Astrocytes are essential regulators of neuronal health, and their dysfunction contributes to neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Using human induced pluripotent stem cell (iPSC)-derived astrocytes carrying ALS-associated VCP mutations, we uncover cell-autonomous activation of the hypoxia response under basal conditions. VCP-mutant astrocytes exhibit increased nuclear hypoxia-inducible factor (HIF)-1ɑ, mitochondrial depolarization, and lipid droplet accumulation. Mimicking hypoxia in control astrocytes by HIF-1ɑ stabilization with dimethyloxalylglycine recapitulates these phenotypes. Transcriptomic and CUT&RUN profiling reveal direct HIF-1ɑ binding to canonical hypoxia-responsive genes in VCP-mutant astrocytes and a transcriptional signature of metabolic reprogramming and mitochondrial dysfunction under normoxia. Furthermore, conditioned medium from hypoxia-exposed astrocytes fails to rescue RNA-binding protein mislocalization in motor neurons, unlike medium from healthy counterparts. Together, these findings demonstrate that aberrant HIF-1ɑ activation drives astrocytic dysfunction and compromises neuronal support, identifying hypoxic stress as an early and functionally consequential event in VCP-mutant ALS, with therapeutic implications for targeting HIF-1ɑ signaling.

Functional stem cell-derived heart models offer new avenues for preclinical, animal-free physiological assessment of drug cardiotoxicity. Yet, comprehensive molecular profiling in these models remains limited, leaving key metabolic drivers of cardiotoxicity unexplored. Here, we leveraged an innovative platform and a topology-guided integration framework to unveil the complex dose- and time-dependent metabolic rewiring of the central carbon metabolism caused by doxorubicin-induced cardiotoxicity (DiC) in human heart tissue. Through cross-modal integration of cardiac functionality and metabolomics in 3D engineered heart tissues, we identified 20 metabolites linked to cardiac contraction and differentially affected by doxorubicin exposure. Nine of them, including carnitine esters and uridine 5'-diphosphate (UDP)-glucuronic acid, were never before implicated in DiC and may represent promising candidates for DiC metabolic rescue. By yielding high-resolution insights into complex biological mechanisms, our platform and mathematical framework enable metabolic and functional assessment of cardiotoxicity in engineered heart models, paving the way for innovative advances in preclinical drug development.

Cerebral organoids generated according to unguided protocols produce neural tissue with exceptional cell diversity and fidelity to in vivo. However, with only minimal extrinsic intervention, the importance of high-quality starting material becomes paramount. Understanding quality and how to maintain it throughout prolonged culture is therefore a crucial foundation for successful organoid differentiation. In this study, we investigate the proteome and phosphoproteome of human pluripotent stem cells to uncover the mechanisms that drive neural organoid competence. We identify aberrant cell-extracellular matrix interaction and increased oxidative metabolism as hallmarks of poor neural differentiators. Drawing on the proteomic data and published literature, we test culture conditions with improved coating matrix, reduction of oxidative stress, and sustained fibroblast growth Factor 2 (FGF2) supply. These adjustments provide some improvement to differentiation, highlighting the importance of optimal culture conditions to maintain high-quality stem cells but also suggesting cell-intrinsic sources of variability.

The common marmoset (Callithrix jacchus) is a genetically modifiable non-human primate increasingly used in biomedical research. Here, we established a method for deriving embryonic stem cells (ESCs) from blastocysts generated by somatic cell nuclear transfer (SCNT) in the marmoset. Injection of histone demethylase Kdm4d mRNA enabled efficient reprogramming of somatic nuclei, allowing blastocyst formation in 14.5% from fibroblasts. Combining this method with a G9a/EHMT2 histone methyltransferase inhibitor improved blastocyst quality and allowed derivation of nuclear transfer ESCs (ntESCs), including wild-type and GFP-transgenic lines. These ntESCs exhibited normal karyotypes and pluripotency. Nuclear and mitochondrial DNA analyses confirmed their nuclear donor origin and cytoplasmic inheritance from recipient oocytes. Transcriptome analysis identified abnormally expressed genes in ntESCs present in a line-dependent and independent manner, suggesting partial reprogramming resistance. Our study establishes a marmoset SCNT method enabling derivation of ntESCs and provides a new platform for preserving and engineering marmoset genetic resources.

