Welcome to another monthly preprint watch, brought to you by the ISEH Publications Committee. This month we delve into several aspects of normal hematopoiesis, including the most interesting preprints on the hematopoietic niche! Moreover, we have multiple preprints submitted by our readers; you should definitely check them out! And if you have a preprint that you want to see highlighted here, do not wait and submit it through our preprint form.
From the Simply Blood Community:
The Nicotinamide Salvage Pathway is a Metabolic Vulnerability of High-Risk MDS Stem Cells
https://www.biorxiv.org/content/10.64898/2025.12.19.695528v1
High-risk myelodysplastic syndrome (MDS) remains a clinically challenging disease with generally poor outcomes for patients, and new strategies to more effectively eradicate malignant hematopoietic stem and progenitor cells (HSPC) at the root of the disease are needed. This study shows that high-risk MDS HSPC possess a distinctive proteomic signature relative to healthy HSPC, typified by increased expression of mitochondrial complex I proteins, which act as NADH dehydrogenases. Consequently, in preclinical models these malignant cells are selectively killed by pharmacological and genetic inhibition of NAMPT, the rate limiting enzyme in the NAD salvage pathway. These studies identify NAMPT as a critical mediator of cellular energetics in high-risk MDS HSPC and a potential therapeutic target for treatment of this disease.
Contact address: eric.pietras@cuanschutz.edu
Social media handles: @ericpietras (Bluesky) @pietras_eric (X)
Aberrant oxidative metabolism selects for TET2-deficient hematopoietic stem and progenitor cells
https://www.biorxiv.org/content/10.64898/2026.02.28.707294v2
This study examining the unique metabolic phenotype of Tet2-deficient hematopoietic stem and progenitor cells that contribute to their selection in clonal hematopoiesis. Importantly, both mouse and human HSPC exhibit aberrant increases in oxidative metabolism linked to increased expression of oxidative phosphorylation genes and changes in the mitochondrial network. Importantly, the increased oxidative metabolism of Tet2-deficient HSPC increases their reliance on the pentose phosphate pathway (PPP) to control their redox state, and mutation of the PPP enzyme glucose-6-phosphate dehydrogenase increases cellular ROS and impairs selective expansion of Tet2-deficient HSPC. Together, these data show that loss of Tet2 drives increased HSPC metabolism, while uncovering a resulting metabolic vulnerability that can suppress selection for Tet2 mutant clones.
Contact address: eric.pietras@cuanschutz.edu
Social media handles: @ericpietras (Bluesky) @pietras_eric (X)
Sustained exposure to CAR-T cell secretome impairs human Hematopoietic Stem Cell function and is reversible by dual TNFα-IFNγ blockade
https://www.biorxiv.org/content/10.64898/2026.03.17.712280v1
Prolonged cytopenias are a frequent complication of chimeric antigen receptor (CAR) T-cell therapies and are associated with increased infection risk and non-relapse mortality. Although inflammatory cytokines released during CAR-T cell activation have been implicated in immune effector cell-associated hematotoxicity (ICAHT), their direct effects on human hematopoietic stem and progenitor cells' (HSPCs) function remains incompletely understood. Here, we established a reductionist model of CAR-T-associated hematotoxicity using conditioned media (CM) derived from activated CD19 CAR-T cells. Sustained exposure of human HSPCs to CAR-T-derived inflammatory secretome impaired HSPC expansion and reduced long-term repopulating capacity in xenotransplantation assays. In contrast, short-term exposure did not abrogate HSPC function, indicating that brief inflammatory signals can initiate durable reprogramming events, with functional consequences emerging during subsequent proliferative expansion. Mechanistically, CAR-T CM induced IFN gamma- (IFNg) and TNF alpha- (TNFa) responsive transcriptional programs in HSPCs and promoted inflammatory myeloid skewing without evidence of apoptosis-dependent stem cell loss. Combined inhibition of IFNg and TNFa restored HSPC expansion, normalized lineage output, reversed inflammatory transcriptional signatures, and rescued in vivo repopulating capacity without impairing CAR-T cytotoxic activity. These findings demonstrate that CAR-T-derived inflammatory signaling can directly impair human HSC function and identify dual IFNg/TNFa blockade as a potential strategy to mitigate CAR-T-associated hematotoxicity while preserving antitumor efficacy.
Contact address: muddinenis@mail.tau.ac.il
Social Media Handle: @sivasai420
Myelopoiesis
Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation
https://www.biorxiv.org/content/10.1101/2025.05.28.656712v2
From the authors: Swann et al. conduct comparative analysis of single cell RNA sequencing data from multiple emergency myelopoiesis models, finding that different perturbations act at various levels of the hematopoietic hierarchy and recruit distinct sets of molecular mechanisms to enhance myelopoiesis. In particular, they identify a conserved myeloid progenitor-based activation module across multiple disease conditions, which informs outcome in human acute myeloid leukemia.
