bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2025–06–15
23 papers selected by
William Grey, University of York



  1. EMBO Rep. 2025 Jun 11.
      Hematopoietic stem and progenitor cells (HSPCs) polarize in contact with the bone marrow stromal cells constituting their niche. Given the role of cell polarity in protection against tumorigenesis and the importance of the niche in the progression of acute myeloid leukemias (AMLs), we investigated the polarization capacities of leukemic blasts. Using engineered micro-niches and centrosome position with respect to the contact site with stromal cells as a proxy for cell polarization, we show that AML cell lines and primary cells from AML patient blasts are unable to polarize in contact with healthy stromal cells. Exposure to AML patient-derived stromal cells compromises the polarization of healthy adult HSPCs and AML blasts from patients. When cultured in "bone-marrow-on-a-chip", stromal cells from a leukemic niche stimulate the migration of healthy HSPCs and AML blast. These results reveal the detrimental influences of both intrinsic transformation and extrinsic contact with transformed stromal cells on the polarization of AML blasts.
    Keywords:  Acute Myeloid Leukemia (AML); Artificial Niche; Bone-marrow-on-a-Chip (BMoC); Hematopoietic Stem and Progenitor Cells (HSPCs); Microwell
    DOI:  https://doi.org/10.1038/s44319-025-00466-w
  2. STAR Protoc. 2025 Jun 05. pii: S2666-1667(25)00281-3. [Epub ahead of print]6(2): 103875
      Here, we present a protocol for isolating and characterizing hematopoietic stem cells (HSCs) from mouse alveolar bone marrow. We describe steps for combining anatomical dissection of the mandibular alveolar region with flow cytometry analysis for identifying HSCs. The protocol enables the isolation of HSCs from a specific bone marrow niche harboring an enriched HSC population. For complete details on the use and execution of this protocol, please refer to Niizuma et al.1.
    Keywords:  Model Organisms; cell Biology; cell culture; cell isolation; flow cytometry; stem cells
    DOI:  https://doi.org/10.1016/j.xpro.2025.103875
  3. iScience. 2025 Jun 20. 28(6): 112547
      In vivo differentiation pathways into several blood cell lineages of Hematopoietic stem cells (HSCs) remain challenging to track over time. Using data from single-cell transplantation assays and mathematical modeling, we examined HSC differentiation kinetics, including the myeloid bypass pathway. We found that myeloid cell production was unchanged with age, whereas B cell production declined, quantitatively confirming myeloid lineage skewing. Estimated dependence on the platelet-bypass correlated with the long-term reconstitution capacity of HSCs. Time-dependent blood cell production patterns calculated by our model distinguished the reconstitution potential of HSCs into subgroups, suggesting a link between the bypass pathway and the multilineage differentiation dynamics of HSCs. Notably, platelet bypass dependence could be determined by the platelet-to-erythrocyte chimerism ratio at 8 weeks after transplantation, serving as a predictive indicator of long-term HSC function. These findings provide quantitative insights into HSC aging and differentiation dynamics, emphasizing the role of the bypass pathway in defining HSC properties.
    Keywords:  Biological constraints; Mathematical biosciences; Stem cells research
    DOI:  https://doi.org/10.1016/j.isci.2025.112547
  4. Development. 2025 Jun 12. pii: dev.204454. [Epub ahead of print]
      Hematopoietic stem cells (HSCs) and more committed progenitors (collectively referred to as HSPCs) emerge from vessels during development, via Endothelial-to-Hematopoietic Transition (EHT). Recently, using the zebrafish embryo, we showed that two EHT cell types emerge from the dorsal aorta, raising the question of their subsequent fate. To address this issue, we established a complex pipeline based on single-cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells, with significant differences in thymus colonization and T-lymphoid lineage commitment. In addition, we investigated implantation of HSPCs in niches, with the support of HSPC signatures (gata2b and cd34/podocalyxin), retrieved from our single-cell datasets. This revealed, at unprecedented resolution, the homing of HSPCs in niches of entire early larvae, including the pronephros, the sub-aortic and caudal regions, as well as the area contacting the supra-intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition, from their emergence to their homing in specific niches.
