技术资料

Small nucleolar RNAs (snoRNAs) are non-coding RNAs that function in ribosome and spliceosome biogenesis,primarily by guiding modifying enzymes to specific sites on ribosomal RNA (rRNA) and spliceosomal RNA (snRNA). However,many orphan snoRNAs remain uncharacterized,with unidentified or unvalidated targets,and studies on additional snoRNA-associated proteins are limited. We adapted an enhanced chimeric eCLIP approach to comprehensively profile snoRNA-target RNA interactions using both core and accessory snoRNA-binding proteins as baits. Using core snoRNA-binding proteins,we confirmed most annotated snoRNA-rRNA and snoRNA-snRNA interactions in mouse and human cell lines and called novel,high-confidence interactions for orphan snoRNAs. While some of these interactions result in chemical modification,others may have modification-independent functions. We showed that snoRNA ribonucleoprotein complexes containing certain accessory proteins,like WDR43 and NOLC1,enriched for specific subsets of snoRNA-target RNA interactions with distinct roles in ribosome and spliceosome biogenesis. Notably,we discovered that SNORD89 guides 2′-O-methylation at two neighboring sites in U2 snRNA that fine-tune splice site recognition. Chimeric eCLIP of snoRNA-associating proteins enables a comprehensive framework for studying snoRNA-target interactions in an RNA-binding protein-dependent manner,revealing novel interactions and regulatory roles in RNA biogenesis. The online version contains supplementary material available at 10.1186/s13059-025-03508-7. View Publication

Lung transplantation is the primary treatment for end-stage lung diseases. However,ischemia-reperfusion injury (IRI) significantly impacts transplant outcomes. 4-Octyl itaconate (4-OI) has shown potential in mitigating organ IRI,although its effects in lung transplantation require further exploration. BEAS-2B cells were used to model transplantation,assessing the effects of 4-OI through viability,apoptosis,and ROS assays. qRT-PCR analyzed cytokine transcription post-cold ischemia/reperfusion (CI/R). RNA sequencing and Gene Ontology analysis elucidated 4-OI’s mechanisms of action,confirmed by Western blotting. ALI-airway and lung transplantation organoid models evaluated improvements in bronchial epithelial morphology and function due to 4-OI. ELISA measured IL-6 and IL-8 levels. Rat models of extended cold preservation and non-heart-beating transplantation assessed 4-OI’s impact on lung function,injury,and inflammation. Our findings indicate that 4-OI (100 µM) during cold preservation effectively maintained cell viability,decreased apoptosis,and reduced ROS production in BEAS-2B cells under CI/R conditions. It also downregulated pro-inflammatory cytokine transcription,including IL1B,IL6,and TNF. Inhibition of Nrf2 partially reversed these protective effects. In cold preservation solutions,4-OI upregulated Nrf2 target genes such as NQO1,HMOX1,and SLC7A11. In ALI airway models,4-OI enhanced bronchial epithelial barrier integrity and ciliary beat function after CI/R. In rat models,4-OI administration improved lung function and reduced pulmonary edema,tissue injury,apoptosis,and systemic inflammation following extended cold preservation or non-heart-beating lung transplantation. Incorporating 4-OI into cold preservation solutions appears promising for alleviating CI/R-induced bronchial epithelial injury and enhancing lung transplant outcomes via Nrf2 pathway activation. The online version contains supplementary material available at 10.1186/s12931-025-03151-7. View Publication

The targeting of cancer stem cells (CSCs) has proven to be an effective approach for limiting tumor progression,thus necessitating the identification of new drugs with anti-CSC activity. Through a high-throughput drug repositioning screen,we identify the antibiotic Nifuroxazide (NIF) as a potent anti-CSC compound. Utilizing a click chemistry strategy,we demonstrate that NIF is a prodrug that is specifically bioactivated in breast CSCs. Mechanistically,NIF-induced CSC death is a result of a synergistic action that combines the generation of DNA interstrand crosslinks with the inhibition of the Fanconi anemia (FA) pathway activity. NIF treatment mimics FA-deficiency through the inhibition of STAT3,which we identify as a non-canonical transcription factor of FA-related genes. NIF induces a chemical HRDness (Homologous Recombination Deficiency) in CSCs that (re)sensitizes breast cancers with innate or acquired resistance to PARP inhibitor (PARPi) in patient-derived xenograft models. Our results suggest that NIF may be useful in combination with PARPi for the treatment of breast tumors,regardless of their HRD status. Subject terms: Breast cancer,Mechanisms of disease,Target identification,Cancer stem cells View Publication

