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Prime editing is a promising approach for correcting pathogenic variants,but its efficiency remains variable across genomic contexts. Here,we systematically evaluated 12 modifications of the PEmax system for correcting the CFTR F508del pathogenic variant that caused cystic fibrosis in patient-derived airway basal cells. We chose EXO1 and FEN1 nucleases to improve the original system. While all tested variants showed comparatively low efficiency in this AT-rich genomic region,4-FEN modification demonstrated significantly improved editing rates (up to 2.13 fold) compared to standard PEmax. Our results highlight two key findings: first,the persistent challenge of AT-rich target sequence correction even with optimized editors,and second,the performance of 4-FEN suggests its potential value for other genomic targets. View Publication

Myeloproliferative Neoplasms (MPN) are malignancies of hematopoietic stem and progenitor cells (HSPCs) that lead to the overproduction of mature blood cells. These disorders include Essential Thrombocythemia (ET),Polycythemia Vera (PV),and Primary Myelofibrosis (PMF),primarily driven by somatic mutations such as JAK2 V617F . Research indicates that mesenchymal stromal cells (MSCs) support fibrosis in PMF,though their role in ET and PV remains less clear. Furthermore,in vivo studies of ET/PV HSPCs remain a challenge due to low engraftment levels in xenograft models. We employed a 3D scaffold model to create an MPN humanized xenograft mouse model,enabling in vivo functional studies of primary MPN progenitor cells and the supportive role of human MSCs. Using this model,we first demonstrated robust hematopoietic support of healthy (HD) HSPCs by PV and ET MSCs. We then investigated the role of MSCs in sustaining JAK2 V617F mutant cells by using a CRISPR‐Cas9 editing model,along with primary PV and ET HSPCs. Our results showed consistent engraftment of CRISPR‐edited JAK2 V617F mutant HSPCs and PV and ET patient‐derived HSPCs in scaffolds seeded with HD,PV,and ET stroma,providing the first in vivo evidence that PV and ET MSCs can sustain both healthy and MPN‐associated hematopoiesis. Furthermore,HD MSCs were also capable of sustaining PV and ET HSPCs in vivo. Overall,we present the first humanized MPN xenograft model that offers valuable insights into how human BM MSCs interact with JAK2 V617F mutant clones. View Publication

Spinal cord injury (SCI) remains a significant clinical challenge and poses a dramatic threat to the life quality of patients due to limited neural regeneration and detrimental post-injury alternations in tissue microenvironment. We developed a therapeutic approach by transplanting spinal neural progenitor cells (spNPGs),derived from human induced pluripotent stem cell (iPSC)-generated neuromesodermal progenitors,into a contusive SCI model in NOD-SCID mice. Single-cell RNA sequencing mapped the in vitro differentiation of iPSC-spNPGs,confirming their specification into spinal neuronal lineages. Single-nucleus transcriptomics at 1 week post-transplantation showed that the grafted cells differentiated in vivo into motor neurons and two interneuron subtypes (V2 and dI4). Additionally,spNPGs integrated into host neural circuits,enhancing synaptic connectivity,while simultaneously modulating the injury microenvironment by shifting microglia and astrocyte polarization toward anti-inflammatory and neuroprotective phenotypes. This dual mechanism promoted axonal regrowth,remyelination,and significant sensorimotor recovery,as evidenced by improved locomotor scores. Our findings highlight the therapeutic potential of human iPSC-spNPGs in reconstructing neural networks and mitigating secondary damage,providing compelling preclinical evidence for advancing stem cell-based SCI therapies. Subject terms: Stem-cell differentiation,Spinal cord injury View Publication

