Wang L, Nakamura Y, Li J
… +18 more, Sievert D, Liu Y, Nguyen T, Jetti PS, Thai E, Zhou RY, Weng J, Meave N, Yadavilli M, Howarth R, Camey K, Banka N, Owusu-Hammond C, Barrows C, Kingsmore SF, Zaki MS, Mukamel E, Gleeson JG
Cell Stem Cell
· 2025 Dec · PMID 41187745
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Thousands of genes are associated with neurodevelopmental disorders (NDDs), yet mechanisms and targeted treatments remain elusive. To fill these gaps, we present a California Institute of Regenerative Medicine (CIRM)-ini...Thousands of genes are associated with neurodevelopmental disorders (NDDs), yet mechanisms and targeted treatments remain elusive. To fill these gaps, we present a California Institute of Regenerative Medicine (CIRM)-initiated NDD biobank of 352 publicly available genetically diverse patient-derived induced pluripotent stem cells (iPSCs), along with clinical details, brain imaging, and genomic data, representing four major categories of disease: microcephaly (MIC), polymicrogyria (PMG), epilepsy (EPI), and intellectual disability (ID). From 35 representative patients, we studied over 6,000 brain organoids for histology and single-cell transcriptomics. Compared with an organoid library from ten neurotypicals, patients showed distinct cellular defects linked to underlying clinical disease categories. MIC showed defects in cell survival and excessive TTR+ cells, PMG showed intermediate progenitor cell junction defects, EPI showed excessive astrogliosis, and ID showed excessive generation of TTR+ cells. Our organoid atlas demonstrates both conserved and divergent NDD category-specific phenotypes, bridging genotype and phenotype. This NDD iPSC biobank can support future disease modeling and therapeutic approaches.
The nucleus basalis of Meynert (nbM), the major cholinergic output of the basal forebrain, regulates cortical modulation, learning, and memory. Dysfunction of the nbM-cortical cholinergic pathway is implicated in neurode...The nucleus basalis of Meynert (nbM), the major cholinergic output of the basal forebrain, regulates cortical modulation, learning, and memory. Dysfunction of the nbM-cortical cholinergic pathway is implicated in neurodegenerative and neurodevelopmental disorders, including Alzheimer's disease (AD) and Down syndrome (DS). Here, we generated human nbM organoids (hnbMOs) from human pluripotent stem cells (hPSCs) containing functional cholinergic projection neurons. Then we reconstructed long-distance cholinergic projections from nbM to the cortex by co-culturing hnbMOs with human fetal brains and transplanting hnbMOs into immunodeficient mice. We further established nbM-cortical assembloids by fusing hnbMOs with human cortical organoids (hCOs). We also established a human-specific cholinergic projection system in transplanted assembloids. Using viral tracing and functional assays, we validated that cholinergic neurons send projections into hCOs and form synaptic connections. Moreover, we captured projection deficits in DS-derived assembloids, demonstrating the utility of this model for studying nbM-related neural circuits and neurological disorders.
Zhu X, Chang Z, Xiao W
… +23 more, Zhang X, Ma M, Wu J, Hu J, Bi Y, Kou X, Zhao Y, Sheng Y, Dong B, Sun J, Chen C, Wu Y, Liu X, Ding W, Jia K, Yao Y, Sun L, Yu X, Wang H, Liu J, Wang Y, Gao S, Gao Y
Transposable elements (TEs) occupy nearly half of the genome and drive developmental innovation, yet the mechanisms of silencing long terminal repeats (LTRs) remain incompletely understood. We demonstrate that methyltran...Transposable elements (TEs) occupy nearly half of the genome and drive developmental innovation, yet the mechanisms of silencing long terminal repeats (LTRs) remain incompletely understood. We demonstrate that methyltransferase-like 3 deficiency reverts naive human embryonic stem cells (hESCs) to a totipotent-like state with reactivation and chromatin resetting of 8C-associated genes, eRNAs, and LTRs, particularly ERV1 and ERVL-MaLR. Moreover, mA on primate-specific L1PA is found to be essential. Mechanistically, L1PA binds 8C-associated LTRs and eRNAs and regulates chromatin through RNA-scaffold complexes with chromatin regulators, where mA directs protein-binding preference. In naive hESCs, mA on L1PA suppresses EP300 binding to ERV1 and enhances KAP1 binding to ERVL-MaLR, thereby restricting LTR activity. In parallel, the mA-L1PA axis or mA on eRNAs limits EP300/H3K27ac occupancy at 8C enhancers. Our findings reveal a conserved mechanism in which humans and mice employ species-specific long interspersed nuclear element-1 subfamilies with mA to regulate LTR activity, underscoring the crucial role of transposons in RNA-chromatin crosstalk during cell fate transitions.
