bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2025–07–06
twenty-one papers selected by
William Grey, University of York



  1. Nat Aging. 2025 Jun 30.
      Aged hematopoietic stem cells (HSCs) exhibit diminished self-renewal and myeloid-biased differentiation with a decline in hematopoiesis and adaptive immune function. However, the molecular regulation of this impaired function remains largely unknown. Here, through an in vivo CRISPR-Cas9-based screen, we uncovered clusterin (Clu) as a driver of biased differentiation. Clu is upregulated in aged HSCs, and its knockout diminishes biased differentiation. Clu promotes mitochondrial hyperfusion by interacting with Mfn2 in aged HSCs, and its ablation attenuates oxidative phosphorylation, improves mitophagy, and reverses myeloid-biased differentiation via the OXPHOS-p38-Cebpb axis. Transplantation of Clu-depleted aged HSCs into middle-aged mice results in balanced hematopoiesis and improved physical functions. Together, our data identify Clu as a critical regulator of aging-associated myeloid bias and reveal an Mfn2-OXPHOS-p38-Cebpb axis as the mechanism underlying how Clu upregulation in aged HSCs leads to myeloid-biased differentiation, providing a target for rejuvenation of aged hematopoietic and immune systems.
    DOI:  https://doi.org/10.1038/s43587-025-00908-z
  2. Cell Stem Cell. 2025 Jul 03. pii: S1934-5909(25)00225-5. [Epub ahead of print]32(7): 1036-1037
      Hematopoietic stem cells (HSCs) with mutations that can cause clonal hematopoiesis of indeterminate potential (CHIP) accumulate during aging. Agarwal et al.1 demonstrate in Nature that intestinal barrier permeability increases with age and enables the microbial metabolite ADP-heptose to reach the bone marrow, thus driving the expansion of DNMT3A-mutant HSCs.
    DOI:  https://doi.org/10.1016/j.stem.2025.06.003
  3. Stem Cell Res Ther. 2025 Jul 01. 16(1): 335
       BACKGROUND: Hematopoietic Stem and Progenitor Cells (HSPCs) gene therapy has shown significant progress, with commercial approval for at least four distinct haematological disorders, and poised for a rapid expansion in the upcoming years. Despite these advancements, the ex vivo culture of HSPCs continues to present significant challenges. The stress induced by ex vivo culture can negatively impact transplantation outcomes, while the need for exogenous cytokine supplementation contributes to the high costs associated with gene therapy products.
    METHODS: We developed genetically modified human bone marrow MSCs (GM-MSCs) secreting cytokines such as Stem cell factor (SCF), Thrombopoietin (TPO), FMS-like tyrosine kinase-3-ligand (FLT3L), and Interleukin-3 (IL3), closely resembling bone marrow cellular niche to augment HSPCs culture.
    RESULTS: HSPCs proliferate on GM-MSCs akin to standard conditions, devoid of external cytokine supplementation and these HSPCs retain their stem cell characteristics, colony-forming potential, stemness gene signatures, and capacity for long-term multilineage reconstitution in NBSGW mice. We demonstrate that our biomimetic feeder layer supports and alleviates stress associated with Homology Directed Repair (HDR) mediated gene-editing of HSPCs for fetal haemoglobin reactivation for a potential application in β-hemoglobinopathies gene therapy.
    CONCLUSION: Our GM-MSCs offer a compelling alternative to traditional cytokine supplementation by establishing a biomimetic bone marrow niche that fosters HSPC expansion while maintaining their stemness. These findings underscore the potential of engineered MSCs to revolutionize ex vivo HSPCs culture, ultimately enhancing their therapeutic value for gene therapy applications.