E2f coordinates the cell cycle and cell fate of hematopoietic progenitors to drive stress myelopoiesis
https://www.biorxiv.org/content/10.1101/2025.06.16.659412v1
This study identifies E2f as a central regulator that simultaneously controls HSPC proliferation, suppresses alternative cell fates via the PRC2 complex (Ezh2), and promotes myeloid differentiation through β-cytokine signaling (CD131). In a preclinical colitis model, combined inhibition of Ezh2 and β-cytokine signaling attenuated stress myelopoiesis and restored colonic homeostasis, positioning this dual targeting as a promising therapeutic strategy for inflammatory diseases.
The differentiation of myeloid progenitors is effected by cascading waves of coordinated gene expression that remodel cellular physiology in a characteristic sequence
https://www.biorxiv.org/content/10.1101/2025.05.25.656046v1
High-resolution genome-wide profiling reveals that gene expression during white blood cell differentiation occurs in coordinated cascading waves — ranging from 8 hours to 3 days — following a defined order: signal transduction, translation, metabolism, and finally innate immunity phenotypes. Two sharp genome-wide transitions mark the initiation of metabolic remodeling and terminal differentiation. These findings highlight that capturing transient intermediate states, not just endpoints, is essential for a complete understanding of hematopoietic differentiation.
In Silico Investigation of the Role of Local and Global Inflammation-Driven Feedback in Myelopoiesis and Clonal Cell Expansion
https://www.biorxiv.org/content/10.1101/2025.08.15.670507v1
A new mathematical model integrating local and systemic inflammatory feedback reveals that while global inflammation enhances hematopoietic resilience, excessive feedback on progenitor cells drives instability and clonal dominance. The model successfully classifies healthy, myelodysplastic, and leukemic states, and shows how mutated clones exploit inflammatory signals to outcompete normal cells. This computational framework identifies critical feedback thresholds governing disease transitions and offers a platform for exploring targeted anti-inflammatory therapies in myeloid malignancies.
Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation
https://www.biorxiv.org/content/10.1101/2025.09.07.674755v3
From the authors: UPR signaling promotes myeloid cell production at the expense of erythroid lineage in steady state. UPR signaling collaborates with the Jak2V617F mutation and increases red blood cell production.
Cigarette Smoke and E-Cigarette Aerosol Extracts Induce Myelopoiesis and Suppress Inflammatory Cytokine Production
https://www.biorxiv.org/content/10.64898/2025.12.21.693601v1
Both cigarette smoke and e-cigarette vapor consistently suppress inflammatory responses in mature myeloid cells while paradoxically driving myeloid expansion and reshaping competitive dynamics between mutant and wild-type progenitors. Chronic in vivo inhalation exposure accelerates HSC aging and increases myeloid proliferation. Together, these findings support a dual model in which tobacco exposure simultaneously blunts innate immunity and creates conditions favoring clonal expansion and premature hematopoietic aging.
Gadd45 regulates fate decisions of myeloid-type blood progenitor cells in Drosophila
https://www.biorxiv.org/content/10.64898/2025.12.16.694615v1
From the authors: Loss of Gadd45 causes a reduction in crystal cells but does not significantly impact macrophage-like plasmatocyte differentiation. Gadd45 overexpression causes myeloid-type progenitor cells to differentiate into lamellocyte, as well as plasmatocyte transdifferentiate to lamellocyte. Gadd45 triggers differentiation by activating a combination of Toll, JNK, and JAK/STAT signaling pathways. Overexpressing Gadd45 does not induce apoptosis but alters the cell cycle behavior of hematopoietic progenitor cells.
Monocyte and Lymphoid Lineages Share a Common Precursor Distinct from Neutrophils in Hematopoiesis
https://www.biorxiv.org/content/10.64898/2025.12.25.696474v1
Using single-cell atlasing and HOPX-based lineage tracing, this study challenges the classical hematopoietic hierarchy by showing that monocytes share a common progenitor with lymphoid lineages rather than with neutrophils. Neutrophils instead commit directly from early multipotent progenitors, diverging early from both lymphoid and monocyte lineages. These findings redefine classical common lymphoid progenitors (CLPs) as lymphoid-monocyte progenitors (LMPs), reshaping our understanding of myeloid lineage specification.