Zhang X, Wu Z, He H
… +21 more, Guan Q, Ouyang Q, Wang R, Xie L, Zhou Y, Feng B, Luo Z, Xu P, Yan W, Hu G, Li J, Zhang M, Zou Y, Xu X, Zhou C, Cheng Q, Liu J, Gao Q, Yang S, Xiong M, Chen Y
The low in vivo yield of midbrain dopaminergic (mDA) neurons and uncertain lineage fates of donor cells following transplantation impede clinical application of human pluripotent stem cell (hPSC)-based cell therapy for P...The low in vivo yield of midbrain dopaminergic (mDA) neurons and uncertain lineage fates of donor cells following transplantation impede clinical application of human pluripotent stem cell (hPSC)-based cell therapy for Parkinson's disease (PD). We developed a three-dimensional (3D) differentiation method, SphereDiff, to generate high-purity mDA progenitors (mDAPs), leading to a significant enrichment of mDA neurons post transplantation. Grafted mDA neurons fully restored dopamine levels and corrected motor deficits in PD model mice. Single-cell spatial transcriptomics revealed a patterned distribution of mDA neuron subtypes and glial cells. Using cross-transplantation single-cell split barcoding (TX-SISBAR), we elucidated the clonal lineage fates of donor cells post transplantation, revealing the mDA neuron and astrocyte fates of mDAPs and glutamatergic neuron fates of diencephalic progenitors. Leveraging these lineage insights, we further refined SphereDiff and eliminated off-target lineage cells. Producing high in vivo efficacy, lineage-defined donor cells supports safer and more effective PD cell therapy in regenerative medicine.
O'Hern C, Caywood S, Aminova S
… +25 more, Kiselev A, Volmert B, Cao W, Wang F, Dionise M, Sewavi ML, Skoric M, Basrai H, Mannering F, Muniyandi P, Popa M, Boulos G, Wolf K, Brown I, Nuñez-Regueiro I, Huang A, Kostina A, Squire L, Wilkerson C, Chalfoun N, Park S, Ashammakhi N, Zhou C, Contag C, Aguirre A
Cell Stem Cell
· 2025 Nov · PMID 41151577
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Yolk-sac-derived embryonic cardiac tissue-resident macrophages (TRMPs) colonize the heart early in development and are essential for proper heart development, supporting tissue remodeling, angiogenesis, electrical conduc...Yolk-sac-derived embryonic cardiac tissue-resident macrophages (TRMPs) colonize the heart early in development and are essential for proper heart development, supporting tissue remodeling, angiogenesis, electrical conduction, efferocytosis, and immune regulation. We present here a human heart-macrophage assembloid (hHMA) model by integrating autologous human pluripotent stem cell (hPSC)-derived embryonic monocytes into heart organoids to generate physiologically relevant TRMPs that persist long-term and contribute to cardiogenesis. Using single-cell transcriptomics, live imaging, and proteomics, we demonstrate that TRMPs modulate cardiac paracrine signaling, perform efferocytosis, and regulate extracellular matrix remodeling and electrical conduction. In a proof-of-concept maturated hHMA model of chronic inflammation, TRMPs adopt pro-inflammatory phenotypes that promote arrhythmogenic activity, consistent with atrial fibrillation through activation of the NOD-like receptor pyrin domain-containing 3 (NLRP3) inflammasome. This system enables detailed mechanistic studies of immune-cardiac interactions and provides a powerful in vitro platform for modeling human heart development and inflammation-driven arrhythmias.
