技术资料

Genome editing is poised to revolutionize treatment of genetic diseases,but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons,which must withstand decades of DNA damage without replicating. This lack of knowledge limits the efficiency and precision of genome editing in clinically relevant cells. To address this,we used induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. We discovered that neurons can take weeks to fully resolve this damage,compared to just days in isogenic iPSCs. Furthermore,Cas9-treated neurons upregulated unexpected DNA repair genes,including factors canonically associated with replication. Manipulating this response with chemical or genetic perturbations allowed us to direct neuronal repair toward desired editing outcomes. By studying DNA repair in postmitotic human cells,we uncovered unforeseen challenges and opportunities for precise therapeutic editing. View Publication

Peripheral nerve and large-scale muscle injuries result in significant disability,necessitating the development of biomaterials that can restore functional deficits by promoting tissue regrowth in an electroactive environment. Among these materials,graphene is favored for its high conductivity,but its low bioactivity requires enhancement through biomimetic components. In this study,we extrusion printed graphene-poly(lactide-co-glycolide) (graphene) lattice scaffolds,aiming to increase bioactivity by incorporating decellularized extracellular matrix (dECM) derived from mouse pup skeletal muscle. We first evaluated these scaffolds using human-induced pluripotent stem cell (hiPSC)-derived motor neurons co-cultured with supportive glia,observing significant improvements in axon outgrowth. Next,we tested the scaffolds with C2C12 mouse and human primary myoblasts,finding no significant differences in myotube formation between dECM-graphene and graphene scaffolds. Finally,using a more complex hiPSC-derived 3D motor neuron spheroid model co-cultured with human myoblasts,we demonstrated that dECM-graphene scaffolds significantly improved axonal expansion towards peripheral myoblasts and increased axonal network density compared to graphene-only scaffolds. Features of early neuromuscular junction formation were identified near neuromuscular interfaces in both scaffold types. These findings suggest that dECM-graphene scaffolds are promising candidates for enhancing neuromuscular regeneration,offering robust support for the growth and development of diverse neuromuscular tissues. View Publication

Heterozygous de novo mutations in the Activity-Dependent Neuroprotective Homeobox (ADNP) gene underlie Helsmoortel-Van der Aa syndrome (HVDAS). Most of these mutations are situated in the last exon and we previously demonstrated escape from nonsense-mediated decay by detecting mutant ADNP mRNA in patient blood. In this study,wild-type and ADNP mutants are investigated at the protein level and therefore optimal detection of the protein is required. Detection of ADNP by means of western blotting has been ambiguous with reported antibodies resulting in non-specific bands without unique ADNP signal. Validation of an N-terminal ADNP antibody (Aviva Systems) using a blocking peptide competition assay allowed to differentiate between specific and non-specific signals in different sample materials,resulting in a unique band signal around 150 kDa for ADNP,above its theoretical molecular weight of 124 kDa. Detection with different C-terminal antibodies confirmed the signals at an observed molecular weight of 150 kDa. Our antibody panel was subsequently tested by immunoblotting,comparing parental and homozygous CRISPR/Cas9 endonuclease-mediated Adnp knockout cell lines and showed disappearance of the 150 kDa signal,indicative for intact ADNP. By means of both a GFPSpark and Flag-tag N-terminally fused to a human ADNP expression vector,we detected wild-type ADNP together with mutant forms after introduction of patient mutations in E. coli expression systems by site-directed mutagenesis. Furthermore,we were also able to visualize endogenous ADNP with our C-terminal antibody panel in heterozygous cell lines carrying ADNP patient mutations,while the truncated ADNP mutants could only be detected with epitope-tag-specific antibodies,suggesting that addition of an epitope-tag possibly helps stabilizing the protein. However,western blotting of patient-derived hiPSCs,immortalized lymphoblastoid cell lines and post-mortem patient brain material failed to detect a native mutant ADNP protein. In addition,an N-terminal immunoprecipitation-competent ADNP antibody enriched truncating mutants in overexpression lysates,whereas implementation of the same method failed to enrich a possible native mutant protein in immortalized patient-derived lymphoblastoid cell lines. This study aims to shape awareness for critical assessment of mutant ADNP protein analysis in Helsmoortel-Van der Aa syndrome. View Publication

