技术资料

SummaryInducible loss-of-function strategies are crucial for understanding gene function. However,creating inducible,multiple-gene knockout models is challenging and time-consuming. Here,we present a protocol for establishing a doxycycline-inducible CRISPR interference (CRISPRi) system to concurrently silence multiple genes in human induced pluripotent stem cells (hPSCs). We describe the steps for establishing host CRISPRi hPSCs,designing and cloning single-guide RNAs (sgRNAs) into a lentivirus plasmid,and establishing monoclonal CRISPRi hPSC lines transduced with sgRNAs. We also detail the procedures for selecting effective CRISPRi clones.For complete details on the use and execution of this protocol,please refer to Matsui et al.1 Graphical abstract Highlights•Dox-inducible CRISPRi system to silence multiple genes concurrently•Instructions for generating CRISPRi hPSCs transduced with four sgRNAs•FOXA1/A2/A3-CRISPRi system represses expression of all three FOXA genes by 95% Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Inducible loss-of-function strategies are crucial for understanding gene function. However,creating inducible,multiple-gene knockout models is challenging and time-consuming. Here,we present a protocol for establishing a doxycycline-inducible CRISPR interference (CRISPRi) system to concurrently silence multiple genes in human induced pluripotent stem cells (hPSCs). We describe the steps for establishing host CRISPRi hPSCs,designing and cloning single-guide RNAs (sgRNAs) into a lentivirus plasmid,and establishing monoclonal CRISPRi hPSC lines transduced with sgRNAs. We also detail the procedures for selecting effective CRISPRi clones. View Publication

Background/Objectives: The limited translatability of preclinical experimental findings to patients remains an obstacle for successful treatment of brain diseases. Relevant models to elucidate mechanisms behind brain pathogenesis,including cell-specific contributions and cell-cell interactions,and support successful targeting and prediction of drug responses in humans are urgently needed,given the species differences in brain and blood-brain barrier (BBB) functions. Human microphysiological systems (MPS),such as Organ-Chips,are emerging as a promising approach to address these challenges. Here,we examined and advanced a Brain-Chip that recapitulates aspects of the human cortical parenchyma and the BBB in one model. Methods: We utilized human primary astrocytes and pericytes,human induced pluripotent stem cell (hiPSC)-derived cortical neurons,and hiPSC-derived brain microvascular endothelial-like cells and included for the first time on-chip hiPSC-derived microglia. Results: Using Tumor necrosis factor alpha (TNF?) to emulate neuroinflammation,we demonstrate that our model recapitulates in vivo-relevant responses. Importantly,we show microglia-derived responses,highlighting the Brain-Chip’s sensitivity to capture cell-specific contributions in human disease-associated pathology. We then tested BBB crossing of human transferrin receptor antibodies and conjugated adeno-associated viruses. We demonstrate successful in vitro/in vivo correlation in identifying crossing differences,underscoring the model’s capacity as a screening platform for BBB crossing therapeutic strategies and ability to predict in vivo responses. Conclusions: These findings highlight the potential of the Brain-Chip as a reliable and time-efficient model to support therapeutic development and provide mechanistic insights into brain diseases,adding to the growing evidence supporting the value of MPS in translational research and drug discovery. View Publication

Neutrophils are essential innate immune cells with unusual anti-microbial properties while dysfunctions of neutrophils lead to severe health problems such as lethal infections. Generation of neutrophils from human induced pluripotent stem cells (hiPSCs) is highly promising to produce off-the-shelf neutrophils for transfusion therapies. However,the anti-microbial potencies of hiPSCs derived neutrophils (iNEUs) remain less documented. Here,we develop a scalable approach to generate iNEUs in a chemical defined condition. iNEUs display typical neutrophil characters in terms of phagocytosis,migration,formation of neutrophil extracellular traps (NETs),etc. Importantly,iNEUs display a strong killing potency against various bacteria such as K.pneumoniae,P.aeruginosa,E.coli and S.aureus. Moreover,transfusions of iNEUs in mice with neutrophil dysfunction largely enhance their survival in lethal infection of different bacteria. Together,our data show that hiPSCs derived neutrophils hold strong anti-microbial potencies to protect severe infections under neutrophil dysfunction conditions.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13619-025-00227-z. View Publication

