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The tumor microenvironment and healing wounds both contain extremely high concentrations of adenosine triphosphate (ATP) compared to normal tissue. The P2Y2 receptor,an ATP-activated purinergic receptor,is typically associated with pulmonary,endothelial,and neurological cell signaling. Here,we examine ATP-dependent signaling in breast epithelial cells and how it is altered in metastatic breast cancer. Using rapid imaging techniques,we show how ATP-activated P2Y2 signaling causes an increase in intracellular Ca 2+ in non-tumorigenic breast epithelial cells,approximately 3-fold higher than their tumorigenic and metastatic counterparts. The non-tumorigenic cells respond to increased Ca 2+ with actin polymerization and localization to the cell edges after phalloidin staining,while the metastatic cells remain unaffected. The increase in intracellular Ca 2+ after ATP stimulation was blunted to control levels using a P2Y2 antagonist,which also prevented actin mobilization and significantly increased cell dissemination from spheroids in non-tumorigenic cells. Furthermore,the lack of Ca 2+ changes and actin mobilization in metastatic breast cancer cells could be due to the reduced P2Y2 expression,which correlates with poorer overall survival in breast cancer patients. This study elucidates the rapid changes that occur after elevated intracellular Ca 2+ in breast epithelial cells and how metastatic cancer cells have adapted to evade this cellular response. View Publication

Acute myeloid leukemia (AML) is associated with unfavorable patient outcomes primarily related to disease relapse. Since specific types of leukemic hematopoietic stem and progenitor cells (HSPCs) are suggested to contribute to AML propagation,this study aimed to identify and explore relapse-initiating HSPC subpopulations present at diagnosis,using single-cell analysis (SCA). We developed unique high-resolution techniques capable of tracking single-HSPC-derived subclones during AML evolution. Each subclone was evaluated for chemo-resistance,in vivo leukemogenic potential,mutational profile,and the cell of origin. In BM samples of 15 AML patients,GMP-like and MLP-like HSPC subpopulations were identified as prevalent at relapse,exhibiting chemo-resistance to commonly used chemotherapy agents cytosine arabinoside (Ara-C) and daunorubicin. Reconstruction of phylogenetic lineage trees combined with genetic analysis of single HSPCs and single-HSPC-derived subclones demonstrated two distinct clusters,originating from MLP-like or GMP-like subpopulations,observed both at diagnosis and relapse. These subpopulations induced leukemia development ex vivo and in vivo. Genetic SCA showed that these relapse-related subpopulations harbored mutated EZH2 and TP53,detected already at diagnosis. This study,using combined molecular,functional,and genomic analyses at the level of single cells,identified patient-specific chemo-resistant HSPC subpopulations at the time of diagnosis,promoting AML relapse. View Publication

This study investigates the use of silver nanoparticles as a potential new treatment for colorectal cancer. Colorectal cancer is one of the most common cancers worldwide,and finding more effective treatments is essential. The researchers tested silver nanoparticles AgNPs with two different surface coatings to see how they affect cancer cells compared to healthy cells. One type of nanoparticles showed significant effects,reducing cancer cell growth and inducing cell death,while the other had minimal impact. These findings suggest that modifying the surface of nanoparticles could help target cancer cells more specifically,leading to treatments that are both more effective and have fewer side effects. This research could pave the way for new therapies for colorectal cancer and other types of cancer,ultimately improving patient outcomes and advancing cancer treatment strategies. View Publication

The in vitro generation of human red blood cells (RBCs) from stem cells,such as induced pluripotent stem cells (iPSCs),holds promise for transfusable RBCs but faces challenges,including RBC maturation,enucleation,and large-scale production. In this study,we evaluated the effect of conditional TAL1 overexpression on in vitro RBC production via hematopoietic cell-forming complex (HCFC) formation from iPSCs because TAL1 is a key regulatory transcription factor essential for erythropoiesis. TAL1 overexpression in iPSCs,either before or after hematopoietic induction,significantly enhanced HCFC formation and hematopoietic differentiation,as evidenced by increased hematopoiesis-related gene expression,a higher yield of glycophorin A (GPA)+/CD71+ cells,and elevated gamma hemoglobin levels. These findings highlight the potential of TAL1 as a powerful regulator of erythropoiesis in vitro and offer a promising strategy for improving RBC production from stem cells. However,the reduced enucleation efficiency observed after TAL1 overexpression indicates a key challenge that must be addressed to optimize the generation of fully functional,transfusable RBCs. Further research is required to balance the benefits of enhanced differentiation with the need for efficient enucleation,which is critical for the production of mature,viable RBCs. View Publication