Phospholipase C gamma 2,proline 522 to arginine (PLCγ2-P522R) is a protective variant that reduces the risk of Alzheimer’s disease (AD). Recently,it was shown to mitigate β-amyloid pathology in a 5XFAD mouse model of AD. Here,we investigated the protective functions of the PLCγ2-P522R variant in a less aggressive APP/PS1 mouse model of AD and assessed the underlying cellular mechanisms using mouse and human microglial models. The effects of the protective PLCγ2-P522R variant on microglial activation,AD-associated β-amyloid and neuronal pathologies,and behavioral changes were investigated in PLCγ2-P522R knock-in variant mice crossbred with APP/PS1 mice. Transcriptomic,proteomic,and functional studies were carried out using microglia isolated from mice carrying the PLCγ2-P522R variant. Finally,microglia-like cell models generated from human blood and skin biopsy samples of PLCγ2-P522R variant carriers were employed. The PLCγ2-P522R variant decreased β-amyloid plaque count and coverage in female APP/PS1 mice. Moreover,the PLCγ2-P522R variant promoted anxiety in these mice. The area of the microglia around β-amyloid plaques was also increased in mice carrying the PLCγ2-P522R variant,while β-amyloid plaque-associated neuronal dystrophy and the levels of certain cytokines,including IL-6 and IL-1β,were reduced. These alterations were revealed through [18F]FEPPA PET imaging and behavioral studies,as well as various cytokine immunoassays,transcriptomic and proteomic analyses,and immunohistochemical analyses using mouse brain tissues. In cultured mouse primary microglia,the PLCγ2-P522R variant reduced the size of lipid droplets. Furthermore,transcriptomic and proteomic analyses revealed that the PLCγ2-P522R variant regulated key targets and pathways involved in lipid metabolism,mitochondrial fatty acid oxidation,and inflammatory/interferon signaling in acutely isolated adult mouse microglia and human monocyte-derived microglia-like cells. Finally,the PLCγ2-P522R variant also increased mitochondrial respiration in human iPSC-derived microglia. These findings suggest that the PLCγ2-P522R variant exerts protective effects against β-amyloid and neuronal pathologies by increasing microglial responsiveness to β-amyloid plaques in APP/PS1 mice. The changes observed in lipid/fatty acid and mitochondrial metabolism revealed by the omics and metabolic assessments of mouse and human microglial models suggest that the protective effects of the PLCγ2-P522R variant are potentially associated with increased metabolic capacity of microglia. The online version contains supplementary material available at 10.1186/s12974-025-03387-6. View Publication

The clinical success of the immune checkpoint inhibitor (ICI) targeting programmed cell death protein 1 (PD-1) has revolutionized cancer treatment. However,the full potential of PD-1 blockade therapy remains unrealized,as response rates are still low across many cancer types. Interleukin-2 (IL-2)-based immunotherapies hold promise,as they can stimulate robust T cell expansion and enhance effector function - activities that could synergize potently with PD-1 blockade. Yet,IL-2 therapies also carry a significant drawback: they can trigger severe systemic toxicities and induce immune suppression by expanding regulatory T cells. To overcome the challenges of PD-1 blockade and IL-2 therapies while enhancing safety and efficacy,we have engineered a novel fusion protein,AWT020,combining a humanized anti-PD-1 nanobody and an engineered IL-2 mutein (IL-2c). The IL-2c component of AWT020 has been engineered to exhibit no binding to the IL-2 receptor alpha (IL-2Rα) subunit and attenuated affinity for the IL-2 receptor beta and gamma (IL-2Rβγ) complex,aiming to reduce systemic immune cell activation,thereby mitigating the severe toxicity often associated with IL-2 therapies. The anti-PD-1 antibody portion of AWT020 serves a dual purpose: it precisely delivers the IL-2c payload to tumor-infiltrating T cells while blocking the immune-inhibitory signals mediated by the PD-1 pathway. AWT020 showed significantly enhanced pSTAT5 signaling in PD-1 expressing cells and promoted the proliferation of activated T cells over natural killer (NK) cells. In preclinical studies using both anti-PD-1-sensitive and -resistant mouse tumor models,the mouse surrogate of AWT020 (mAWT020) demonstrated markedly enhanced anti-tumor efficacy compared to an anti-PD-1 antibody,IL-2,or the combination of an anti-PD-1 antibody and IL-2. In addition,the mAWT020 treatment was well-tolerated,with minimal signs of toxicity. Immune profiling revealed that mAWT020 preferentially expands CD8 + T cells within tumors,sparing peripheral T and NK cells. Notably,this selective tumoral T-cell stimulation enables potent tumor-specific T-cell responses,underscoring the molecule’s enhanced efficacy and safety. The AWT020 fusion protein offers a promising novel immunotherapeutic strategy by integrating PD-1 blockade and IL-2 signaling,conferring enhanced anti-tumor activity with reduced toxicity. View Publication