Cytolysin A (ClyA) is a pore‐forming protein from a strongly silenced gene in non‐pathogenic Escherichia coli,including typical commensal isolates in the intestinal microbiome of healthy mammalian hosts. Upon overproduction,ClyA‐expressing bacteria display a cytolytic phenotype. However,it remains unclear whether sublytic amounts of native ClyA play a role in commensal E. coli ‐host interactions in vivo. Here,we show that sublytic amounts of ClyA are released via outer membrane vesicles (OMVs) and affect host cells in a remarkable manner. OMVs isolated from ClyA + E. coli were internalised into cultured colon cancer cells. The OMV‐associated ClyA caused reduced levels of cancer‐activating proteins such as H3K27me3,CXCR4,STAT3 and MDM2 via the EZH2/H3K27me3/microRNA 622/CXCR4 signalling axis. Our results demonstrate that sublytic amounts of ClyA in OMVs from non‐pathogenic E. coli can influence the stability of the EZH2 protein,reducing its activity in epigenetic regulation,causing elevated level of the tumour suppressor protein p53. View Publication

The limited proliferative capacity of erythroid precursors is a major obstacle to generate sufficient in vitro-derived red blood cells for clinical purposes. While BMI1,a Polycomb Repressive Complex 1 member,is both necessary and sufficient to drive extensive proliferation of self-renewing erythroblasts,its mechanism of action remains poorly understood. Here we report that BMI1 overexpression leads to 10 billion-fold increase in self-renewal of human erythroblasts,which can terminally mature and agglutinate with typing reagent monoclonal antibodies. BMI1 and RING1B occupancy,along with repressive histone marks,are present at known BMI1 target genes,including the INK-ARF locus,consistent with altered cell cycle kinetics following BMI1 inhibition. Upregulation of BMI1 target genes with low repressive histone modifications,including key regulators of cholesterol homeostasis,along with functional studies,suggest that both cholesterol import and synthesis are essential for BMI1-associated self-renewal. We conclude that BMI1 regulates erythroid self-renewal not only through gene repression but also through gene activation and offer a strategy to expand immature erythroid precursors for eventual clinical uses. Subject terms: Self-renewal,Cell growth,Stem-cell research View Publication

Viral transduction is a critical step in the manufacturing of genetically modified T cells for immunotherapies,yet conventional transduction methods suffer from low to medium efficiency,high vector consumption,and limited scalability. To address these challenges,we introduce the Transduction Boosting Device (TransB),an innovative,automated,and closed-system platform designed to enable efficient and scalable gene delivery and overcome the limitations of conventional transduction methods. TransB improves cell-virus interactions by facilitating proximity between target cells and viral vectors. TransB demonstrated up to 1-fold decrease in processing time,3-fold reduction in viral vector consumption,and 0.7-fold increase in transduction efficiency compared to 24—well plate method for donor T cell transduction in studies evaluating its impact on transduction process. Comparison studies transducing T cells from three different donors with Lenti-GFP vectors showed that TransB achieved an average 0.5-fold improvement in transduction efficiencies while maintaining comparable post-transduction cell recovery,viability,growth,and phenotype compared to 24—well plate. Furthermore,TransB delivered consistent performance across two different input cell numbers demonstrating scalability of the process. These findings suggest that TransB could significantly shorten the transduction time,reduce the transduction cost and improve the transduction efficiency for manufacturing genetically modified T cell therapies. It shows strong potential as a robust,efficient,and scalable platform to enhance T cell therapy manufacturing and help overcome current manufacturing challenges in the field. The online version contains supplementary material available at 10.1186/s12967-025-06836-1. View Publication

Transplantation of engineered B cells has demonstrated efficacy in HIV disease models. B cell engineering may also be utilized for the treatment of cancer. Recent studies have highlighted that B cell activity is associated with favorable clinical outcomes in oncology. In mice,polyclonal B cells have been shown to elicit anti-cancer responses. As a potential novel cell therapy,we demonstrate that engineering B cells to target a tumor-associated antigen enhances polyclonal anti-tumor responses. We observe that engineered B cells expressing an anti-HPV B cell receptor internalize the antigen,enabling subsequent activation of oncoantigen-specific T cells. Secreted antibodies from engineered B cells form immune complexes,which are taken up by antigen-presenting cells to further promote T cell activation. Engineered B cells hold promise as novel,multi-modal cell therapies and open new avenues in solid tumor targeting. View Publication

