技术资料

This study presents a comprehensive transcriptomic analysis of feeder-free extended pluripotent stem cells (ffEPSCs) and their parental human embryonic stem cells (ESCs),providing new insights into understanding human early development and cellular heterogeneity of pluripotency. Leveraging Smart-seq2-based single-cell RNA sequencing (scRNA-seq),we have compared gene expression profiles between ESCs and ffEPSCs and uncovered distinct subpopulations within both groups. Through pseudotime analysis,we have mapped the transition process from ESCs to ffEPSCs,revealing critical molecular pathways involved in the shift from a primed pluripotency to an extended pluripotent state. Additionally,we have employed repeat sequence analysis based on the latest T2T database and identified the stage-specific repeat elements contributing to regulating pluripotency and developmental transitions. This dataset deepens our understanding on early pluripotency and highlights the role of repeat sequences in early embryonic development. Our findings thus offer valuable resources for researchers in stem cell biology,pluripotency,early embryonic development,and potential cell therapy and regenerative medical applications. View Publication

This study investigates the impact of sodium channel protein type 1 subunit alpha (SCN1A) gene knockout (SCN1A KO) on brain development and function using cerebral organoids coupled with a multiomics approach. From comprehensive omics analyses,we found that SCN1A KO organoids exhibit decreased growth,dysregulated neurotransmitter levels,and altered lipidomic,proteomic,and transcriptomic profiles compared to controls under matrix-free differentiation conditions. Neurochemical analysis reveals reduced levels of key neurotransmitters,and lipidomic analysis highlights changes in ether phospholipids and sphingomyelin. Furthermore,quantitative profiling of the SCN1A KO organoid proteome shows perturbations in cholesterol metabolism and sodium ion transportation,potentially affecting synaptic transmission. These findings suggest dysregulation of cholesterol metabolism and sodium ion transport,with implications for synaptic transmission. Overall,these insights shed light on the molecular mechanisms underlying SCN1A-associated disorders,such as Dravet syndrome,and offer potential avenues for therapeutic intervention. View Publication

Using live-cell microscopy,we find that loss of VPS13C in human neurons disrupts lysosomal morphology and dynamics with increased inter-lysosomal tethers,leading to impaired lysosomal motility and defective lysosomal function as well as a decreased phospho-Rab10-mediated lysosomal stress response. Loss-of-function mutations in VPS13C are linked to early-onset Parkinson’s disease (PD). While VPS13C has been previously studied in non-neuronal cells,the neuronal role of VPS13C in disease-relevant human dopaminergic neurons has not been elucidated. Using live-cell microscopy,we investigated the role of VPS13C in regulating lysosomal dynamics and function in human iPSC-derived dopaminergic neurons. Loss of VPS13C in dopaminergic neurons disrupts lysosomal morphology and dynamics with increased inter-lysosomal contacts,leading to impaired lysosomal motility and cellular distribution,as well as defective lysosomal hydrolytic activity and acidification. We identified Rab10 as a phospho-dependent interactor of VPS13C on lysosomes and observed a decreased phospho-Rab10-mediated lysosomal stress response upon loss of VPS13C. These findings highlight an important role of VPS13C in regulating lysosomal homeostasis in human dopaminergic neurons and suggest that disruptions in Rab10-mediated lysosomal stress response contribute to disease pathogenesis in VPS13C-linked PD. View Publication

Ribosomal RNA (rRNA) genes exist in multiple copies arranged in tandem arrays known as ribosomal DNA (rDNA). The total number of gene copies is variable,and the mechanisms buffering this copy number variation remain unresolved. We surveyed the number,distribution,and activity of rDNA arrays at the level of individual chromosomes across multiple human and primate genomes. Each individual possessed a unique fingerprint of copy number distribution and activity of rDNA arrays. In some cases,entire rDNA arrays were transcriptionally silent. Silent rDNA arrays showed reduced association with the nucleolus and decreased interchromosomal interactions,indicating that the nucleolar organizer function of rDNA depends on transcriptional activity. Methyl-sequencing of flow-sorted chromosomes,combined with long read sequencing,showed epigenetic modification of rDNA promoter and coding region by DNA methylation. Silent arrays were in a closed chromatin state,as indicated by the accessibility profiles derived from Fiber-seq. Removing DNA methylation restored the transcriptional activity of silent arrays. Array activity status remained stable through the iPS cell re-programming. Family trio analysis demonstrated that the inactive rDNA haplotype can be traced to one of the parental genomes,suggesting that the epigenetic state of rDNA arrays may be heritable. We propose that the dosage of rRNA genes is epigenetically regulated by DNA methylation,and these methylation patterns specify nucleolar organizer function and can propagate transgenerationally. View Publication