Pancreatic cancer is one of the most malignant cancers,and limited therapeutic options are available. The induction of ferroptosis is considered to be a novel,promising strategy that has potential in cancer treatment,and ferroptosis inducers may be new options for eradicating malignant cancers that are resistant to traditional drugs. The exact mechanism underlying the function of sorcin in the initiation and progression of pancreatic cancer remains unclear. The expression of sorcin in cancer tissues was assessed by analyzing TCGA,GEO and immunohistochemical staining data,and the function of sorcin in the induction of ferroptosis in pancreatic cancer cells was investigated. The mechanism underlying the function of sorcin was revealed through proteomics,co-IP,Ch-IP,and luciferase assays. Natural product screening was subsequently performed to screen for products that interact with sorcin to identify new ferroptosis inducers. We first showed that sorcin expression was positively correlated with the survival and tumor stages of patients with pancreatic cancer,and we revealed that sorcin inhibited ferroptosis through its noncalcium binding function. Furthermore,we discovered that sorcin interacted with PAX5 in the cytoplasm and inhibited PAX5 nuclear translocation,which in turn decreased FBXL12 protein expression and then reduced ALDH1A1 ubiquitination,thus inhibiting ferroptosis. Moreover,an in-house natural product screen revealed that celastrol inhibited the interaction of sorcin and PAX5 by directly binding to the Cys194 residue of the sorcin protein; disruption of the sorcin-PAX5 interaction promoted the nuclear translocation of PAX5,induced the expression of FBXL12,increased the ubiquitylation of ALDH1A1,and eventually induced ferroptosis in pancreatic cancer cells. In this study,we revealed the mechanism of action of sorcin,which is a druggable target for inducing ferroptosis,we identified celastrol as a novel agent that induces ferroptosis,and we showed that disrupting the sorcin-PAX5 interaction is a promising therapeutic strategy for treating pancreatic cancer. The online version contains supplementary material available at 10.1186/s13045-025-01680-8. View Publication

Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) are remarkably effective for treating EGFR-mutant non-small cell lung cancer (NSCLC). However,patients inevitably develop acquired drug resistance,resulting in recurrence or metastasis. It is important to identify novel effective therapeutic targets to reverse acquired TKI resistance. Bioinformatics analysis revealed that nicotinamide N-methyltransferase (NNMT) was upregulated in EGFR-TKI resistant cells and tissues via EGR1-mediated transcriptional activation. High NNMT levels were correlated with poor prognosis in EGFR-mutated NSCLC patients,which could promote resistance to EGFR-TKIs in vitro and in vivo. Mechanistically,NNMT catalyzed the conversion of nicotinamide to 1-methyl nicotinamide by depleting S-adenosyl methionine (the methyl group donor),leading to a reduction in H3K9 trimethylation (H3K9me3) and H3K27 trimethylation (H3K27me3) and subsequent epigenetic activation of EGR1 and ALDH3A1. In addition,ALDH3A1 activation increased lactic acid levels,which further promoted NNMT expression via p300-mediated histone H3K18 lactylation on its promoter. Thus,NNMT mediates the formation of a double positive feedback loop via EGR1 and lactate,EGR1/NNMT/EGR1 and NNMT/ALDH3A1/lactate/NNMT. Moreover,the combination of a small-molecule inhibitor for NNMT (NNMTi) and osimertinib exhibited promising potential for the treatment of TKI resistance in an NSCLC osimertinib-resistant xenograft model. The combined contribution of these two positive feedback loops promotes EGFR-TKI resistance in NSCLC. Our findings provide new insight into the role of histone methylation and histone lactylation in TKI resistance. The pivotal NNMT-mediated positive feedback loop may serve as a powerful therapeutic target for overcoming EGFR-TKI resistance in NSCLC. The online version contains supplementary material available at 10.1186/s12943-025-02285-y. View Publication

Multiple sclerosis (MS) is a chronic inflammatory disease characterized by immune‐mediated demyelination of the central nervous system,resulting in extensive neurological deficit and remyelination impairment. We have previously found that interleukin‐four induced one (IL4I1) protein modulates CNS inflammation and enhances remyelination in mouse models of experimental demyelination. However,it remained unclear if IL4I1 regulates lymphocyte activity in MS. To assess the therapeutic potential of IL4I1 in MS,we investigated the impact of IL4I1 treatment on human lymphocytes from peripheral blood mononuclear cells (PBMCs) obtained from healthy individuals and MS patients. We found that IL4I1 increased the relative densities of Th2 and regulatory T‐cells,while reducing Th17 cell density in healthy control (HC) samples. Furthermore,IL4I1‐treated lymphocytes promoted CNS remyelination when grafted into demyelinated spinal cord lesions in mice. We found that baseline endogenous IL4I1 expression was reduced in people with MS. However,unlike HCs,IL4I1 treatment had no significant effect on IL17 or TOB1 expression in lymphocytes derived from MS patients. These results suggest that IL4I1 skews CD4 + T‐cells to a regulatory state in healthy human lymphocytes,which may be essential for promoting remyelination. However,IL4I1 appears unable to exert its influence on lymphocytes in MS,indicating that impaired IL4I1‐mediated activity may underlie MS pathology. View Publication