    Keywords:  Gene therapy; Hematopoietic stem and progenitor cells; Homology-directed gene editing; Mesenchymal stromal cells; Β-hemoglobinopathies
    DOI:  https://doi.org/10.1186/s13287-025-04474-4
  4. Stem Cells. 2025 Jul 03. pii: sxaf047. [Epub ahead of print]
      Hematopoietic aging is characterized by diminished stem cell regenerative capacity and an increased risk of hematologic dysfunction. We previously identified that the prostaglandin-degrading enzyme 15-hydroxyprostaglandin dehydrogenase (15-PGDH) regulates hematopoietic stem cell activity. Here, we expand on this work and demonstrate that in aged mice, (1) 15-PGDH expression and activity remain conserved in the bone marrow and spleen, suggesting it remains a viable therapeutic target in aging, (2) prolonged PGDH inhibition (PGDHi) significantly increases the frequency and number of phenotypic hematopoietic stem and progenitor cells across multiple compartments, with transcriptional changes indicative of enhanced function, (3) PGDHi-treated bone marrow enhances short-term hematopoietic recovery following transplantation, leading to improved peripheral blood output and accelerated multilineage reconstitution, and (4) PGDHi confers a competitive advantage in primary hematopoietic transplantation while mitigating age-associated myeloid bias in secondary transplants. Notably, these effects occur without perturbing steady-state blood production, suggesting that PGDHi enhances hematopoiesis under regenerative conditions while maintaining homeostasis. Our work identifies PGDHi as a translatable intervention to rejuvenate aged HSCs and mitigate hematopoietic decline.
    Keywords:  aging; drug target; hematopoietic stem cell transplantation; hematopoietic stem cells; stem cells
    DOI:  https://doi.org/10.1093/stmcls/sxaf047
  5. Stem Cell Reports. 2025 Jun 25. pii: S2213-6711(25)00175-4. [Epub ahead of print] 102571
      The ineffective hematopoiesis of myelodysplastic syndrome (MDS) suggests that hematopoietic stem and progenitor cells (HSPCs) are defective. Here, we demonstrate that NUP98::HOXD13 (NHD13) MDS mice have significantly decreased functional HSPCs. Moreover, in contrast to wild-type (WT) bone marrow (BM), lineage-positive (Lin+) BM cells from NHD13 mice have self-renewal potential. Specific subsets of NHD13 Lin+ cells that express B220 and Kit antigens were able to self-renew and generate MDS in WT recipients. Although this unique B220+Kit+ phenotype could be found in WT as well as NHD13 BM, the population was markedly increased in NHD13 BM. Further characterization using Mac1 and Gr1 markers revealed that both Mac1+Gr1+B220+Kit+ and Mac1-Gr1- B220+Kit+ populations showed self-renewal and led to an MDS phenotype in WT recipients. Taken together, these findings demonstrate that as normal hematopoiesis derived from typical HSPCs decreases in NHD13 mice, committed hematopoietic progenitor cells proliferate, self-renew, and initiate MDS.
    Keywords:  MDS-initiating cell; NHD13; hematopoiesis; kit; myelodysplastic syndrome; stem cells
    DOI:  https://doi.org/10.1016/j.stemcr.2025.102571
  6. Nat Commun. 2025 Jul 01. 16(1): 5639
      The hematopoietic stem cell and multipotent progenitor (HSC/MPP) pool dynamically responds to stress to adapt blood output to specific physiological demands. In β-thalassemia (Bthal), severe anemia and ineffective erythropoiesis generate expansion of erythroid precursors and a chronic stress status in the bone marrow (BM) microenvironment. However, the response to the BM altered status at the level of the HSC/MPP compartment in terms of lineage commitment has not been investigated. Bulk and single-cell RNA-sequencing reveal that Bthal HSCs/MPPs are expanded and activated with enhanced priming along the whole Ery differentiation trajectory. Consistently, HSC/MPP showed an altered TGFβ expression and autophagy transcriptional signatures along with a declined dormancy state. We discovered that the altered TGFβ signaling fosters the Ery potential of HSCs by reducing their autophagic levels, and in vivo stimulation of autophagy is sufficient to rescue the imbalance of the HSC compartment. Our findings identify the interplay between TGFβ and HSC autophagy as a key driver in the context of non-malignant hematopoiesis.