Autophagy is a cytoprotective mechanism responsible for the maintenance and long-term survival of various cell types, including stem cells. However, its role in the germline stem cell (GSC) niche remains unexplored. We demonstrate that autophagy flux in female Drosophila GSCs is low and dependent on the core autophagy gene, Atg5. However, the maintenance of Atg5 GSCs within the GSC niche was unaffected even under nutrient stress. In contrast, disruption of autophagy within the cap cells (niche cells) leads to the loss of both cap cells and GSCs during aging. Further, reduced autophagy in cap cells severely impairs the crucial GSC self-renewal signal mediated by BMP-pMad emanating from the cap cells at the onset of midlife. Autophagy was essential for the long-term survival of cap cells. Our study reveals a differential role for autophagy, which is dispensable in GSCs but necessary in niche cells, where it supports signaling and survival to maintain GSCs.

Perturb-seq is a powerful approach to systematically assess how genes and enhancers impact the molecular and cellular pathways of development and disease. However, technical challenges have limited its application in stem-cell-based systems. Here, we benchmarked Perturb-seq across multiple CRISPRi modalities, on diverse genomic targets, in multiple human pluripotent stem cells, during directed differentiation to multiple lineages, and across multiple single guide RNA (sgRNA) delivery systems. To ensure cost-effective production of large-scale Perturb-seq datasets as part of the Impact of Genomic Variants on Function (IGVF) consortium, our optimized protocol dynamically assesses experiment quality across the weeks-long procedure. Our analysis of 1,996,260 sequenced cells across benchmarking datasets reveals shared regulatory networks linking disease-associated enhancers and genes with downstream targets during cardiomyocyte differentiation. This study establishes open tools and resources for interrogating genome function during stem cell differentiation.

Charcot-Marie-Tooth type 2A (CMT2A) is an inherited sensory-motor axonopathy caused by mutations in the Mitofusin2 (MFN2) gene, coding for MFN2 protein. No curative treatment has been developed to date. The advent of induced pluripotent stem cell (iPSC) has provided unprecedented opportunities to understand complex neurological disorders. In CMT2A research, patient-specific iPSCs can be differentiated in motor and sensory neurons, thereby establishing reliable in vitro disease models. Here, we review current available iPSC-based models of CMT2A, focusing on pathogenetic insights derived from these studies and discussing challenges and potential of iPSC-derived models in elucidating disease mechanisms, providing innovative platforms for testing, and developing novel effective therapeutic strategies.

OCT4 is a master regulator of pluripotency, with expression restricted to pluripotent and germ cells. Its expression is controlled by two cis-regulatory elements: the distal (DE) and proximal (PE) enhancers. Although widely used as markers for pluripotent stem cells (PSCs), their biological roles have remained incompletely defined. Here, we generated PSC lines and mouse models with targeted deletions of the Oct4 DE and PE. Our findings reveal that the DE is dispensable for sustaining the primed pluripotent state but required for the naive state, whereas the PE is necessary for the primed state but not for the naive state. Notably, PE-deficient naive mouse PSCs retained the capacity to differentiate into somatic lineages in vitro and to contribute chimeras. In contrast, deletion of either enhancer in vivo resulted in early embryonic lethality. These models offer powerful genetic tools to dissect the regulation of Oct4 expression during pluripotency and early development.

This Forum article explores 4,481 YouTube videos about stem cells to map how medical knowledge is shaped online. By analyzing content and user metrics, the article identifies key mediators and influential creators, revealing a complex discourse dominated by celebrity influencers in the promotion and discussion of putative stem cell treatments.

Recent studies highlight the critical role of mitochondria in hematopoiesis, especially in stem cell function and erythroid maturation. To explore mitochondrial contributions to cell lineage commitment of hematopoietic progenitors, we utilized Cars2-mutant mice, an ideal model for this purpose. CARS2, a mitochondrial isoform of cysteinyl-tRNA synthetase, has cysteine persulfide synthase (CPERS) activity. Our new mouse model, with reduced CPERS activity, showed that the Cars2 mutation led to mitochondrial inhibition and anemia by suppressing erythroid commitment in megakaryocyte-erythroid progenitors (MEPs). This suppression was reproduced using mitochondrial electron transport chain inhibitors. We identified two distinct MEP populations based on the mitochondrial content: mitochondria-rich MEPs favored erythroid differentiation, while the mitochondria-poor MEPs favored megakaryocyte differentiation. These findings reveal critical contributions of mitochondria to the MEP lineage selection, acting as a "mitochondrial navigation" for lineage commitment.