In mice, the repressive histone mark H3K27me3 undergoes both region-specific inheritance and erasure during the parental-to-embryonic transition, with the underlying mechanisms poorly understood. Here, we show that PRC2,...In mice, the repressive histone mark H3K27me3 undergoes both region-specific inheritance and erasure during the parental-to-embryonic transition, with the underlying mechanisms poorly understood. Here, we show that PRC2, which catalyzes H3K27me3, binds both classic Polycomb targets and noncanonical H3K27me3 domains in growing oocytes but dissociates from chromatin in fully grown oocytes. After fertilization, PRC2 rebinds noncanonical H3K27me3 domains before relocating to Polycomb targets in blastocysts. Interestingly, the binding and activity of PRC2 are restricted by a maternal inhibitory factor, EZH inhibitory protein (EZHIP), which co-binds with PRC2. Upon knockout of Ezhip, hyperactive PRC2 promiscuously deposits H3K27me3 genome-wide. This overwrites H3K27me3 memories at noncanonical imprinted genes and paradoxically causes derepression of H3K27me3 targets, defective X chromosome inactivation, and diluted chromatin PRC2. H3K27me3 restoration at Polycomb targets after implantation is also attenuated, accompanied by sub-lethality. These data unveil principles of epigenetic inheritance that both insufficient and excessive heterochromatic marks cause loss of epigenetic memories and repression.
Jing Y, Lu H, Li J
… +15 more, He Z, Zhao L, Zhang C, Huang Z, Liu L, Sun S, Ma S, Rodriguez Esteban C, Fu X, Zhao G, Izpisua Belmonte JC, Zhang W, Qu J, Wang S, Liu GH
Ovarian aging plays a pivotal role in female reproductive health, with implications for treatment strategies and quality of life. However, the potential of a single pharmaceutical agent to mitigate primate ovarian aging...Ovarian aging plays a pivotal role in female reproductive health, with implications for treatment strategies and quality of life. However, the potential of a single pharmaceutical agent to mitigate primate ovarian aging remains largely unexplored. Our 3.3-year study in monkeys demonstrates that oral vitamin C has geroprotective effects against ovarian aging. Vitamin C diminishes key aging biomarkers, including oxidative stress and follicular depletion. Using a single-cell transcriptomic clock, we show that vitamin C can reduce the biological age of oocytes by 1.35 years and somatic cells by 5.66 years. This effect is partly mediated by the NRF2 pathway, which alleviates ovarian cell senescence and inflammation. Our findings highlight the role of vitamin C in combating primate ovarian aging and provide insights for developing interventions against human ovarian aging.
The spatiotemporal regulation of morphogenetic signals, along with local tissue mechanics, guides morphogenesis and determines the shape of the embryo. However, how these signals integrate into developmental circuits rem...The spatiotemporal regulation of morphogenetic signals, along with local tissue mechanics, guides morphogenesis and determines the shape of the embryo. However, how these signals integrate into developmental circuits remains poorly understood. Here, we developed a light-inducible strategy to induce BMP4 signaling with precise spatial coordinates in human pluripotent stem cells. Light-controlled BMP4 induces SMAD1-5 phosphorylation, resulting in amnion differentiation, and relies on a tension-dependent induction of WNT and NODAL for mesoderm differentiation. In response to BMP4 signaling, the mechanosensitive transcription factor YAP1 accumulates in the nucleus, where it represses WNT3 mRNA, regulating the induction of the three germ layers. Based on these findings, we developed a mathematical model that integrates tissue mechanics into morphogen dynamics, quantitatively explaining tissue-scale responses to BMP4 signaling. Thus, light induction of the morphogen BMP4 in human stem cell models elucidated the interplay between tissue mechanics and signaling at the onset of gastrulation.
Dong Z, Wit N, Agarwal A
… +8 more, Reid AJ, Dubal D, Beier S, Mahbubani KT, Saeb-Parsy K, van den Ameele J, Nathan JA, Rawlins EL
Cell Stem Cell
· 2025 Nov · PMID 41075787
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Human lungs experience dynamic oxygen tension during development. Here, we show that hypoxia directly regulates human lung epithelial cell identity using tissue-derived organoids. Fetal multipotent lung epithelial progen...Human lungs experience dynamic oxygen tension during development. Here, we show that hypoxia directly regulates human lung epithelial cell identity using tissue-derived organoids. Fetal multipotent lung epithelial progenitors remain undifferentiated in a self-renewing culture condition under normoxia but spontaneously differentiate toward multiple airway cell types and inhibit alveolar differentiation under hypoxia. Using chemical and genetic tools, we demonstrate that hypoxia-induced airway differentiation depends on hypoxia-inducible factor (HIF) activity, with HIF1α and HIF2α differentially regulating progenitor fate decisions. KLF4 and KLF5 are direct HIF targets that promote basal and secretory cell fates. Moreover, hypoxia is sufficient to convert alveolar type 2 cells derived from both human fetal and adult lungs to airway cells, including aberrant basal-like cells that exist in human fibrotic lungs. These findings reveal roles for hypoxia and HIF activity in the developing human lung epithelium and have implications for aberrant cell fate changes in pathological lungs.
