技术资料

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

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

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

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

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

Human norovirus (HuNoV) is a major cause of enteric infectious gastroenteritis and is classified into several genotypes based on its capsid protein amino acid sequence and nucleotide sequence of the polymerase gene. Among these,GII.4 is the major genotype worldwide. Epidemiological studies have highlighted the prevalence of GII.2. Although recent advances using human tissue– and induced pluripotent stem cell (iPSC)–derived intestinal epithelial cells (IECs) have enabled in vitro replication of multiple HuNoV genotypes,GII.2 HuNoV could replicate only in tissue-derived IECs and not in iPSC-derived IECs. We investigated the factors influencing GII.2 HuNoV replication in IECs,focusing on histo-blood group antigens. We also assessed the immunogenicity of GII.2 virus-like particles (VLPs) and their ability to induce neutralizing antibodies. Antibody cross-reactivity was tested to determine whether GII.2 VLPs could neutralize other HuNoV genotypes,including GII.4,GII.3,GII.6,and GII.17. Our findings indicated that GII.2 HuNoV replication in vitro requires the presence of both H and B antigens. Moreover,GII.2 VLPs generated neutralizing antibodies effective against both GII.2 and GII.4 but not against GII.3,GII.6,or GII.17. Comparatively,GII.2 and GII.17 VLPs induced broader neutralizing responses than GII.4 VLPs. The findings of this study suggests that GII.2 and GII.17 VLPs may be advantageous as HuNoV vaccine candidates because they elicit neutralizing antibodies against the predominant GII.4 genotype,which could be particularly beneficial for infants without prior HuNoV exposure. These insights will contribute to the development of effective HuNoV vaccines. View Publication

Polo-like kinase 1 (PLK1),a key regulator of the G2/M phase in mitosis,is frequently overexpressed in numerous tumors. Although PLK1 inhibitors have emerged as promising therapeutic agents for cancer,their use has been linked to significant anemia in a subset of patients,yet the underlying mechanisms remain poorly understood. In this study,we utilized an in vitro human umbilical cord blood-derived CD34 + cell-based erythroid differentiation system,alongside a murine model,to investigate the impact of PLK1 inhibitors on erythropoiesis. Our results indicate that PLK1 inhibitors,specifically GSK461364 and BI6727,significantly suppress the proliferation of erythroid cells,resulting in G2/M phase cell cycle arrest,increased apoptosis in erythroid cells,and the formation of abnormally nucleated late-stage erythroblasts. In vivo,administration of PLK1 inhibitors in mice induced severe anemia,as evidenced by a marked reduction in red blood cells and hemoglobin levels. More specifically,PLK1 inhibition impaired the differentiation and erythroid commitment of hematopoietic stem cells in the bone marrow,resulting in abnormal accumulation of BFU-E cells and reduced proliferation and differentiation of CFU-E,and a decrease in the number of terminal erythrocytes. Mechanistically,PLK1 inhibitors primarily induce apoptosis in erythroid cells by reducing Mitochondrial membrane potential and arresting the cell cycle at the G2/M phase. Overall,our findings underscore the critical role of PLK1 in erythropoiesis and shed light on the mechanisms underlying PLK1 inhibitor-induced anemia,providing essential guidance for developing strategies to prevent and manage anemia in clinical applications of PLK1-targeted therapies. View Publication

This study aimed to evaluate different combinations of three dietary supplements for potential additive or synergistic effects in an in vitro Parkinson’s Disease model. The complex and diverse processes leading to neurodegeneration in each patient with a neurodegenerative disorder cannot be effectively addressed by a single medication. Instead,various combinations of potentially neuroprotective agents targeting different disease mechanisms simultaneously may show improved additive or synergistic efficacy in slowing the disease progression and allowing the agents to be utilized at lower doses to minimize side effects. We evaluated four possible combinations of the three selected supplements: tauroursodeoxycholic acid (TUDCA),co-enzyme Q10 (CoQ10),and creatine,chosen for their effects on different targets that had previously shown neuroprotective effects in preclinical models. We evaluated the following combinations: (1) TUDCA+CoQ10,(2) TUDCA+Creatine,(3) CoQ10 + Creatine,and (4) TUDCA+CoQ10 + Creatine. We used induced pluripotent stem cell (iPSC) derived human dopaminergic neurons from a patient with Parkinson’s disease and healthy control,as well as microglial cells,to evaluate for an additive or synergistic effect of these combinations on neurodegeneration and neuroinflammation. We used neurofilament heavy chain,tubulin filament,and proinflammatory cytokines as metrics. We have identified a triple combination of these supplements that showed an additive protective effect across all these endpoints. Indeed,the agents in that combination could address the majority of the known pathways leading to neurodegeneration,such as accumulation of misfolded α -synuclein,mitochondrial dysfunction,reactive oxygen species,and neuroinflammation. We demonstrated that the combination of TUDCA,CoQ10,and creatine exerts an additive effect in in vitro models of a neurodegenerative disease,surpassing the efficacy of each compound individually. This combination shows strong potential as a candidate for further preclinical confirmatory studies and clinical trials as a neuroprotective treatment for patients with,or at risk for,Parkinson’s disease. View Publication