Lung cancer-fueled emergency myelopoiesis is characterized by an increase of S100A9+ and LCN2+ hematopoietic stem and progenitor cells
https://www.biorxiv.org/content/10.64898/2026.02.24.707656v1
Lung cancer systemically disrupts bone marrow hematopoiesis, skewing progenitor output toward granulocyte-monocyte lineages at the expense of mature neutrophils and B cells, as demonstrated by integrated single-cell profiling and two-photon microscopy in both mouse models and human NSCLC samples. S100A9 and Lipocalin-2 (LCN2) are upregulated across the entire hematopoietic trajectory, with S100A9 acting as an upstream regulator of LCN2. In vivo inhibition of S100A9 with Tasquinimod reduced tumor growth and reshaped BM secretion profiles, suggesting therapeutic potential in immunotherapy-refractory lung cancer.
Lymphopoiesis
Super-silencers are crucial for development and carcinogenesis in B cells
https://www.biorxiv.org/content/10.1101/2025.06.27.662063v1
B-cell super-silencers are potent repressive chromatin regions that silence developmentally important genes, and are disproportionately enriched for cancer-associated mutations and translocation breakpoints. In B-cell lymphoma, up to 13% convert into super-enhancers, reactivating oncogenes such as BCL6 and BACH2, which show heightened sensitivity to bromodomain inhibitor JQ1. Their repressive mechanism is partly sequence-dependent, with CpG content determining whether they block enhancer-promoter interactions or suppress local chromatin looping, collectively positioning super-silencer dysregulation as a primary driver of B-cell malignancy.
Decoding human B cell ontogeny in prenatal and adult bone marrow and in vitro models via single-cell multiomics
https://www.biorxiv.org/content/10.1101/2025.08.31.672613v1
A comprehensive single-cell multiomics atlas of over 500,000 prenatal and adult bone marrow cells reveals that while B cell development follows broadly similar trajectories, prenatal progenitors display leukemia-associated features, including enhanced proliferation, higher RAG1/RAG2 activity, and lower bone marrow retention signals. A novel postnatal 'lateCLP' subset functionally equivalent to prenatal 'preProB' cells was identified, clarifying developmental stage correspondences across ontogeny. Additionally, a new hiPSC-based experimental model faithfully recapitulates key B cell differentiation stages, providing a powerful resource for investigating the molecular origins of pediatric hematological malignancies.
Serum-free differentiation platform for the generation of B lymphocytes and natural killer cells from human CD34+ cord blood progenitors
https://www.biorxiv.org/content/10.1101/2025.05.22.655473v1
From the authors: This article presents a novel, fully humanized, serum-free co-culture system that efficiently directs cord blood-derived HSC into B and natural killer (NK) cells. By using human bone marrow stromal cells and recombinant human cytokines, it overcomes the limitations of murine-based models and better mimics human blood cell development. This platform enables improved disease modeling and therapeutic testing relevant to human hematopoiesis.
Arid2 promotes Follicular B-cell differentiation and antibody responses in vivo
https://www.biorxiv.org/content/10.1101/2025.10.01.678812v1
Conditional knockout studies reveal that ARID2, a subunit of the PBAF chromatin remodeling complex frequently mutated in B cell leukemias, is a critical regulator of normal B cell differentiation. Its loss disrupts stage-specific gene expression programs, particularly B cell receptor signaling, impairing follicular B cell output without affecting proliferation or survival. Functionally, ARID2-deficient mice show impaired germinal center responses and reduced IgG production, linking its chromatin remodeling activity to both early lymphopoiesis and mature B cell function.
Histone methyltransferase DOT1L differentially affects the development of dendritic cell subsets
https://www.biorxiv.org/content/10.1101/2025.09.05.674429v1
DOT1L-mediated H3K79 methylation differentially regulates dendritic cell subset development: its loss reduces myeloid progenitors and plasmacytoid DCs (pDCs), while expanding cDC2s. Dot1l-knockout DCs fail to produce IFNα upon stimulation and show upregulated MHC class II surface expression alongside enriched antigen presentation pathways. These findings establish DOT1L as a key epigenetic suppressor of antigen presentation and a subset-specific regulator of DC development through its methyltransferase activity.
T cell development from expanded hematopoietic progenitors reveals progression control by Lmo2, Erg, Spi1, Hoxa9, and Meis1
https://www.biorxiv.org/content/10.1101/2025.04.22.649893v1
Using an optimized serum-free expansion system combined with single-cell RNA sequencing and CRISPR knockouts, this study maps the earliest transcriptional and chromatin events in T cell commitment. It shows that initial Notch activation immediately opens chromatin at the TCR-Cβ locus. Systematic gene knockouts identify Ikzf1, Hes1, Gabpa, and Myb as required for T-lineage entry, while Lmo2, Erg, and Meis1 act as developmental brakes. Notably, Lmo2 — a stem cell and leukemia-associated factor — strongly restrains T cell program initiation, with its deletion accelerating TCRβ transcription and activation of key T cell transcription factors.