    DOI:  https://doi.org/10.1038/s41467-025-60676-7
  7. J Biol Chem. 2025 Jul 01. pii: S0021-9258(25)02281-1. [Epub ahead of print] 110431
      CD45 is the most abundant glycoprotein on the surface of all nucleated hematopoietic-lineage cells, comprising multiple isoforms generated by alternative splicing of three exons ("A", "B", "C") that are exquisitely restricted across hematopoietic development. Despite CD45's ubiquitous expression on hematopoietic cells, its function(s) remain rather obscure. Here, we report that discrete CD45 isoforms expressed uniquely by immature human hematopoietic cells are distinguished as functional glycoforms ("isoglycoforms") that bind E-selectin. Moreover, our studies indicate that "CD45RA", a marker of human acute myeloid leukemia (AML) cells, identifies a distinct isoglycoform of CD45 containing all splice exon-encoded peptides. This isoglycoform, "CD45RABC-E", is directly upregulated by AML cells and demarcates these malignant cells from mature human leukocytes and the native human hematopoietic stem cell. Further analyses revealed that treatment-resistant AML highly expresses CD45RABC-E. Our findings thus unveil heretofore unrecognized functions of CD45 and define a novel CD45 isoglycoform that delineates AML cells from life-sustaining human hematopoietic cells.
    Keywords:  CD15s; CD45; CD45 isoform; E-selectin; E-selectin ligand; isoglycoform; sLeX; sialyl Lewis X; translational glycobiology
    DOI:  https://doi.org/10.1016/j.jbc.2025.110431
  8. Nat Commun. 2025 Jul 04. 16(1): 6170
      Hematopoietic stem cells (HSC) with multilineage potential are critical for T cell reconstitution after allogeneic hematopoietic cell transplantation (allo-HCT). The Kitlo HSC subset is enriched for multipotential precursors, but their T cell potential remains poorly characterized. Using a preclinical allo-HCT mouse model, we demonstrate that Kitlo HSCs provide superior thymic recovery and T cell reconstitution, resulting in improved immune responses to post-transplant infection. Kitlo HSCs with augmented bone marrow (BM) lymphopoiesis mitigate age-associated thymic alterations and enhance T cell recovery in middle-aged mice. Mechanistically, chromatin profiling reveals Kitlo HSCs exhibiting higher activity of lymphoid-specifying transcription factors, such as, ZBTB1. Zbtb1 deletion diminishes HSC engraftment and T cell potential; by contrast, reinstating Zbtb1 in megakaryocytic-biased Kithi HSCs rescues hematopoietic engraftment and T cell potential in vitro and in vivo. Furthermore, age-associated decline in Kitlo HSCs is associated with diminished T lymphopoietic potential in aged BM precursors; meanwhile, Kitlo HSCs in aged mice maintain enhanced lymphoid potential, but their per-cell capacity is diminished. Lastly, we observe an analogous human BM KITlo HSC subset with enhanced lymphoid potential. Our results thus uncover an age-related epigenetic regulation of lymphoid-competent Kitlo HSCs for T cell reconstitution.
