参考文献

Prime Editing can rewrite genes in living cells by allowing point mutations,deletions,or insertion of small DNA sequences with high precision. However,its safe and efficient delivery into human stem cells remains a technical challenge. In this report,we engineer Nanoscribes,virus-like particles that encapsidate ribonucleoprotein complexes of the Prime Editing system and allow their delivery into recipient cells. We identify key features that unlock the potential of Nanoscribes,including the use of multiple fusogens,the improvement of pegRNAs structures,their encoding by a Pol II system and the optimization of Prime-Editors. Nanoscribes edit HEK293T with an efficiency of 68% at the HEK3 locus with increased fidelity over DNA-transfection and support pegRNA-multiplexing. Importantly,Nanoscribes permit editing of myoblasts,hiPSCs and hiPSCs-derived hematopoietic stem cells with an editing efficiency up to 25%. Nanoscribes is an asset for development of next generation genome editing approaches using VLPs. Subject terms: CRISPR-Cas9 genome editing,Genetic vectors,Nanoparticles View Publication

Non-Small Cell Lung Cancer (NSCLC) is the leading cause of cancer death worldwide. Although immune checkpoint inhibitors (ICIs) have shown remarkable clinical efficacy,they can also induce a paradoxical cancer acceleration,known as hyperprogressive disease (HPD),whose causative mechanisms are still unclear. This study investigated the mechanisms of ICI resistance in an HPD-NSCLC model. Two primary cell cultures were established from samples of a NSCLC patient,before ICI initiation (“baseline”,NSCLC-B) and during HPD (“hyperprogression”,NSCLC-H). The cell lines were phenotypically and molecularly characterized through immunofluorescence,Western Blotting and RNA-Seq analysis. To assess cell plasticity and aggressiveness,cellular growth patterns were evaluated both in vitro and in vivo through 2D and 3D cell growth assays and patient-derived xenografts establishment. In vitro investigations,including the evaluation of cell sensitivity to interferon-gamma (IFN-γ) and cell response to PD-L1 modulation,were conducted to explore the influence of these factors on cell plasticity regulation. NSCLC-H exhibited increased expression of specific CD44 isoforms and a more aggressive phenotype,including organoid formation ability,compared to NSCLC-B. Plastic changes in NSCLC-H were well described by a deep transcriptome shift,that also affected IFN-γ–related genes,including PD-L1. IFN-γ–mediated cell growth inhibition was compromised in both 2D-cultured NSCLC-B and NSCLC-H cells. Further,the cytokine induced a partial activation of both type I and type II IFN-pathway mediators,together with a striking increase in NSCLC-B growth in 3D cell culture systems. Finally,low IFN-γ doses and PD-L1 modulation both promoted plastic changes in NSCLC-B,increasing CD44 expression and its ability to produce spheres. Our findings identified plasticity as a relevant hallmark of ICI-mediated HPD by demonstrating that ICIs can modulate the IFN-γ and PD-L1 pathways,driving tumor cell plasticity and fueling HPD development. The online version contains supplementary material available at 10.1186/s12967-024-06023-8. View Publication

Genome editing using CRISPR-Cas systems is a promising avenue for the treatment of genetic diseases. However,cellular and humoral immunogenicity of genome editing tools,which originate from bacteria,complicates their clinical use. Here we report reduced immunogenicity (Red)(i)-variants of two clinically relevant nucleases,SaCas9 and AsCas12a. Through MHC-associated peptide proteomics (MAPPs) analysis,we identify putative immunogenic epitopes on each nuclease. Using computational modeling,we rationally design these proteins to evade the immune response. SaCas9 and AsCas12a Redi variants are substantially less recognized by adaptive immune components,including reduced binding affinity to MHC molecules and attenuated generation of cytotoxic T cell responses,yet maintain wild-type levels of activity and specificity. In vivo editing of PCSK9 with SaCas9.Redi.1 is comparable in efficiency to wild-type SaCas9,but significantly reduces undesired immune responses. This demonstrates the utility of this approach in engineering proteins to evade immune detection. Subject terms: Protein design,Immunogenetics,CRISPR-Cas9 genome editing View Publication

Optical aberrations hinder fluorescence microscopy of thick samples,reducing image signal,contrast,and resolution. Here we introduce a deep learning-based strategy for aberration compensation,improving image quality without slowing image acquisition,applying additional dose,or introducing more optics. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks,making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained ‘de-aberration’ networks outperforms alternative methods,providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal,light-sheet,multi-photon,and super-resolution microscopy. In all cases,the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation,including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos. Subject terms: Microscopy,Fluorescence imaging View Publication

Our study highlights the role of epigenetic machinery in transformation of normal pluripotent stem cells to variant pluripotent state. We demonstrate the importance of non-histone protein methylation,which underlie the EMT and abnormal differentiation behaviour of variant hESCs. View Publication

