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USH2A mutations are the leading cause of autosomal recessive retinitis pigmentosa (RP),a progressive blinding disease marked by photoreceptor degeneration. Animal models fail to recapitulate the features of USH2A RP seen in humans,and its earliest pathogenic events remain unknown. Here,we established a human model of USH2A RP using retinal organoids derived from patient induced pluripotent stem cells and CRISPR-Cas9-engineered isogenic-USH2A−/− induced pluripotent stem cells. Methods: We assessed organoids for cellular,molecular,and morphological defects using serial live imaging and whole organoid and fixed section analyses. Results: Both patient-derived and isogenic-USH2A−/− organoids showed preferential rod photoreceptor loss followed by widespread degeneration,consistent with the clinical phenotype. Additionally,isogenic-USH2A−/− organoids showed early defects in proliferation and structure. Conclusions: Our findings suggest that molecular changes precede overt photoreceptor loss in USH2A RP,and pathogenesis may begin before clinical symptoms emerge. By defining early and late disease features,we provide new insight on the developmental origins of USH2A RP to guide therapeutic strategies. View Publication

The maintenance of a basal immunoinflammatory signature in hematopoietic stem/progenitor cells (HSPCs) constitutes a fundamental regulatory axis governing hematopoietic competence and immune effector generation. While epigenetic repressors constrain this inflammatory phenotype,the molecular amplifiers that preserve this critical state remain undefined. Through integrated single-cell transcriptomic/epigenomic profiling and functional interrogation,we identify Setd2-mediated H3K36me3 as an indispensable epigenetic amplifier sustaining baseline inflammation in murine HSPCs. Setd2 ablation specifically eliminated interferon (IFN)-enriched HSPC subpopulations and attenuated inflammatory signaling cascades. Functionally,Setd2-deficient HSPCs exhibited impaired IFNγ responsiveness,compromised B-lymphopoiesis,and diminished reconstitution capacity due to Lin−c-Kit+Sca1high cell depletion. Paradoxically,Setd2 loss conferred resistance to IFNγ-induced HSPCs exhaustion,which may contribute to the maintenance of Setd2-deficient HSPCs in our myelodysplastic syndrome (MDS) model under the inflammatory milieu. Mechanistically,Setd2 sustained chromatin accessibility and enhancer (H3K27ac) activity at inflammatory gene loci. This work delineates a critical link between Setd2-mediated chromatin regulation,baseline inflammation,HSPC function,and immune competence,providing insights into inflammatory dysregulation in hematopoietic malignancies like MDS. View Publication

Aggregated α-synuclein (αSyn) is a pathological hallmark of Parkinson’s disease (PD),yet other protein aggregates,including tau,are commonly observed in PD brains. This suggests that PD is not solely a synucleinopathy but may involve multiple,coexisting proteinopathies. Mutations in LRRK2,particularly the G2019S (GS),are the most common cause of familial PD. LRRK2-PD has been associated with both αSyn and tau pathology; however the mechanistic links between LRRK2 dysfunction and protein aggregation remain incompletely defined. Here we opted to investigate whether LRRK2 contributes to αSyn and tau pathology through common molecular pathways or via distinct cellular mechanisms. Viral vector-mediated αSyn overexpression in GS LRRK2 knock-in mice led to enhanced dopaminergic neurodegeneration,increased phosphorylated αSyn levels,pronounced neuroinflammation,and accumulation of lysosomal proteins,suggesting impaired αSyn clearance and immune activation as key drivers. Human iPSC-derived dopaminergic neurons from GS LRRK2 PD patients mirrored these findings. In contrast viral vector-mediated overexpression of tau in GS LRRK2 knock-in mice promoted tau phosphorylation but did not significantly affect neuroinflammation,lysosomal markers,or neurodegeneration,indicating a primarily cell-autonomous mechanism. Our results reveal a mechanistic divergence in how GS LRRK2 impacts αSyn and tau pathologies,supporting the notion that LRRK2 kinase activity contributes to PD pathogenesis through different pathways,thereby highlighting its potential as a therapeutic target in both familial and sporadic PD. View Publication