    DOI:  https://doi.org/10.1038/s41467-025-61125-1
  9. Nat Commun. 2025 Jul 01. 16(1): 5470
      High doses of ionizing radiation (IR) cause severe damage to the hematopoietic system. However, the heterogeneity of hematopoietic stem and progenitor cells (HSPCs) in response to IR stress remains largely uncharacterized. Here, we present a dynamic single cell transcriptomic landscape and elucidate the complex crosstalk between HSPCs and the bone marrow (BM) microenvironment during IR-induced regeneration process. We reveal that BMP4 signaling in HSPCs confers IR resistance, and a single administration of BMP4 or SB4 can rescue mice from the IR-induced mortality. Furthermore, we identify BMPR2+ HSCs as a radiation resistant subset, displaying distinct epigenetic landscapes from BMPR2- HSCs under radiation stress. BMPR2+ HSCs sustain a strong self-renewal capacity primarily by reducing the H3K27me3 modification on the Nrf2 gene in response to radiation stress. In Nrf2 knockout mice, we demonstrate that Nrf2 is a critical downstream functional gene for BMP4-BMPR2 signaling on HSCs to resist IR-induced damage. Collectively, we provide insights into the molecular intricacies underlying HSPC heterogeneity and BM niche after radiation exposure, and we uncover that BMP4-BMPR2 signaling may serve as a promising target for developing innovative and effective intervention strategies to mitigate IR-induced hematopoietic injury.
    DOI:  https://doi.org/10.1038/s41467-025-60557-z
  10. Nat Commun. 2025 Jul 01. 16(1): 5475
      Age-related decline in the ability of bone marrow (BM) to recruit transplanted hematopoietic stem and progenitor cells (HSPCs) limits the potential of HSPC-based medicine. Using in vivo imaging and manipulation combined with integrative metabolomic analyses, we show that, with aging, degradation of non-neurogenic acetylcholine disrupts the local Chrm5-eNOS-nitric oxide signaling, reducing arterial dilation and decreasing both BM blood flow and sinusoidal wall shear stress. Consequently, aging BM microenvironment impairs transendothelial migration of transplanted HSPCs, and their BM homing efficiency is reduced, mediated by decreased activation of Piezo1. Notably, pharmacological activation of Piezo1 improves HSPC homing efficiency and post-transplant survival of aged recipients. These findings suggest that age-related dysregulation of local arteries leads to impaired HSPC homing to BM by decreasing shear stress. Modulation of these mechanisms may improve the efficacy and safety of clinical transplantation in elderly patients.
    DOI:  https://doi.org/10.1038/s41467-025-60515-9
  11. Mol Biol Rep. 2025 Jun 30. 52(1): 657
      Nowadays, hematopoietic stem cell transplantation (HSCT) and hematopoietic cell transfusion are the accepted therapy for patients with both malignant and nonmalignant hematological disorders. Due to the limited availability of donors and hematopoietic cells, the generation of hematopoietic cells from pluripotent stem cells (PSCs) is considered as a promising alternative source for hematopoietic cells in therapeutic applications. PSCs are undifferentiated cells capable of both self-renewal and differentiation into various hematopoietic lineages, including HSCs, hematopoietic progenitor cells (HPCs), and adult hematopoietic cells in vitro, offer significant potential. Therefore, ex vivo production of patient-specific hematopoietic stem cells (HSCs) derived from renewable sources such as PSCs serves as an experimental tool for investigating the field of regenerative medicine research and can be utilized for treating hematological diseases, especially when no other options are available. This review aims to provide an overview of recent advancements in inducing hematopoietic cells from PSCs, emphasizing the potential implications for future therapeutic interventions.
    Keywords:  ESCs; Hematopoietic differentiation; MIAMI; USSC; VSEL; iPSC
    DOI:  https://doi.org/10.1007/s11033-025-10730-w
  12. Trends Cancer. 2025 Jul 03. pii: S2405-8033(25)00144-X. [Epub ahead of print]
      Menin has emerged as a promising therapeutic target in acute myeloid leukemia (AML). The menin-MLL1 interaction promotes an oncogenic transcriptional program that drives leukemogenesis in HOX-mediated acute leukemias, including KMT2A-rearranged (KMT2Ar), nucleophosmin 1-mutated (NPM1m), and NUP98-rearranged (NUP98r) AML, prompting development of menin inhibitors for treatment of these subtypes. Successes in clinical investigation have led to recent FDA approval of revumenib for KMT2Ar AML, with numerous trials examining menin inhibitors as monotherapy and in combination with other antileukemic drugs ongoing. Although menin inhibitors represent a major advancement in AML treatment, acquired resistance is an evolving barrier to efficacy. Here, we examine the biological rationale for menin inhibition and discuss the landscape of clinical trials and resistance mechanisms associated with menin inhibitors.
