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SUMMARY During cell fate transitions,cells remodel their transcriptome,chromatin,and epigenome; however,it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here,we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that,following heterokaryon formation,the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG,conversely,has significant nascent RNA transcription only at 48 h after cell fusion but,strikingly,exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent. In brief Martinez-Sarmiento et al. demonstrate that,during heterokaryon reprogramming,global chromatin decondensation and loss of repressive histone modifications occur at late stages after cell fusion. Activation of OCT4 precedes global chromatin decompaction and does not require the opening of its local genomic region. Conversely,NANOG activation occurs after OCT4 activation,and the NANOG locus undergoes opening prior to its transcriptional activation. Graphical Abstract View Publication

CRISPR-based gene activation (CRISPRa) is a strategy for upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here,we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific,CRISPRa-responsive cis-regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells,which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis-regulatory elements in both K562 cells and iPSC-derived excitatory neurons,we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1?Mb,including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type,implying a dependency on either chromatin landscape and/or additional trans-acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate genes in a cell type-specific manner. Scalable CRISPRa screening of cis-regulatory elements in non-cancer cell lines has proved challenging. Here,the authors describe a scalable,CRISPR activation screening framework to identify regulatory element-gene pairs in diverse cell types including cancer cells and neurons. View Publication

hiPSC-derived blood–brain barrier (BBB) models are valuable for pharmacological and physiological studies,yet their translational potential is limited due to insufficient cell phenotypes and the neglection of the complex environment of the BBB. This study evaluates the plasma compatibility with hiPSC-derived microvascular endothelial-like cells to enhance the translational potential of in vitro BBB models. Therefore,plasma samples (sodium/lithium heparin,citrate,EDTA) and serum from healthy donors were tested on hiPSC-derived microvascular endothelial-like cells at concentrations of 100%,75%,and 50%. After 24 h,cell viability parameters were assessed. The impact of heparin-anticoagulated plasmas was further evaluated regarding barrier function and endothelial phenotype of differentiated endothelial-like cells. Finally,sodium-heparin plasma was tested in an isogenic triple-culture BBB model with continuous TEER measurements for 72 h. Only the application of heparin-anticoagulated plasmas did not significantly alter viability parameters compared to medium. Furthermore,heparin plasmas improved barrier function without increasing cell density and induced a von Willebrand factor signal. Finally,continuous TEER measurements of the triple-culture model confirmed the positive impact of sodium-heparin plasma on barrier function. Consequently,heparin-anticoagulated plasmas were proven to be compatible with hiPSC-derived microvascular endothelial-like cells. Thereby,the translational potential of BBB models can be substantially improved in the future. View Publication

The translocator protein 18 kDa (TSPO) is a multifunctional outer mitochondrial membrane protein associated with various aspects of mitochondrial physiology and multiple roles in health and disease. Here,we aimed to analyse the role of TSPO in the regulation of mitochondrial and cellular functions in a human neuronal cell model. We used the CRISPR/Cas9 technology and generated TSPO knockout (KO) and control (CTRL) variants of human-induced pluripotent stem cells (hiPSCs). In a multimodal phenotyping approach,we investigated cellular and mitochondrial functions in neural progenitor cells (NPCs),astrocytes,and neurons differentiated from hiPSC CTRL and TSPO KO cell lines. Our analysis revealed reduced mitochondrial respiration and glycolysis,altered Ca2+ levels in the cytosol and mitochondrial matrix,a depolarised MMP,and increased levels of reactive oxygen species,as well as a reduced cell size. Notably,TSPO deficiency was accompanied by reduced expression of the voltage-dependent anion channel (VDAC). We also observed a reduced TSPO and VDAC expression in cells derived from patients suffering from major depressive disorder (MDD). Considering the modulatory function of TSPO and the similar functional phenotype of cells derived from patients with depression,we discuss a role of TSPO in the etiology or pathology of MDD. In summary,our findings indicate a general impairment of mitochondrial function in TSPO knockout (KO) cells. This deepens our insight into the intricate role of TSPO in a range of physiological and pathological processes. View Publication