Using anonymized, biobanked samples for induced pluripotent stem cells (iPSCs) creates new and unresolved ethical dilemmas. To elucidate the issues, we studied the perspectives of community members and bioethicists involved in the collection of the Yoruba Resident in Ibadan, Nigeria (YRI) HapMap samples. We found support for broad consent, commercial use of samples, more benefit sharing, sustained engagement of the community and local researchers, particularly for novel research, where a long time has elapsed between samples' collection and new research projects, and in the oversight of biobanked samples. Broad consent was durable when coupled with sustained community engagement, transparent governance, and practical mechanisms for reciprocal benefit.

Variants in the SHANK2 gene, linked to neurodevelopmental disorders like autism, were studied using human iPSC-derived neurons and multielectrode arrays. We compared two isogenic pairs of SHANK2 cell lines and found that SHANK2 networks exhibited a hyperconnectivity phenotype at the network level. These networks showed a significantly increased frequency and reduced duration of network burst events compared to controls. SHANK2 network activity was hypersynchronous, with stronger functional correlations between recording channels. Spikes within SHANK2 network bursts formed high-frequency trains, creating a distinctive burst shape. Calcium-dependent reverberating super bursts (RSBs) were common in control networks but rare in SHANK2 networks. Treatment with the group 1 mGluR agonist (S)-3,5-dihydroxyphenylglycine (DHPG) fully rescued SHANK2 network hypersynchrony, restored RSB detection, and improved network burst frequency and duration. The findings demonstrate that SHANK2 variants cause functional hyperconnectivity, which can be rescued by pharmacologically regulating glutamatergic neurotransmission.

RPGRIP1 encodes a connecting cilium (CC) protein essential for normal photoreceptor cell development and maintenance. Damaging variants in RPGRIP1 cause severe inherited retinal disease (IRD) and currently incurable vision loss, with mouse studies showing promising preclinical gene augmentation therapy results. Almost one-half of variants in RPGRIP1 in the ClinVar database are variants of uncertain significance (VUS), hindering genetic diagnosis for affected individuals and, hence, access to clinical trials of novel therapies and other management options. Here, we use human induced pluripotent stem cell (iPSC)-derived retinal organoids to model RPGRIP1-associated IRD, detecting biomarkers of disease including CC interactome dysfunction, stress response, and proteostasis abnormalities. In parallel, utilizing these novel disease biomarkers, we demonstrate the pathogenicity of a missense VUS, RPGRIP1 c.2108T>C p.(Ile703Thr). In addition, RPGRIP1 gene augmentation therapy rescued disease phenotypes, further supporting the utility of these biomarkers of RPGRIP1-IRD for reclassifying VUS and testing response to therapy.

Oligodendrocyte precursor cells (OPCs) display functional plasticity beyond myelination. Kuwata et al. explore how hypoxia shapes OPC features after ischemic stroke. Combining single-cell transcriptomics with in vivo and ex vivo models, they reveal oxygen-dependent OPC phenotypes promoting angiogenesis and remyelination, highlighting OPC versatility and potential for novel stroke cell therapies.

Stem cell-derived models are a powerful tool for studying biology and are increasingly paving the way for cell-based therapies. However, understanding precisely which cell types are present and how closely they recapitulate in vivo cells remains challenging. Single-cell genomics, coupled with annotation methods, provides a framework for evaluating the congruence of stem cells with in vivo biology. Here, we explore approaches to cell annotation and discuss the challenges of implementing these methods in stem cell-derived models. We provide recommendations for the application of these methods, as well as our vision for the future of stem cell annotation using cell manifolds.

Cell differentiation is regulated by transcription factors (TFs), but specific TFs needed for mammalian differentiation pathways are not fully understood. For example, during spinal motor neuron (MN) differentiation, 1,370 TFs are transcribed, yet only 55 have reported functional relevance. We developed a method combining pluripotent stem cell differentiation, single-cell transcriptomics, and a CRISPR-based TF loss-of-function screen and applied it to MN differentiation. The CRISPR screen identified 245 genes important for mouse MN differentiation, including 116 TFs. This screen uncovered important genes not showing differential transcription and identified a regulatory hub at the MN progenitor (pMN) stage. A secondary human screen of 69 selected candidates revealed a conservation between mouse pMN and human pMN and ventral pMN (vpMN) regulations. The validation of three hits required for efficient human MN differentiation supported the effectiveness of our approach. Collectively, our strategy offers a framework for identifying important TFs in various differentiation pathways.