    Keywords:  KMT2A; NPM1; acute myeloid leukemia; menin inhibitors
    DOI:  https://doi.org/10.1016/j.trecan.2025.06.002
  13. Nat Genet. 2025 Jul 01.
      The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal hematopoiesis is not well defined. We conducted whole-genome sequencing on 1,276 single-cell-derived hematopoietic stem and progenitor cell (HSPC) colonies from ten patients with multiple myeloma treated with chemotherapies and six normal donors. Melphalan treatment significantly increased the mutational burden, producing a distinctive mutation signature, whereas other chemotherapeutic agents had minimal effects. Consequently, the clonal diversity and architecture of post-treatment HSPCs resemble those observed in normal elderly individuals, particularly through the progression of oligoclonal hematopoiesis, thereby suggesting that chemotherapy accelerates clonal aging. Integrated phylogenetic analysis of matched therapy-related myeloid neoplasm samples traced their clonal origin to a single-HSPC clone among multiple competing clones, supporting a model of oligoclonal to monoclonal transformation. These findings underscore the need for further systematic research on the long-term hematological consequences of cancer chemotherapy.
    DOI:  https://doi.org/10.1038/s41588-025-02235-w
  14. Leukemia. 2025 Jun 30.
      VEXAS syndrome is a clonal hematopoietic disorder characterized by hyperinflammation, bone marrow failure, and high mortality. The molecular hallmark of VEXAS is somatic mutations at methionine 41 (M41) in the E1 ubiquitin enzyme, UBA1. These mutations induce a protein isoform switch, but the mechanisms underlying disease pathogenesis remain unclear. Here, we developed a human cell model of VEXAS syndrome by engineering the male monocytic THP1 cell line to express the common UBA1M41V mutation. We found that mutant UBA1M41V cells exhibit aberrant UBA1 isoform expression, increased vacuolization, and upregulation of the unfolded protein response, recapitulating key features of VEXAS. Moreover, proteomic analyses revealed dysregulated ubiquitination and proteotoxic stress in UBA1M41V cells, with alterations in inflammatory and stress-response pathways. Functional studies demonstrated that UBA1M41V cells were highly sensitive to genetic or pharmacological inhibition of E1 ubiquitin enzymes. Treatment with the E1 enzyme inhibitor TAK-243 preferentially suppressed colony formation of UBA1M41V cells as compared to WT cells. Moreover, UBA1M41V cells exhibited greater sensitivity to TAK-243 in competition assays and showed increased apoptosis. Interestingly, TAK-243 preferentially inhibited UBA6 activity over UBA1, suggesting that UBA6 may compensate for UBA1 dysfunction in UBA1M41V cells. Targeting UBA6 using shRNA or the UBA6-specific inhibitor phytic acid further revealed an acquired dependency on UBA6 in UBA1M41V cells. Phytic acid selectively impaired growth and colony formation in UBA1M41V cells while sparing WT cells, highlighting a potential therapeutic vulnerability. Together, these findings establish a novel human model of VEXAS syndrome, identify key roles for UBA1 and UBA6 in disease pathogenesis, and demonstrate that UBA6 inhibition represents a promising therapeutic strategy for selectively targeting UBA1 mutant clones.