    Keywords:  Hematopoietic stem cells; MARS-seq; Niches; RNAscope; Single-cell transcriptomics; Zebrafish
    DOI:  https://doi.org/10.1242/dev.204454
  5. Blood. 2025 Jun 10. pii: blood.2024028033. [Epub ahead of print]
      TET2 is among the most commonly mutated genes in both clonal hematopoiesis and myeloid malignancies, thus, the ability to identify selective dependencies in TET2 deficient cells has broad translational significance. Here, we identify regulators of Tet2 knockout (KO) hematopoietic stem and progenitor cell (HSPC) expansion using an in vivo CRISPR-Cas9 KO screen, in which nucleotide barcoding enabled large-scale clonal tracing of Tet2 deficient HSPCs in a physiological setting. Our screen identified candidate genes, including Ncoa4, that are selectively required for Tet2 KO clonal outgrowth compared to wild-type (WT). Ncoa4 targets ferritin for lysosomal degradation (ferritinophagy), maintaining intracellular iron homeostasis by releasing labile iron (Fe2+) in response to cellular demands. In Tet2-deficient HSPCs, increased mitochondrial ATP production correlates with increased cellular iron requirements, and in turn, promotes Ncoa4-dependent ferritinophagy. Restricting iron availability reduces Tet2 KO stem cell numbers, revealing a dependency in TET2-mutated myeloid neoplasms.
    DOI:  https://doi.org/10.1182/blood.2024028033
  6. bioRxiv. 2025 May 29. pii: 2025.05.28.656712. [Epub ahead of print]
      Hematopoietic stem and progenitor cells (HSPC) respond to infections, inflammation, and regenerative challenges using a collection of cellular and molecular mechanisms termed emergency myelopoiesis (EM) pathways. However, it remains unclear how various EM inducers regulate HSPCs using shared or distinct molecular mechanisms. Here, we generate a comprehensive and generalizable cell annotation method (HemaScribe) and a refined quantitative model of hematopoietic differentiation (HemaScape) using single cell RNA sequencing (scRNA-seq) of HSPCs, which we apply to a broad range of EM modalities. We uncover multiple strategies to enhance myelopoiesis acting at different levels of the HSPC hierarchy, which are associated with both unique and shared transcriptional response modules. In particular, we identify a myeloid progenitor-based module of EM engagement across diverse inflammatory challenges, which informs outcome in adult and pediatric human acute myeloid leukemia. Collectively, our work illuminates fundamental regulatory mechanisms in hematopoietic regeneration that have direct translational applications in disease contexts.
    HIGHLIGHTS: New HemaScribe method for hematopoietic progenitor annotation in scRNA-seq datasetsDifferent emergency myelopoiesis (EM) inducers act at distinct hematopoiesis levelsUnique and shared transcriptional response modules enacted by different EM inducersA myeloid progenitor EM module informs outcome in acute myeloid leukemia.
    eTOC BLURB: 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.
    GRAPHICAL ABSTRACT:
    DOI:  https://doi.org/10.1101/2025.05.28.656712
  7. bioRxiv. 2025 Jun 07. pii: 2025.06.06.657881. [Epub ahead of print]
      Resistance to combination regimens containing the BCL-2 inhibitor venetoclax in acute myeloid leukemia (AML) is a growing clinical challenge for this extensively utilized agent. We previously established the anti-leukemic properties of ceramide, a tumor-suppressive sphingolipid, in AML and demonstrated that upregulated expression of acid ceramidase (AC), a ceramide-neutralizing enzyme, supported leukemic survival and resistance to BH3 mimetics. Here, we report the anti-leukemic efficacy and mechanisms of co-targeting AC and BCL-2 in venetoclax-resistant AML. Analysis of the BeatAML dataset revealed a positive relationship between increased AC gene expression and venetoclax resistance. Targeting AC enhanced single-agent venetoclax cytotoxicity and the venetoclax + cytarabine combination in AML cell lines with primary or acquired venetoclax resistance. SACLAC + venetoclax was equipotent to the combination of venetoclax + cytarabine at reducing cell viability when evaluated ex vivo across a cohort of 71 primary AML patient samples. Mechanistically, SACLAC + venetoclax increased ceramide to levels that trigger a cytotoxic integrated stress response (ISR), ISR-mediated NOXA protein upregulation, mitochondrial dysregulation, and caspase-dependent cell death. Collectively, these data demonstrate the efficacy of co-targeting AC and BCL-2 in AML and rationalize targeting AC as a therapeutic approach to overcome venetoclax resistance.