Microtubule anchoring and coupling of CD20 to the RhoA/Rock1 pathway
https://www.biorxiv.org/content/10.1101/2025.05.29.656301v2
CD20 maintains the resting state of naïve B cells through PKCδ-mediated phosphorylation. It recruits 14-3-3 adaptor proteins, linking CD20 to the GEF-H1/microtubule network that stabilizes the IgD-BCR nanocluster. Upon anti-CD20 antibody binding, microtubules disassemble and GEF-H1 is replaced by a RhoA-GTP/ROCK1 complex, triggering actomyosin contractility. This study reveals CD20 as an active orchestrator of the microtubule-to-actin cytoskeletal switch in B lymphocytes, with direct implications for optimizing anti-CD20 therapeutic protocols.
Optimized Ex Vivo Differentiation of CD103+ Dendritic Cells and High-Efficiency Retroviral Transduction of Mouse Bone Marrow HSCs
https://www.biorxiv.org/content/10.1101/2025.09.21.677651v1?rss=1
A two-stage ex vivo culture system efficiently generates CD103+ cDC1-like dendritic cells from mouse bone marrow progenitors, recapitulating their in vivo counterparts. Combined with a high-efficiency retroviral transduction method (ecotropic pseudotyped virus and retronectin-coated plates), this platform enables robust HSC genetic manipulation. Together, these tools provide a powerful framework for dissecting cDC1 biology and advancing dendritic cell-based immunotherapy research.
Feeder-free generation of functional dendritic cells from human pluripotent stem cells
https://www.biorxiv.org/content/10.1101/2025.11.13.687739v1?rss=1
A feeder-free differentiation platform generates CD1c+CD141+ conventional dendritic cells from human pluripotent stem cells (hPSC-cDCs), resembling tissue-resident cDC2 subsets. The protocol was optimized through a Design-of-Experiments framework to improve efficiency and reduce cytokine demand. The hPSC-cDCs demonstrate superior antigen uptake, cytokine responses, and CD8+ T cell priming compared to conventional monocyte-derived DCs.
Three-Dimensional Epigenome Roadmap of Human B-cell Differentiation Uncovers Mechanisms of Humoral Immunity and Oncogenesis
https://www.biorxiv.org/content/10.64898/2025.12.22.695871v1
The authors generated a comprehensive 3D epigenomic atlas, spanning nine B cell differentiation stages, linking nearly half a million enhancers to target genes. That reveals that B cell identity is established through large additive and synergistic enhancer networks. Memory B cells retain primed chromatin loops enabling accelerated responses upon antigen re-exposure, uncovering a 3D epigenetic basis for immune memory.
MLL3 and MLL4 sustain hematopoietic stem cell multipotency by opposing a B-cell default state
https://www.biorxiv.org/content/10.64898/2025.12.24.696404v1
From the authors: MLL3 and MLL4 act redundantly in HSCs to sustain transcription factor and enhancer networks that support multipotency. Simultaneous loss of MLL3 and MLL4 drives hematopoietic progenitors into a uniform B-cell-like default state
B Lymphocyte Protein Factories produced by Hematopoietic Stem Cell Gene Editing
https://www.biorxiv.org/content/10.64898/2026.01.16.699998v1
By gene-editing small numbers of HSPCs, this study programs B cell progeny to produce long-term, high-level therapeutic antibodies upon antigen-driven clonal expansion. Edited cells achieved protective serum antibody levels against HIV-1, malaria, and influenza, with the anti-influenza broadly neutralizing antibody conferring universal protection against lethal heterologous challenge.
Cbfb2 gene dosage programs the differential lymphoid lineage developmental potential of fetal and adult hematopoietic progenitors
https://www.biorxiv.org/content/10.64898/2026.03.02.708762v1
CBFβ2 gene dosage acts as a quantitative switch governing fetal-versus-adult lymphopoiesis. Its reduction unlocks fetal-like competence in adult progenitors and enables robust generation of IL-17-producing γδ T cells through promoter-level chromatin remodeling. Fetal niches further amplify this latent potential, selectively favoring innate-like γδ T cell differentiation over conventional αβ T cell output. Notch1 haploinsufficiency phenocopies CBFβ2 reduction, linking quantitative RUNX:CBFβ and NOTCH1 signaling to innate lymphocyte developmental programming and revealing unexpected plasticity in adult hematopoiesis.