    DOI:  https://doi.org/10.1038/s41375-025-02671-x
  15. Cell Stem Cell. 2025 Jun 24. pii: S1934-5909(25)00228-0. [Epub ahead of print]
      Clonal hematopoiesis (CH) is associated with many age-related diseases, but its interaction with Alzheimer's disease (AD) remains unclear. Here, we show that TET2-mutant CH is associated with a 47% reduced risk of late-onset AD (LOAD) in the UK Biobank, whereas other drivers of CH do not confer protection. In a mouse model of AD, transplantation of Tet2-mutant bone marrow reduced cognitive decline and β-amyloid plaque formation, effects not observed with Dnmt3a-mutant marrow. Bone-marrow-derived microglia-like cells were detected at an increased rate in Tet2-mutant marrow recipients, and TET2-mutant human induced pluripotent stem cell (iPSC)-derived microglia were more phagocytic and hyperinflammatory than DNMT3A-mutant or wild-type microglia. Strikingly, single-cell RNA sequencing (scRNA-seq) revealed that macrophages and patrolling monocytes were increased in brains of mice transplanted with Tet2-mutant marrow in response to chemokine signaling. These studies reveal a TET2-specific protective effect of CH on AD pathogenesis mediated by peripheral myeloid cell infiltration.
    Keywords:  Alzheimer’s disease; DNMT3A; TET2; clonal hematopoiesis; inflammation; microglia, peripheral immune cells; myeloid cell activation; phagocytosis
    DOI:  https://doi.org/10.1016/j.stem.2025.06.006
  16. Blood Cancer Discov. 2025 Jul 03.
      The World Health Organization (WHO) 5th edition and International Consensus Classification (ICC) for myeloid neoplasms both incorporate empirical numerical thresholds to morphologic and molecular features defining certain disease entities. However, the clinical implications of these thresholds remain unclear. We analyzed a large cohort (N=6,976) of patients with myeloid neoplasms to evaluate the impact of proposed, yet different numerical thresholds for variant allele frequency of genetic mutations or hematologic parameters set forth by WHO 5th and ICC for classification of SF3B1-mutated (SF3B1m) myelodysplastic neoplasms (MDS), NPM1m acute myeloid leukemia (AML), and oligomonocytic-chronic myelomonocytic leukemia (O-CMML). Our analysis demonstrated the clonal burden of SF3B1m in MDS informs biological classification and prognosis, supported the notion that NPM1 mutation should be AML-defining regardless of blast percentage, highlighted the prognostic impact of the cumulative number of myelodysplasia-related mutations in NPM1-mutated AML, and provided evidence that integrating specific molecular signatures could improve accuracy of O-CMML classification.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-25-0047
  17. Blood Rev. 2025 Jun 23. pii: S0268-960X(25)00063-3. [Epub ahead of print] 101318
      Leukaemia is caused by genetic mutations within haematopoietic stem and progenitor cells, leading to the production of immature blasts. While mouse models have been instrumental in studying disease mechanisms and testing therapies, their limitations contribute to 90 % failure rate of new therapies in clinical trials. This is often attributed to the choice of model utilised, and failure of mouse models to accurately replicate the complexity of the human disease. This review examines different leukaemia mouse models, including transgenic, syngeneic and xenografts, discussing their phenotype, advantages and limitations. Finally, we describe advanced technologies for in vitro modelling of haematopoiesis and leukaemia. These models provide a promising platform for tumour microenvironment research, and a robust human-relevant pipeline for drug screening, reducing our reliance on in vivo testing. The information in this review will enable researchers to make informed decisions on the most appropriate models to carry out pre-clinical testing in the future.