Natural killer (NK) cells are cytotoxic immune cells that can eliminate target cells without prior stimulation. Human induced pluripotent stem cells (iPSCs) provide a robust source of NK cells for safe and effective cell-based immunotherapy against aggressive cancers. In this in vitro study,a feeder-free iPSC differentiation was performed to obtain iPSC-NK cells,and distinct maturational stages of iPSC-NK were characterized. Mature cells of CD56bright CD16bright phenotype showed upregulation of CD56,CD16,and NK cell activation markers NKG2D and NKp46 upon IL-15 exposure,while exposure to aggressive atypical teratoid/rhabdoid tumor (ATRT) cell lines enhanced NKG2D and NKp46 expression. Malignant cell exposure also increased CD107a degranulation markers and stimulated IFN-? secretion in activated NK cells. CD56bright CD16bright iPSC-NK cells showed a ratio-dependent killing of ATRT cells,and the percentage lysis of CHLA-05-ATRT was higher than that of CHLA-02-ATRT. The iPSC-NK cells were also cytotoxic against other brain,kidney,and lung cancer cell lines. Further NK maturation yielded CD56?ve CD16bright cells,which lacked activation markers even after exposure to interleukins or ATRT cells - indicating diminished cytotoxicity. Generation and characterization of different NK phenotypes from iPSCs,coupled with their promising anti-tumor activity against ATRT in vitro,offer valuable insights into potential immunotherapeutic strategies for brain tumors. Graphical abstractImage 1 Highlights•Natural killer (NK) cells were derived from human induced pluripotent stem cells (iPSCs) in the absence of feeder cells.•Various maturational subtypes of iPSC-NK cells were characterized,and the phenotypic and functional properties were studied.•iPSC-NK cells of CD56bright CD16bright phenotype expressed activation markers in response to interleukin stimuli.•iPSC-NK cells were cytotoxic toward human atypical teratoid and rhabdoid tumor (ATRT) cells and other human cancer cells.•The cytotoxicity of iPSC-NK cells against various cancer cells in vitro might be translated into an in vivo immunotherapy. View Publication

SummaryMolecular information on the early stages of human retinal development remains scarce due to limitations in obtaining early human eye samples. Pluripotent stem cell-derived retinal organoids (ROs) provide an unprecedented opportunity for studying early retinogenesis. Using a combination of single cell RNA-seq and spatial transcriptomics we present for the first-time a single cell spatiotemporal transcriptome of RO development. Our data demonstrate that ROs recapitulate key events of retinogenesis including optic vesicle/cup formation,presence of a putative ciliary margin zone,emergence of retinal progenitor cells and their orderly differentiation to retinal neurons. Combining the scRNA- with scATAC-seq data,we were able to reveal cell-type specific transcription factor binding motifs on accessible chromatin at each stage of organoid development,and to show that chromatin accessibility is highly correlated to the developing human retina,but with some differences in the temporal emergence and abundance of some of the retinal neurons. Graphical abstract Highlights•Single cell analyses reveal putative ciliary margin (pCM) presence in retinal organoids•PCM harbors early RPCs which differentiate to late RPCs and retinal neurons•Single cell ATAC-seq data reveal novel TF binding motifs in RPCs and retinal neurons•RO development largely recapitulates retinogenesis Genetics; Molecular biology; Neuroscience; Cell biology; Omics View Publication