    DOI:  https://doi.org/10.1101/2025.06.06.657881
  8. Stem Cell Res Ther. 2025 Jun 09. 16(1): 298
       BACKGROUND: Dobutamine hydrochloride (DH), a common inotropic drug used for heart failure, has recently been discovered to inhibit Yes-Associated Protein (YAP). YAP is a key component of the Hippo signaling pathway and plays a crucial role in the regulation of hematopoietic cell growth. The decrease in YAP activity has been shown to increase hematogenic differentiation and the generation of hematopoietic stem and progenitor cells (HSPCs) from human induced pluripotent stem cells (hiPSCs). Therefore, this study investigates the effect of DH on enhancing the hematopoietic differentiation of hiPSCs toward HSPCs.
    METHODS: This study used isogenic hiPSCs to study the effect of DH during various stages of their hematogenic differentiation using an in vitro culture system. The differentiating hiPSCs were cultured under specific conditions, including defined differentiation media composition and controlled oxygen tension throughout the differentiation process. The percentages of iPSC-derived HSPCs were assessed using flow cytometry to evaluate the expression of HSPC markers, including CD34⁺, CD43⁺, and CD45⁺/⁻. The HSPC production yield and the multilineage differentiation capacity of the resulting hiPSC-derived HSPCs were determined at the end of culture.
    RESULTS: The findings indicate that DH treatment significantly inhibits YAP activity and increases the hematogenic differentiation of hiPSCs and the yield of HSPCs at the end of culture. Specifically, inhibiting YAP activity with DH during the transition of hiPSCs from the hematoendothelial progenitor (HE) stage to the hematopoietic stage (endothelial to hematopoietic transition, EHT) proved to be the most effective in increasing HSPC production from hiPSCs.
    CONCLUSIONS: This study highlights the potential of the inotropic drug DH as a novel agent to enhance hematogenic differentiation and improve the yield of hiPSC-derived hematopoietic stem and progenitor cells (HSPCs). DH was found to significantly inhibit YAP activity, which in turn promoted hematopoietic specification, particularly when administered during the critical endothelial-to-hematopoietic transition (EHT) stage. These findings suggest that repurposing DH could offer a valuable strategy to increase the efficiency of hiPSC-derived HSPC production, advancing its potential for therapeutic and clinical applications in regenerative medicine and hematopoietic cell therapies.
    Keywords:  Dobutamine hydrochloride; Hematopoietic stem cells; Hippo pathway; YAP; iPSCs
    DOI:  https://doi.org/10.1186/s13287-025-04427-x
  9. Clin Exp Med. 2025 Jun 07. 25(1): 190
      It is well known that multiple myeloma (MM) cells are highly dependent on the bone marrow (BM) microenvironment. However, the complex interactions and signaling pathways between MM cells and BM stromal cells remain inadequately defined. In this study, we employed an in vitro coculture model to investigate these interactions. We found that coculturing MM cells with BM-derived HS5 stromal cells stimulated the secretion of hyaluronic acid (HA) and interleukin-6 (IL-6), and significantly increased the expression of CD44 and F-actin stress fibers polymerization in MM cells. Among the three hyaluronan synthase (HAS) isoforms, HAS3 mRNA expression was most significantly elevated in MM cells following coculture with HS5. This coculture also resulted in upregulation of HAS3 and IL-6 mRNA in MM cells. Notably, MM cells in direct contact with HS5 cells exhibited higher proliferative capacity compared to those not in contact with the stromal cells. Additionally, coculturing MM cells with HS5 led to the formation of membrane protrusions in MM cells, with CD44 enrichment observed at these polarized regions. Further analysis revealed that Rac1 co-localizes with CD44 on MM cells within the coculture system, suggesting that Rac1 signaling plays a critical role in CD44-mediated cytoskeletal rearrangements. Importantly, silencing CD44 expression in MM cells reduced F-actin polymerization, as well as impaired MM cell migration and adhesion to HS5. Our findings highlight the involvement of the HA/CD44/F-actin pathway in MM-BM migration and adhesion, suggesting that CD44 may serve as a novel therapeutic target to disrupt the MM-BM microenvironment.