Osteoporosis (OP) could lead to the alteration of bone marrow microenvironment and non-homeostasis of hematopoiesis,which could increase the incidence of hematologic malignancies. However,whether myeloid-biased hematopoiesis occurred and contributed to the leukemogenesis under the condition of OP remains unclear. Results: This study successfully induced a mouse model for OP by hindlimb unloading,which shows increased myeloid cells and decreased B cells in the peripheral blood (PB). Furthermore,our study demonstrates that the myeloid-biased subset of HSPCs (hematopoietic stem and progenitor cells) with reduced differentiation and apoptosis,including multipotent progenitor 3 (MPP3) and granulocyte-monocyte progenitors (GMPs),were expanded in the OP mice. The expansion of myeloid-biased HSPCs contributes to the accumulation of HSPCs in the bone marrow and increased myeloid cells in the PB of OP mice. In the expanded pool of HSPCs,OP mice specifically enriched subsets were identified and profiled by single cell RNA-seq,including subHSCs from primitive HSCs,MPP3-1 from MPP3,GMP5 from GMPs,MkP2 from megakaryocyte progenitors and EryP1 from erythrocyte progenitors. Meanwhile,those OP-HU mice enriched subsets shared significantly up- and down-regulated genes enriched in chromatin modification and cell differentiation and apoptosis such as Bromodomain-containing protein 4 (Brd4),encoding an important chromatin remodeling protein,and Proteinase 3 (Prtn3). Moreover,the specific transcription factors corresponding to the expansion of subHSCs,MPP3-1,GMP5 and EryP1 in OP-HU mice were identified as Zfp951,Nfic,Maz and Ezh2. Finally,inhibition of BRD4 in vivo could partially restore the phenotype of OP-HU mice and the expression of genes regulating HSPC expansion,differentiation and apoptosis. Conclusions: First of all,our study shows that OP could induce the unbalanced hematopoiesis and enhances the myeloid-biased hematopoiesis. Secondly,OP mice enriched subsets of HSPCs were identified and characterized with enhanced chromatin remodeling,reduced differentiation and resistance to apoptosis. Finally,this study demonstrate that Brd4 regulated gene programs endow the myeloid-biased subsets of HSPCs with tumor cell-like characters in OP mice,which may increase the incidence of the leukemic evolution. This study sheds light on the importance for the prevention of myeloid leukemogenesis in human with OP. View Publication

Different innate immune cell types are known to release extracellular traps (ETs) in response to invasive pathogens,including parasites. These ETs function to trap,immobilize,and eventually kill pathogens. In line with this,monocytes and macrophages have been shown to release ETs,known as monocyte/macrophage extracellular traps (METs). Toxoplasma gondii (T. gondii) is an apicomplexan zoonotic parasite that infects humans and homeothermic animals. While most studies have focused on prolonged exposure of immune cells to T. gondii,this study characterized the early innate immune reaction of mononuclear phagocytes to vital T. gondii tachyzoites. Methods: Primary human and bovine monocytes,monocytic THP-1 cells,and THP-1 cell-derived macrophages (M0-,M1-,and M2-like) were exposed to T. gondii tachyzoites for 4 h. Scanning electron microscopy (SEM),transmission electron microscopy (TEM),immunofluorescencemicroscopy,and confocal microscopy were used to visualize cell activation and the presence of METs. Additionally,the release of pro-inflammatory cytokines interleukin (IL)-1β and IL-6,and expression of Toll-like receptor (TLR) 2 and TLR4 were analyzed. Results and discussion: Microscopic analysis illustrated the activation of all cell types tested within 4 h of exposure to T. gondii tachyzoites. Numerous tachyzoites were found intracellularly in THP-1 cell-derived M1-like macrophages. Furthermore,the co-localization of extracellular DNA (extDNA) and histones in extracellular web-like fibers proved classical characteristics of extruded T. gondii-induced METs,although this was a rare event. In primary human monocytes,an increased release of IL-1β and IL-6 was observed following exposure to T. gondii tachyzoites. When co-stimulated with lipopolysaccharide (LPS),primary human monocytes showed an enhanced release of IL-1β and IL-6 in response to T. gondii. In contrast to monocytic THP-1 cells,THP-1 cell-derived M1-like macrophages released IL-1β in response to T. gondii tachyzoite exposure. When additionally stimulated by LPS,all THP-1 cell-derived macrophages showed an enhanced release of IL-1β,and monocytic THP-1 cells an increased release of IL-6 in response to T. gondii tachyzoites. This study provides insights into the early innate immune response of human and bovine mononuclear phagocytes to T. gondii. While cytokine secretion was prominent,MET formation was rare in the early response (i.e. < 4 h of exposure) to T. gondii tachyzoites. View Publication