Human induced pluripotent stem cells (hiPSCs) generate multiple clones with inherent heterogeneity,leading to variations in their differentiation capacity. Previous studies have primarily addressed line-to-line variations in differentiation capacity,leaving a gap in the comprehensive understanding of clonal heterogeneity. Here,we aimed to profile the heterogeneity of hiPSC clones and identify predictive biomarkers for cardiomyocyte (CM) differentiation capacity by integrating transcriptomic,epigenomic,endogenous retroelement,and protein kinase phosphorylation profiles. We generated multiple clones from a single donor and validated that these clones exhibited comparable levels of pluripotency markers. The clones were classified into two groups based on their differentiation efficiency to CMs—productive clone (PC) and non-productive clone (NPC). We performed RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin with sequencing (ATAC-seq). NPC was enriched in vasculogenesis and cell adhesion,accompanied by elevated levels of phosphorylated ERK1/2. Conversely,PC exhibited enrichment in embryonic organ development and transcription factor activation,accompanied by increased chromatin accessibility near transcription start site (TSS) regions. Integrative analysis of RNA-seq and ATAC-seq revealed 14 candidate genes correlated with cardiac differentiation potential. Notably,TEK and SDR42E1 were upregulated in NPC. Our integrative profiles enhance the understanding of clonal heterogeneity and highlight two novel biomarkers associated with CM differentiation. This insight may facilitate the identification of suboptimal hiPSC clones,thereby mitigating adverse outcomes in clinical applications. View Publication

Mitochondrial function is modulated by its interaction with the endoplasmic reticulum (ER). Recent research indicates that these contacts are disrupted in familial models of amyotrophic lateral sclerosis (ALS). We report here that this impairment in the crosstalk between mitochondria and the ER impedes the use of glucose-derived pyruvate as mitochondrial fuel,causing a shift to fatty acids to sustain energy production. Over time,this deficiency alters mitochondrial electron flow and the active/dormant status of complex I in spinal cord tissues,but not in the brain. These findings suggest mitochondria-associated ER membranes (MAM domains) play a crucial role in regulating cellular glucose metabolism and that MAM dysfunction may underlie the bioenergetic deficits observed in ALS. The bioenergetic deficits observed in Amyotrophic Lateral Sclerosis result from the disruption of mitochondria-associated ER membranes. Here,the authors show that this disruption impairs the use of glucose-derived pyruvate,which over time hinders mitochondrial electron flow. View Publication

Human pancreatic islets regulate organ development and metabolic homeostasis,with dysfunction leading to diabetes. Human pluripotent stem cells (hPSCs) provide a potential alternative source to cadaveric human pancreatic islets for replacement therapy in diabetes. However,human islet-like organoids (HILOs) generated from hPSCs in vitro often exhibit heterogeneous immature phenotypes such as aberrant gene expression and inadequate insulin secretion in response to glucose. Here we show that FXYD Domain Containing Ion Transport Regulator 2 (FXYD2) marks and regulates functional maturation and heterogeneity of generated HILOs,by controlling the ? cell transcriptome necessary for glucose-stimulated insulin secretion (GSIS). Despite its presence in mature ? cells,FXYD2 is diminished in hPSC-derived ?-like cells. Mechanistically,we find that FXYD2 physically interacts with SRC proto-oncogene,non-receptor tyrosine kinase (SRC) protein to regulate FXYD2-SRC-TEAD1 signaling to modulate ? cell transcriptome. We demonstrate that FXYD2High HILOs significantly outperform FXYD2Low counterparts to improve hyperglycemia in STZ-induced diabetic immune deficient mice. These results suggest that FXYD2 marks and regulates human ? cell maturation via channel-sensing signal transduction and that it can be used as a selection marker for functional heterogeneity of stem cell derived human islet organoids. Tacto et al. uncover a key marker that enables the selection of functional,transplantable human islets derived from stem cells,potentially paving the way for more precise and effective diabetes cell therapy. View Publication