Viruses depend on host metabolic pathways and flaviviruses are specifically linked to lipid metabolism. During dengue virus infection lipid droplets are degraded to fuel replication and Zika virus (ZIKV) infection depends on triglyceride biosynthesis. Here,we systematically investigated the neutral lipid–synthesizing enzymes diacylglycerol O-acyltransferases (DGAT) and the sterol O-acyltransferase (SOAT) 1 in orthoflavivirus infection. Downregulation of DGAT1 and SOAT1 compromises ZIKV infection in hepatoma cells but only SOAT1 and not DGAT inhibitor treatment reduces ZIKV infection. DGAT1 interacts with the ZIKV capsid protein,indicating that protein interaction might be required for ZIKV replication. Importantly,inhibition of SOAT1 severely impairs ZIKV infection in neural cell culture models and cerebral organoids. SOAT1 inhibitor treatment decreases extracellular viral RNA and E protein level and lowers the specific infectivity of virions,indicating that ZIKV morphogenesis is compromised,likely due to accumulation of free cholesterol. Our findings provide insights into the importance of cholesterol and cholesterol ester balance for efficient ZIKV replication and implicate SOAT1 as an antiviral target. Exploring the role of neutral lipid-synthesizing enzymes in Zika virus infection using different cell culture models,inhibition of cholesterol esterification is found to impair ZIKV morphogenesis. View Publication

ABSTRACTExtracellular vesicles (EVs) and secretory factors play crucial roles in intercellular communication,but the molecular mechanisms and dynamics governing their interplay in human pluripotent stem cells (hPSCs) are poorly understood. Here,we demonstrate that hPSC?secreted milk fat globule?EGF factor 8 (MFGE?8) is the principal corona protein at the periphery of EVs,playing an essential role in controlling hPSC stemness. MFGE?8 depletion reduced EV?mediated self?renewal and survival in hPSC cultures. MFGE?8 in the EV corona bound to integrin ?v?5 expressed in the peripheral zone of hPSC colonies. It activated cyclin D1 and dynamin?1 via the AKT/GSK3? axis,promoting the growth of hPSCs and facilitating the endocytosis of EVs. Internalization of EVs alleviated oxidative stress and cell death by transporting redox and stress response proteins that increased GSH levels. Our findings demonstrate the critical role of the extracellular association of MFGE?8 and EVs in modulating the self?renewal and survival of hPSCs. View Publication

Monkeypox virus (MPV) is known to inflict injuries and,in some cases,lead to fatalities in humans. However,the underlying mechanisms responsible for its pathogenicity remain poorly understood. We investigated functions of MPV core proteins,H3L,A35R,A29L,and I1L,and discovered that H3L induced transcriptional perturbations and injuries. We substantiated that H3L upregulated IL1A expression. IL1A,in consequence,caused cellular injuries,and this detrimental effect was mitigated when countered with IL1A blockage. We also observed that H3L significantly perturbed the transcriptions of genes in cardiac system. Mechanistically,H3L occupied the promoters of genes governing cellular injury,leading to alterations in the binding patterns of H3K27me3 and H3K4me3 histone marks,ultimately resulting in expression perturbations. In vivo and in vitro models confirmed that H3L induced transcriptional disturbances and cardiac dysfunction,which were ameliorated when IL1A was blocked or repressed. Our study provides valuable insights into comprehensive understanding of MPV pathogenicity,highlights the significant roles of H3L in inducing injuries,and potentially paves the way for the development of therapeutic strategies targeting IL1A. View Publication