BackgroundSpecific microglia responses are thought to contribute to the development and progression of neurodegenerative diseases,including Parkinson’s disease (PD). However,the phenotypic acquisition of microglial cells and their role during the underlying neuroinflammatory processes remain largely elusive. Here,according to the multiple-hit hypothesis,which stipulates that PD etiology is determined by a combination of genetics and various environmental risk factors,we investigate microglial transcriptional programs and morphological adaptations under PARK7/DJ-1 deficiency,a genetic cause of PD,during lipopolysaccharide (LPS)-induced inflammation.MethodsUsing a combination of single-cell RNA-sequencing,bulk RNA-sequencing,multicolor flow cytometry and immunofluorescence analyses,we comprehensively compared microglial cell phenotypic characteristics in PARK7/DJ-1 knock-out (KO) with wildtype littermate mice following 6- or 24-h intraperitoneal injection with LPS. For translational perspectives,we conducted corresponding analyses in human PARK7/DJ-1 mutant induced pluripotent stem cell (iPSC)-derived microglia and murine bone marrow-derived macrophages (BMDMs).ResultsBy excluding the contribution of other immune brain resident and peripheral cells,we show that microglia acutely isolated from PARK7/DJ-1 KO mice display a distinct phenotype,specially related to type II interferon and DNA damage response signaling,when compared with wildtype microglia,in response to LPS. We also detected discrete signatures in human PARK7/DJ-1 mutant iPSC-derived microglia and BMDMs from PARK7/DJ-1 KO mice. These specific transcriptional signatures were reflected at the morphological level,with microglia in LPS-treated PARK7/DJ-1 KO mice showing a less amoeboid cell shape compared to wildtype mice,both at 6 and 24 h after acute inflammation,as also observed in BMDMs.ConclusionsTaken together,our results show that,under inflammatory conditions,PARK7/DJ-1 deficiency skews microglia towards a distinct phenotype characterized by downregulation of genes involved in type II interferon signaling and a less prominent amoeboid morphology compared to wildtype microglia. These findings suggest that the underlying oxidative stress associated with the lack of PARK7/DJ-1 affects microglia neuroinflammatory responses,which may play a causative role in PD onset and progression.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12974-024-03164-x. View Publication

Introduction: Africa,home to 1.4 billion people and the highest genetic diversity globally,harbors unique genetic variants crucial for understanding complex diseases like neurodegenerative disorders. However,African populations remain underrepresented in induced pluripotent stem cell (iPSC) collections,limiting the exploration of population-specific disease mechanisms and therapeutic discoveries. Methods: To address this gap,we established an open-access African Somatic and Stem Cell Bank. Results: In this initial phase,we generated 10 rigorously characterized iPSC lines from fibroblasts representing five Nigerian ethnic groups and both sexes. These lines underwent extensive profiling for pluripotency,genetic stability,differentiation potential,and Alzheimer's disease and Parkinson's disease risk variants. Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology was used to introduce frontotemporal dementia-associated MAPT mutations (P301L and R406W). Discussion: This collection offers a renewable,genetically diverse resource to investigate disease pathogenicity in African populations,facilitating breakthroughs in neurodegenerative research,drug discovery,and regenerative medicine. Highlights: We established an open-access African Somatic and Stem Cell Bank. 10 induced pluripotent stem cell lines from five Nigerian ethnic groups were rigorously characterized. Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology was used to introduce frontotemporal dementia-causing MAPT mutations. The African Somatic and Stem Cell Bank is a renewable,genetically diverse resource for neurodegenerative research. View Publication