Here we systematically investigated genomic alterations from the initiation of induced pluripotent stem (iPS) cell generation to induced mesenchymal stromal/stem cell differentiation. We observed a total of ten copy number alterations (CNAs) and five single-nucleotide variations (SNVs) during the phases of reprogramming,differentiation and passaging. We identified a higher frequency of CNAs and SNVs in iPS cells generated using the Sendai virus (SV) method compared with those generated with episomal vectors (Epi). Specifically,all SV-iPS cell lines exhibited CNAs during the reprogramming phase,while only 40% of Epi-iPS cells showed such alterations. Additionally,SNVs were observed exclusively in SV-derived cells during passaging and differentiation,with no SNVs detected in Epi-derived lines. Gene expression analysis revealed upregulation of chromosomal instability-related genes in late-passage SV-iPSCs,further indicating increased genomic instability. Notably,TP53 mutations were identified,underscoring the vulnerability of the gene and the critical need for careful genomic scrutiny when preparing iPS cells and derived cell lines. Genomic instability in induced pluripotent stem cells revealedThis study explores the potential of using induced pluripotent stem (iPS) cells to create mesenchymal stem (MS) cells for medical treatments. iPS cells can be reprogrammed from regular cells and can become any cell type,including MS cells,which are important for tissue repair. However,a concern is that iPS cells might develop genetic changes that could affect their safety. Here researchers investigated these genetic changes during the creation and growth of iPS cells and their transformation into MS cells using advanced techniques such as chromosomal microarray and next-generation sequencing,alongside conventional methods. The study found that iPS cells often develop genetic alterations,which can persist as they are turned into MS cells. The results suggest that while iPS cells hold promise for regenerative medicine,careful monitoring of genetic stability is crucial. Future research should focus on improving methods to ensure safety of iPS cell-derived therapies.This summary was initially drafted using artificial intelligence,then revised and fact-checked by the author. View Publication

Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by hypermethylation of expanded CGG repeats (>200) in the FMR1 gene leading to gene silencing and loss of Fragile X Messenger Ribonucleoprotein (FMRP) expression. FMRP plays important roles in neuronal function,and loss of FMRP in mouse and human FXS cell models leads to aberrant synaptic signaling and hyperexcitability. Multiple drug candidates have advanced into clinical trials for FXS,but no efficacious treatment has been identified to date,possibly as a consequence of poor translation from pre-clinical animal models to human. Here,we use a high resolution all-optical electrophysiology platform applied to multiple FXS patient-derived and CRISPR/Cas9-generated isogenic neuronal cell lines to develop a multi-parametric FXS disease phenotype. This neurophysiological phenotype was optimized and validated into a high throughput assay based on the amount of FMRP re-expression and the number of healthy neurons in a mosaic network necessary for functional rescue. The resulting highly sensitive and multiparameter functional assay can now be applied as a discovery platform to explore new therapeutic approaches for the treatment of FXS. Deep functional characterization of Fragile X syndrome patient and isogenic neurons using all-optical electrophysiology and machine learning identifies a validated,FMR1-dependent cellular phenotype compatible with high throughput drug screening. View Publication

SummaryMotivated by the cellular heterogeneity in complex tissues,particularly in brain and induced pluripotent stem cell (iPSC)-derived brain models,we developed a complete workflow to reproducibly characterize cell types in complex tissues. Our approach combines a flow cytometry (FC) antibody panel with our computational pipeline CelltypeR,enabling dataset aligning,unsupervised clustering optimization,cell type annotating,and statistical comparisons. Applied to human iPSC derived midbrain organoids,it successfully identified the major brain cell types. We performed fluorescence-activated cell sorting of CelltypeR-defined astrocytes,radial glia,and neurons,exploring transcriptional states by single-cell RNA sequencing. Among the sorted neurons,we identified subgroups of dopamine neurons: one reminiscent of substantia nigra cells most vulnerable in Parkinson’s disease. Finally,we used our workflow to track cell types across a time course of organoid differentiation. Overall,our adaptable analysis framework provides a generalizable method for reproducibly identifying cell types across FC datasets in complex tissues. Graphical abstract Highlights•CelltypeR is a flow cytometry and computational pipeline for cell type quantification•Identified brain cell types in midbrain organoids and measured changes in proportions•Enriched selected populations using FACS and characterized by single-cell RNA sequencing•Identified substantia nigra–like dopaminergic neurons sensitive in Parkinson’s disease Neuroscience; Cell biology; Omics View Publication