SummaryProtein turnover is a critical component of gene expression regulation and cellular homeostasis,yet methods for measuring turnover rates that are scalable and applicable to different models are still needed. We introduce an improved D2O (heavy water) labeling strategy to investigate the landscape of protein turnover in cell culture,with accurate calibration of per-residue deuterium incorporation in multiple cell types. Applying this method,we mapped the proteome-wide turnover landscape of pluripotent and differentiating human induced pluripotent stem cells (hiPSCs). Our analysis highlights the role of APC/C (anaphase-promoting complex/cyclosome) and SPOP (speckle-type POZ protein) degrons in the fast turnover of cell-cycle-related and DNA-binding hiPSC proteins. Upon pluripotency exit,many short-lived hiPSC proteins are depleted,while RNA-binding and -splicing proteins become hyperdynamic. The ability to identify fast-turnover proteins also facilitates secretome profiling,as exemplified in hiPSC-cardiomyocyte and primary human cardiac fibroblast analysis. This method is broadly applicable to protein turnover studies in primary,pluripotent,and transformed cells. Graphical abstract Highlights•D2O labeling measures protein turnover in primary,pluripotent,and transformed cells•D2O incorporates into multiple amino acids in vitro,including Ala,Glu,Asp,and Pro•Protein turnover analysis shows hiPSC differentiation alters fast-turnover proteins•We show application to secretome analysis in human cardiac myocytes and fibroblasts MotivationDynamic stable isotope labeling by amino acids in cell culture coupled with mass spectrometry is commonly used to measure protein turnover in cell culture but requires altering culture medium composition and may not label some peptides. We describe a simple and convenient alternative for measuring protein turnover kinetics in cultured cells by adding low-volume D2O (heavy water) to standard tissue culture media. Addressing a critical gap,we determined the number of deuterium-accessible atoms on all 20 proteinogenic amino acids across multiple cell types. This allows accurate interpretation of D2O-labeled mass spectra to measure protein turnover kinetics and secretome flux on a proteome scale. Alamillo et al. present a D2O labeling mass spectrometry method to measure protein turnover rates that is compatible with multiple cell cultures and medium formulations. The method reveals a parsimonious protein turnover landscape in human induced pluripotent stem cells and identifies hyperdynamic proteins that are unique to self-renewal states. View Publication

To build in vitro tissues for therapeutic applications,it is essential to replicate the spatial distribution of cells that occurs during morphogenesis in vivo. However,it remains technically challenging to simultaneously regulate the geometric alignment and aggregation of cells during tissue fabrication. Here,we introduce the acoustofluidic bioassembly induced morphogenesis,which is the combination of precise arrangement of cells by the mechanical forces produced by acoustofluidic cues,and the morphological and functional changes of cells in the following in vitro and in vivo cultures. The acoustofluidic bioassembly can be used to create tissues with regulated nano-,micro-,and macro-structures. We demonstrate that the neuromuscular tissue fabricated with the acoustofluidic bioassembly exhibits enhanced contraction dynamics,electrophysiology,and therapeutic efficacy. The potential of the acoustofluidic bioassembly as an in situ application is demonstrated by fabricating artificial tissues at the defect sites of living tissues. The acoustofluidic bioassembly induced morphogenesis can provide a pioneering platform to fabricate tissues for biomedical applications. Tissue engineering is essential for drug screening and regenerative medicine. Here,authors developed an acoustofluidic method that can induce morphogenesis of therapeutic tissues at varied dimensions/scales. View Publication

The blood-brain barrier (BBB) serves as a highly intricate and dynamic interface connecting the brain and the bloodstream,playing a vital role in maintaining brain homeostasis. BBB dysfunction has been associated with multiple neurodegenerative diseases,including amyotrophic lateral sclerosis (ALS); however,the role of the BBB in neurodegeneration is understudied. We developed an ALS patient-derived model of the BBB by using cells derived from 5 patient donors carrying C9ORF72 mutations. Brain microvascular endothelial-like cells (BMEC-like cells) derived from C9ORF72-ALS patients showed altered gene expression,compromised barrier integrity,and increased P-glycoprotein transporter activity. In addition,mitochondrial metabolic tests demonstrated that C9ORF72-ALS BMECs display a significant decrease in basal glycolysis accompanied by increased basal and ATP-linked respiration. Moreover,our study reveals that C9-ALS derived astrocytes can further affect BMECs function and affect the expression of the glucose transporter Glut-1. Finally,C9ORF72 patient-derived BMECs form leaky barriers through a cell-autonomous mechanism and have neurotoxic properties towards motor neurons.Graphical Abstract Supplementary InformationThe online version contains supplementary material available at 10.1186/s12987-024-00528-6. View Publication

