技术资料

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. Subject terms: Genetics research,Acute myeloid leukaemia View Publication

Kidney organoids derived from human induced pluripotent stem cells lack a proper vasculature,hampering their applicability. Transplantation prevents the loss of organoid endothelial cells (ECs) observed in vitro,and promotes vascularization. In this study,we transplanted kidney organoids in chicken embryos and deployed single-cell RNA sequencing of ~12,000 organoid ECs to delineate their molecular landscape and identify key changes associated with transplantation. Transplantation significantly altered EC phenotypic composition. Consistent with angiogenesis,proliferating EC populations expanded 8 days after transplantation. Importantly,ECs underwent a major vein-to-arterial phenotypic shift. One of the transplantation-specific arterial EC populations,characterized by laminar shear stress response and Notch signalling,showed a similar transcriptome as human fetal kidney arterial/afferent arteriolar ECs. Consistently,transplantation-induced transcriptional changes involved proangiogenic and arteriogenic SOX7 transcription factor upregulation and regulon enrichment. These findings point to blood flow and candidate transcription factors such as SOX7 as possible targets to enhance kidney organoid vascularization. Subject terms: Nephrons,Transcriptomics,Angiogenesis,Angiogenesis,Stem cells,Stem-cell differentiation View Publication

Prenatal nicotine exposure impairs fetal cortical grey matter volume,but the precise cellular mechanisms remain poorly understood. This study elucidates the role of nicotinic acetylcholine receptors (nAChRs) in progenitor cells and radial glia (RG) during human cortical development. We identify two nAChR subunits—CHRNA7 and the human-specific CHRFAM7A—expressed in SOX2+ progenitors and neurons,with CHRFAM7A particularly enriched along RG endfeet. nAChR activation in organotypic slices and dissociated cultures increases RG proliferation while decreasing neuronal differentiation,whereas nAChR knockdown reduces RG and increases neurons. Single-cell RNA sequencing reveals that nicotine exposure downregulates key genes in excitatory neurons (ENs),with CHRNA7 or CHRFAM7A selectively modulating these changes,suggesting an evolutionary divergence in regulatory pathways. Furthermore,we identify YAP1 as a critical downstream effector of nAChR signaling,and inhibiting YAP1 reverses nicotine-induced phenotypic alterations in oRG cells,highlighting its role in nicotine-induced neurodevelopmental pathophysiology. Subject terms: Neuronal development,Developmental neurogenesis,Neural stem cells View Publication

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. Subject terms: Haematopoietic stem cells,Haematological diseases,Autophagy View Publication

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 UBA1 M41V mutation. We found that mutant UBA1 M41V 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 UBA1 M41V cells,with alterations in inflammatory and stress-response pathways. Functional studies demonstrated that UBA1 M41V 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 UBA1 M41V cells as compared to WT cells. Moreover,UBA1 M41V 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 UBA1 M41V cells. Targeting UBA6 using shRNA or the UBA6-specific inhibitor phytic acid further revealed an acquired dependency on UBA6 in UBA1 M41V cells. Phytic acid selectively impaired growth and colony formation in UBA1 M41V 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. Subject terms: Haematological cancer,Cell signalling View Publication

Aplastic anemia (AA) is a life-threatening bone marrow (BM) failure syndrome characterized by pancytopenia. Recent studies revealed that dysfunctional endothelial progenitor cells (EPCs),critical components of the BM microenvironment,are involved in hematopoietic-dysfunction-related diseases,including AA. However,the mechanism underlying EPC damage in AA remains unknown. Here we find that transforming growth factor-β (TGF-β) signaling is hyperactive in dysfunctional AA EPCs with impaired hematopoietic support and immune regulatory ability,and TGF-β inhibition promotes hematopoiesis and immune rebalance by repairing dysfunctional EPCs. Through impaired EPC and AA murine models,we validated that TGF-β inhibition restores EPC dysfunction to improve hematopoiesis and immune status in vitro and in vivo. RNA sequencing and real-time quantitative polymerase chain reaction provided further validation. These results indicate that dysfunctional BM EPCs with hyperactive TGF-β signaling are involved in AA. TGF-β inhibition promotes multilineage hematopoiesis recovery and immune balance by repairing dysfunctional EPCs,providing a potential therapeutic strategy for AA. Subject terms: Experimental models of disease,Translational research View Publication