SUMMARY Individuals with Williams syndrome (WS),a neurodevelopmental disorder caused by hemizygous loss of 26–28 genes at 7q11.23,characteristically portray a hypersocial phenotype. Copy-number variations and mutations in one of these genes,GTF2I,are associated with altered sociality and are proposed to underlie hypersociality in WS. However,the contribution of GTF2I to human neurodevelopment remains poorly understood. Here,human cellular models of neurodevelopment,including neural progenitors,neurons,and three-dimensional cortical organoids,are differentiated from CRISPR-Cas9-edited GTF2I-knockout (GTF2I-KO) pluripotent stem cells to investigate the role of GTF2I in human neurodevelopment. GTF2I-KO progenitors exhibit increased proliferation and cell-cycle alterations. Cortical organoids and neurons demonstrate increased cell death and synaptic dysregulation,including synaptic structural dysfunction and decreased electrophysiological activity on a multielectrode array. Our findings suggest that changes in synaptic circuit integrity may be a prominent mediator of the link between alterations in GTF2I and variation in the phenotypic expression of human sociality. Graphical Abstract In brief GTF2I is thought to influence the phenotypic expression of human sociality and is implicated in neurodevelopmental disease. Adams et al. use hiPSC-derived cell platforms to investigate the role of GTF2I in human neurodevelopment. Loss of GTF2I promotes increased cell death,reduced synaptic integrity,and decreased electrical activity of cortical organoids. View Publication

IntroductionAccumulating evidence indicates that the increased presence of astrocytes is fundamentally linked to the neurological dysfunctions observed in individuals with Down syndrome (DS). REST (RE1-silencing transcription factor),as a chromatin modifier,regulates 15,450 genes in humans. REST is a key regulatory element that governs astrocyte differentiation,development,and the maintenance of their physiological functions. The downregulation of REST may disrupt the homeostatic balance of astrocytes in DS.MethodsThis study aims to elucidate the role of REST in DS-astrocytes through comprehensive transcriptomic analysis and experimental validation.ResultsTranscriptomic analysis identified that REST-targeted differentially expressed genes (DEGs) in DS astrocytes are enriched in pathways associated with inflammatory response. Notably,our findings in astrocytes derived from DS human induced pluripotent stem cells (hiPSCs) show that the loss of nucleus REST leads to an upregulation of inflammatory mediators and markers indicative of the presence of reactive astrocytes. Lithium treatment,which restored nucleus REST in trisomic astrocytes,significantly suppressed the expression of these inflammatory mediators and reactive astrocyte markers.DiscussionThese findings suggest that REST is pivotal in modulating astrocyte functionality and reactivity in DS. The loss of REST in DS-astrocytes prompts the formation of reactive astrocytes,thereby compromising central nervous system homeostasis. Lithium treatment possesses the potential to rescue astrocyte reactivity in DS by restoring nucleus REST expression. View Publication

Background?-catenin,acting as the core effector of canonical Wnt signaling pathway,plays a pivotal role in controlling lineage commitment and the formation of definitive endoderm (DE) during early embryonic development. Despite extensive studies using various animal and cell models,the ?-catenin-centered regulatory mechanisms underlying DE formation remain incompletely understood,partly due to the rapid and complex cell fate transitions during early differentiation.ResultsIn this study,we generated new CTNNB1-/- human ES cells (hESCs) using CRISPR-based insertional gene disruption approach and systematically rescued the DE defect in these cells by introducing various truncated or mutant forms of ?-catenin. Our analysis showed that a truncated ?-catenin lacking both N- and C-terminal domains (?N148C) could robustly rescue the DE formation,whereas hyperactive ?-catenin mutants with S33Y mutation or N-terminal deletion (?N90) had limited ability to induce DE lineage. Notably,the ?N148C mutant exhibited significant nuclear translocation that was positively correlated with successful DE rescue. Transcriptomic analysis further uncovered that two weak ?-catenin mutants lacking the C-terminal transactivation domain (CTD) activated primitive streak (PS) genes,whereas the hyperactive ?-catenin mutants activated mesoderm genes.ConclusionOur study uncovered an unconventional regulatory function of ?-catenin through weak transactivation,indicating that the levels of ?-catenin activity determine the lineage bifurcation from mesendoderm into endoderm and mesoderm.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13578-024-01279-5. View Publication