    Keywords:  CD44; F-actin; Hyaluronic acid; Interleukin-6; Multiple myeloma cells; Stromal cells
    DOI:  https://doi.org/10.1007/s10238-025-01649-4
  10. bioRxiv. 2025 May 28. pii: 2025.05.23.655671. [Epub ahead of print]
      During cancer development, mutations promote gene expression changes that cause transformation. Leukemia is frequently associated with aberrant HOXA expression driven by translocations in nucleoporin genes or KMT2A , and mutations in NPM1 . How disparate mutations converge on this regulatory pathway is not understood. Here we demonstrate that mutant NPM1 (NPM1c) forms nuclear condensates in multiple human cell lines, mouse models, and primary patient samples. We show NPM1c phase separation is necessary and sufficient to coordinate the recruitment of NUP98 and KMT2A to condensates. Through extensive mutagenesis and pharmacological destabilization of phase separation, we find that NPM1c condensates are necessary for regulating gene expression, promoting in vivo expansion, and maintaining the undifferentiated leukemic state. Finally, we show that nucleoporin and KMT2A fusion proteins form condensates that are biophysically indistinguishable from NPM1c condensates. Together, these data define a new condensate underlying leukemias that we term coordinating bodies (C-bodies), and propose C-bodies as a therapeutic vulnerability.
    DOI:  https://doi.org/10.1101/2025.05.23.655671
  11. Biochim Biophys Acta Rev Cancer. 2025 Jun 09. pii: S0304-419X(25)00113-1. [Epub ahead of print] 189371
      The tumor microenvironment plays an important role in cancer onset and progression. Its significance has been increasingly addressed in myeloid neoplasms. Such a shift marks a departure from the usual tumor-centered approach to a more comprehensive and integrated understanding of the interplay between myeloid tumors and their surroundings. On this note, we aimed to summarize, in this review, an up-to-date take on how a pro-inflammatory milieu influences clonal selection of genetically altered hematopoietic stem cells towards myeloid malignancies at the expense of their healthy counterpart; the role of NLRP3 inflammasome, a major component of the innate immunity and source of interleukin-1β, over acute myeloid leukemia development and performance; and, alongside post-translational modifications, how autophagy represents a major NLRP3 inflammasome regulator.
    Keywords:  Acute myeloid leukemia; Inflammation; Innate immunity; Leukemic stem cell; Myeloid neoplasm; NLRP3 inflammasome
    DOI:  https://doi.org/10.1016/j.bbcan.2025.189371
  12. Cell Rep. 2025 Jun 09. pii: S2211-1247(25)00545-5. [Epub ahead of print]44(6): 115774
      KRAS mutations drive tumorigenesis, but their role in ferroptosis regulation remains unclear. Here, we construct wild-type KRAS (KRASWT) and KRASG12D-mutant cancer cells and demonstrate that G12D-mutant cells exhibit increased viability and reduced ferroptosis upon RSL3 or erastin treatment. These cells show diminished lipid peroxidation and mitochondrial damage, indicating ferroptosis resistance. KRASG12D activates MEK/ERK signaling to phosphorylate LDHA, enhancing glycolysis and lactate production. Exogenous lactate supplementation similarly protects WT cells from ferroptosis. Mechanistically, G12D-mutation-derived lactate induces glutamate-cysteine ligase (GCL) modifier (GCLM) lactylation, a process catalyzed by acetyl-coenzyme A (CoA) acetyltransferase 2 (ACAT2). Inhibition of GCLM lactylation either through the mutation of the lactylation site or by knockdown of ACAT2 diminished the enzymatic activity of GCL and suppressed glutathione synthesis. Importantly, ACAT2 depletion overcomes ferroptosis resistance in KRASG12D-mutant tumors in vivo. Our findings reveal a KRASG12D-driven metabolic adaptation linking GCLM lactylation to ferroptosis resistance, proposing ACAT2 inhibition as a therapeutic strategy for KRAS-mutant cancers.