Spaceflight provides a unique environment that profoundly influences stem cell biology. Experiments aboard the International Space Station (ISS) and in simulated microgravity have revealed altered stem cell proliferation...Spaceflight provides a unique environment that profoundly influences stem cell biology. Experiments aboard the International Space Station (ISS) and in simulated microgravity have revealed altered stem cell proliferation, differentiation, and stress responses, unveiling possibilities for modeling impacts of spaceflight and harnessing microgravity for biomanufacturing. Stem cell-derived organoids and tissue models flown in space are yielding insights into development, disease, and aging mechanisms, while in-space biomanufacturing efforts demonstrate accelerated stem cell expansion and tissue formation for potential translational and clinical applications. Finally, as humanity prepares for long-duration lunar and Martian missions, space-based stem cell research offers transformative biomedical applications but also raises new technical, regulatory, workforce development, and ethical challenges.
Cell Stem Cell
· 2025 Oct · PMID 41043402
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Recent studies highlight microglial replacement as a promising therapeutic approach for neurological disease. Wu et al. demonstrated that transplanted bone marrow-derived cells halted ALSP progression, while Mader et al....Recent studies highlight microglial replacement as a promising therapeutic approach for neurological disease. Wu et al. demonstrated that transplanted bone marrow-derived cells halted ALSP progression, while Mader et al. introduced a strategy that avoids systemic bone marrow ablation toxicity and reduces immune rejection, collectively validating this strategy's therapeutic potential.
In this issue of Cell Stem Cell, Huang et al. address the challenge of creating organoids that more closely replicate kidney spatial patterning and function. They develop region-specific progenitor assembloids mimicking...In this issue of Cell Stem Cell, Huang et al. address the challenge of creating organoids that more closely replicate kidney spatial patterning and function. They develop region-specific progenitor assembloids mimicking native architecture. After transplantation into mice, which further promotes differentiation, they demonstrate functional and disease modeling capability.
In this issue of Cell Stem Cell, Márquez-Valadez, Gallardo-Caballero, and Llorens-Martín report that adult hippocampal neurogenesis (AHN) is differentially disrupted in neuropsychiatric disorders. Their findings highligh...In this issue of Cell Stem Cell, Márquez-Valadez, Gallardo-Caballero, and Llorens-Martín report that adult hippocampal neurogenesis (AHN) is differentially disrupted in neuropsychiatric disorders. Their findings highlight the role of the neurogenic niche and lifestyle, supporting the view of human AHN as a dynamic process sensitive to biology and behavior.
Chan et al. show that enteric neurons influence lipid metabolism in gastric cancer organoids, affecting dependencies on key enzymes. Using CRISPR screening and metabolic analysis, their work highlights how microenvironme...Chan et al. show that enteric neurons influence lipid metabolism in gastric cancer organoids, affecting dependencies on key enzymes. Using CRISPR screening and metabolic analysis, their work highlights how microenvironmental signals impact tumor metabolism and potential treatment targets in gastric cancer.
The generation of stem-cell-based embryo models has ushered in a new era for human embryology, but improving their reproducibility and lineage fidelity has remained a challenge. In this issue of Cell Stem Cell, Chen et a...The generation of stem-cell-based embryo models has ushered in a new era for human embryology, but improving their reproducibility and lineage fidelity has remained a challenge. In this issue of Cell Stem Cell, Chen et al. and Oura et al. develop refined strategies to assemble human post-implantation embryo models with greater accuracy and efficiency, setting a new standard for the field.
Two recent studies from the Silva and Hanna groups optimized chemical induction and culture conditions to derive extraembryonic lineages directly from embryonic stem cells (ESCs) without transgenes, enabling mouse stem c...Two recent studies from the Silva and Hanna groups optimized chemical induction and culture conditions to derive extraembryonic lineages directly from embryonic stem cells (ESCs) without transgenes, enabling mouse stem cell-based embryo models (SCBEMs) to reproducibly advance to the E8.5-E8.75 stage.
