Preprint Watch: May

 

Welcome to this month’s Preprint Watch, where we highlight some of the latest and most interesting preprints for the ISEH community. This time, we’re diving into studies using less explored animal models, new angles on normal and pathological lymphopoiesis, and several exciting technologies pushing the boundaries of advanced cell culture.

We’re also thrilled to chat with Christiana Georgiou from the Lo Celso Lab in London, UK, who will share more details about her recent work on HSC heterogeneity in the context of malaria infection!
As usual, we are more than happy to highlight your new preprint, you just have to submit it at https://www.iseh.org/Preprintwatch! 

From the Simply Blood Community:

Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers
https://www.biorxiv.org/content/10.1101/2025.01.31.635709v1

From the authors: We identified the KDM4 family of H3K9 demethylases as subtype-agnostic therapeutic targets for diffuse large B-cell lymphoma. Inhibition of the KDM4 family antagonizes transcriptional networks essential for B cell identity, epigenetically rewires heterochromatin and elicits cytotoxicity through DNA replication stress-induced cGAS-STING activation.
Contact address: mnajia@broadinstitute.org

Mesenchymal Stromal Cells regulate human Hematopoietic Stem Cell survival, engraftment and regeneration via PGE2/cAMP signaling pathway
https://www.biorxiv.org/content/10.1101/2023.11.09.566361v2

From the authors: We identify a stromal PGE2/cAMP/CREB signaling axis that protects human HSPCs from DNA damage–induced apoptosis by repressing pro-apoptotic ASPP1 and PUMA and stabilizing MCL1 expression. Pharmacologic activation of this pathway enhances long-term engraftment and self-renewal of irradiated HSPCs in vivo.
Contact address: mmilyavsky@post.tau.ac.il

A subset of Haematopoietic Stem Cells resists Plasmodium infection-induced stress by uncoupling interferon sensing and metabolic activation
https://www.biorxiv.org/content/10.1101/2025.04.09.647965v1

The authors investigated how HSCs respond to inflammation during infection using a murine malaria model. They identified two HSC subsets with differing proliferation rates, metabolic rate and response to interferon. The study reveals that a metabolically distinct reserve pool of HSCs remains functional during infection, not by avoiding inflammation, but by preserving a stem-like metabolic profile.
Contact address: christiana.georgiou@imperial.ac.uk

STEM AND PROGENITOR CELLS BIOLOGY

p16.1 and p16.2, new HSPC markers, play redundant roles in zebrafish T-cell lymphopoiesis
https://www.biorxiv.org/content/10.1101/2025.01.21.634058v1?rss=1

The authors used the zebrafish model to characterize two previously undescribed genes, p16.1 and p16.2, expressed in early HSPCs. They found that these genes play redundant roles in embryonic thymopoiesis, as their knockdown impaired HSPC lymphoid commitment and thymic homing, though double mutants showed no phenotype. These findings identify two new HSPC markers functionally linked to lymphoid fate and underscore the heterogeneity of emerging HSPCs.

Regulation of hematopoietic stem cell (HSC) proliferation by Epithelial Growth Factor Like-7 (EGFL7)
https://www.biorxiv.org/content/10.1101/2025.01.21.634107v1?rss=1

The authors investigated the role of Epithelial Growth Factor Like-7 (EGFL7) in hematopoiesis. They found that EGFL7 deficiency led to reduced bone marrow cellularity and fewer HSPCs due to increased quiescence and disrupted cell-cycle progression. Treatment with recombinant EGFL7 reversed these defects and promoted HSC expansion, especially after genotoxic stress. 

Antioxidant role of the GABA shunt in regulating redox balance in blood progenitors during Drosophila hematopoiesis
https://www.biorxiv.org/content/10.1101/2025.01.31.635852v1?rss=1

The authors examined how blood progenitor cells regulate redox balance during lymph gland development. They found that pyruvate oxidation via the TCA cycle generates ROS, while de novo glutathione (GSH) synthesis counteracts oxidative stress. Disrupting this pathway causes metabolic imbalance and ROS dysregulation, highlighting a GABA-driven framework for redox homeostasis in progenitor cells.