    Keywords:  CP: Cancer; CP: Metabolism; GCLM; KRAS mutation; ferroptosis; glutamate-cysteine ligase modifier; pancreatic cancer; protein lactylation
    DOI:  https://doi.org/10.1016/j.celrep.2025.115774
  13. Cancer Drug Resist. 2025 ;8 23
      Acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) are genetically heterogeneous malignancies of hematopoietic stem cells, characterized by complex mutations and a high risk of drug resistance and relapse. Patient-derived xenograft (PDX) models are dynamic entities transplanted with leukemia stem cells (LSCs), retaining patients' biological and genetic characteristics. By elucidating LSCs, clonal dynamics, and microenvironment interaction, PDXs facilitate the preclinical evaluation of therapy sensitivity, including immunotherapies, epigenetic therapies, and other agents targeting mutated proteins or apoptosis. The application of PDXs has provided translational evidence for various studies with reliable clinical relevance. Additionally, conventional PDXs remain a robust tool in identifying drug resistance compared with other models, and their potential is further unleashed when examined in large cohorts or combined with novel technologies, which not only enhances our understanding of acute leukemia biology but also enables the discovery and identification of novel biomarkers. In this review, we present the application of PDX models for acute leukemia resistance, including mechanism investigation, therapy evaluation, and associated challenges.
    Keywords:  Patient-derived xenografts; acute leukemia; leukemia stem cells
    DOI:  https://doi.org/10.20517/cdr.2025.18
  14. Haematologica. 2025 Jun 12. 0
      Acute myeloid leukemia (AML) patients with high PRDM16 expression frequently experience induction failure and have a poor prognosis. However, the molecular mechanisms underlying these clinical features remain elusive. We found that murine AML cells transformed by MLL::AF9 fusion and oncogenic short-isoform Prdm16 overexpression (hereafter, MF9/sPrdm16) exhibited resistance to cytarabine (AraC), but not to anthracycline, both in vitro and in vivo. Intriguingly, MF9/sPrdm16 cells displayed a gene expression signature of high oxidative phosphorylation (OxPHOS) and increased mitochondrial respiration. The inhibition of mitochondrial respiration with metformin or tigecycline abrogated AraC resistance in MF9/sPrdm16 cells via an energetic shift toward low OxPHOS status. Furthermore, sPrdm16 upregulated Myc and the glutamine transporter Slc1a5, activating TCA cycle and glutaminolysis. Of note, both OxPHOS and MYC-target gene signatures were significantly enriched in AML patient samples with high PRDM16 expression. Together, we showed that PRDM16 overexpression activates mitochondrial respiration through metabolic reprogramming via MYC-SLC1A5-Glutaminolysis axis, thereby conferring AraC resistance on AML cells. These results suggest that targeting mitochondrial respiration might be a novel treatment strategy to overcome chemoresistance in AML patients with high PRDM16 expression.