Previous studies have indicated that the presence of cancer stem cells may be a contributing factor to the development of metastasis in colorectal cancer patients. Cancer stem cells represent a small subpopulation within the tumor mass that exhibits heightened resistance to treatment and possesses the capacity for self-replication,epithelial–mesenchymal transition,and the generation of new tumors. The tumor microenvironment secretes and releases several molecules that facilitate the self-renewal of cancer stem cells and provide support for colorectal cancer progression. microRNAs are involved in direct cell-to-cell signaling and paracrine signaling between tumor cells and other tumor microenvironment components. They could act as tumor suppressors or oncomiRs,and their deregulation is involved in colorectal cancer progression and cancer stem cell formation. In our previous studies,we demonstrated the oncosuppressive function of miR-486-5p in colorectal cancer; these findings prompted us to conduct a more detailed investigation into its role in cancer stem cell phenotypes. Background: Colorectal cancer (CRC) is the third diagnosed cancer worldwide. Forty-four percent of metastatic colorectal cancer patients were diagnosed at an early stage. Despite curative resection,approximately 40% of patients will develop metastases within a few years. Previous studies indicate the presence of cancer stem cells (CSCs) and their contribution to CRC progression and metastasis. miRNAs deregulation plays a role in CSCs formation and in tumor development. In light of previous studies,we investigated the role of miR-486-5p to understand its role in CSC better. Methods: The expression of miR-486-5p was assessed in adherent cells and spheres generated from two CRC cell lines to observe the difference in expression in CSC-enriched spheroids. Afterward,we overexpressed and underexpressed this miRNA in adherent and sphere cultures through the transfection of a miR-486-5p mimic and a mimic inhibitor. Results: The results demonstrated that miR-486-5p exhibited a notable downregulation in CSC models,and its overexpression led to a significant decrease in colony size. Conclusions: In this study,we confirmed that miR-486-5p plays an oncosuppressive role in CRC,thereby advancing our understanding of the role of this microRNA in the CSC phenotype. View Publication

Cancer stem cells (CSCs) play a key role in non-small cell lung cancer (NSCLC) chemoresistance and metastasis. In this study,we used two NSCLC cell lines to investigate the regulating effect of hypoxia in the induction and maintenance of CSC traits. Our study demonstrated hypoxia-induced stemness and chemoresistance at levels comparable to those in typical CSC sphere culture. Activation of the NF-κB pathway (by transfection of NF-κB-p65) plays a key role in NSCLC CSCs and chemoresistance. Disulfiram (DS),an anti-alcoholism drug,showed a strong in vitro anti-CSC effect. It blocked cancer cell sphere reformation and clonogenicity,synergistically enhanced the cytotoxicity of four anti-NSCLC drugs (doxorubicin,gemcitabine,oxaliplatin and paclitaxel) and reversed hypoxia-induced resistance. The effect of DS on CSCs is copper-dependent. A very short half-life in the bloodstream is the major limitation for the translation of DS into a cancer treatment. Our team previously developed a poly lactic-co-glycolic acid (PLGA) nanoparticle encapsulated DS (DS-PLGA) with a long half-life in the bloodstream. Intra venous injection of DS-PLGA in combination with the oral application of copper gluconate has strong anticancer efficacy in a metastatic NSCLC mouse model. Further study may be able to translate DS-PLGA into cancer applications. View Publication

Introduction: Pathogenic variants in the OFD1 gene are linked to a spectrum of syndromes that exhibit partial clinical overlap. Hemizygous loss-of-function variants are considered lethal in males,while heterozygous loss-of-function variants generally result in oro-facial-digital syndrome type 1. A reported phenotype,Simpson–Golabi–Behmel syndrome type 2,was published once but remains controversial,with many specialists questioning its validity and arguing about its continued listing in the OMIM database. Methods: To investigate the genetic and phenotypic characteristics of the patients,we performed clinical exome sequencing,family-based genetic analysis,X-inactivation studies,electron microscopy,and detailed clinical assessments. Results: Three patients from unrelated families carrying loss-of-function variants in the OFD1 gene were identified,emphasizing the diverse phenotypic spectrum of OFD1 -associated disorders. The first patient,a female with a heterozygous frameshift variant p.(Gln398LeufsTer2),was diagnosed with oro-facial-digital syndrome type 1. The second patient,a male with a heterozygous nonsense variant p.(Gln892Ter),presented with features resembling Simpson–Golabi–Behmel syndrome type 2,as previously reported under this diagnosis. The third patient,a male with another heterozygous nonsense variant p.(Glu879Ter),exhibited isolated primary ciliary dyskinesia without any syndromic features. Conclusions: This study contributes to the growing body of evidence on the expanding phenotypic spectrum of OFD1 -associated disorders. It underscores the need for further investigation into the molecular mechanisms underlying the diverse presentations and the necessity of re-evaluating diagnostic classifications for conditions such as SGBS2 in the context of variants in the OFD1 gene. View Publication

The only cure of HIV has been achieved in a small number of people who received a hematopoietic stem cell transplant (HSCT) comprising allogeneic cells carrying a rare,naturally occurring,homozygous deletion in the CCR5 gene. The rarity of the mutation and the significant morbidity and mortality of such allogeneic transplants precludes widespread adoption of this HIV cure. Here,we show the application of CRISPR/Cas9 to achieve >90% CCR5 editing in human,mobilized hematopoietic stem progenitor cells (HSPC),resulting in a transplant that undergoes normal hematopoiesis,produces CCR5 null T cells,and renders xenograft mice refractory to HIV infection. Titration studies transplanting decreasing frequencies of CCR5 edited HSPCs demonstrate that <90% CCR5 editing confers decreasing protective benefit that becomes negligible between 54% and 26%. Our study demonstrates the feasibility of using CRISPR/Cas9/RNP to produce an HSPC transplant with high frequency CCR5 editing that is refractory to HIV replication. These results raise the potential of using CRISPR/Cas9 to produce a curative autologous HSCT and bring us closer to the development of a cure for HIV infection. Subject terms: HIV infections,CRISPR-Cas9 genome editing,Retrovirus,Translational research View Publication