    Keywords:  Haematopoiesis; In vitro models; Leukaemia; Leukaemic stem cell; Mouse models
    DOI:  https://doi.org/10.1016/j.blre.2025.101318
  18. Blood. 2025 Jul 03. pii: blood.2025028935. [Epub ahead of print]
      TP53-Y220C is a recurrent hotspot mutation in cancers and leukemias. It is observed predominantly in acute myeloid leukemia (AML)/myelodysplastic syndromes among hematological malignancies and is associated with poor outcome. The mutation creates a structural pocket in the p53 protein. PC14586 (rezatapopt) is a small molecule designed to bind to this pocket and thus restore a p53-wild type (p53-WT) conformation. We demonstrate that PC14586 converts p53-Y220C into a p53-WT conformation and activates p53 transcriptional targets, but surprisingly induces limited/no apoptosis in TP53-Y220C AML. Mechanistically, MDM2 induced by PC14586-activated conformational p53-WT and the nuclear exporter XPO1 reduce the transcriptional activities of p53, which are fully restored by inhibition of MDM2 and/or XPO1. Importantly, p53-WT protein can bind to BCL-2, competing with BAX in the BH3 binding pocket of BCL-2 and also binds to BCL-xL and MCL-1. However, such binding by PC14586-activated conformational p53-WT is not detected. Pharmacological inhibition of the BCL-2/BAX interaction with venetoclax fully compensates for this deficiency, induces massive cell death in AML cells and stem/progenitor cells in vitro and prolongs survival of TP53-Y220C AML xenografts in vivo. Collectively, we identified transcription-dependent and -independent mechanisms that limit the apoptogenic activities of reactivated conformational p53-WT and suggest approaches to optimize apoptosis induction in TP53-mutant leukemia. A clinical trial of PC14586 in TP53-Y220C AML/myelodysplastic syndromes has recently been initiated (NCT06616636).
    DOI:  https://doi.org/10.1182/blood.2025028935
  19. Nat Commun. 2025 Jul 01. 16(1): 5852
      Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) enables paired measurement of surface protein and mRNA expression in single cells using antibodies conjugated to oligonucleotide tags. Due to the high copy number of surface protein molecules, sequencing antibody-derived tags (ADTs) allows for robust protein detection, improving cell-type identification. However, variability in antibody staining leads to batch effects in the ADT expression, obscuring biological variation, reducing interpretability, and obstructing cross-study analyses. Here, we present ADTnorm, a normalization and integration method designed explicitly for ADT abundance. Benchmarking against 14 existing scaling and normalization methods, we show that ADTnorm accurately aligns populations with negative- and positive-expression of surface protein markers across 13 public datasets, effectively removing technical variation across batches and improving cell-type separation. ADTnorm enables efficient integration of public CITE-seq datasets, each with unique experimental designs, paving the way for atlas-level analyses. Beyond normalization, ADTnorm includes built-in utilities to aid in automated threshold-gating as well as assessment of antibody staining quality for titration optimization and antibody panel selection. Applying ADTnorm to an antibody titration study, a published COVID-19 CITE-seq dataset, and a human hematopoietic progenitors study allowed for identifying previously undetected phenotype-associated markers, illustrating a broad utility in biological applications.
    DOI:  https://doi.org/10.1038/s41467-025-61023-6
  20. FEBS Open Bio. 2025 Jun 30.
      Emerging evidence has demonstrated that ribosomes are not homogeneous structures with non-specialized functions. There are now several reports of heterogeneity in the composition and functional specialization of ribosomes. Ribosome heterogeneity functions in regulating the translation of specific mRNAs, and thus plays important roles in embryonic development. However, the panorama of ribosome heterogeneity during embryonic hematopoiesis has not yet been portrayed. Here, by leveraging our single-cell transcriptomic data and a published proteomic dataset, we depict the landscape of ribosomal heterogeneity during endothelial-to-hematopoietic transition (EHT). By precisely distinguishing the different ribosomal components, we found their number and expression levels showed dynamic changes during EHT. We also report stage-specific signatures of ribosomal components. For example, RPL27 and RACK1 exhibited up-regulated expression both in dual-omics analysis and immunofluorescence experiments during EHT. Interestingly, further spatial structure analysis revealed that RACK1 localized at the bottom of 40S small ribosomal subunit, indicating its potential role in regulating ribosome function. Taken together, our study not only highlights the ribosome heterogeneity during EHT, but also provides new clues to explore how these heterogeneous machineries regulate mRNA translation.
    Keywords:  definitive hematopoiesis; endothelial to hematopoietic transition; mRNA translation; ribosome heterogeneity
    DOI:  https://doi.org/10.1002/2211-5463.70078