Eosinophils are major effector cells in type 2 immune responses,contributing to host defense and allergic diseases. They also contribute to maintaining tissue homeostasis by regulating various immune cell types,including neutrophils. Here we show that eosinophils directly associate with neutrophils in the lungs of asthma-induced mice. Eosinophil-specific deficiency of the short-chain fatty acid receptor,GPR43,results in hyperactivation of eosinophils and increases the expression of neutrophil chemoattractants and PECAM-1,thereby enhancing the interaction between eosinophils and neutrophils. This interaction exposes neutrophils to eosinophil-derived IL-4 and GM-CSF,which induce the conversion of conventional neutrophils into more pathogenic,Siglec-Fhi neutrophils capable of enhancing Th17 cell differentiation and aggravating asthma symptoms in mouse models. Our results thus implicate GPR43 as a critical regulator of eosinophils,and describe eosinophil-mediated modulation of neutrophil differentiation and function. Eosinophils contribute to type 2 immunity,but their interaction with neutrophils in this context is incompletely understood. Here the authors use mouse asthma models and in vitro culture to show that eosinophil-specific deficiency of GPR43 promotes Siglec-Fhi neutrophil differentiation and downstream induction of Th17 to aggravate lung inflammation and asthma. View Publication

How the neuroectoderm-derived eye field breaks symmetry to specify iris muscle is not well understood. Recent studies have begun to transcriptionally characterize mouse iris muscle; however,little is known about the transcriptional foundation of human iris development. Human pluripotent stem cells (hPSCs) enable the study of iris muscle specification. Here we compare iris smooth muscle from native adult iris tissues to evaluate successful specification of iris muscle from hPSC lines. We utilize a previously published eye-like organoid protocol that specified cells of the eye field to also generate iris muscle. We describe a population transcriptionally similar to native iris and describe an iris muscle gene signature. Human iris muscle not only contains pigment,but also expresses pigment synthesis genes and is responsive to acetylcholine. Integration of single-cell RNA-seq datasets confirm the similarity between the iris muscle to the adult iris,establishing the usefulness of the model in studying neuroectoderm-derived iris muscle specification,and related diseases. Single-cell RNA sequencing reveals that iris muscle,derived from neuroectoderm,can form in stem cell–derived eye organoids – enabling the modelling of iris muscle pathologies like aniridia and proliferative vitreoretinopathy. View Publication