    DOI:  https://doi.org/10.3324/haematol.2024.287265
  15. bioRxiv. 2025 May 26. pii: 2025.05.21.655403. [Epub ahead of print]
      Mitochondria are dynamic organelles that undergo continuous morphological changes, yet exhibit unique, cell-type-specific structures. In rod photoreceptor cells of the retina, these structures include elongated mitochondria in the inner segments and a distinct, large, circular mitochondrion in each presynaptic terminal. The mechanisms underlying the establishment and maintenance of these specialized mitochondrial morphologies, along with their functional significance, are not well understood. Here, we investigate the roles of mitochondrial fusion proteins mitofusin 1 (MFN1) and mitofusin 2 (MFN2) in shaping these structures and maintaining photoreceptor cell health. Rod photoreceptor cell-specific ablation of MFN1 and MFN2 resulted in mitochondrial fragmentation by one month of age, suggesting that mitochondrial fusion is essential for the development of photoreceptor cell-specific mitochondrial structures. Notably, the layer structures of the retina examined by light microscopy appeared unaffected at this age. Following this time period, significant photoreceptor cell degeneration occurred by three months of age. Furthermore, we showed that impaired mitochondrial fusion perturbed the balance of proteins involved in glycolysis, oxidative phosphorylation (OXPHOS), and β-oxidation, highlighting the critical role of mitochondrial fusion in ensuring the proper levels of proteins necessary for optimal energy metabolism. Additionally, we identified upregulation of cellular stress pathways such as endoplasmic reticulum (ER) stress and unfolded protein response (UPR), which arise in response to energy deprivation, and cytoprotective biosynthetic pathways mediated by CCAAT/enhancer-binding protein gamma (C/EBPγ) and mammalian target of rapamycin complex 1 (mTORC1) signaling. In summary, our findings indicate that mitochondrial fusion through MFN1 and MFN2 is vital for the development of unique mitochondrial structures and proper energy production, underscoring the fundamental importance of mitochondrial dynamics in photoreceptor cell function and survival.
    Significance Statements: Rod photoreceptor cells exhibit unique mitochondrial morphologies and high energy requirements. In this report, we examined how these unique mitochondrial structures are established and their biological significance. We identified that mitochondrial fusion is essential for the development of characteristic mitochondrial morphologies in rod photoreceptor cells. Furthermore, we demonstrated that impaired mitochondrial fusion disrupts the equilibrium of proteins associated with OXPHOS, glycolysis, and β-oxidation, ultimately leading to an imbalance in cellular energy homeostasis. Our findings also revealed activation of cellular stress pathways, including ER stress and the UPR, which are likely triggered by energy depletion. Additionally, we identified activation of cytoprotective biosynthetic pathways that are engaged to preserve cellular homeostasis and function.
    DOI:  https://doi.org/10.1101/2025.05.21.655403
  16. Proc Natl Acad Sci U S A. 2025 Jun 17. 122(24): e2424985122
      PARP7 is an enzyme that uses donor substrate NAD+ to attach a single ADP-ribose moiety onto proteins related to immunity, transcription, and cell growth and motility. Despite the importance of PARP7 in these processes, PARP7 signaling networks remain underresearched. Here, we used genome-wide CRISPR screens and multiplex quantitative proteomics in distinct lung cancer cell lines treated with a PARP7 inhibitor to better understand PARP7 molecular functions. We find that manipulating the aryl hydrocarbon receptor (AHR) transcriptional activity mediates PARP7 inhibitor sensitivity and triggers robust changes to the AHR-controlled proteome (AHR-ome). One of the striking features of such AHR-ome remodeling was the downregulation of filamins A and B concurrent with the induction of the corresponding E3 ubiquitin ligase ASB2. We also show that suppressor of cytokine signaling 3 (SOCS3) crosstalks to AHR. Inhibition of PARP7 in SOCS3 knockout cells leads to reduced viability compared to wild-type cells treated with a PARP7 inhibitor. Our results reveal signaling interplay between PARP7, AHR, and SOCS3 and establish an invaluable resource to study the role of PARP7 in the regulation of AHR signaling and innate immunity through its ADP-ribosyl transferase activity.