Neurodevelopmental studies employing animal models encounter challenges due to interspecies differences and ethical concerns. Maturing neurons of human origin,undergoing several developmental stages,present a powerful alternative. In this study,human embryonic stem cell (H9 cell line) was differentiated into neural stem cells and subsequently matured into neurons over 30 days. Ion AmpliSeq™ was used for transcriptomic characterization of human stem cell-derived neurons at multiple time points. Data analysis revealed a progressive increase of markers associated with neuronal development and astrocyte markers,indicating the establishment of a co-culture accommodating both glial and neurons. Transcriptomic and pathway enrichment analysis also revealed a more pronounced GABAergic phenotype in the neurons,signifying their specialization toward this cell type. The findings confirm the robustness of these cells across different passages and demonstrate detailed progression through stages of development. The model is intended for neurodevelopmental applications and can be adapted to investigate how genetic modifications or exposure to chemicals,pharmaceuticals,and other environmental factors influence neurons and glial maturation. View Publication

The ten‐eleven translocation family of enzymes (TET1/2/3) promotes DNA demethylation and is essential for hematopoiesis. While the roles of TET1 and TET2 are well‐studied in hematopoiesis,the requirement of TET3 in embryonic and adult hematopoiesis is less investigated. In this study,by characterizing embryonic and adult hematopoiesis in Tie2 +/cre ; Tet3 f/f mice,we have established a requirement for TET3 in regulating hematopoietic stem cells (HSCs; CD150 + CD48 – ). We found that loss of TET3 in the fetal liver and adult bone marrow causes a reduction in the percent of long‐term HSCs (LT‐HSCs; CD150 + CD48 – CD34 – ). This was accompanied by reduced colony forming capacity of TET3‐deficient HSCs in vitro and reduced contribution of HSCs after a competitive bone marrow transplantation in vivo. TET3 deficiency increased DNA methylation at several cell cycle regulator genes leading to their down regulation. This is consistent with,and likely underpins,the reduced number of quiescent HSCs in TET3‐deficient bone marrow. These findings uncover a new role for TET3 in HSC homeostasis during embryonic and adult hematopoiesis. View Publication

Metabolic reprogramming of amino acids represents a vulnerability in cancer cells,yet the mechanisms underlying serine metabolism in acute myeloid leukemia (AML) and leukemia stem/initiating cells (LSCs/LICs) remain unclear. Here,we identify RNA N 6 -methyladenosine (m 6 A) modification as a key regulator of serine biosynthesis in AML. Using a CRISPR/Cas9 screen,we find that depletion of m 6 A regulators IGF2BP3 or METTL14 sensitizes AML cells to serine and glycine (SG) deprivation. IGF2BP3 recognizies m 6 A on mRNAs of key serine synthesis pathway (SSP) genes (e.g.,ATF4,PHGDH,PSAT1 ),stabilizing these transcripts and sustaining serine production to meet the high metabolic demand of AML cells and LSCs/LICs. IGF2BP3 silencing combined with dietary SG restriction potently inhibits AML in vitro and in vivo,while its deletion spares normal hematopoiesis. Our findings reveal the critical role of m 6 A modification in the serine metabolic vulnerability of AML and highlight the IGF2BP3/m 6 A/SSP axis as a promising therapeutic target. Subject terms: Acute myeloid leukaemia,Cancer metabolism View Publication

Mounting evidence indicates that exosomes derived from human umbilical cord mesenchymal stem cells (hucMSCs-exosomes) combine the advantages of hucMSC pluripotency with their nanoscale dimensions,enhancing their clinical potential through prolonged circulation half-life. Despite these promising characteristics,research on their immunological toxicity remains insufficient. This study focuses on the impact of hucMSC-exosomes on the general toxicity and immunopathological indicators. When mice received tail vein injections of 6 × 10 10 hucMSC-exosomes particles,we observed no significant changes in body weight,feed intake,blood composition,organ indices,or histopathological findings throughout the 14 days observation period. Similarly,blood levels of immunoglobulins,cytokines,and lymphocyte subpopulations remained stable. The hucMSC-exosomes produced no detectable negative effects on immune organs including the thymus,spleen,and bone marrow. These findings indicate that intravenous administration of 6 × 10 10 particles of hucMSC-exosomes appears relatively safe at the murine level. This assessment of safety and immunological impact following intravenous hucMSC-exosomes infusion offers experimental support for potential clinical applications and future analyses in this field. View Publication

In Alzheimer’s disease,amyloid beta (Aβ) and tau pathology are thought to drive synapse loss. However,there is limited information on how endogenous levels of tau,Aβ and other biomarkers relate to patient characteristics,or how manipulating physiological levels of Aβ impacts synapses in living adult human brain. Using live human brain slice cultures,we report that Aβ 1-40 and tau release levels vary with donor age and brain region,respectively. Release of other biomarkers such as KLK-6,NCAM-1,and Neurogranin vary between brain region,while TDP-43 and NCAM-1 release is impacted by sex. Pharmacological manipulation of Aβ in either direction results in a loss of synaptophysin puncta,with increased physiological Aβ triggering potentially compensatory synaptic transcript changes. In contrast,treatment with Aβ-containing Alzheimer’s disease brain extract results in post-synaptic Aβ uptake and pre-synaptic puncta loss without affecting synaptic transcripts. These data reveal distinct effects of physiological and pathological Aβ on synapses in human brain tissue. Subject terms: Alzheimer's disease,Alzheimer's disease View Publication

