discovery of a first-in-class small molecule inhibitor of IGF2BP3, an oncofetal RNA-binding protein overexpressed in B-acute lymphoblastic leukemia (B-ALL). Through biochemical and cell-based screening, they identify I3IN-002, which effectively disrupts IGF2BP3–mRNA interactions, alters gene expression, impairs leukemic cell proliferation, and induces apoptosis. Importantly, I3IN-002 is well tolerated in mice and demonstrates strong anti-leukemic activity in a syngeneic MLL-Af4 model, providing a promising framework for targeting IGF2BP3 therapeutically.
Cell state transitions drive the evolution of disease progression in B-lymphoblastic leukemia
https://www.biorxiv.org/content/10.1101/2025.04.21.649796v1?rss=1
This study models stochastic transitions between B-ALL cell states, revealing that CD34+/CD38- stem-like cells arise through de-differentiation, particularly in BCR::ABL1-positive patients. High self-renewal in this compartment correlates with minimal residual disease, while BCR::ABL1-negative cases favor other cell states. Transition patterns remain stable between diagnosis and relapse, and the model demonstrates that routine flow cytometry can infer both prognosis and genotype.
Genomic and Immunogenomic Profiling of Extramedullary Acute Myeloid Leukemia Reveals Actionable Clonal Branching and Frequent Immune Editing
https://www.biorxiv.org/content/10.1101/2025.04.18.649610v1?rss=1
Extramedullary AML (eAML) exhibits clonal branching from bone marrow in over a third of cases, often involving FLT3, IDH2, and NPM1 mutations, with RAS pathway alterations and HLA class II losses indicating immune editing. Relapsed cases consistently acquire FLT3 aberrations, highlighting actionable targets, and the study emphasizes the importance of genomic profiling for accurate diagnosis and therapeutic guidance.
Pan-cancer Analysis Identified Ectopic RUNX1T1 Associated with Lineage Plasticity
https://www.biorxiv.org/content/10.1101/2025.04.18.649575v1?rss=1
In this work, scientists looked at HOX gene expression patterns to map cancer cell lineages and identify lineage-plastic subtypes in prostate, lung, and AML, which exhibited altered HOX codes. These subtypes consistently showed elevated RUNX1T1, suggesting it as a pan-cancer marker and key mediator of lineage plasticity, with potential implications for therapy resistance.
MOLECULAR HEMATOPOIESIS
Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions
https://www.biorxiv.org/content/10.1101/2025.04.16.649256v1?rss=1
In this work, scientists looked at how the transcription factor MYB controls enhancer function in leukemia. They found that degrading MYB disrupted precise enhancer-promoter interactions, reduced enhancer activity, and downregulated target genes. Strikingly, the MYB transactivation domain alone was sufficient to create enhancer-like regions and drive long-range chromatin interactions, showing that MYB activity can directly nucleate enhancers and sustain transcriptional programs in cancer.
Directing stem cell differentiation by chromatin state approximation
https://www.biorxiv.org/content/10.1101/2025.04.24.650451v1?rss=1
In this work, scientists looked at how to optimize cell differentiation for regenerative medicine by comparing chromatin profiles of lab-grown cells with their in vivo counterparts. Using erythroblast generation as a test case, they showed that iteratively selecting the most in vivo–like cells led to improved differentiation outcomes. Analysis of regulatory sequences also revealed transcription factors and ligands that help overcome roadblocks, highlighting a data-driven strategy to refine protocols for producing complex cell types
Erythrocytosis-inducing PHD2 mutations implicate biological role for N-terminal prolyl-hydroxylation in HIF1α oxygen-dependent degradation domain
https://www.biorxiv.org/content/10.1101/2025.04.22.650142v3
In this work, scientists looked at how EGLN1 mutations disrupt the oxygen-sensing enzyme PHD2, which regulates HIF degradation. By studying seven patient-associated variants, they showed that all mutants impaired PHD2 structure or catalytic activity. One mutant, P317R, retained the ability to hydroxylate the main C-terminal site but failed to act on the N-terminal proline, revealing its unexpected importance. These findings demonstrate that dysregulated HIF control drives PHD2-linked erythrocytosis and highlight a broader role for N-terminal hydroxylation in hypoxic signaling.
TECH WATCH AND MODELING
Capsule-Based Single-Cell Genome Sequencing
https://www.biorxiv.org/content/10.1101/2025.03.14.643253v1?rss=1
In this work, scientists looked at a new semi-permeable capsule (SPC) technology designed to handle single cells for genomic studies. These capsules protect cellular contents while allowing selective molecular exchange, enabling efficient culture, unbiased nucleic acid amplification, and high-quality single-cell whole genome sequencing. SPC-based sequencing produced uniform coverage with minimal contamination and captured lineage marks in a proof-of-concept tracing experiment. This approach broadens the single-cell genomics toolkit, enabling sensitive variant detection and large-scale lineage reconstruction.
High-throughput single cell -omics using semi-permeable capsules
https://www.biorxiv.org/content/10.1101/2025.03.14.642805v1?rss=1
In this work, scientists looked at semi-permeable capsules (SPCs) as a versatile platform for high-throughput single-cell analyses. Unlike droplet systems, SPCs enable long-term cell cultivation and clonal expansion while supporting nucleic acid assays such as digital PCR, genome sequencing, and scRNA-seq. Applying this approach to blood cells from patients with hematopoietic disorders, they showed that CapSeq delivers superior transcript capture and revealed AML-associated transcriptional changes in granulocytes and monocytes. The technology offers a scalable, biocompatible tool to capture cellular heterogeneity and advance clinical single-cell genomics.
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.
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