The work highlights the different calcium channels involved in controlling protein synthesis in neurons,and shows the dysfunction of this process in Alzheimer’s disease neurons. Calcium signaling is integral for neuronal activity and synaptic plasticity. We demonstrate that the calcium response generated by different sources modulates neuronal activity–mediated protein synthesis,another process essential for synaptic plasticity. Stimulation of NMDARs generates a protein synthesis response involving three phases—increased translation inhibition,followed by a decrease in translation inhibition,and increased translation activation. We show that these phases are linked to NMDAR-mediated calcium response. Calcium influx through NMDARs elicits increased translation inhibition,which is necessary for the successive phases. Calcium through L-VGCCs acts as a switch from translation inhibition to the activation phase. NMDAR-mediated translation activation requires the contribution of L-VGCCs,RyRs,and SOCE. Furthermore,we show that IP3-mediated calcium release and SOCE are essential for mGluR-mediated translation up-regulation. Finally,we signify the relevance of our findings in the context of Alzheimer’s disease. Using neurons derived from human fAD iPSCs and transgenic AD mice,we demonstrate the dysregulation of NMDAR-mediated calcium and translation response. Our study highlights the complex interplay between calcium signaling and protein synthesis,and its implications in neurodegeneration. View Publication

Inflammatory cytokines,including interleukin 6 (IL6),are associated with ion channel remodeling and enhance the propensity to alterations in cardiac rhythm generation and propagation,in which the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels play a crucial role. Hence,we investigated the consequences of exposure to IL6 on HCN channels in cell models and human atrial biopsies. In murine atrial HL1 cells and in cardiomyocytes derived from human induced pluripotent stem cells (hiPS-CMs),IL6 elicited STAT3 phosphorylation,a receptor-mediated downstream signaling. Downregulation of HCN1,2,4 by IL6 was observed after 24–48 h; in hiPS-CMs,this effect was reverted by 24 h of application of tocilizumab,a human IL6 receptor antagonist. In parallel,hiPS-CM action potentials (APs) showed a reduced spontaneous frequency. Moreover,we assessed IL6 and HCN expression in dilated left atrial samples from patients with mitral valve disease,an AF-prone condition. IL6 levels were increased in dilated atria compared to controls and positively correlated with echocardiographic atrial dimensions. Interestingly,the highest IL6 transcript levels and the lowest HCN4 and HCN2 expression were in these samples. In conclusion,our data uncovered a novel link between IL6 and cardiac HCN channels,potentially contributing to atrial electrical disturbances and a higher risk of dysrhythmias in conditions with elevated IL6 levels. View Publication

BackgroundAniridia is a rare panocular disease caused by gene mutation in the PAX6,which is essential for eye development. Aniridia is inherited in an autosomal dominant manner,but its phenotype can vary significantly among individuals with the same mutation. Animal models,such as drosophila,zebrafish,and rodents,have been used to study aniridia through Pax6 deletions. Recently,patient-derived limbal epithelial stem cells (LESCs) and human-induced pluripotent stem cells (hiPSCs) have been used to model the disease in vitro,providing new insights into therapeutic strategies.MethodsIn this study,corneal organoids were generated from hiPSCs derived from aniridia patients with three different PAX6 nonsense mutations,allowing for a detailed comparison between diseased and healthy control models. These organoids structurally mimicked the human cornea and were used to investigate histologic and metabolomic differences between healthy and aniridia-derived samples.ResultsUntargeted metabolomic analysis revealed significant metabolic differences between wild-type (WT) and aniridia-associated keratopathy (AAK) hiPSCs. Further metabolomic profiling at different time points demonstrated distinct metabolic shifts,with amino acid metabolism pathways being consistently enriched in AAK organoids.ConclusionsThis study emphasizes the profound impact of AAK mutations on metabolism,particularly in amino acid biosynthesis and energy metabolism pathways.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12886-024-03831-w. View Publication