The development of patient-derived cardiac disease models has advanced rapidly due to the progress of human-induced pluripotent stem cell (hiPSC) technologies. Many protocols detail individual parts of the entire workflow,from handling hiPSCs and differentiating them into cardiomyocytes to live contraction imaging via widefield/phase-contrast and fluorescence microscopy. Here,we propose a streamlined protocol that guides users through hiPSC culture,differentiation,expansion,and functional imaging of hiPSC cardiomyocytes. First,hiPSC maintenance and handling procedures are outlined. Differentiation occurs over a two-week period,followed by selective expansion to increase the yield of hiPSC cardiomyocytes. Comprehensive characterization and quantification enable detailed contraction profiling of these cells. Designed to be low-cost,this protocol is suited for applications in drug discovery,screening,and clinical testing of patient-specific phenotypes. The addition of cardiomyocyte expansion and automated analysis distinguishes our protocol from current approaches. View Publication

Alcohol use disorder (AUD) is the most prevalent substance use disorder worldwide. Acamprosate and naltrexone are anti-craving drugs used in AUD pharmacotherapy. However,molecular mechanisms underlying their anti-craving effect remain unclear. This study utilized a patient-derived induced pluripotent stem cell (iPSC)-based model system and anti-craving drugs that are used to treat AUD as “molecular probes” to identify possible mechanisms associated with alcohol craving. We examined the pathophysiology of craving and anti-craving drugs by performing functional genomics studies using iPSC-derived astrocytes and next-generation sequencing. Specifically,RNA sequencing performed using peripheral blood mononuclear cells from AUD patients with extreme values for alcohol craving intensity prior to treatment showed that inflammation-related pathways were highly associated with alcohol cravings. We then performed a genome-wide assessment of chromatin accessibility and gene expression profiles of induced iPSC-derived astrocytes in response to ethanol or anti-craving drugs. Those experiments identified drug-dependent epigenomic signatures,with IRF3 as the most significantly enriched motif in chromatin accessible regions. Furthermore,the activation of IRF3 was associated with ethanol-induced endoplasmic reticulum (ER) stress which could be attenuated by anti-craving drugs,suggesting that ER stress attenuation might be a target for anti-craving agents. In conclusion,we found that craving intensity was associated with alcohol consumption and treatment outcomes. Our functional genomic studies suggest possible relationships among craving,ER stress,IRF3 and the actions of anti-craving drugs. View Publication

Enzymatic dissociation of human pluripotent stem cells (hPSCs) into single cells during routine passage leads to massive cell death. Although the Rho-associated protein kinase inhibitor,Y-27632 can enhance hPSC survival and proliferation at high seeding density,dissociated single cells undergo apoptosis at clonal density. This presents a major hurdle when deriving genetically modified hPSC lines since transfection and genome editing efficiencies are not satisfactory. As a result,colonies tend to contain heterogeneous mixtures of both modified and unmodified cells,making it difficult to isolate the desired clone buried within the colony. In this study,we report improved clonal expansion of hPSCs using a retinoic acid analogue,TTNPB. When combined with Y-27632,TTNPB synergistically increased hPSC cloning efficiency by more than 2 orders of magnitude (0.2% to 20%),whereas TTNPB itself increased more than double cell number expansion compared to Y-27632. Furthermore,TTNPB-treated cells showed two times higher aggregate formation and cell proliferation compared to Y-27632 in suspension culture. TTNPB-treated cells displayed a normal karyotype,pluripotency and were able to stochastically differentiate into all three germ layers both in vitro and in vivo. TTNBP acts,in part,by promoting cellular adhesion and self-renewal through the upregulation of Claudin 2 and HoxA1. By promoting clonal expansion,TTNPB provides a new approach for isolating and expanding pure hPSCs for future cell therapy applications. A retinoic acid analogue,TTNPB,improves clonal expansion in adherent and suspension culture of hPSCs by promoting cellular adhesion and self-renewal through the upregulation of Claudin 2 and HoxA1. View Publication