Background: Acute Lung Injury (ALI) and its most severe form,Acute Respiratory Distress Syndrome (ARDS),are critical pulmonary conditions characterized by life-threatening acute hypoxic respiratory failure,affecting over three million individuals globally each year. ALI involves alveolar inflammation and disruption of the alveolar-capillary barrier,primarily driven by neutrophil infiltration and the release of inflammatory mediators. In our previous study using a lipopolysaccharide (LPS)-induced mouse model of ALI,we demonstrated that C6,a peptide inhibitor of voltage-gated proton channels (Hv1),ameliorates lung injury,identifying Hv1 as a potential therapeutic target. However,(i) whether the anti-inflammatory effects of C6 are translatable to a clinically relevant live bacterial infection model,and (ii) the molecular mechanisms underlying these anti-inflammatory effects,remain unknown,and are a crucial next step towards targeted rational drug development. Methods: To induce ALI,we used an intratracheal Pseudomonas aeruginosa infection model,a gram-negative bacterium relevant in ventilated and immunocompromised patients. A separate group of infected mice also received intravenous treatment with C6 (4 mg/kg). Lung injury severity was evaluated using histopathological analysis. Bronchoalveolar lavage (BAL) fluid was collected to quantify neutrophil infiltration and proinflammatory cytokines concentrations. In addition,reactive oxygen species (ROS) production and intracellular calcium levels in BAL neutrophils were measured. RNA sequencing of BAL neutrophils was conducted to assess C6-induced transcriptional changes. Key findings were validated in vitro using human neutrophils. Results: C6 mitigates P. aeruginosa-induced ALI in mice by reducing neutrophil infiltration into the alveolar space by ~ 86%,improving lung injury scores,decreasing BAL fluid proinflammatory cytokine levels,and suppressing neutrophil ROS production and intracellular calcium levels. RNA sequencing of BAL neutrophils revealed 51 downregulated genes,including key regulators of neutrophil migration,cytokine release,and ROS production; only three genes were upregulated and they also have roles in neutrophil immune defense. In human neutrophils,C6 similarly inhibited chemotaxis and reduced ROS and cytokine release,and calcium influx. Conclusions: Targeting Hv1 with C6 effectively protects against P. aeruginosa-induced ALI by limiting neutrophil recruitment and activation. These findings establish C6 as a promising therapeutic candidate against infectious ALI and provide important mechanistic insights into its immunomodulatory effects on neutrophils. View Publication

Cutaneous tuberculosis (CTB) is an infectious disease highly associated with extracellular matrix remodeling and granuloma-driven fibrosis. Fibroblasts play crucial roles in this fibrotic process,but their specific roles in Mycobacterium tuberculosis (Mtb) skin infections remain unclear due to the lack of proper in vitro models. Here,we demonstrate that skin organoids (SKOs) derived from human induced pluripotent stem cells can model CTB infected by Mtb. Single-cell RNA analyses reveal an increase in fibroblasts,upregulation of genes involved in collagen synthesis,and enhanced collagen degradation induced by MMP2 and MMP14 in Mtb-infected SKOs. This is accompanied by the destruction of nerve cells and adipocytes. Importantly,the onset of fibrosis in Mtb-infected SKOs is dependent on the activation of the PI3K-AKT signaling pathway and transcription factor AP1 in fibroblasts. Pharmacological inhibition of PI3K-AKT and AP1 alleviates fibrosis and collagen deposition. Our findings have uncovered distinct alterations in cell populations during Mtb-induced skin fibrosis,highlighting the crucial roles of PI3K-AKT and AP1. The study demonstrates the utility of SKOs for investigating CTB pathogenesis and evaluating potential antifibrotic treatments. Cutaneous tuberculosis is an infectious disease associated with extracellular matrix remodeling and granuloma-driven fibrosis. Here,the authors present an in vitro model of this disease using skin organoids infected with Mycobacterium tuberculosis,and describe infection-induced alterations in specific pathways and cell populations. View Publication