CXCR4 coordinates adhesion, migration, and development of human NK cells
https://www.biorxiv.org/content/10.64898/2026.03.12.711152v1
This study shows that CXCR4 and its ligand CXCL12 regulate NK cell maturation by mediating adhesion and contact-dependent motility within stromal niches. CXCR4 blockade disrupted integrin-dependent stromal engagement and impaired NK cell generation from CD34+ precursors. High-resolution imaging reveals direct crosstalk between CXCR4 and integrins, providing a mechanistic basis for the chemokine-dependent modulation. Findings from WHIM syndrome patients carrying CXCR4 gain-of-function mutations treated with plerixafor confirm the in vivo relevance of this axis in NK cell trafficking and development.
MKpoiesis
Treatment with the ribosome biogenesis inhibitor CX-5461 increases platelet count in humans and enhances murine megakaryopoiesis
https://www.biorxiv.org/content/10.1101/2025.06.15.659730v1?rss=1
The authors observed unexpectedly that the ribosome biogenesis inhibitor CX-5461 stimulates platelet production in both cancer patients and mice. The inhibitor drove selective expansion of megakaryocytes and MK-biased progenitors, independently of thrombopoietin (Tpo) signaling. Single-cell RNAseq confirmed enhanced megakaryocyte progenitor differentiation, and CX-5461 treatment mitigated carboplatin-induced thrombocytopenia by accelerating platelet recovery without altering function or lifespan. These findings reveal a novel TPO-independent thrombopoietic mechanism and identify CX-5461 as a candidate therapeutic for managing thrombocytopenia in cancer treatment.
Molecular Control of Non-Muscle Myosin II-A Aggregation and Intracellular Dynamics by motor- or tail-specific MYH9 Mutations
https://www.biorxiv.org/content/10.1101/2025.05.20.654665v1?rss=1
In MYH9-related disease, the motor domain mutation N93K reduces functional Non-Muscle Myosin II-A (NM2-A) by enhancing filament stability and forming concentration-dependent aggregates that sequester both mutant and wild-type NM2-A. In contrast, the tail mutation E1841K forms independent aggregates that exclude wild-type NM2-A, limiting its dominant-negative impact. These distinct aggregation behaviors provide a molecular explanation for the greater clinical severity observed with motor versus tail domain mutations in MYH9-RD patients.
Shared and distinct sequence-function signatures define different modes of human TpoR activation
https://www.biorxiv.org/content/10.1101/2025.09.09.675271v1?rss=1
In this work, the authors performed deep mutational scanning and AlphaFold 3 modeling, which reveal that synthetic agonists and oncogenic mutations activate the thrombopoietin receptor (hTpoR) through a shared left-handed parallel helix dimer interface. Conversely, native Tpo induces a structurally distinct right-handed "splayed" dimer insensitive to transmembrane substitutions. These two activation modes reconcile prior conflicting biochemical models and provide a mechanistic framework for designing selective therapeutics in myeloproliferative diseases.
The alarmin Interleukin-33 modulates platelet proteome, function and biogenesis
https://www.biorxiv.org/content/10.64898/2025.12.19.695476v1
From the authors: IL-33 impacts platelet inflammation-related proteins and adhesion. IL-33 receptor is expressed by subsets of MK progenitors in mouse and human
ATP11A and ATP11C are plasma membrane phosphatidylserine flippases in in vitro human megakaryocytes.
https://www.biorxiv.org/content/10.64898/2026.01.30.702765v1
Using CRISPR-Cas9 knockout in hiPSC-derived megakaryocytes, this study identifies the ATPases ATP11A and ATP11C as the flippase proteins responsible for maintaining phosphatidylserine (PS) asymmetry at the platelet plasma membrane. While single knockouts retained normal flippase activity, ATP11A/11C double knockout abolished NEM-sensitive PS internalisation, mirroring the constitutive PS exposure seen in CDC50A knockouts. These findings close a critical gap in understanding pro-coagulant platelet biology, with direct implications for thrombotic disease.
Megakaryocyte activation and mobilization from the bone marrow in response to trauma and hemorrhagic shock in mice
https://www.biorxiv.org/content/10.64898/2026.02.10.704825v1
Using a murine trauma-hemorrhage model, this study demonstrates that severe injury induces rapid changes in megakaryocyte morphology and sinusoidal mobilization within one hour, accompanied by elevated alpha-granule protein levels in the bone marrow. Co-culture experiments confirm that soluble bone marrow factors from injured mice are sufficient to recapitulate these changes in naive megakaryocytes. These findings reveal a previously unrecognized hyperacute remodeling of the bone marrow microenvironment following trauma that rapidly alters megakaryocyte activity.