    Keywords:  ADP-ribosylation; CRISPR; PARP; aryl hydrocarbon receptor; proteomics
    DOI:  https://doi.org/10.1073/pnas.2424985122
  17. J Am Chem Soc. 2025 Jun 10.
      A major challenge in evaluating the suitability of ∼700 known and putative E3 ligases for target protein degradation (TPD) is the lack of ligase-specific binders. Here, we use genetic code expansion (GCE) to express in living cells an E3 ligase with a site-specifically encoded, tetrazine-containing noncanonical amino acid (Tet-ncAA). Then, using click chemistry, we conjugate the incorporated Tet with a strained trans-cyclooctene (sTCO) tethered to a neosubstrate protein binder. The resulting covalent E3 ligase-binder construct can then be evaluated for the TPD of the neosubstrate. We first demonstrate that cereblon (CRBN) has a rather high plasticity for TPD by studying CRBN containing Tet-ncAA at a variety of surface positions. When these CRBN forms are covalently tethered to an sTCO-linker-JQ1 reagent, they all successfully recruit BRD2/4 for degradation, with the efficiency depending on the placement of the Tet-ncAA and the linker length. The results highlight the ability of this approach to map E3 surfaces and identify optimal TPD interfaces and pockets. Applying this strategy to speckle-type POZ protein (SPOP), an E3 ligase with no known specific ligand, we demonstrate that multiple sites on its surface can support TPD, revealing the potential for PROTAC-type development. This E3-ligand-free degrader (ELF degrader) platform preserves the native state of E3 ligases, enables the interrogation of any E3 surface region in live cells, and is applicable to a broad range of E3 ligases. ELF degraders represent a versatile approach to define functional degron sites, guide degrader design, and unlock new E3 ligases, those without known ligands, for therapeutic applications.
    DOI:  https://doi.org/10.1021/jacs.5c02741
  18. Int J Mol Sci. 2025 May 30. pii: 5269. [Epub ahead of print]26(11):
      Humanized mice generated by hematopoietic stem cell (HSC) transplantation are limited by the immune system developed being allogeneic to the tumor. We have innovated a platform to reconstitute an autologous human immune system (HIS) in immunodeficient NOG-EXL mice from mobilized peripheral blood (MPB)-CD34 cells, along with PDX generated from the same patient's tumor tissue. Patients consented under an IRB-approved protocol for tumor biopsy and HSC apheresis at Emory University. HSC collection included mobilization with G-CSF and plerixafor, immunomagnetic bead isolation with CliniMACS, and cryopreservation of CD34+ cells. PDX were established from biopsies or surgical specimens by passaging into immunodeficient mice. Irradiated NOG-EXL mice were engrafted with HSCs by intravenous transplantation of CD34+ HSC. Engraftment of human T cells, B cells, and myeloid cells in peripheral blood was assessed by serial flow cytometry of blood samples, with final assessment of immune components in spleen and bone marrow at 30 weeks. Twenty-eight PDX models were generated from 43 patients with HNSCC; 1 patient underwent apheresis. HSC engraftment in blood was observed in 100% of NOG-EXL mice at 8 weeks post-transplant, with 5-20% hCD45+ cells present in the periphery. B-cell development was predominant at early time points and declined over time. Human T-cell and subset development of CD4+ and CD8+ T cells were observed in blood from 15 weeks post-transplant. Strong development of the myeloid lineage (CD33+) was observed starting at 8 weeks and persisted throughout the study. These data demonstrate that mobilization and apheresis of HNSCC patients is technically and clinically feasible and may allow the establishment of autologous HIS-PDX mice.
    Keywords:  PDX; autologous stem cells; autologous xenograft; immunograft
    DOI:  https://doi.org/10.3390/ijms26115269
  19. bioRxiv. 2025 May 29. pii: 2025.05.26.655807. [Epub ahead of print]
      Hundreds of mitochondrial-destined proteins rely on N-terminal presequences for organellar targeting and import. While generally described as positively charged amphipathic helices, presequences lack a consensus motif and thus likely promote the import of proteins into mitochondria with variable efficiencies. Indeed, the concept of presequence "strength" critically underlies biological models such as stress sensing, yet a quantitative analysis of what dictates "strong" versus "weak" presequences is lacking. Furthermore, the extent to which presequence strength affects mitochondrial function and cellular fitness remains unclear. Here, we capitalize on the high-throughput and kinetic nature of the MitoLuc mitochondrial protein import assay to quantify multiple aspects of presequence strength. We find that select presequences, including those that regulate the mitochondrial unfolded protein response (UPR mt ), are sufficient to impart differential import efficiencies during mitochondrial uncoupling. Surprisingly, we find that presequences beyond those classically associated with stress signaling promote highly variable import efficiency in stressed and basal (i.e., non-stressed) conditions in vitro, suggesting that presequence strength may influence a broader array of processes than currently appreciated. We exploit this variability to demonstrate that only presequences that promote robust import in vitro can fully rescue defects in respiratory growth in Complex IV-deficient yeast, suggesting that presequence strength dictates metabolic potential. Collectively, our findings demonstrate that presequence strength can describe numerous metrics, such as total imported protein, maximal import velocity, or sensitivity to uncoupling, suggesting that the annotation of presequences as "weak" versus "strong" requires more nuanced characterization than is typically performed. Importantly, we find that such variability in presequence strength meaningfully affects cellular fitness in processes beyond stress signaling, suggesting that organisms may broadly exploit presequence strength to fine-tune mitochondrial import and thus organellar homeostasis.