Insulin-dependent diabetes could be treated by supplying patients with primary pancreatic islets or other types of insulin-secreting cells. Functional insulin-secreting cells can be induced in situ from the murine stomach using defined genetic factors, offering a promising method to directly produce autologous insulin-secreting cells. Here, we modeled whether such gastric insulin-secreting (GINS) cells could be generated in vivo from human stomach tissues. We produced human gastric organoids (hGOs) from human embryonic stem cells engineered with inducible expression of reprogramming factors. The hGOs were stably transplanted for 6 months and showed robust cytodifferentiation resembling the human stomach in structure and cellular composition. Upon hGO maturation in vivo, we activated the reprogramming factors and observed the formation of insulin cells, which secreted insulin into the circulation and ameliorated experimental diabetes. Our modeling indicates that GINS cells can be induced from human stomach tissues in vivo, warranting further therapeutic development for this technology.

The human intestinal epithelial barrier is shaped by biological and biomechanical cues, including growth factor gradients and fluid flow. While these factors are known to affect adult stem cell (ASC)-derived intestinal epithelial cells in vitro, their impact on human induced pluripotent stem cell (hiPSC)-derived cells is largely unexplored. Here, we compare the cellular composition and gene expression profiles of hiPSC-derived intestinal epithelial cells exposed to various medium compositions and cultured as organoids, in Transwell and microfluidic intestine-on-chip systems. Modulating key signaling pathways (WNT, NOTCH, bone morphogenetic protein [BMP], and mitogen-activated protein kinase [MAPK]) influenced the presence of dividing, absorptive, and secretory epithelial lineages. Upon differentiation, intestinal epithelial cells expressed genes encoding digestive enzymes, nutrient transporters, and drug-metabolizing enzymes. Notably, these pathways were most enhanced in the intestine-on-chip system, along with an expression profile that suggests a more mature state. These findings highlight the potential of hiPSC-derived intestinal cells to model important intestinal functions and guide the selection of optimal culture conditions for specific applications.

Direct reprogramming is a technique for elucidating the mechanisms that control cell-fate decisions and holds promise as a therapeutic strategy. We previously showed that a specific combination of three transcription factors (FOXA3, HNF1A, and HNF6) can induce direct reprogramming of human umbilical vein endothelial cells (HUVECs) into human induced hepatic progenitor cells (hiHepPCs). However, low reprogramming efficiency limits their application in research and therapy. Here, we show that activation of the canonical Wnt signaling pathway increases the reprogramming efficiency of HUVECs to hiHepPCs by rapidly inducing chromatin remodeling and gene expression changes in the transduced HUVECs. Moreover, endogenous Wnt activation, mainly mediated by WNT2B, is required for the initiation of direct reprogramming from HUVECs to hiHepPCs. Wnt activation that allows rapid induction of hiHepPCs enables efficient production of a large amount of hiHepPCs, which is an advantage in research and clinical applications using hiHepPCs and their descendants.

The master cell bank (MCB) system is essential for regenerative cell therapy. We have developed induced pluripotent stem cell (iPSC)-based immortalized megakaryocyte progenitor cell lines (imMKCLs) as an MCB for iPSC-derived platelet (iPSC-PLT) transfusion. However, imMKCLs exhibit both thrombopoietic and immune-skewed properties, with enhanced immune activity impairing platelet production. The link between immune properties and thrombopoietic efficiency remains unclear. Here, we demonstrate that proliferating imMKCLs in G1 and G2/M interphases contribute to platelet generation, while lysine acetyltransferase 7 (KAT7) suppresses immune-biased dominancy to maintain these interphases. KAT7 inhibition with WM3835 increases G0 cells, mimicking imMKCL aging, and induces cGAS-STING activation, chromatin instability, and the secretion of tumor necrosis factor (TNF)-α, interferon (IFN)-β, and other pro-inflammatory cytokines. Additionally, TNF-α treatment recapitulates the transition to G0 seen with KAT7 loss. These findings identify KAT7 as a key regulator of imMKCL proliferation by preventing immune-skewed properties, highlighting its potential as a quality control marker in iPSC-PLT manufacturing.