Preprint Watch: July

Welcome to the July edition of Simply Blood Preprint Watch! Whether you're reading this from the lab or taking a well-earned break, we’ve got you covered with 25 fresh preprints that span hematopoietic development, leukemogenesis, and the latest in tech development.

This month, we’re especially excited to feature two community-submitted preprints — thank you for sharing your work with us! Keep them coming via https://www.iseh.org/Preprints or by emailing us at info@iseh.org. 

We also had the chance to discuss with Dr. Abdullah Khan, from the Radcliffe Department of Medicine, Oxford UK, about his most recent preprint and an exciting approach to protocol sharing and optimization. Stay tuned for that conversation!

From the Simply Blood Community:

comBO: A combined human bone and lympho-myeloid bone marrow organoid for pre-clinical modelling of haematopoietic disorders
https://www.biorxiv.org/content/10.1101/2025.02.16.638505v1?rss=1

The authors present comBOs, a next-generation human bone marrow organoid model that integrates osteolineage, vascular, lymphoid, and myeloid components derived from iPSCs. Cultured in a granular microgel scaffold under physiologically relevant conditions, comBOs support the creation of “chimeroids” that incorporate healthy or diseased adult cells, enabling faithful modeling of human hematopoietic microenvironments. 

X:@AbAttacks, Bluesky: @abattacks.bsky.social‬

Genetic variation reveals a homeotic long noncoding RNA that modulates human hematopoietic stem cells
https://www.biorxiv.org/content/10.1101/2025.07.16.664824v1

From the authors: This study identifies a genetic variant (rs17437411) within the HOXA locus that disrupts a antisense lncRNA, termed as HOTSCRAMBL, leading to reduced blood cell counts and impaired HSC self-renewal. We found that HOTSCRAMBL regulates HOXA gene (particularly HOXA9) expression and splicing in an SRSF2-dependent manner, with functional consequences in both normal hematopoiesis and HOXA9-dependent leukemias.

Contact address: plyu@broadinstitute.org
Bluesky: @lvchosen1.bsky.social‬ or @bloodgenes.bsky.social‬


STEM AND PROGENITOR CELLS BIOLOGY

CD34 serves as an intrinsic innate immune guardrail protecting stem cells from replicating retroviruses
https://www.biorxiv.org/content/10.1101/2025.03.15.643450v1?rss=1

Stem cells resist HIV infection, partly due to the intrinsic antiviral role of CD34, a surface marker of hematopoietic stem and progenitor cells. This study shows that CD34 impairs HIV-1 infectivity not by blocking entry or integration, but by incorporating into virions and rendering them non-infectious. Loss of CD34—via CRISPR knockout or differentiation—enhances HIV replication in stem cells. 

Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation
https://www.biorxiv.org/content/10.1101/2025.03.24.645017v1?rss=1

This study identifies a protective non-coding variant, rs17834140-T, which reduces clonal hematopoiesis (CH) and myeloid cancer risk by downregulating the RNA-binding protein MSI2 in hematopoietic stem cells. The variant slows clonal expansion and alters an MSI2-regulated RNA network critical for HSC maintenance. Functional modeling confirms that lower MSI2 levels suppress the dominance of ASXL1-mutant clones. These findings reveal post-transcriptional regulation as a key modulator of CH risk and point to MSI2 as a potential therapeutic target.

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?rss=1

From the authors: CD45-targeted radioimmunotherapy more effectively suppresses the hematopoietic system than non- targeted radiation delivery. The bone marrow vascular niche is differentially reprogrammed by CD45-targeted radioimmunotherapy compared to non-targeted radiation delivery.

Loss of transcriptional factor Zbtb33 fails to induce clonal hematopoiesis in mice but plays a role in tumor immunity
https://www.biorxiv.org/content/10.1101/2025.04.10.648125v1?rss=1

From the authors: CH is linked to mutations in hematopoietic stem cells, but the role of Zbtb33 in CH remains unclear. To investigate this, we examined the function of Zbtb33 under physiological conditions and in response to external stimuli. Additionally, we explored whether Zbtb33 mutations cooperate with other genetic mutations to drive clonal hematopoiesis.