Huang B, Medina P, He J
… +33 more, Zeng Z, Kim S, Romo J, Koppitch K, Zhang CC, Gyarmati G, Park Y, Bohovyk R, N'Guetta PY, Guo J, Ma T, Schreiber ME, Xu C, Pham J, Parvez RK, Su J, Xia MW, Liu Z, Perin L, El-Nachef D, Murry CE, Kumar S, O'Brien L, Zimmerman KA, Ichida J, Lindström NO, Pastor-Soler NM, Hallows KR, Staruschenko A, Peti-Peterdi J, Jiang C, McMahon AP, Li Z
Cell Stem Cell
· 2025 Oct · PMID 40967224
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Current kidney organoids do not recapitulate the kidney's complex spatial patterning and function, limiting their applications. The human kidney comprises one million nephrons, derived from nephron progenitor cells, that...Current kidney organoids do not recapitulate the kidney's complex spatial patterning and function, limiting their applications. The human kidney comprises one million nephrons, derived from nephron progenitor cells, that connect to an arborized ureteric progenitor cell-derived collecting system. Here, we develop spatially organized mouse and human kidney progenitor assembloid (KPA) models in which the nephrons undergo extensive development and fuse to a centrally located collecting system, recapitulating kidney progenitor self-assembly processes observed in vivo. KPAs show dramatically improved cellular complexity and maturity and exhibit several aspects of major kidney functions in vitro and in vivo. Modeling human autosomal dominant polycystic kidney disease (ADPKD) with genome-edited, in vivo-grown human KPAs recapitulated the cystic phenotype and the molecular and cellular hallmarks of the disease and highlighted the crosstalk among cyst epithelium, stroma, and macrophages. The KPA platform opens new avenues for high-fidelity disease modeling and lays a strong foundation for kidney regenerative medicine.
Adult mammalian hearts are non-regenerative, and a majority of studies examining repair and potential regeneration post-myocardial infarction (MI) have focused on cardiomyocyte (CM) proliferation and infarcted zones. Her...Adult mammalian hearts are non-regenerative, and a majority of studies examining repair and potential regeneration post-myocardial infarction (MI) have focused on cardiomyocyte (CM) proliferation and infarcted zones. Here, we observed aberrantly high expression of lysozyme 2 (Lyz2) in injured mouse hearts at both local injury sites and at remote zones, with sustained Lyz2 expression conspicuous in endocardial cells of non-regenerative hearts. Although traditionally conceptualized as a myeloid marker, we demonstrate that LYZ2 functions as an injury-specific, positive regulator of lysosomal degradation capacity that mediates pathogenic degradation of the extracellular matrix. We observed an anti-apoptotic benefit to CMs upon disrupting LYZ2/LYZ function in mice and in a human endomyocardium experimental model. Harnessing these insights, we show that both Lyz2 knockout (KO) and pharmacological inhibition of lysosomal degradation confer rapid functional recovery in injured non-regenerative hearts. Thus, targeting a remote injury response in a non-CM cell type rapidly promotes post-MI recovery of non-regenerative hearts.
Rao RC, Arduini BL, Borden S
… +13 more, Sareen D, Svendsen C, Lee P, Ryan C, Kodati S, Nyaiburi C, Wolsieffer K, Oh E, Park S, Ford G, Dionne K, Temple S, Stern J
Cell Stem Cell
· 2025 Nov · PMID 40961946
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Retinal pigment epithelium (RPE) cell atrophy in dry age-related macular degeneration (AMD) compromises photoreceptor cell function, leading to vision loss. Stem cell-based RPE replacement therapy aims to reverse disease...Retinal pigment epithelium (RPE) cell atrophy in dry age-related macular degeneration (AMD) compromises photoreceptor cell function, leading to vision loss. Stem cell-based RPE replacement therapy aims to reverse disease progression and restore vision. RPESC-RPE-4W, a post-mitotic adult RPE stem cell-derived RPE (RPESC-RPE) progenitor cell product, exhibits consistent safety and efficacy in preclinical studies. The first-in-human clinical trial of RPESC-RPE-4W completed low-dose cohort 1 interventions (NCT04627428). Six subjects received a subretinal suspension of 50,000 RPESC-RPE-4W cells. No significant inflammation, tumor, or product-related serious adverse events were observed. Best-corrected visual acuity in the three worse-seeing group A subjects improved by an average of +21.67 letters from baseline at 12 months. Three better-seeing group B subjects improved by an average of +3.0 letters at 6 months. The positive safety and tolerability outcomes for low-dose cohort 1 enabled dose escalation to mid-dose RPESC-RPE-4W therapy for dry AMD.