Delayed Trp53 activation protects Dnmt3a-mutant hematopoietic stem cells from inflammatory attrition
https://www.biorxiv.org/content/10.1101/2025.01.27.635076v1?rss=1

This work investigates how DNMT3A R882H mutations confer a selective advantage in HSCs during clonal hematopoiesis. Mutant HSCs resist inflammatory and genotoxic stress by delaying activation of the p53-p21-DREAM axis, enabling sustained proliferation without exhaustion under conditions like IL-1β-induced emergency granulopoiesis. The findings point to impaired TP53 signaling as a driver of DNMT3A-mutant clone fitness.

Single-cell transcriptional profiling reveals a novel RAB13+ endothelial subpopulation and profibrotic mesenchymal cells in the aged human bone marrow
https://www.biorxiv.org/content/10.1101/2025.01.28.635238v1?rss=1

Using single-cell RNA sequencing (scRNA-seq), the authors characterized molecular and functional alterations in the human bone marrow microenvironment during aging. They found that aged endothelial cells (ECs) exhibit mitochondrial dysfunction, prothrombotic features, and compromised vascular integrity, including the emergence of a senescent subset. Similarly, mesenchymal stem cells (MSCs) from aged individuals showed impaired matrix remodeling and epithelial-mesenchymal transition (EMT).

A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells
https://www.biorxiv.org/content/10.1101/2025.02.04.636388v1?rss=1

The authors performed over 1,000 single-cell transplants of murine long-term HSCs to map functional heterogeneity and clonal reconstitution dynamics. They found that reconstitution kinetics serve as a unifying indicator of HSC potency, with slower-engrafting cells being more functionally robust. Over time, HSCs showed a shift toward faster kinetics and reduced potency, aligning along a linear hierarchy. Altogether, the study offers a revised model for interpreting HSC diversity.

HSCs and Tregs cooperate to preserve extramedullary hematopoiesis under chronic inflammation
https://www.biorxiv.org/content/10.1101/2025.02.05.636492v1?rss=1

This work uncovers how chronic inflammation reshapes HSC behavior outside the bone marrow. Using a mouse model of autoinflammatory disease, the authors identified extramedullary HSCs in blood, spleen, and inflamed tissues, marked by upregulation of Cd53 and immunoregulatory genes. These CD53+ HSCs function as antigen-presenting cells that promote regulatory T cell (Treg) development, while Tregs, in turn, support HSC maintenance. 

Single-Cell RNA Sequencing Reveals Hemocyte Heterogeneity, Differentiation Trajectories, and Viral Tropism in Shrimp (Macrobrachium rosenbergii) Infected with Decapod Iridescent Virus 1
https://www.biorxiv.org/content/10.1101/2025.02.10.637476v1?rss=1

Using scRNA-seq, the authors mapped hemocyte diversity in the Giant River Prawn (Macrobrachium rosenbergii) before and after infection with Decapod Iridescent Virus 1 (DIV1). They identified 12 transcriptionally distinct hemocyte clusters, with DIV1 promoting expansion of susceptible populations and accelerating differentiation toward immune-active granulocytes. This study offers the first single-cell atlas of shrimp hemocytes under viral infection and identifies candidate targets for improving disease resistance in aquaculture.

PATHOLOGICAL HEMATOPOIESIS

B-cell-Specific Wwox Deletion Promotes Plasmablastic Tumor Development and Pro-Inflammatory Signatures in a Myeloma Mouse Model
https://www.biorxiv.org/content/10.1101/2025.01.29.635577v1?rss=1

By combining Wwox deletion with MYC activation in a murine myeloma model, the authors recreated two key oncogenic events found in B cell malignancies. The resulting mice developed aggressive plasmablastic tumors and lymphomas with reduced survival. Transcriptomic and mutational profiling of plasma cells and tumors revealed inflammatory activation, genomic instability, and hypermutation linked to Aid/Apobec overexpression and disrupted DNA damage response. 

RAS pathway activation drives clonal selection and monocytic differentiation in FLT3 and BCL2 inhibitor resistance
https://www.biorxiv.org/content/10.1101/2025.02.02.636108v1?rss=1

From the authors: Mutational and non-mutational RAS signaling activation drives clonal selection, monocytic differentiation and treatment resistance to FLT3 and BCL2 inhibition in AML. MEK inhibition can resensitize resistant AML cells, suggesting therapeutic potential for combined FLT3, BCL2 and RAS pathway inhibition in AML.

