Stem Cell Reports最新文献

Homeostasis in the intestinal epithelium depends on intestinal stem cells (ISCs). A reduction in the function of ISCs, caused by a decline of canonical Wnt signaling in ISCs, contributes to a reduced regenerative potential of the aged intestine. The composition of the intestinal microbiota changes upon aging. We report here that aging-associated changes in the composition of the microbiota result in reduced canonical Wnt signaling through Ascl2 in ISCs, which causes a decline in the regenerative potential of aged ISCs in vivo. We demonstrate, using microbiota transfer experiments, that interestingly, elevated levels of Akkermansia muciniphila in the intestine cause a reduction of Ascl2-mediated canonical Wnt signaling in ISCs and thus reduced regeneration of the aged epithelium. The composition of the intestinal microbiota thus plays a critical role in regulating the function of ISCs. Our data imply potential therapeutic approaches via modulation of the composition of microbiota for aging-associated changes in the function of ISCs.

The olfactory epithelium is one of the few regions of the nervous system that sustains neurogenesis throughout life. Its experimental accessibility makes it especially tractable for studying molecular mechanisms that drive neural regeneration in response to injury. In this study, we used single-cell sequencing to identify transcriptional and epigenetic processes involved in determining olfactory epithelial stem cell fate during injury-induced regeneration. By combining gene expression and accessible chromatin profiles of individual lineage-traced olfactory stem cells, we identified transcriptional heterogeneity among activated stem cells at a stage when cell fates are being specified. We further identified a subset of resting cells that appears poised for activation, characterized by accessible chromatin around silent genes prior to their expression in response to injury. These results provide evidence for a latent activated stem cell state in which a subset of quiescent olfactory epithelial stem cells are epigenetically primed to support injury-induced regeneration.

Canavan disease (CD) is a severe neurodegenerative disorder caused by aspartoacylase (ASPA) deficiency, leading to N-acetyl-L-aspartic acid (NAA) accumulation and spongy degeneration. While several therapeutic candidates improve outcomes in CD mouse models when delivered before symptom onset, there remains a need for treatments targeting established disease pathology. Here, we demonstrate that transplantation with human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs) expressing a functional ASPA gene (ASPA iNPCs) can rescue disease manifestations in symptomatic CD (Nur7) mice. When administered at postnatal day 21 (P21), ASPA iNPCs successfully engrafted, differentiated into neural lineage cells, and restored ASPA activity as revealed by reduced NAA level. Transplanted mice showed a significant reduction in brain and cerebrospinal fluid (CSF) NAA levels, decreased vacuolation across multiple brain regions, improved myelination, and enhanced motor function 6-month post-transplantation. Our findings demonstrate that ASPA iNPC transplantation can effectively reverse established CD pathology, suggesting therapeutic potential for treating symptomatic patients.

Altered microglial lipid metabolism is heavily implicated in Alzheimer's disease (AD) and aging. Recently, protocols were developed to generate human induced pluripotent stem cell-derived microglia-like cells (iMGL) to study microglial function in vitro, including embryoid body-based methods and induced transcription factor (iTF)-dependent approaches. Here, we performed comparative lipidomics on iMGL from these methods and report major differences in multiple lipid classes, including triglycerides (TGs), a storage form of fatty acids implicated in microglial reactivity. TGs are strongly increased in iTF microglia due to the absence of a media supplement (B-27). Supplementing iTF microglia with B-27, or its component L-carnitine, reduces TGs and promotes a homeostatic state. B-27 also renders iTF microglia metabolically responsive to immune stimuli. Overall, our data show that iMGL differentiation methods have a major impact on microglial lipidomes and warrant attention when studying AD and neuroinflammatory processes involving lipids.

The clinical outcome of human immunodeficiency virus type-1 (HIV-1) infection varies greatly among individuals, ranging from rapid disease progression to natural viral suppression. While viral and environmental factors contribute, host genetics are considered major determinants of disease trajectory. To enable mechanistic studies of host factors underlying disease outcomes, we generated 50 induced pluripotent stem cell (iPSC) lines from 18 participants of the Multicenter AIDS Cohort Study (MACS), spanning a spectrum of clinical trajectories. Reprogrammed MACS lines are confirmed to be HIV-1 negative and Sendai vector-free. We validate their pluripotency and demonstrate robust differentiation into macrophages capable of productive HIV-1 infection. These MACS-iPSC lines offer a genetically diverse resource to model HIV-1 infection in vitro, where clinical progression is known. Crucially, their capacity to differentiate into HIV-1 target cells and other disease-relevant lineages makes them a powerful tool to uncover host determinants of HIV-1 pathogenesis and advance targeted treatment and curative strategies.