BackgroundMale factor infertility (MFI) is responsible for 50% of infertility cases and in 15% of the cases sperm is absent due to germ cell aplasia. Human induced pluripotent stem cell (hiPSC)-derived spermatogonial stem cells (hSSCs) could serve as an autologous germ cell source for MFI in patients with an insufficient sperm yield for assisted reproductive technology (ART). The endocannabinoid system (ECS) has been implicated to play a role in mouse embryonic stem cells (mESCs) and the human testicular environment. However,the contribution of the ECS in hiPSCs and hiPSC-derived hSSCs is currently unknown. Here,we aimed to assess whether hiPSCs and hiPSC-derived hSSCs are regulated by components of the ECS and whether manipulation of the ECS could increase the yield of hiPSC-derived SSCs and serve as an autologous cell-based source for treatment of MFI.MethodsWe reprogrammed human dermal fibroblasts (hDFs) to hiPSCs,induced differentiation of hSSC from hiPSCs and evaluated the presence of ECS ligands (AEA,2-AG) by LC/MS,receptors (CB1R,CB2R,TRPV1,GPR55) by qPCR,flow cytometry and immunofluorescent labeling. We then examined the efficacy of endogenous and synthetic selective ligands (ACPA,CB65,CSP,ML184) on proliferation of hiPSCs using real-time cell analysis (RTCA) and assessed the effects of on CB2R agonism on hiPSC pluripotency and differentiation to hSSCs.ResultshiPSCs from hDFs expressed the pluripotency markers OCT4,SOX2,NANOG,SSEA4 and TRA-1-60; and could be differentiated into ID4+,PLZF?+?hSSCs. hiPSCs and hiPSC-derived hSSCs secreted AEA and 2-AG at 10??10 ??10??9 M levels. Broad expression of all ECS receptors was observed in both hiPSCs and hiPSC-derived hSSCs,with a higher CB2R expression in hSSCs in comparison to hiPSCs. CB2R agonist CB65 promoted proliferation and differentiation of hiPSCs to hiPSC-hSSCs in comparison to AEA,2-AG,ACPA,CSP and ML184. The EC50 of CB65 was determined to be 2.092?×?10??8 M for support of pluripotency and preservation of stemness on hiPSCs from 78 h. CB65 stimulation at EC50 also increased the yield of ID4?+?hSSCs,PLZF?+?SSPCs and SCP3?+?spermatocytes from day 10 to 12.ConclusionsWe demonstrated here for the first time that stimulation of CB2R results in an increased yield of hiPSCs and hiPSC-derived hSSCs. CB65 is a potent CB2R agonist that can be used to increase the yield of hiPSC-derived hSSCs offering an alternative source of autologous male germ cells for patients with MFI. Increasing the male germ/stem cell pool by CB65 supplementation could be part of the ART-associated protocols in MFI patients with complete germ cell aplasia.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40659-025-00596-4. View Publication

Patients with breast cancer show altered expression of genes within the pectoralis major skeletal muscle cells of the breast. Through analyses of The Cancer Genome Atlas (TCGA)-breast cancer (BRCA),we identified three previously uncharacterized putative novel tumor suppressor genes expressed in normal muscle cells,whose expression was downregulated in breast tumors. We found that NEDD4 binding protein 2-like 1 (N4BP2L1),pleckstrin homology domain-containing family A member 4 (PLEKHA4),and brain-enriched guanylate kinase-associated protein (BEGAIN) that are normally highly expressed in breast myoepithelial cells and smooth muscle cells were significantly downregulated in breast tumor tissues of a cohort of 50 patients with this cancer. Our data revealed that the low expression of PLEKHA4 in patients with menopause below 50 years correlated with a higher risk of breast cancer. Moreover,we identified N4BP2L1 and BEGAIN as potential biomarkers of HER2-positive breast cancer. Furthermore,low BEGAIN expression in breast cancer patients with blood fat,heart problems,and diabetes correlated with a higher risk of this cancer. In addition,protein and RNA expression analysis of TCGA-BRCA revealed N4BP2L1 as a promising diagnostic protein biomarker in breast cancer. In addition,the in silico data of scRNA-seq showed high expression of these genes in several cell types of normal breast tissue,including breast myoepithelial cells and smooth muscle cells. Thus,our results suggest their possible tumor-suppressive function in breast cancer and muscle development. View Publication