Overall survival of acute myeloid leukemia (AML) remains limited. Inhibitors of the master mitotic kinase PLK1 have emerged as promising therapeutics,demonstrating efficacy in an undefined subset of patients with AML. However,the clinical success of PLK1 inhibitors remains hindered by a lack of predictive biomarkers. The Fanconi anemia (FA) pathway,a tumor-suppressive network comprised of at least 22 genes,is frequently mutated in sporadic AML. In this study,we demonstrate that FA pathway disruption sensitizes AML cells to PLK1 inhibition. Mechanistically,we identify novel interactions between PLK1 and both FANCA and FANCD2 at mitotic centromeres. We demonstrate that PLK1 inhibition impairs recruitment of FANCD2 to mitotic centromeres,induces damage to mitotic chromosomes,and triggers mitotic collapse in FANCA-deficient cells. Our findings indicate that PLK1 inhibition targets mitotic vulnerabilities specific to FA pathway–deficient cells and implicate FA pathway mutations as potential biomarkers for the identification of patients likely to benefit from PLK1 inhibitors. This work demonstrates that FA pathway mutations,which are frequently observed in sporadic AML,induce hypersensitivity to PLK1 inhibition,providing rationale for a novel synthetic lethal therapeutic strategy for this patient population. View Publication

The airway epithelium represents a central barrier against pathogens and toxins while playing a crucial role in modulating the immune response within the upper respiratory tract. Understanding these mechanisms is particularly relevant for red foxes ( Vulpes vulpes ),which serve as reservoirs for various zoonotic pathogens like rabies or the fox tapeworm ( Echinococcus multilocularis ). The study aimed to develop,establish,and validate an air-liquid interface (ALI) organoid model of the fox respiratory tract using primary airway epithelial cells isolated from the tracheas and main bronchi of hunted red foxes. The resulting ALI cultures exhibited a structurally differentiated,pseudostratified epithelium,characterised by ciliated cells,mucus secretion,and tight junctions,as confirmed through histological and immunohistochemical analysis. Functional assessments using a paracellular permeability assay and measurement of transepithelial electrical resistance,demonstrated a tight epithelial barrier. The potential of model’s utility for studying innate immune responses to respiratory infections was validated by exposing the cultures to lipopolysaccharide,phorbol-12-myristate-13-acetate and ionomycin,and nematode somatic antigens. Quantitative PCR revealed notable changes in the expression of pro-inflammatory cytokines TNF and IL-33. This in vitro model represents a significant advancement in respiratory research for non-classical species that may act as important wildlife reservoirs for a range of zoonotic pathogens. View Publication

Brain organoids have been proposed as suitable human brain model candidates for a variety of applications. However,the lack of appropriate maturation limits the transferability of such functional tools. Here,we present a method to facilitate neuronal maturation by integrating astrocyte-secreted factors into hPSC-derived 2D and 3D neural culture systems. We demonstrate that protein- and nutrient-enriched astrocyte-conditioned medium (ACM) accelerates neuronal differentiation with enlarged neuronal layer and the overproduction of deep-layer cortical neurons. We captured the elevated changes in the functional activity of neuronal networks within ACM-treated organoids using comprehensive electrophysiological recordings. Furthermore,astrocyte-secreted cues can induce lipid droplet accumulation in neural cultures,offering protective effects in neural differentiation to withstand cellular stress. Together,these data indicate the potential of astrocyte secretions to promote neural maturation. Subject terms: Neurological models,Neuronal development View Publication

Cervical cancer (CC) remains a major health challenge with high mortality rates due to chemoresistance and immune escape. However,the underlying mechanisms remain unclear. We investigated the role of TAB2 in CC using cisplatin‐resistant and parental cell lines. Cell proliferation,migration,sphere formation and T cell‐mediated killing assays were performed. Western blot and qRT‐PCR analysed protein and mRNA expression. NF‐κB pathway involvement was examined using the BAY 11–7082 inhibitor. TAB2 expression was significantly elevated in cisplatin‐resistant CC cells. TAB2 overexpression promoted chemoresistance and immune escape through NF‐κB pathway activation. Conversely,TAB2 knockdown or NF‐κB inhibition sensitised resistant cells to cisplatin and enhanced T cell‐mediated killing. The resistant phenotype could be rescued by restoring PD‐L1 expression. Our findings reveal TAB2 as a critical regulator of both chemoresistance and immune escape in CC through NF‐κB pathway activation. This suggests TAB2 as a potential therapeutic target for overcoming treatment resistance in CC. View Publication