Th2 inflammation and epithelial-mesenchymal transition (EMT) play crucial roles in the pathophysiology of chronic rhinosinusitis with nasal polyps (CRSwNP). This study aimed to investigate the hypothesis that MMP-12,produced by M2 macrophages,induces EMT in nasal epithelial cells,thereby contributing to airway inflammation and remodeling in CRSwNP. The expression levels of MMP-12 were measured by RT-PCR in CRS nasal mucosa and THP-1 cells. mRNA and protein levels of E-cadherin,vimentin,α-SMA,and fibronectin were determined using RT-PCR,western blotting,and immunofluorescence staining in primary nasal epithelial cells and air-liquid interface culture. The expression of MMP-12 was significantly increased in CRSwNP and M2-like THP-1 cells. In co-culture with primary nasal epithelial cells and M2-like THP-1 cells,E-cadherin expression was inhibited,and fibronectin,vimentin,and α-SMA expression were increased. MMP-12 decreased E-cadherin but induced fibronectin,vimentin,and α-SMA mRNA and protein expression in primary nasal epithelial cells and air-liquid interface culture. MMP408,an MMP-12 inhibitor,inhibited EMT-related factors. These findings suggest that MMP-12 expression in M2 macrophages induces EMT in nasal epithelial cells and may contribute to the pathogenesis of CRSwNP. View Publication

Micropapillary adenocarcinoma (MPC) is an aggressive histological subtype of lung adenocarcinoma (LUAD). MPC is composed of small clusters of cancer cells exhibiting inverted polarity. However,the mechanism underlying its formation is poorly understood. Here we show that hypoxia is involved in MPC formation. Hypoxia induced the formation of MPC-like structures (MLSs) in a three-dimensional culture system using A549 human LUAD cells,and HIF-1α was indispensable for MLS formation. RNA sequencing analysis demonstrated that A549 cells forming MLSs exhibited a gene expression signature similar to that of lung MPC. Moreover,MLS formation enhanced the resistance of A549 cells to natural killer cell cytotoxicity. Our findings suggest that hypoxia drives lung MPC formation through HIF-1α and that immune escape from natural killer cells might underlie the aggressiveness of MPC. View Publication

The lack of a robust system to reproducibly propagate HRV-C,a family of viruses refractory to cultivation in standard cell lines,has substantially hindered our understanding of this common respiratory pathogen. We sought to develop an organoid-based system to reproducibly propagate HRV-C,and characterize virus-host interaction using respiratory organoids. We demonstrate that airway organoids sustain serial virus passage with the aid of CYT387-mediated immunosuppression,whereas nasal organoids that more closely simulate the upper airway achieve this without any intervention. Nasal organoids are more susceptible to HRV-C than airway organoids. Intriguingly,upon HRV-C infection,we observe an innate immune response that is stronger in airway organoids than in nasal organoids,which is reproduced in a Poly(I:C) stimulation assay. Treatment with α-CDHR3 and antivirals significantly reduces HRV-C viral growth in airway and nasal organoids. Additionally,an organoid-based immunofluorescence assay is established to titrate HRV-C infectious particles. Collectively,we develop an organoid-based system to reproducibly propagate the poorly cultivable HRV-C,followed by a comprehensive characterization of HRV-C infection and innate immunity in physiologically active respiratory organoids. The organoid-based HRV-C infection model can be extended for developing antiviral strategies. More importantly,our study has opened an avenue for propagating and studying other uncultivable human and animal viruses. Subject terms: Virus-host interactions,Viral pathogenesis,Respiratory tract diseases View Publication

Although acute myeloid leukemia (AML) affects hematopoietic stem cell (HSC)-supportive microenvironment,it is largely unknown whether leukemia-modified bone marrow (BM) microenvironment can be remodeled to support normal hematopoiesis after complete remission (CR). As a key element of BM microenvironment,endothelial progenitor cells (EPCs) provide a feasible way to investigate BM microenvironment remodeling. Here,we find reduced and dysfunctional BM EPCs in AML patients,characterized by impaired angiogenesis and high ROS levels,could be partially remodeled after CR and improved by N-acetyl-L-cysteine (NAC). Importantly,HSC-supporting ability of BM EPCs is partially recovered,whereas leukemia-supporting ability is decreased in CR patients. Mechanistically,the transcriptome characteristics of leukemia-modified BM EPCs return to near-normal after CR. In a classic AML mouse and chemotherapy model,BM vasculature and normal hematopoiesis are reversed after CR. In summary,we provide further insights into how leukemia-modified BM microenvironment can be remodeled to support normal hematopoiesis after CR,which can be further improved by NAC. Subject terms: Translational research,Acute myeloid leukaemia View Publication

Metaplastic breast cancer (MpBC) is a highly chemoresistant subtype of breast cancer with no standardized therapy options. A clinical study in anthracycline-refractory MpBC patients suggested that nitric oxide synthase (NOS) inhibitor NG-monomethyl-l-arginine (L-NMMA) may augment anti-tumor efficacy of taxane. We report that NOS blockade potentiated response of human MpBC cell lines and tumors to phosphoinositide 3-kinase (PI3K) inhibitor alpelisib and taxane. Mechanistically,NOS blockade leads to a decrease in the S-nitrosylation of c-Jun NH 2 -terminal kinase (JNK)/c-Jun complex to repress its transcriptional output,leading to enhanced tumor differentiation and associated chemosensitivity. As a result,combined NOS and PI3K inhibition with taxane targets MpBC stem cells and improves survival in patient-derived xenograft models relative to single-/dual-agent therapy. Similarly,biopsies from MpBC tumors that responded to L-NMMA+taxane therapy showed a post-treatment reversal of epithelial-to-mesenchymal transition and decreased stemness. Our findings suggest that combined inhibition of iNOS and PI3K is a unique strategy to decrease chemoresistance and improve clinical outcomes in MpBC. Subject terms: Breast cancer,Cell signalling,Cancer therapy View Publication