The Kifc3 Motor Protein Controls Centrosomal Factor Cep192 in Ontogenic Coordination of Megakaryocyte Development
https://www.biorxiv.org/content/10.64898/2026.03.20.713234v1
The kinesin Kifc3 is identified as a key regulator of ontogenic megakaryopoiesis, with its knockdown in neonatal megakaryocytes inducing adult-type morphogenesis. It also enhanced platelet release through centrosomal dispersion of Cep192, which promotes cellular process extensions via actin remodeling. This Kifc3-Cep192 pathway operates downstream of the Mkl1/Dyrk1a axis, governing fetal-to-adult megakaryocyte transition. Kifc3 inhibition recapitulates these effects, suggesting therapeutic potential for thrombocytopenia in premature infants, post-cord blood transplantation, and Down Syndrome-associated leukemogenesis.
Erythropoiesis
Canonical nuclear envelope protein emerin regulates structure and integrity of the erythrocyte plasma membrane
https://www.biorxiv.org/content/10.1101/2025.06.06.658339v1?rss=1
Emerin, canonically known as a nuclear envelope protein, is also expressed at the red blood cell plasma membrane, where it regulates membrane protein localization and cytoskeletal dynamics. Loss of emerin in mice reduces RBC volume and hemoglobin content, with males additionally showing increased RBC number and osmotic resistance. Human EMD mutations associate with altered mean corpuscular volume, and Emery-Dreifuss muscular dystrophy patients display consistent mild RBC phenotypes, establishing a non-canonical, cell-specific role for emerin in anuclear cells.
Direct and indirect regulation of fetal globin transcript by RNA-binding protein IGF2BP1
https://www.biorxiv.org/content/10.1101/2025.09.09.675143v1?rss=1
The m6A RNA-binding protein IGF2BP1 promotes fetal hemoglobin (HBG1/2) expression through two distinct mechanisms: indirect suppression of BCL11A via activation of its repressor HIC2, and direct binding to HBG1/2 transcripts to enhance their translation through stop codon-proximal m6A-modified coding sequences. These findings reveal a previously unappreciated physical interaction between heterochronic RNA-binding proteins and globin transcripts. This dual regulatory mechanism deepens understanding of developmental hemoglobin switching and may inform therapeutic strategies for reactivating fetal hemoglobin in hemoglobinopathies.
Near completely reversing the γ- to β-globin switch by enhancer release, retargeting and reinforcing
https://www.biorxiv.org/content/10.64898/2026.01.30.702713v1
This study shows that simultaneous editing of CACCC and TGACCA motifs disrupts the KLF1-mediated genomic interaction, while relieving epigenetic repression of HBG, redirecting the locus control region from β- to γ-globin and achieving near-complete reversal of hemoglobin switching. These findings demonstrate that gene competition and epigenetic silencing jointly govern globin switching, with enhancer-promoter specificity determined by transcription factor clusters binding to both elements. This dual-editing strategy also represents a promising therapeutic approach for β-hemoglobinopathies.
Regulation of BCL11A DNA binding and expression in human erythrocyte precursor HUDEP-2 cells
https://www.biorxiv.org/content/10.64898/2026.02.06.704516v1
Structural analysis reveals that BCL11A recognizes the TGNCCA motif through distinct strand-specific interactions, potentially promoting BCL11A oligomerization on DNA. Epigenetic inhibition of DNA methylation reactivates fetal hemoglobin in HUDEP-2 cells, with the EZH2 inhibitor FTX6058 notably reducing BCL11A transcription, via LIN28B. A drug screening of 213 IMiD-derived compounds identifies consistent downregulation of IKZF1 and ZFP91 as part of BCL11A's regulatory network, collectively revealing new therapeutic avenues for HbF reactivation in β-hemoglobinopathies.
A cell-nonautonomous heme acquisition pathway enables erythroid hemoglobinization under stress
https://www.biorxiv.org/content/10.64898/2026.02.10.705195v1
This study reveals that erythroblasts are not heme-autonomous, instead importing extracellular heme through the plasma membrane permease HRG1, which accumulates during stress erythropoiesis. HRG1 loss impairs heme uptake, blocks terminal erythroid differentiation, and causes anemia, while partial HRG1 loss in β-thalassemic mice reduces ineffective erythropoiesis. These findings uncover intercellular heme sharing as a critical mechanism in red cell production and identify HRG1 as a promising therapeutic target in hemoglobinopathies.
Erythropoietin Mediates Glycerophospholipid Remodeling During Human Early Erythropoiesis
https://www.biorxiv.org/content/10.64898/2026.02.20.707106v1
Single-cell transcriptomics and untargeted lipidomics reveal that erythropoietin (Epo) drives a transient upregulation of lipid metabolic pathways during the BFU-E to CFU-E progenitor transition, resulting in Epo-dependent remodeling of specific glycerophospholipid species. Epo is further required to maintain key enzymes for phosphatidylcholine and phosphatidylethanolamine synthesis in differentiating erythroid cells. These findings uncover a previously unrecognized role for Epo in shaping membrane lipid composition during early erythropoiesis, with implications for understanding lipid dysregulation in anemia and bone marrow failure diseases.