    DOI:  https://doi.org/10.1101/2025.05.26.655807
  20. Haematologica. 2025 Jun 12. 0
      The evaluation of bone marrow pathology is essential for diagnosing and classifying myeloproliferative neoplasms (MPNs). However, morphological assessments of bone marrow trephine (BMT) sections by hematopathologists are inherently subjective; thus, an accurate and objective diagnostic system is needed. Based on U2-Net, UNeXt, and ResNet, we developed an automatic quantitative analysis platform of BMT sections from MPNs patients and nonneoplastic cases (n=342 total) to enhance the accuracy of diagnosis and classification of MPNs. Bone marrow metrics, including marrow cellularity, the myeloid-to-erythroid (M: E) ratio, megakaryocyte morphology and distribution, and the grading of marrow fibrosis (MF), were quantitatively analyzed (with an accuracy of approximately 0.9) based on the accuracy segmentation and identification of various cells and tissues (with an intersection over union (IoU) of roughly 0.8). A bone marrow classification model incorporating bone marrow metrics, a clinical classification model utilizing clinical features, and a comprehensive classification model that includes both bone marrow metrics and clinical features were developed using random forest classifiers to differentiate MPN subtypes and nonneoplastic conditions. The bone marrow and comprehensive classification models reached a macro-average area under the curve (AUC) of 0.96 for differentiating MPN subtypes and nonneoplastic cases. The clinical classification model attained a macro-average AUC of 0.92. This platform is highly accurate for quantitatively analyzing bone marrow pathology and classifying MPN subtypes and nonneoplastic cases. It can be a potentially auxiliary diagnostic tool for hematopathologists when dealing with patients with suspected MPNs.
    DOI:  https://doi.org/10.3324/haematol.2024.286123
  21. bioRxiv. 2025 May 27. pii: 2025.05.23.655825. [Epub ahead of print]
      In vitro hematopoiesis systems can be used to define mechanisms for blood cell formation and function, produce cell therapeutics, and model blood cell contributions to systemic disease. Hematopoietic progenitor cell (HPC) production remains inefficient, precluded by knowledge gaps related to specification and morphogenesis of specialized hemogenic endothelial cells, which undergo an endothelial-to-hematopoietic transition (EHT) to form HPCs. We elected to define changes in gene expression and chromatin organization during HPC formation to reveal regulatory mechanisms. Using paired single cell RNA/ATAC sequencing together with Hi-C, we profiled cells before and after EHT. Pathway analysis and pseudotime inferences confirmed a continuum of stromal and endothelial cells undergoing development into HE cells and lineage-based HPCs in vitro . In these cell types, we characterize cis-regulatory elements and transcriptional regulatory activities that facilitate EHT and HPC homeostasis, including for SNAI1, SOX17, TGFβ, STAT4, as well as for GFI1b and KLF1 in megakaryocyte- and erythroid-biased progenitors, respectively. We then leveraged our insights into chromatin organization among in vitro -derived cells to assess enrichments corresponding to human trait variation reported in human genome wide association studies. HPCs revealed locus enrichment for quantitative blood traits and autoimmune disease predisposition, which were particularly enriched in myeloid- and lymphoid-biased populations. Stromal and endothelial cells from our in vitro cultures were specifically enriched for accessible chromatin at blood pressure loci. Our findings reveal genes and mechanisms governing in vitro hematopoietic development and blood cell-related disease pathology.
    DOI:  https://doi.org/10.1101/2025.05.23.655825