Cancer stem cells (CSCs) are responsible for colorectal cancer (CRC) chemoresistance,recurrence,and metastasis. Therefore,identifying molecular stemness targets that are involved in tumor growth is crucial for effective treatment. Here,we performed an extensive in vitro and in vivo molecular and functional characterization,revealing the pivotal role of the lysine methyltransferase SET and MYND Domain Containing 3 (SMYD3) in colorectal cancer stem cell (CRC-SC) biology. Specifically,we showed that SMYD3 interacts with and methylates c-MYC at K158 and K163,thereby modulating its transcriptional activity,which is implicated in stemness and colorectal malignancy. Our in vitro data suggest that SMYD3 pharmacological inhibition or its stable genetic ablation affects the clonogenic and self-renewal potential of patient-derived CRC-SCs and organoids by altering their molecular signature. Moreover,we found that SMYD3 stable knock-out or pharmacological inhibition drastically reduces CRC tumorigenicity in vivo and CRC-SC metastatic potential. Overall,our findings identify SMYD3 as a promising therapeutic target acting directly on c-MYC,with potential implications for countering CRC-SC proliferation and metastatic dissemination. Subject terms: Gastrointestinal cancer,Cancer stem cells View Publication

Several years after the COVID‐19 pandemic,the impact of SARS‐CoV‐2 on immunity and the potential protective role of Bacillus Calmette–Guérin (BCG) vaccination through trained immunity remain a subject of investigation. This study aimed to determine the long‐term impact of SARS‐CoV‐2 on immune cells and the association between BCG vaccination,latent infections and COVID‐19 severity and sepsis progression. We conducted a prospective analysis of patients who recovered from mild/severe/critical COVID‐19 ( n = 97,3–17 months after COVID‐19) and sepsis patients ( n = 64). First,we assessed the impact of COVID‐19 and its severity on immune cell frequencies and expression of functional markers. Further,we analysed plasma titres of anti‐ Toxoplasma gondii /cytomegalovirus/BCG antibodies and their association with COVID‐19 severity and sepsis outcome. To examine monocyte responses to secondary challenge,monocytes isolated from COVID‐19 convalescent patients,BCG vaccinated and unvaccinated volunteers were stimulated with SARS‐CoV‐2 and LPS. Post‐COVID‐19 patients showed immune dysregulation regardless of disease severity characterised by altered expression of activation and functional markers in myeloid (CD39,CD64,CD85d,CD11b) and lymphoid cells (CD39,CD57,TIGIT). Strikingly,post‐critical COVID‐19 patients showed elevated expression of CD57 in CD8 + T cells compared to other severity groups. A trend toward improved outcomes in BCG‐seropositive COVID‐19/sepsis patients was observed,although this may be confounded by age differences between groups. In contrast,the monocyte response to stimulation appeared unaffected by COVID‐19 severity. These findings highlight the long‐term alterations of immune cells in post‐COVID‐19 patients,emphasising the substantial impact of COVID‐19 on immune function. View Publication

Ageing-dependent low-grade inflammation is a hallmark of central nervous system (CNS) diseases. Vascular and immune abnormalities are implicated in the progression of gliomas and occur in the early stages of Alzheimer's disease (AD); however,the mechanisms by which these alterations manifest in the brain parenchyma remain unclear. Using RNAseq,scRNAseq,bioinformatics tools and a cohort of patients with glioma and Alzheimer's disease for validation of results,we have established an analysis of blood–brain barrier (BBB) dysfunction and neuron loss. A mouse model for glioblastoma pathology was also used that reversed BBB disruption and neuron loss,with the incorporation of the IDH mutation. Finally,we established a characterization of the relevant immune populations with an IHC analysis and transcriptional profile. In this study,molecular analyses of the brain ecosystem revealed that blood–brain barrier dysfunction and neuronal synapse integrity exhibit significant threshold-dependent changes that correlate directly and inversely,respectively,with brain ageing (significant changes at 57 years) and the progression of AD and gliomas (survival of 1525 vs 4084 days for patients with High vs Low BBB dysfunction). Using human samples and mouse models,we identified immunoageing processes characterized by an imbalance between pro-inflammatory and anti-inflammatory signals. This dysregulation promotes the extravasation of monocyte-derived macrophages (85% increase of cells),particularly those with a suppressive phenotype,alongside an increase in inflammatory cytokine levels. Notably,our data show that vascular normalization in a glioma model can reverse neuronal loss and attenuate the aggressiveness of the tumours. Finally,tumour development can be prevented by reactivating the ageing immune system. We propose that the ageing brain represents a common,BBB dysfunction-associated process driving chronic inflammation. This inflammation is regulated by TREM2+/TIM3+ suppressive myeloid cells,which play a central role in disease progression. Our findings suggest that targeting these pathways could offer therapeutic strategies to mitigate CNS pathologies linked to ageing,characterized by toxic neuroinflammation and myeloid dysfunction. This study was funded by ISCIII and co-funded by the European Union. View Publication