It has been reported that human embryonic stem cells (hESCs) treated with BMP4 and inhibitors of TGF? signaling (A83-01) and FGF signaling (PD173074),called BAP,can efficiently differentiate to extraembryonic (ExE) cells in vitro. Due to restricted access to human embryos,it is ethically impossible to test the developmental potential of ExE cells in vivo. Here,we demonstrate that most ExE cells expressed molecular markers for both trophoblasts (TBs) and amniotic cells (ACs). Following intra-uterine transplantation,ExE cells contributed to the mouse placenta. More interestingly,ExE cells could chimerize with the mouse blastocyst as,after injection into the blastocyst,they penetrated its trophectoderm. After implantation of the injected blastocysts into surrogate mice,human cells were found at E14 in placental labyrinth,junction zones,and even near the uterine decidua,expressed placental markers,and secreted human chorionic gonadotropin. Surprisingly,ExE cells also contributed to cartilages of the chimeric embryo with some expressing the chondrogenic marker SOX9,consistent with the mesodermal potential of TBs and ACs in the placenta. Deleting MSX2,a mesodermal determinant,restricted the contribution of ExE cells to the placenta. Thus,we conclude that hESC-derived ExE cells can chimerize with the mouse blastocyst and contribute to both the placenta and cartilages of the chimera consistent with their heteogenious nature. Intra-uterus and intra-blastocyst injections are novel and sensitive methods to study the developmental potential of ExE cells. View Publication

Human GWAS have shown that obesogenic FTO polymorphisms correlate with lean mass,but the mechanisms have remained unclear. It is counterintuitive because lean mass is inversely correlated with obesity and metabolic diseases. Here,we use CRISPR to knock-in FTOrs9939609-A into hESC-derived tissue models,to elucidate potentially hidden roles of FTO during development. We find that among human tissues,FTOrs9939609-A most robustly affect human muscle progenitors’ proliferation,differentiation,senescence,thereby accelerating muscle developmental and metabolic aging. An edited FTOrs9939609-A allele over-stimulates insulin/IGF signaling via increased muscle-specific enhancer H3K27ac,FTO expression and m6A demethylation of H19 lncRNA and IGF2 mRNA,with excessive insulin/IGF signaling leading to insulin resistance upon replicative aging or exposure to high fat diet. This FTO-m6A-H19/IGF2 circuit may explain paradoxical GWAS findings linking FTOrs9939609-A to both leanness and obesity. Our results provide a proof-of-principle that CRISPR-hESC-tissue platforms can be harnessed to resolve puzzles in human metabolism. Human GWAS paradoxically linked FTO SNPs to both lean mass and sarcopenia/obesity. Here,Guang et al used CRISPR-edited stem cells to reveal that an obesogenic FTO SNP accelerates both muscle development and aging,by increasing RNA m6A demethylation. View Publication

Mutation in CUL4B gene is one of the most common causes for X-linked intellectual disability (XLID). CUL4B is the scaffold protein in CUL4B-RING ubiquitin ligase (CRL4B) complex. While the roles of CUL4B in cancer progression and some developmental processes like adipogenesis,osteogenesis,and spermatogenesis have been studied,the mechanisms underlying the neurological disorders in patients with CUL4B mutations are poorly understood. Here,using 2D neuronal culture and cerebral organoids generated from the patient-derived induced pluripotent stem cells and their isogenic controls,we demonstrate that CUL4B is required to prevent premature cell cycle exit and precocious neuronal differentiation of neural progenitor cells. Moreover,loss-of-function mutations of CUL4B lead to increased synapse formation and enhanced neuronal excitability. Mechanistically,CRL4B complex represses transcription of PPP2R2B and PPP2R2C genes,which encode two isoforms of the regulatory subunit of protein phosphatase 2 A (PP2A) complex,through catalyzing monoubiquitination of H2AK119 in their promoter regions. CUL4B mutations result in upregulated PP2A activity,which causes inhibition of AKT and ERK,leading to premature cell cycle exit. Activation of AKT and ERK or inhibition of PP2A activity in CUL4B mutant organoids rescues the neurogenesis defect. Our work unveils an essential role of CUL4B in human cortical development. View Publication