Stem Cell Reports最新文献

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.

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.

Previous studies showed the polycomb repressive complex 2 (PRC2) co-factor Jarid2 represses self-renewal transcriptional networks in mouse multipotent progenitor cells (MPPs). But only a fraction of de-repressed HSC-specific genes were associated with loss of H3K27me3, implying Jarid2 may have non-canonical (PRC2-independent) functions in hematopoiesis. We sought to delineate these potential PRC2-independent functions by comparing stem and progenitor cells genetically deficient for either Jarid2 or Ezh2 (enzymatic component of PRC2). Loss of Ezh2 increased myeloid differentiation but with a defect in lymphopoiesis. In contrast, loss of Jarid2 enhanced multi-lineage differentiation proportionally. Single-cell transcriptomics showed loss of Jarid2 had minimal impact across progenitor populations, but loss of Ezh2 led to accumulation of lymphoid-biased MPP4 cells and B cell progenitors in the bone marrow. Functional assays confirmed a differentiation block at the pre-pro-B cell stage. These data suggest the major PRC2-dependent function of Jarid2 in hematopoietic progenitors is restriction of myeloid differentiation potential.

Recombinant human erythropoietin (EPO) is widely used to treat anemia. EPO has immunomodulatory effects extending beyond erythropoiesis, but its impact on lympho-hematopoiesis remains insufficiently explored. The objective of this study was to investigate B lymphopoiesis in the context of hyper-EPOemia-induced stress hematopoiesis. Using an EPO supplementation model in C57BL/6 mice, we found that EPO exerts contrasting effects on early B cell development. EPO supplementation promotes the transition from common lymphoid progenitors (CLPs) to pre-pro-B cells but impairs the pre-pro-B to pro-B transition, in part by downregulating interleukin-7 (IL-7) receptor expression. Remarkably, EPO promotes the emergence of atypical B cell precursors, including M-CSFR/CD115-expressing CLPs and CD11b and CD16/32-expressing pre-pro-B cells. Gene expression profiling revealed that EPO reprograms early B cell precursors, upregulating myeloid-type genes, while downregulating B lymphoid identity genes. In conclusion, our results show that hyper-EPOemia interferes with the earliest stages of B cell development, while promoting the emergence of mixed-lineage "myeloid-like" B cells.

Alternative promoters are critical for lineage-specific gene expression; however, their systematic roles in hematopoiesis remain unclear. Here, we analyze 532 RNA sequencing (RNA-seq) datasets to construct a high-resolution promoter activity landscape. We identify 1,074 high-impact promoters, including novel lineage-specific switches in Pou2f1 and Ikzf1. Pou2f1 P1 is active in T/NK cells/monocytes, while P2 is B-cell-/progenitor-specific. Ikzf1 P1 is active in B cells/monocytes, and P2 is T-cell-specific. CRISPRi-mediated repression validated their lineage-specific functions. We further pinpoint the following driving transcription factors: Spi1 (Ikzf1 P1), Foxo1 (Ikzf1 P2), Yy1 (Pou2f1 P1), and Pax5 (Pou2f1 P2). This study provides novel insights into promoter-mediated regulation in hematopoietic lineages and a foundation for targeting promoter-specific mechanisms in disease.

Hematopoietic stem cells (HSCs) self-renew to sustain stem cell pools and differentiate into all types of blood cells, whose properties are tightly regulated by epigenetic and transcriptional networks. Here, we identified DHX9 as a critical regulator of HSC maintenance. Dhx9 deletion caused bone marrow failure and impaired hematopoietic reconstitution in murine primary and secondary transplantation recipients due to loss of HSCs and defective self-renewal capacity. Further investigations revealed that Dhx9 deficiency led to aberrant cell cycle entry, increased apoptosis, and elevated ROS, which compromise HSC function. Mechanistically, DHX9 interacts with CBP/p300 acetyltransferase and maintains H3 acetylation at hematopoietic gene promoters to facilitate transcription activation. Inhibition of CBP/p300 disrupted their expression, whereas the enhancement of H3K27ac levels partially rescued hematopoietic defects caused by Dhx9 deficiency in both mouse models and human CD34⁺ cells. This study highlights DHX9 as a crucial factor linking epigenetic modifications with transcriptional programs in HSC biology.

Alternative splicing events have emerged as a rapid regulatory layer in gene expression. Lin et al. demonstrate that alternative splicing is widespread during muscle stem cell activation. Its functional importance is illustrated through an RNA-binding fox 1-homolog 2 (RBFOX2)-dependent splice choice in the Notch regulator Numb, showing how inclusion of a single exon can tune Notch signaling to regulate the transition from quiescence to activation.

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.

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.