CD38,an ecto-enzyme involved in NAD + catabolism,is highly expressed in exhausted CD8 + T cells and has emerged as an attractive target to improve response to immune checkpoint blockade (ICB) by blunting T cell exhaustion. However,the precise role(s) and regulation of CD38 in exhausted T cells and the efficacy of CD38-directed therapeutic strategies in human cancer remain incompletely defined. Here,we show that CD38 + CD8 + T cells are induced by chronic TCR activation and type I interferon stimulation and confirm their association with ICB resistance in human melanoma. Disrupting CD38 restores cellular NAD + pools and improves T cell bioenergetics and effector functions. Targeting CD38 restores ICB sensitivity in a cohort of patient-derived organotypic tumor spheroids from explanted melanoma specimens. These results support further preclinical and clinical evaluation of CD38-directed therapies in melanoma and underscore the importance of NAD + as a vital metabolite to enhance those therapies. View Publication

Maturation of human pluripotent stem (hPS) cell-derived cardiomyocytes is critical for their use as a model system. Here we mimic human heart maturation pathways in the setting of hPS cell-derived cardiac organoids (hCOs). Specifically,transient activation of 5′ AMP-activated protein kinase and estrogen-related receptor enhanced cardiomyocyte maturation,inducing expression of mature sarcomeric and oxidative phosphorylation proteins,and increasing metabolic capacity. hCOs generated using the directed maturation protocol (DM-hCOs) recapitulate cardiac drug responses and,when derived from calsequestrin 2 ( CASQ2 ) and ryanodine receptor 2 ( RYR2 ) mutant hPS cells exhibit a pro-arrhythmia phenotype. These DM-hCOs also comprise multiple cell types,which we characterize and benchmark to the human heart. Modeling of cardiomyopathy caused by a desmoplakin ( DSP ) mutation resulted in fibrosis and cardiac dysfunction and led to identifying the bromodomain and extra-terminal inhibitor INCB054329 as a drug mitigating the desmoplakin-related functional defect. These findings establish DM-hCOs as a versatile platform for applications in cardiac biology,disease and drug screening. Subject terms: Tissue engineering,Differentiation,Cardiomyopathies View Publication

Glioblastoma (GBM) is a rapidly growing,aggressive brain tumor with very poor prognosis without currently effective therapies. The immunosuppressive nature of the tumor microenvironment (TME) in GBM hinders the development of effective tumor-eradicating immunotherapies. This hostile TME can be modulated by administering immune-activating cytokines in combination with agents inducing tumor cell death. To achieve these objectives,we sought to harness the cancer-selective cell death-inducing properties of an enhanced “Superkine” version of melanoma differentiation associated gene-7/interleukin-24,IL-24S,and the immune-activating properties of IL-15 to modulate the TME of GBM to maximize therapeutic outcomes. A fusion “Superkine” ( FSK ) comprised of IL‐24S linked to IL-15 was generated,and antitumor effects were evaluated when transduced by a type 5 adenovirus (Ad.5) in a GBM immunocompetent mouse tumor model. To target the delivery of Ad.5 FSK systemically,we employed an innovative approach of focused ultrasound (FUS) paired with microbubbles (MBs),FUS-DMB (FUS plus double MB),to safely transport the FSK engineered Ad.5 construct into mouse brain to overcome limitations of systemic viral delivery and selectivity of the blood-brain barrier. The FSK stimulated higher tumor regression and enhanced survival in vivo than the individual “Superkine” or cytokine in GBM cancer models. Apoptosis of GBM cells was induced,as well as increased tumor infiltration of T cells,dendritic cells,macrophages and natural killer (NK) cells. The antitumor-inducing activity of FSK is a consequence of induction of cancer-specific growth suppression and induction of apoptosis (IL-24S) as well as diverse effects on immune cells (IL-15 and IL-24S). Antibody neutralization indicates that a primary immune mediator of anticancer activity of FSK is through recruitment and activation of NK cells. Global cytokine analyses indicated no changes in inflammatory cytokines during therapy,suggesting that this strategy will be safe. In summary,treatment with an FSK,consisting of a fusion of IL-24S to IL-15,promotes GBM cell killing and remodeling of the TME by recruiting and activating immune cells supporting the feasibility of developing safe and effective cancer immunotherapeutic fusion proteins and selective delivery in the brain for the therapy of GBM. View Publication