Loss of Zbtb33 fails to induce clonal hematopoiesis and does not synergize with Tet or Tp53 mutations. However, it plays a significant role in regulating cancer immunity and the tumor microenvironment.

Deciphering of single-cell chromatin accessibility and transcriptome reveals the discrepancy for ex vivo human erythropoiesis
https://www.biorxiv.org/content/10.1101/2025.04.15.648947v1

Using single-cell chromatin and transcriptome profiling, this study maps ex vivo human erythropoiesis from cord blood, bone marrow, and iPSCs, revealing key developmental constraints. Early differentiation is hindered by myeloid bias linked to low glutamine activity, while iPSC-derived erythropoiesis shows deficiencies in cell cycle and hypoxia signaling. The analysis defines a high-resolution erythroid trajectory and underscores the regulatory role of chromatin accessibility. Weak cell–cell communication in ex vivo systems highlights a potential target to enhance erythrocyte regeneration for clinical applications.

15-PGDH inhibition promotes hematopoietic recovery and enhances HSC function during aging
https://www.biorxiv.org/content/10.1101/2025.04.11.648417v1

From the authors: We identify 15-hydroxyprostaglandin dehydrogenase inhibition (PGDHi) as a strategy to enhance hematopoietic stem cell function in aging. In aged mice, PGDHi expands stem and progenitor populations, accelerates hematopoietic recovery after transplantation, and reduces myeloid bias while maintaining steady-state blood production. These findings highlight a potential therapeutic approach to restore hematopoietic resilience and improve regenerative outcomes in aging.


PATHOLOGICAL HEMATOPOIESIS

Fetal context conveys heritable protection against MLL-rearranged leukemia that depends on MLL3
https://www.biorxiv.org/content/10.1101/2025.03.11.642680v1?rss=1

This study reveals a fetal-specific resistance to MLL::ENL-driven leukemia, explaining the rarity of congenital leukemias despite frequent prenatal MLL rearrangements. In fetal hematopoietic progenitors, MLL::ENL induces differentiation and loss of self-renewal, preventing transformation—a barrier absent when the oncogene is expressed postnatally. This resistance is maintained by the histone methyltransferase MLL3 and can be bypassed by cooperating mutations like NrasG12D. These findings uncover a heritable, MLL3-dependent fetal protection mechanism against leukemogenesis.

Harnessing ALDH1A2 vulnerability in T-cell acute lymphoblastic leukemia
https://www.biorxiv.org/content/10.1101/2025.03.11.642712v1?rss=

This study identifies ALDH1A2 as a T-ALL-specific survival factor regulated by the TAL1 oncogene and absent in most other hematologic malignancies. Pharmacologic inhibition of ALDH1A2 effectively kills leukemic cells across diverse T-ALL subtypes, including relapsed patient samples. These findings position ALDH1A2 as a novel therapeutic target and highlight ALDH inhibition as a promising strategy for treating refractory T-ALL.

Leukemic Cells Manipulate MSCs Bioelectrical Signals to Reshape the Bone Marrow Niche
https://www.biorxiv.org/content/10.1101/2025.03.10.642319v1?rss=1

This study shows that pediatric AML blasts reprogram mesenchymal stromal cells (MSCs) by depolarizing their membrane potential and downregulating the CaV1.2 calcium channel. This bioelectrical shift promotes a leukemia-supportive phenotype, marked by heightened calcium oscillations. Restoring CaV1.2 expression or inducing MSC hyperpolarization reverses these effects and diminishes leukemic support. These findings highlight electrical reprogramming of the bone marrow niche as a novel therapeutic target in AML.

Targeting Monoallelic CREBBP/EP300 Mutations in Germinal Center-Derived B-Cell Lymphoma with a First-in-Class Histone Acetyltransferase Activator
https://www.biorxiv.org/content/10.1101/2025.03.13.642871v1?rss=1

This study introduces YF2, a first-in-class activator of CREBBP/EP300 histone acetyltransferases, which restores function in GC B-cell lymphomas harboring monoallelic HAT mutations. YF2 enhances auto-acetylation and selectively kills HAT-mutant lymphoma cells by boosting acetylation of targets like H3K27, p53, and BCL6. It also upregulates immune pathways and antigen presentation, modulates the germinal center reaction, and promotes B-cell maturation. In vivo, YF2 is well tolerated and extends survival, offering a promising therapeutic strategy for HAT-deficient lymphomas.