Background: Lung cancer is a leading cause of cancer-related mortality worldwide,with heterogeneity and acquired resistance posing major challenges to treatment. Advances in next-generation sequencing (NGS) have enabled comprehensive genomic profiling,yet there remains a need for robust patient-derived models to study tumor biology and inform precision medicine. This study aims to establish and characterize patient-derived lung cancer organoids (LCOs) using whole-genome sequencing (WGS) to explore their genomic landscape and therapeutic potential. Methods: We established a panel of LCOs from resected tumors and malignant pleural effusions (MPEs) of 14 non-small cell lung cancer (NSCLC) patients. Organoids were authenticated and subjected to WGS to profile somatic single nucleotide variants (SNVs),insertions/deletions (InDels),copy number variations (CNVs),structural variants (SVs),and microsatellite instability (MSI). Bioinformatic analyses were performed to annotate mutations,assess tumor mutation burden (TMB),and explore mutational signatures. Furthermore,deep learning-based drug response prediction and in vitro drug sensitivity assays were conducted to evaluate therapeutic potentials in the established LCOs. Results: In the established LCOs,WGS revealed recurrent mutations in TP53,TTN,MUC16,and FLG,with approximately 80% of somatic variants located in non-coding regions,highlighting the potential role of regulatory elements in lung cancer pathogenesis. Early and locally advanced-stage tumor-derived LCOs exhibited higher TMB and MSI compared to those from advanced-stage disease,suggesting greater clonal diversity prior to therapeutic intervention. Drug screening demonstrated the feasibility of using genomic data for drug prediction,but requires more advanced models to fully utilize the WGS data. Conclusions: Our comprehensive genomic characterization of patient-derived LCOs provides valuable insights into the mutational landscape and evolutionary dynamics of lung cancer. These well-annotated organoid models serve as a powerful resource for investigating tumor biology and developing genomically informed therapeutic strategies. View Publication

Clonal hematopoiesis (CH),a prevalent and premalignant state in the elderly,has been detected in young individuals under selective pressures such as hematopoietic cell transplantation (HCT). However,the origin of CH and mutational processes underlying CH driver mutations in young blood systems remain unclear. Here,we used genome‐wide somatic mutation profiles to retrospectively trace the origin of DNMT3A‐mutant CH in three individuals,14–41 years after childhood HCT. Both the rate and spectrum of somatic mutations in individuals with posttransplant CH were consistent with normal age‐associated mutagenesis. Phylogenetic analysis revealed that DNMT3A‐mutant HSPCs were present in the donor before 6.8 years of age,including during fetal development,despite being undetectable with a limit of detection of variant allele frequency of 0.001 at the time of transplantation. These findings were validated by comparing the observed mutations to expected age‐dependent mutational signatures. Our results reveal that undetectable DNMT3A‐mutant clones in young donors can expand into significant CH clones within decades upon transplantation. The rapid expansion of these clones in this context indicates that specific environmental pressures,rather than solely mutation acquisition,drive the development of CH. View Publication

Background: Chronic myocarditis (CMYO) progresses to fibrosis and heart failure,yet no therapies effectively target fibrosis. Fibroblast activation protein (FAP) marks pathogenic myofibroblasts,but its therapeutic potential remains unexplored in inflammatory settings.Methods: Using bulk/scRNA-seq of human myocarditis samples,we identified FAP as a fibrosis-specific marker. We engineered FAP-targeted CAR-T (FAP.CAR-T) cells and tested their efficacy in autoimmune (EAM) and viral (CVB3) myocarditis models. Human cardiac organoids (hCOs) treated with IL-17A modeled inflammatory fibrosis.Results: FAP expression correlated with fibrosis severity in patients (r = 0.96,P = 0.0028). In EAM and CVB3 models,FAP.CAR-T cells reduced fibrosis by 65% and 55%,respectively (P < 0.001),restored ejection fraction to higher than 65%. hCOs treated with FAP.CAR-T cells showed 55% less fibrosis (P < 0.05). No toxicity was observed in healthy mice.Conclusions: FAP.CAR-T cells eliminate fibrosis-driving myofibroblasts,reversing cardiac dysfunction in chronic myocarditis. This strategy,validated in human organoids,offers translatable immunotherapy for fibrosis-driven heart disease. View Publication