Extracellular vesicles (EVs) derived from human organoids are phospholipid bilayer-bound nanoparticles that carry therapeutic cargo. However,the low yield of EVs remains a critical bottleneck for clinical translation. Vertical-Wheel bioreactors (VWBRs),with unique design features,facilitate the scalable production of EVs secreted by human blood vessel organoids (BVOs) under controlled shear stress,using aggregate- and microcarrier-based culture systems. Human induced pluripotent stem cell-derived BVOs cultured as aggregates or on Synthemax II microcarriers within VWBRs (40 and 80 rpm) were compared to static controls. The organoids were characterized by metabolite profiling,flow cytometry,and gene expression of EV biogenesis markers. EVs were characterized by nanoparticle tracking analysis,electron microscopy,and Western blotting. Lipidomics provided insights into EV lipid composition,while functional assays assessed the impact of EVs in a D-galactose-induced senescence model. VWBR cultures showed more aerobic metabolism and higher expression of EV biogenesis genes compared to the static control. EVs from different conditions were comparable in size,but the yields were significantly higher for microcarrier and dynamic cultures than static aggregates. Lipidomic profiling revealed minimal variation (< 0.36%) in total lipid content; however,distinct differences were identified in lipid chain lengths and saturation levels,affecting key pathways such as sphingolipid and neurotrophin signaling. Human BVO EVs demonstrated the abilities of reducing oxidative stress and increasing cell proliferation in vitro. Human BVOs differentiated in VWBRs (in particular 40 rpm) produce 2–3 fold higher yield of EVs (per mL) than static control. The bio manufactured EVs from VWBRs have exosomal characteristics and therapeutic cargo,showing functional properties in in vitro assays. This innovative approach establishes VWBRs as a scalable platform for producing functional EVs with defined lipid profiles and therapeutic potential,paving the way for future in vivo studies. The online version contains supplementary material available at 10.1186/s13287-025-04317-2. View Publication

Chronic obstructive pulmonary disease (COPD) is a heterogeneous syndrome,resulting in inconsistent findings across studies. Identifying a core set of genes consistently involved in COPD pathogenesis,independent of patient variability,is essential. We integrated lung tissue sequencing data from patients with COPD across two centers. We used weighted gene co-expression network analysis and machine learning to identify 13 potential pathogenic genes common to both centers. Additionally,a gene-based model was constructed to distinguish COPD at the molecular level and validated in independent cohorts. Gene expression in specific cell types was analyzed,and Mendelian randomization was used to confirm associations between candidate genes and lung function/COPD. Preliminary in vitro functional validation was performed on prioritized core candidate genes. Tissue inhibitor of metalloproteinase 4 (TIMP4) was identified as a key pathogenic gene and validated in COPD cohorts. Further analysis using single-cell sequencing from mice and patients with COPD revealed that TIMP4 is involved in ciliated cells. In primary human airway epithelial cells cultured at the air-liquid interface,TIMP4 overexpression reduced ciliated cell numbers. We developed a 13-gene model for distinguishing COPD at the molecular level and identified TIMP4 as a potential hub pathogenic gene. This finding provides insights into shared disease mechanisms and positions TIMP4 as a promising therapeutic target for further investigation. The online version contains supplementary material available at 10.1186/s12931-025-03238-1. View Publication

Human brain development requires generating diverse cell types,a process explored by single-cell transcriptomics. Through parallel meta-analyses of the human cortex in development (seven datasets) and adulthood (16 datasets),we generated over 500 gene co-expression networks that can describe mechanisms of cortical development,centering on peak stages of neurogenesis. These meta-modules show dynamic cell subtype specificities throughout cortical development,with several developmental meta-modules displaying spatiotemporal expression patterns that allude to potential roles in cell fate specification. We validated the expression of these modules in primary human cortical tissues. These include meta-module 20,a module elevated in FEZF2 + deep layer neurons that includes TSHZ3,a transcription factor associated with neurodevelopmental disorders. Human cortical chimeroid experiments validated that both FEZF2 and TSHZ3 are required to drive module 20 activity and deep layer neuron specification but through distinct modalities. These studies demonstrate how meta-atlases can engender further mechanistic analyses of cortical fate specification. Subject terms: Developmental neurogenesis,Gene regulatory networks View Publication