Transitory enhancement of GATA2 chromatin engagement during early erythroid differentiation
https://www.biorxiv.org/content/10.64898/2026.03.05.709895v1
Combining single-molecule live-cell imaging with CUT&Tag profiling, this study reveals that early erythroid differentiation is paradoxically characterized by a transient increase in long-lived GATA2 chromatin binding, before declining upon further maturation. Genome-wide mapping identifies two classes of early GATA2 targets: promoter-proximal sites enriched for GATA/RUNX motifs and distal enhancer elements with composite GATA/E-box signatures. These findings reframe the GATA2-to-GATA1 transition as a kinetically regulated process rather than simple GATA2 silencing, revealing transcription factor binding dynamics as a key regulatory layer in lineage commitment.
Niche
A new double reporter strategy reveals a subset of non-migratory hematopoietic stem cells localized in a dynamic bone marrow niche
https://www.biorxiv.org/content/10.1101/2025.07.20.665772v1
Using a dual Hoxb5-mKO2/Vwf-GFP reporter strategy, intravital microscopy reveals that highly pure long-term HSCs remain non-migratory in homeostasis, during stress-induced proliferation, and during ageing, challenging the prevailing model that HSC activation requires relocation to alternative niches. These HSCs reside in contact with vasculature and LepR+ perivascular cells, and increased megakaryopoiesis following platelet depletion dynamically brings megakaryocytes into their proximity. These findings uncover previously unrecognized niche dynamics during regeneration while establishing that HSC activation is spatially fixed within the perivascular niche.
A bone marrow stromal secretome screen identifies semaphorin 3A as a regulator of hematopoiesis
https://www.biorxiv.org/content/10.1101/2025.08.07.669162v1
From the authors: Borger et al. characterize the secretome of revitalized bone marrow stromal cells and identify a novel role of the protein semaphorin 3A in regulating hematopoietic stem and progenitor cell proliferation in steady state and stress conditions.
Niche-targeted therapy via YAP/TAZ activation enhances hematopoietic regeneration
https://www.biorxiv.org/content/10.1101/2025.08.21.671455v1
From the authors: YAP/TAZ enable BM niche cells to sense injury and restore their structure and function, thereby promoting hematopoietic regeneration. Pharmacological activation of YAP/TAZ enhances BM niche resilience and accelerates hematopoietic recovery after myelosuppressive therapies.
Vcam1 in endothelial and stromal cells regulates hematopoietic stem cell contact with the niche
https://www.biorxiv.org/content/10.1101/2025.08.30.673252v1
From the authors: blood stem cell interaction with the niche microenvironment during development is critical for establishing a robust stem cell pool into adulthood. This study determines the niche cell types that present Vcam1 in the embryo and allow interaction with blood stem cells.
High-resolution spatial profiling of the hematopoietic landscape of the murine lung
https://www.biorxiv.org/content/10.1101/2025.09.25.678618v1
From the authors: This work represents the highest resolution gene expression mapping of the spatial symbiosis between the hematopoietic and pulmonary systems. Pulmonary megakaryocytes localize within distinct vascular and stromal neighborhoods.
Degeneration and Impaired Resilience of Skull Bone and Hematopoietic Bone Marrow
https://www.biorxiv.org/content/10.1101/2025.10.02.679940v1
This work reveals that skull marrow is among the most vulnerable sites of age-related decline: loss of mesenchymal and osteoprogenitors, adipocyte accumulation, vascular senescence, mitochondrial dysfunction, and heightened inflammation. Proteomic profiling further shows that vertebral niches are relatively spared from these hallmarks, contrasting sharply with skull marrow deterioration. These findings redefine the geography of bone marrow ageing and position the skull as a clinically relevant target for preserving hematopoietic and immune health.
Quantitative Multicolored Deep Imaging of Human Bones Reveals a Composite Osteo-Sinusoidal Niche for Mesenchymal Stromal Cells.
https://www.biorxiv.org/content/10.1101/2025.10.07.680053v1
Using DeepBone, a novel tissue-clearing protocol combining simultaneous mRNA and protein detection, this study spatially maps human bone marrow mesenchymal stromal/stem cells (BM-MSCs). The authors revealed that the native niche in young bone is enriched in vasculature, sinusoids, bone matrix, and adipocytes, while aged bone shows loss of these preferential associations. Proliferative BM-MSCs localize predominantly along blood vessels, and a specialized young-bone niche features sinusoids coiled around trabeculae enriched in R-type vessels. These findings provide a physiological foundation for developing tissue-engineering strategies that faithfully recapitulate the native BM-MSC microenvironment.