Induced pluripotent stem cells (iPSCs) are widely used to model human genetic diseases. The most common strategy involves collecting cells from relevant individuals and then reprogramming them into iPSCs. This strategy is very powerful,but finding enough individuals with a specific genetic disease can be challenging,especially since most are rare. In addition,making numerous iPSC lines is time-consuming and expensive. As a result,most studies have included relatively small numbers of iPSC lines,sometimes from the same individual. Considering the experimental variability obtained using different iPSC lines,there has been great interest in delineating the most efficient number of lines needed to achieve a robust and reproducible result. Several recommendations have been published,although most conclusions have been based on methods where experimental variance from individual cases is difficult to separate from technical issues related to the preparation of iPSCs. The current study used gene expression profiles determined by RNA sequencing (RNAseq) to empirically evaluate the impact of the number of unique individuals and the number of replicate iPSC lines from each individual for modeling Lesch-Nyhan disease (LND). This disease is caused by mutations in the HPRT1 gene,which encodes the enzyme hypoxanthine-guanine phosphoribosyltransferase. Results for detecting disease-relevant changes in gene expression depended on the analytical method employed,and whether or not statistical procedures were used to address multiple iPSC lines from the same individual. In keeping with prior studies,the best results were obtained with iPSC lines from 3-4 unique individuals per group. In contrast to prior studies,results were improved with 2 lines per individual,without statistical corrections for duplicate lines from the same individual. In the current study where all lines were produced in parallel using the same methods,most variance in gene expression came from technical factors unrelated to the individual from whom the iPSC lines were prepared. View Publication

Immunotherapy has emerged as a key modality in cancer treatment,yet its effectiveness varies significantly among patients,often due to the metabolic stress imposed by the tumor microenvironment. Hypoxia,a major factor in the tumor microenvironment,results from the high metabolic rate of tumor cells and inadequate vascularization,impairing immune cells’ function and potentially influencing gene expression profiles. Despite the widespread use of quantitative real-time PCR in immunological studies,to the best of our knowledge,data on reference gene stability in human peripheral blood mononuclear cells under hypoxic conditions is limited. In our study,we assessed the expression stability of commonly used reference genes ( S18,HPRT,IPO8,RPL13A,SDHA,PPIA,and UBE2D2 ) in both non-stimulated and CD3/CD28-activated peripheral blood mononuclear cells cultured under normoxic,hypoxic (1% O 2 ),and chemically induced hypoxic conditions for 24 h. Analysis using four different algorithms—delta Ct,geNorm,NormFinder,and BestKeeper—identified RPL13A,S18,and SDHA as the most suitable reference genes for human peripheral blood mononuclear cells under hypoxic conditions. In contrast,IPO8 and PPIA were found to be the least suitable housekeeping genes. The study provides essential insights into the stability of reference genes in peripheral blood mononuclear cells under hypoxic conditions,a critical but understudied aspect of immunological research. Given the significant impact of hypoxia on T cell metabolism and function in the tumor microenvironment,selecting reliable reference genes is crucial for accurate gene expression analysis. Our findings will be valuable for future studies investigating hypoxia-driven metabolic reprogramming in immune cells,ultimately contributing to a better understanding of T cell responses in cancer immunotherapy. View Publication