Homoharringtonine Promotes FTO Degradation to Suppress LILRB4-Mediated Immune Evasion in Acute Monocytic Leukemia
https://www.biorxiv.org/content/10.1101/2025.03.15.643466v1?rss=1

This study reveals that homoharringtonine (HHT), beyond its role as a protein synthesis inhibitor, suppresses immune evasion in acute monocytic leukemia (AML-M5) by targeting the FTO/m6A/LILRB4 pathway. HHT promotes degradation of the m6A demethylase FTO, leading to increased RNA methylation and reduced LILRB4 expression, a key immune checkpoint. Reduced LILRB4 enhances CD8+ T cell-mediated killing of leukemic cells, highlighting HHT’s potential to improve immunotherapy efficacy in monocytic AML.

Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies
https://www.biorxiv.org/content/10.1101/2025.03.15.643352v1?rss=1

This study demonstrates that FFPE-compatible Hi-C can reliably detect genomic rearrangements in clinical lymphoid cancer biopsies, matching and extending findings from standard FISH assays. Hi-C reveals oncogene rearrangements, enhancer hijacking events, and novel non-coding alterations involving therapeutic targets like PD-1 ligands. Additionally, it distinguishes functional classes of rearrangements and maps topological changes affecting MYC regulation. These results highlight Hi-C as a powerful tool for comprehensive structural and regulatory insights from archived clinical samples.

Individualized pseudogenes networks for survival prognosis in B-cell acute lymphoblastic leukemia
https://www.biorxiv.org/content/10.1101/2025.03.14.643224v1?rss=1

In pediatric B-ALL, pseudogene co-expression patterns were analyzed in 1,416 patients, identifying subgroups with distinct survival outcomes. The pseudogene EEF1A1P12 emerged as a key hub, and the interaction between RPL7P10 and RPS3AP36 served as a strong survival predictor. This study highlights pseudogene networks as valuable prognostic markers in B-ALL and a potential avenue for precision oncology.

Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell Resolution
https://www.biorxiv.org/content/10.1101/2025.03.19.644196v1?rss=1

From the authors: Using primary template-directed amplification single cell whole genome sequencing (PTA-enabled scWGS), single pALL cells contain several fold more mutations per cell than detected in bulk sequencing, which, when multiplied across billions of cells, reveal hidden population-scale genetic complexity. Some phenotypes in pALL are heritable, including treatment resistance, where we identify pre-existing rare clones with relapse-associated mutations that preferentially survive four weeks of standard treatment in patients.

TP53 Inactivation Confers Resistance to the Menin Inhibitor Revumenib in Acute Myeloid Leukemia
https://www.biorxiv.org/content/10.1101/2025.03.24.644993v1?rss=1

This study reveals that TP53 mutations cause de novo resistance to the menin inhibitor revumenib in AML with KMT2A rearrangements or NPM1 mutations. Resistance involves impaired TP53 target activation and altered BCL-2/MCL-1 expression. Combining revumenib with the MCL-1 inhibitor MIK665 restores sensitivity, suggesting TP53 mutation as a biomarker and supporting dual therapy in resistant AML.

Single cell transcriptional evolution of myeloid leukaemia of Down syndrome
https://www.biorxiv.org/content/10.1101/2025.04.01.646181v1?rss=1

Children with Down syndrome face a 150-fold higher risk of myeloid leukemia (ML-DS), which evolves from a preleukemic stage called TAM. Using single-cell RNA sequencing and phylogenetics, the study shows that transcriptional changes driven by GATA1 mutations in TAM persist throughout ML-DS progression, shaping the leukemia’s gene expression. This work maps the transcriptional evolution of ML-DS and offers a framework for understanding mutation impacts in disease context.