Red bone marrow hosts metabolically active anucleate adipocytes that support hematopoiesis
https://www.biorxiv.org/content/10.64898/2025.12.02.691590v1
Using a high-yield isolation method, this study characterizes human regulatory bone marrow adipocytes (rBMAds) as a novel anucleate adipocyte subtype that retains organelles and active lipid and glucose metabolism, yet unlike rodent counterparts, lacks lipolytic activity. These cells actively secrete hematopoiesis-supporting factors, establishing them as functional contributors to the bone marrow niche. Their properties suggest they arise from constitutive BMAds through terminal differentiation, defining a previously unrecognized adipocyte subtype critical for bone marrow homeostasis.
CYB5R3 Controls Sex-Specific Stress Erythropoiesis via Heme-Biosynthesis
https://www.biorxiv.org/content/10.64898/2025.12.04.692104v1
From the authors: CYB5R3 is required for effective stress erythropoietic induction, with a more pronounced impact in males. Erythroid-specific CYB5R3 deficiency creates a heme-limited state, impairing erythroblast differentiation and maturation.
Redefining the topology of the human bone marrow using augmented spatial transcriptomic analysis
https://www.biorxiv.org/content/10.64898/2025.12.22.694222v1
Spatial transcriptomic profiling of over 5 million cells across 30 human bone marrow samples reveals spatially restricted hematopoietic trajectories and extends understanding of the HSC niche. It also identifies distinct immune and stromal co-enriched neighborhoods associated with fibrosis in myeloproliferative neoplasms. A machine learning model trained on spatial transcriptomic data quantifies microenvironmental deviation, uncovering previously unrecognized inter- and intra-individual heterogeneity in MPN.
A single cell atlas defines perinatal factors that drive murine bone marrow development
https://www.biorxiv.org/content/10.64898/2026.01.21.700817v1
A single-cell atlas spanning late gestation through 18 months of age defines murine BMSC progenitor identities and developmental trajectories, revealing how CAR cells and osteoblasts establish hematopoietic niches prior to HSC colonization. EBF1-3 transcription factors emerge as key temporal regulators of niche establishment, with their activity linked to systemic metabolic, inflammatory, and hypoxic signals driving postnatal CAR cell emergence. These findings provide unprecedented resolution into the sequential cellular and molecular events governing bone marrow colonization and lifelong hematopoietic niche maturation.
Leptin Receptor+ cells create a perisinusoidal niche for thrombopoiesis in the bone marrow by synthesizing CXCL14
https://www.biorxiv.org/content/10.64898/2026.01.27.702029v1
From the authors: Leptin Receptor+ stromal cells regulate terminal differentiation in megakaryocytes in addition to maintaining stem and progenitor cells. CXCL14 from Leptin Receptor+ cells promotes the formation of platelets by remodeling lipid metabolism in megakaryocytes in the bone marrow
Altered stem cell properties of human hematopoietic stem and progenitor cells based on bone region location
https://www.biorxiv.org/content/10.64898/2026.02.25.707977v1
While HSPCs isolated from the medullary cavity and trabecular compartment display comparable cell-intrinsic functional outputs, extracellular vesicles derived from the trabecular microenvironment specifically inhibit cell cycle progression and promote HSPC quiescence. These findings reveal that anatomically distinct bone marrow compartments exert differential regulation through paracrine extracellular vesicle signaling rather than cell-intrinsic programming. This identifies the trabecular niche as a specialized microenvironment with a protective role in maintaining HSPC quiescence.
NicheSphere reveals Spp1⁺ macrophages as central hubs coordinating fibrotic remodeling in myeloproliferative neoplasms
https://www.biorxiv.org/content/10.64898/2026.03.16.711605v1
Using single-cell sequencing, dual lineage-tracing, and the novel NicheSphere computational framework, this study identifies SPP1⁺ macrophages as central communication hubs driving bone marrow fibrosis in myeloproliferative neoplasms through WNT, JAK-STAT, TNFα, and TGF-β signaling with osteoCAR cells, fibroblasts, and megakaryocytes. Mechanistically, SPP1 promotes integrin-mediated adhesion and IL-1β secretion, while IL-1 cytokines reciprocally induce Spp1 and collagen expression, forming a self-sustaining fibroinflammatory loop. Genetic ablation of Spp1 reduced inflammation and restored macrophage function, establishing SPP1⁺ macrophages as promising therapeutic targets in progressive bone marrow fibrosis.
Blog post contributed by Alessandro Donada, PhD (Bluesky: @alessandrodonada.bsky.social) of the ISEH Publications Committee.
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