Rare coding mutations cause ~45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases,but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs),we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity,often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context,four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing,we used the MPRA data to develop a regression model,EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together,we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD. View Publication

Preclinical data have confirmed that human pluripotent stem cell-derived cardiomyocytes (PSC-CMs) can remuscularize the injured or diseased heart,with several clinical trials now in planning or recruitment stages. However,because ventricular arrhythmias represent a complication following engraftment of intramyocardially injected PSC-CMs,it is necessary to provide treatment strategies to control or prevent engraftment arrhythmias (EAs). Here,we show in a porcine model of myocardial infarction and PSC-CM transplantation that EAs are mechanistically linked to cellular heterogeneity in the input PSC-CM and resultant graft. Specifically,we identify atrial and pacemaker-like cardiomyocytes as culprit arrhythmogenic subpopulations. Two unique surface marker signatures,signal regulatory protein ? (SIRPA)+CD90?CD200+ and SIRPA+CD90?CD200?,identify arrhythmogenic and non-arrhythmogenic cardiomyocytes,respectively. Our data suggest that modifications to current PSC-CM-production and/or PSC-CM-selection protocols could potentially prevent EAs. We further show that pharmacologic and interventional anti-arrhythmic strategies can control and potentially abolish these arrhythmias. Selvakumar,Clayton et al. use a porcine model of myocardial infarction and PSC-CM transplantation and identify atrial and pacemaker-like cardiomyocytes as the cause of engraftment arrhythmias and surface marker signatures to distinguish between arrhythmogenic and non-arrhythmogenic cardiomyocytes. View Publication

Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During the cell cycle,nuclear speckles dissolve following phosphorylation of their protein components. Here,we identify the PP1 family as the phosphatases that counteract kinase-mediated dissolution. PP1 overexpression increases speckle cohesion and leads to retention of mRNA within speckles and the nucleus. Using APEX2 proximity labeling combined with RNA-sequencing,we characterize the recruitment of specific RNAs. We find that many transcripts are preferentially enriched within nuclear speckles compared to the nucleoplasm,particularly chromatin- and nucleus-associated transcripts. While total polyadenylated RNA retention increases with nuclear speckle cohesion,the ratios of most mRNA species to each other are constant,indicating non-selective retention. We further find that cellular responses to heat shock,oxidative stress,and hypoxia include changes to the phosphorylation and cohesion of nuclear speckles and to mRNA retention. Our results demonstrate that tuning the material properties of nuclear speckles provides a mechanism for the acute control of mRNA localization. Here the authors study how interactions with nuclear speckles help localize mRNA in cells. They find that modifications of the proteins in these structures affects their cohesion and can modulate mRNA retention under stress. View Publication

PurposeLittle is known about the development of Bruch's membrane (BrM),the structure separating and supporting the retina and choroid,nor whether differentiation of human pluripotent stem cell (hPSC)-derived retinal pigment epithelium (RPE) accurately replicates BrM. This has relevance for tissue engineering strategies,both in the development of accurate in vitro models,and effective RPE transplant strategies. Here,we investigated BrM-associated protein production in human fetal tissue and hPSC-derived RPE.MethodsThe presence of laminin,elastin,fibronectin,and types I/III/IV collagen was examined in human fetal eyes at 6 to 21 post-conception weeks (PCWs) and hPSC-derived RPE cultures at 1 to 6 weeks in culture using immunohistochemistry/immunocytochemistry and quantitative PCR (qPCR).ResultsIn human fetal retina,laminin and fibronectin were present from 6 PCW,type IV collagen from 8 PCW,elastin from 12 PCW,type I collagen by 17 PCW,and type III collagen from 21 PCW. BrM layering was discernible from 12 PCW,becoming distinct by 17 PCW. In hPSC-derived RPE cultures,basement membranes containing laminin and fibronectin were present from week 1,type IV collagen from week 2,and type I collagen from week 4. Type III collagen was present at all timepoints,although not localized as a basement membrane. Elastin was absent at all timepoints.ConclusionsBrM-like membrane synthesis in hPSC-derived RPE largely recapitulates the temporal sequence seen in human development,excluding elastin. These support the utility of hPSC-derived RPE in in vitro systems to model RPE/retina interactions in health and disease,and inform cell therapy approaches,as de novo BrM-like membrane has the potential to support transplanted donor RPE. View Publication