The Immune-Modulatory Function of Megakaryocytes in the Hematopoietic Niche of Myeloproliferative Neoplasms
https://www.biorxiv.org/content/10.1101/2025.04.01.646152v1?rss=1

From the authors: JAK2V617F mutant MKs reprogram the marrow immune microenvironment to promote neoplastic HSC expansion in MPNs. LINE-1 activation in diseased MKs triggers chronic inflammation and immune dysfunction in MPNs.

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

This study uncovers TTLL4 as a selective vulnerability in NPM1-mutated AML (Acute Myeloid Leukemia), where it glutamylates NPM1c at E126 to stabilize its cytoplasmic mislocalization and maintain a differentiation block. Genetic or pharmacologic inhibition of TTLL4 reduces NPM1c glutamylation, restores myeloid differentiation, and impairs leukemic growth. TTLL4 loss mirrors the effects of NPM1c degradation and aligns transcriptionally with known therapeutic targets. These results position TTLL4 as a promising druggable epigenetic regulator in NPM1c-driven AML.


MOLECULAR HEMATOPOIESIS

Regulation of Alternative Polyadenylation Events by PABPC1 Affects Erythroid Progenitor Cell Expansion
https://www.biorxiv.org/content/10.1101/2025.03.17.643825v1?rss=1

This study maps the alternative polyadenylation (APA) landscape during early erythropoiesis and identifies dynamic APA shifts essential for erythroid maturation. PABPC1 emerges as a key regulator, with its depletion impairing progenitor proliferation and differentiation. Mechanistically, reduced PABPC1 alters APA usage of targets like TSC22D1, leading to gene overexpression and disrupted cell fate. These findings reveal APA as a critical post-transcriptional layer in erythroid development and disease.

MLL1 complex is a critical regulator of fetal hemoglobin repression
https://www.biorxiv.org/content/10.1101/2025.03.24.645036v1?rss=1

This study identifies the MLL1 complex, specifically its components MEN1 and KMT2A, as key repressors of fetal and embryonic hemoglobin via direct regulation of BCL11A in erythroid cells. Knockdown or pharmacological inhibition of MENIN reduces BCL11A expression, leading to increased γ- and ε-globin and higher fetal hemoglobin (HbF) production in both cell lines and primary human progenitors. These findings highlight MENIN inhibitors as promising candidates for treating sickle cell disease and β-thalassemia by reactivating HbF expression.

RNA Editors Sculpt the Transcriptome During Terminal Erythropoiesis
https://www.biorxiv.org/content/10.1101/2025.04.03.647020v1?rss=1

This study uncovers that the RNA decay pathway involving ZCCHC6 and DIS3L2 is essential for terminal erythropoiesis and globin switching. Loss of these enzymes in mouse models and human cells leads to the accumulation of RNA-rich erythroid precursors and persistent fetal γ-globin expression, revealing a post-transcriptional mechanism that complements transcriptional regulation during hemoglobin switching. These insights provide new targets for enhancing γ-globin stabilization, with implications for treating hemoglobinopathies.


TECH WATCH AND MODELING

Inferring Phylogenetic Trees of Cancer Evolution from Longitudinal Single-Cell Copy Number Profiles
https://www.biorxiv.org/content/10.1101/2025.03.17.643834v1?rss=1

NestedBD-Long is a novel phylogenetic method that integrates longitudinal temporal data into evolutionary analyses of cancer using a birth-death model on copy number variations. Unlike traditional static approaches, it maps real-world time directly onto evolutionary trees, improving accuracy in reconstructing tumor progression and clonal dynamics. This tool enhances understanding of cancer evolution, treatment resistance, and metastasis by linking mutation timing with clinical timelines, and is publicly available for research use.

Multi-step genomics on single cells and live cultures in sub-nanoliter capsules
https://www.biorxiv.org/content/10.1101/2025.03.14.642839v1?rss=1

This study introduces CAGEs—capsules with amphiphilic gel envelopes—that enable selective retention of cells, mRNA, and DNA while allowing reagent exchange, facilitating multi-step, high-throughput single-cell assays, including live-cell analyses. By barcoding DNA and RNA within CAGEs, the authors capture transcriptomes from tens of thousands of expanding clones, enabling detailed tracking of gene expression persistence. This platform broadens the scope of scalable single-cell genomics by integrating live-cell functional assays with molecular profiling.

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.