Senolytics restore hematopoietic stem cell function in sickle cell disease
https://www.biorxiv.org/content/10.1101/2025.02.08.636742v1?rss=1

The authors demonstrated that Sickle Cell Disease (SCD) imposes stress on the bone marrow, leading to HSPC dysfunction characterized by oxidative stress, senescence, and DNA damage. Both human and murine SCD HSPCs showed impaired hematopoietic potential, with mice exhibiting a loss of transplantable stem cells. Treatment with the senolytic agent ABT-263 restored HSPC function in SCD mice. 

Single Cell Resolution Tracking of Cutaneous T-Cell Lymphoma Reveals Clonal Evolution in Disease Progression
https://www.biorxiv.org/content/10.1101/2025.02.11.637715v1?rss=1

This study delivers a comprehensive multi-omics analysis of cutaneous T-cell lymphoma (CTCL) progression using 114 serial samples from 35 patients. By integrating genomic, transcriptomic, and epigenomic data at single-cell resolution, the authors uncovered recurrent mutations linked to immune evasion, PI3K signaling, and PD-1 pathways. Frequent mutations in chromatin modifiers such as EZH2 suggest epigenetic therapies, including EZH1/2 inhibitors, may hold promise for CTCL treatment.

The cellular state space of AML unveils novel NPM1 subtypes with distinct clinical outcomes and immune evasion properties
https://www.biorxiv.org/content/10.1101/2025.02.12.637826v1?rss=1

From the authors: The bulk transcriptional profiles of AML are mainly driven by a diverse set of cellular signatures. Single-cell RNA-sequencing of the most common AML subtypes reveals marked heterogeneity extending beyond current genomic classification schemes. NPM1-mutated AML can be divided into two new classes, with distinct immune evasion mechanisms and survival after transplantation.

Signals from the bone marrow B cell niches shape pre-leukemic fate in murine B cell acute lymphoblastic leukemia
https://www.biorxiv.org/content/10.1101/2025.02.14.638228v1?rss=1

Using a murine model of spontaneous B-ALL, this study reveals that bone marrow niche-derived signals—specifically Galectin-1—shape pre-leukemic B cell fate. Disrupting Galectin-1 expression in the microenvironment reduced pre-leukemic cell proliferation and delayed leukemia onset, promoting a more mature BCR+ B-ALL phenotype. Notably, Galectin-1 deficiency skewed secondary mutations toward IL-7R signaling rather than affecting both IL-7R and pre-BCR pathways. 

Comparative analysis of macrophage feeder systems reveals distinct behaviors and key transcriptional shifts in chronic lymphocytic leukemia cells via coculture
https://www.biorxiv.org/content/10.1101/2025.02.13.638101v1?rss=1

From the authors: In this brief report, we evaluated various macrophage coculture systems for their CLL-feeding potential, phagocytosis capacity, induction of treatment resistance in CLL cells, and their impact on the transcriptional profiles of CLL cells.

MOLECULAR HEMATOPOIESIS

Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes
https://www.biorxiv.org/content/10.1101/2025.01.27.635124v1?rss=1

This study investigates the epigenetic landscape of the inactive X chromosome (Xi) in naïve and activated female B cells, uncovering a dynamic interplay between Xist RNA and histone modifications during X-Chromosome Inactivation (XCI). While naïve B cells lack H2AK119Ub and H3K9me3 on the Xi, they retain DNA methylation and H3K27me3, maintaining an Xist-dependent memory of inactivation. Upon mitogenic stimulation, H3K27me3 persists independently of Xist, whereas H2AK119Ub reaccumulates in a Xist-dependent, temporally regulated manner. 

CDK9 interacts with a RanGTP-NEMP1-Importin β complex to regulate erythroid enucleation
https://www.biorxiv.org/content/10.1101/2025.02.03.636174v1?rss=1

From the authors: Importin β physically interacts with CDK9 in erythroid cells and is a novel regulator of erythroid enucleation. Functional assays show that CDK9 and importin β act prior to calcium-dependent actin-mediated nuclear extrusion.

Dynamics of Fanconi anemia protein D2 in association with nuclear lipid droplet formation
https://www.biorxiv.org/content/10.1101/2025.02.05.636583v1?rss=1

This study reveals a previously unrecognized role for FANCD2, a central Fanconi anemia (FA) protein, in lipid metabolism. While FA is primarily known for defects in DNA repair, the authors show that FANCD2 interacts with lipid metabolism regulators and that its deficiency leads to decreased fatty acid levels. These findings suggest that FANCD2 integrates responses to both genotoxic and metabolic stress.