The recently identified proton-activated chloride (PAC) channel is ubiquitously expressed,and it regulates several proton-sensitive physiological and pathophysiological processes. While the PAC channel is activated by strong acids due to the binding of protons to extracellular binding sites,here,we describe the way in which weak acids inhibit the PAC channel by a mechanism involving a distinct extracellular binding site. Whole-cell patch clamp was performed on wildtype HEK293T cells,PAC-knockout HEK293 cells expressing human (h)PAC mutant constructs,and on hiPSC-derived cardiomyocytes. Proton-induced cytotoxicity was examined in HEK293T cells. Acetic acid inhibited endogenous PAC channels in HEK 293T cells in a reversible,concentration-dependent,and pH-dependent manner. The inhibition of PAC channels was also induced by lactic acid,propionic acid,itaconic acid,and β-hydroxybutyrate. Weak acids also inhibited recombinant wildtype hPAC channels and PAC-like currents in hiPSC-derived cardiomyocytes. Replacement of the extracellular arginine 93 by an alanine (hPAC–Arg93Ala) strongly reduced the inhibition by some weak acids,including arachidonic acid. Although lactic acid inhibited PAC,it did not reduce the proton-induced cytotoxicity examined in wildtype HEK 293 cells. To conclude,weak acids inhibit PAC via an extracellular mechanism involving Arg93. These data warrant further investigations into the regulation of the PAC channel by endogenous weak acids. View Publication

Due to the complexity of modeling tumor-host interactions within the tumor microenvironment in vitro,we developed a 3D heterotypic cellular breast cancer (BC) model. We generated spheroid models using MCF7,MDA-MB-231,and SK-BR-3 cell lines alongside cancer-associated (BrC4f) and normal (BN120f) fibroblasts in ultra-low attachment plates. Stromal spheroids (3Df) were formed using a liquid overlay technique (graphical abstract). The YT cell line and peripheral blood NK (PB-NK) cells were used as immune components in our 3D model. In this study,we showed that stromal cells promoted tumor cell aggregation into spheroids,regardless of the initial proliferation rates,with NK cells accumulating in fibroblast-rich regions. The presence of CAFs within the model induced alterations in the expression levels of MICA/B and PD-L1 by tumor cells within the 3D-2 model. The feasibility of utilizing a 3D cell BC model in combination with cytokines and PB-NKs was evaluated. We observed that IL-15 and IL-2 enhanced NK cell activity within spheroids,whereas TGFβ had varying effects on proliferation depending on the cell type. Stimulation with IL-2 and IL-15 or TGFβ1 altered PB-NK markers and stimulated their differentiation into ILC1-like cells in 3D models. These findings underscore the regulatory function of CAFs in shaping the response of the tumor microenvironment to immunotherapeutic interventions. View Publication

HexaBody-CD27 (GEN1053/BNT313) is an investigational novel agonistic CD27 antibody engineered to enhance T-cell costimulation and promote antitumor immunity. Through the introduction of a hexamerization-enhancing mutation in the IgG Fc domain,HexaBody-CD27 was designed to drive clustering and activation of CD27 via intermolecular Fc:Fc interactions between membrane-bound antibodies,independent of crosslinking by FcγR-bearing cells. HexaBody-CD27 carries an Fc-silencing mutation to prevent T-cell depletion through Fc-mediated effector functions. In vitro,HexaBody-CD27 induced CD27 receptor signaling independent of FcγR-mediated crosslinking in a reporter assay. It also enhanced T-cell proliferation,cytotoxic activity and proinflammatory cytokine secretion in primary human lymphocytes. In contrast to benchmark IgG1 CD27 antibodies,HexaBody-CD27 did not induce phagocytosis of T cells in vitro. HexaBody-CD27 promoted ex vivo tumor infiltrating lymphocyte (TIL) expansion in non-small cell lung cancer (NSCLC) specimens,in particular of CD8 + TILs. The combination of HexaBody-CD27 with an anti-PD-1 antibody enhanced T-cell proliferation,cytokine secretion,and cytotoxic activity in vitro compared to either compound alone. In conclusion,HexaBody-CD27 enhanced T-cell activation and effector functions in an FcγR-crosslinking-independent manner,without inducing T-cell depletion. The immune agonist activity of HexaBody-CD27 was potentiated in combination with PD-1 blockade. View Publication