Transcription factors (TFs) mediate gene expression changes during differentiation and development. However, how TF biophysical properties and abundance dynamically regulate specific cell state transitions remains poorly understood. Using automated live-cell single-molecule tracking (SMT) in intestinal organoid models, we revealed an expression-level-independent decrease in the fraction of immobile sex-determining region Y box 9 (SOX9) molecules during differentiation from ∼48% to ∼38%, largely dependent on DNA binding. Strikingly, long-term SOX9 overexpression caused organoids to transition from budding to spheroid morphology accompanied by increased proliferation and a loss in gene expression signatures for intestinal identity and function. In this fetal-like reprogrammed state, a larger fraction of partially self-interacting SOX9 molecules (∼61%) binds to DNA. Our results suggest context-dependent SOX9 single-molecule dynamics during adult intestinal differentiation and fetal-like reversion in consequence to long-term SOX9 overexpression. Our work underpins the power of our automated live-cell SMT framework to generate testable hypotheses toward unraveling molecular mechanisms underlying tissue-level phenotypes.

Brain tumors are the most common solid cancer in children, with radiotherapy being a primary treatment. Proton therapy, with its precise dose distribution, is increasingly being used in these patients to minimize damage to the developing brain. However, the biological effects of proton irradiation on the human brain remain unclear. To investigate this, human cortical organoids were exposed to conventional photons, plateau protons, and spread-out Bragg peak (SOBP) protons, followed by comparative transcriptomic profiling. While photons and protons induced similar transcriptional profiles characterized by apoptosis and downregulation of DNA replication, SOBP protons uniquely downregulated genes involved in brain development and synaptic signaling. Functional calcium imaging, cell deconvolution analysis, and immunostaining indicated that SOBP protons impaired neural network function, due to reduced synaptic density and loss in excitatory neuron progenitors. These findings underscore the distinct biological effects of SOBP protons and their potential impact on the developing brain.

Dynamic epigenetic changes guide retinal progenitor cells (RPCs) toward diverse neuronal subtypes and Müller glia during retinal development. However, the epigenetic mechanisms that maintain RPC proliferative and neurogenic potential throughout the final stages of retinal cell genesis remain poorly understood. Here, we integrate RNA sequencing and assay for transposase-accessible chromatin sequencing (ATAC-seq) to investigate how mouse RPC progenitor competence is regulated. Our analysis reveals conserved chromatin accessibility and gene expression profiles in mouse RPCs throughout retinal cell genesis. Notably, the histone methyltransferase Setd8, which catalyzes H4K20 monomethylation, remains persistently expressed in RPCs but is barely detectable in adult Müller glia. Setd8 deletion in developing RPCs reduces proliferation, triggers apoptosis, and disrupts retinal laminar organization and ocular axis length. Additionally, Setd8 deficiency impairs the chromatin accessibility that is normally preserved in RPCs, leading to a partial acquisition of a transcriptomic profile associated with terminally differentiated cells. Our study indicates that Setd8 safeguards mouse RPC identity by maintaining RPC-specific chromatin accessibility, thereby ensuring proper retinal development.

Pigs are important for disease model generation, xenotransplantation, and interspecies organogenesis. Porcine induced pluripotent stem cells (piPSCs) should enable these efforts, but have not been generated to meet the attributes, such as feeder-free culture, robust development potential, and blastocyst generation through nuclear transfer. We report an improved strategy to generate such piPSCs. We show that chemically defined medium 3 promotes the formation of epithelium-like colonies in porcine reprogramming, which allows further reprogramming under the new medium cocktail LACID. The resulting piPSCs have key features, including flat morphology with feeder-free culture, generating robust teratoma and blastoids, forming chimeric blastocysts, and readily edited with CRISPR-Cas9. Lastly, nuclear transfer with piPSCs can develop into blastocysts. Despite maintaining a primed pluripotent state, our results suggest that the newly established LACID piPSCs may be ideal for applications in regenerative medicine. This method may be further improved to generate naive or totipotent stem cells.

The mammalian cornea is endowed with stem cells (SCs) that have lifelong regenerative activity. The niche for these cells is the limbus, and damage to it or its SCs results in limbal stem cell deficiency (LSCD). Despite the numerous studies that employ single-cell RNA sequencing, the identity of these cells remains an enigma principally because their spatial positioning is lost upon dissociation. These adversities were avoided via on-tissue spatial transcriptomics where Krt16 and Nkiras1 were differentially expressed. Krt16 was dynamically expressed in the developing limbus, correlated with slow-cycling label-retaining limbal epithelial SCs and was induced during corneal injury, observations consistent with marking functional SCs. Additionally, we established Nkiras1 as a novel maker of limbal neutrophils. Because current gold-standard treatments for LSCD include SC transplantation, our data will inform future studies in delivering a more reliable standard therapy that incorporates an identifiable SC population to improve clinical outcomes.