Transient alterations in nucleosome distribution and sensitivity to nuclease define the THP-1 monocyte to macrophage transition
https://www.biorxiv.org/content/10.1101/2025.02.11.637703v1?rss=1

From the authors: Nucleosome distribution is largely static during PMA-induced monocyte differentiation while nucleosome sensitivity is highly dynamic and is associated with gene expression, active chromatin marks, transcription factor binding, and higher-order chromatin structure.

Dynamic nucleosome redistribution and increases in nucleosome sensitivity underpin THP-1 macrophage response to LPS
https://www.biorxiv.org/content/10.1101/2025.02.11.637695v1?rss=1

From the authors: following LPS stimulation, a subset of nucleosomes in macrophage immune promoters undergo transient redistribution, whereas the majority of nucleosomes show changes in MNase sensitivity that are largely uncoupled from gene expression.

TECH WATCH AND MODELING

A High-Throughput Bone Marrow 3D Co-Culture System to Develop Resistance to B Cell Receptor Signaling Targeted Agents in B Cell Non-Hodgkin Lymphoma
https://www.biorxiv.org/content/10.1101/2025.01.14.632958v1?rss=1

The authors developed a high-throughput 3D co-culture model using lymphoma cells, primary bone marrow stromal cells (BMSCs), and a fibrin gel matrix. This system revealed that BMSCs dampen responses to PI3K and BTK inhibitors and support tumor growth. Proteomic analysis identified IGFBP-3, Serpin E1, and PTX-3 as candidate resistance mediators. 

Multiparametric optimization of human primary B-cell cultures using Design of Experiments
https://www.biorxiv.org/content/10.1101/2025.01.16.633474v1?rss=1

The authors developed a primary human B-cell culture system using engineered CD40L-expressing feeder cells and cytokines BAFF, IL-4, and IL-21. A Design of Experiments (DOE) framework was employed to optimize culture conditions and parse the contribution of each component. The study found CD40L and IL-4 to be essential for B-cell survival, proliferation, and IgE class switching, while BAFF had minimal impact and IL-21 provided modest support.

Stochastic Modeling of Hematopoietic Stem Cell Dynamics
https://www.biorxiv.org/content/10.1101/2025.01.27.635091v1?rss=1

From the authors: this study addresses the challenge of characterizing hematopoietic stem cell (HSC) dynamics by developing a flexible, user-friendly stochastic spatial model of long-term and short-term HSCs. The model captures observed cellular variability and heterogeneity, predicts homeostatic dynamics, can be adapted to simulate stress-induced perturbations like apoptosis, and incorporates a spatial component to analyze HSC movement within a bone marrow niche.

SAMHD1 Knockout iPSC model enables high lenti-viral transduction in myeloid cell types
https://www.biorxiv.org/content/10.1101/2025.02.04.636295v1?rss=1

In this study, the authors quantified population bottlenecks during differentiation from induced pluripotent stem cells (iPSCs) to macrophages. They created and validated SAMHD1 knockout (KO) iPSCs, inducing macrophages via two protocols and confirming functionality. To boost lentiviral transduction, they generated SAMHD1 KO iPSCs expressing CRISPR-dCas9-KRAB and showed enhanced gene transfer efficiency in both macrophages and microglia. This model supports robust gene knockdown and high-throughput functional genomics in mature iPSC-derived myeloid cells, offering a scalable platform for studying innate immunity and chronic inflammation.

EpiFoundation: A Foundation Model for Single-Cell ATAC-seq via Peak-to-Gene Alignment
https://www.biorxiv.org/content/10.1101/2025.02.05.636688v1?rss=1

The authors introduce EpiFoundation, a foundation model tailored to scATAC-seq data. EpiFoundation uses non-zero peak filtering to enrich input density and uses paired scRNA-seq data for cross-modality supervision, aligning epigenetic and transcriptomic signals. They trained the model on a curated dataset of 100,000+ cells with paired scRNA-seq and scATAC-seq profiles (MiniAtlas), offering a robust framework for single-cell epigenomic analysis.

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.