Stem Cell Reports最新文献

Carriers of two apolipoprotein L1 gene risk variants (RVs), termed G1 and G2, are at increased risk for chronic kidney disease. This study utilized induced pluripotent stem cells (iPSCs) derived from two patients homozygous for G1 and G2 to model human apolipoprotein L1 (APOL1)-mediated kidney disease (AMKD) in kidney organoids. Single-cell transcriptomic analysis and immunofluorescence imaging showed APOL1 upregulation in podocytes after interferon-gamma (IFN-γ) treatment. Transcriptomics and spatial dynamic metabolomics demonstrated a significant reduction in oxidative phosphorylation and tricarboxylic acid (TCA) cycle activity, along with upregulation of glycolysis and hypoxia signaling in RV podocytes. Isolated RV glomeruli exhibited no increase in maximal respiration rate following IFN-γ treatment, while iPSC-derived RV podocytes displayed a reduced number of mitochondrial branches and shorter branch length. This model presents early metabolic reprogramming of RV podocytes upon inflammatory injury and compelling evidence that mitochondrial dysfunction plays a pivotal role in the early pathophysiology of AMKD.

Human induced pluripotent stem cell (iPSC)-derived neurons are often heterogeneous, posing challenges for disease modeling and cell therapy. We previously developed single-cell glycan and RNA sequencing (scGR-seq) to analyze the glycome and transcriptome simultaneously. Here, we applied scGR-seq to examine heterogeneous populations of human iPSC-derived neurons. We identified four subpopulations: mature neurons, immature neurons, undifferentiated neural progenitor cells (undiffNPCs), and mesenchymal cells (MCs). Lectin-binding patterns indicated high α1,3-fucose expression in undiffNPCs. MCs exhibited strong binding of a poly-LacNAc-recognizing lectin (rLSLN) and high expression of B3GNT2, a poly-LacNAc synthetic enzyme. Pseudotime analysis revealed that a subpopulation of NPCs acquired mesenchymal features and differentiated into MCs. Immunocytochemistry confirmed the specific detection of undiffNPCs and MCs using anti-Lewis X (α1,3-fucosylated glycan) antibodies and rLSLN. Beyond identifying cell heterogeneity, scGR-seq enables the discovery of glycan markers and detection probes for iPSC-derived cells, aiding in their further cell processing and manipulation.

The extracellular matrix (ECM) forms a dynamic microenvironment, known as the "niche," that influences muscle stem cell (MuSC) behavior. Its composition and topology remain underexplored. Using bioinformatics analysis of publicly available transcriptomic data, we profiled the matrisome of skeletal muscle-resident cells and identified quiescent MuSCs as key ECM producers. Their matrisome includes novel markers such as the basement membrane zone genes Col19a1 and Lama3, ECM assembly regulators Thsd4 and Aebp1, and notably, matrisome genes linked to neurogenesis. Light-sheet immunofluorescence microscopy of selected ECM components in isolated murine myofiber bundles revealed niche-specific ECM components associated with MuSCs. Upon activation, these cells shifted their gene expression, downregulating niche-associated ECM genes while upregulating those involved in basement membrane disruption and cell motility. These findings identify distinct matrisome signatures in quiescent and activated MuSCs, emphasizing the critical role of ECM in locally regulating MuSC states and highlighting its therapeutic potential for muscle regeneration.

Here, we conducted temporal RNA sequencing (RNA-seq) profiling of human induced pluripotent stem cells (hiPSCs) and induced pluripotent stem cell (iPSC)-derived motor neurons (iMNs) carrying C9orf72, FUS, TARDBP, or SOD1 mutations in both patients with amyotrophic lateral sclerosis (ALS) and healthy individuals. We discovered dysregulated gene expression and alternative splicing (AS) throughout iMN development and maturation, and iMNs with mutations in ALS-associated genes displayed enrichment of cytoskeletal defects and synaptic alterations from the premature stage to mature iMNs. Our findings indicate that synaptic gene dysfunction is a common molecular hallmark of familial ALS, which may result in neuronal susceptibility and progressive motor neuron degeneration. Analysis of upstream splicing factors revealed that differentially expressed RNA-binding proteins (RBPs) in iMNs from patients with ALS may cause abnormal AS events. Overall, our research provides a comprehensive and valuable resource for gaining insights into the shared mechanisms of familial ALS pathogenesis during motor neuron development and maturation in iMN models.

Hematopoietic stem cells (HSCs) arise in embryogenesis from a specialized hemogenic endothelium (HE) via endothelial-to-hematopoietic transition (EHT). While induced pluripotent stem cells (iPSCs) give rise to HE with robust hemogenic potential, bona fide HSC generation from iPSCs remains challenging. We map single-cell dynamics of EHT from iPSCs and integrate it with human embryo datasets to identify ligand-receptor interactions that drive transcriptional divergence between iPSC-derived and embryonic cell states. The expression of endothelial genes predicted to be regulated by FGF signaling was incompletely repressed during iPSC-derived EHT. FGF activity declined at the onset of EHT to enable normal hematopoiesis in the zebrafish, and chemical inhibition of FGF signaling during EHT enhanced HSC and progenitor generation in the zebrafish and from iPSCs. In summary, we generate a single-cell map of iPSC-derived EHT, identify ligand-receptor interactions that can improve iPSC differentiation, and uncover elevated FGF signaling as a barrier to hematopoiesis.

The human macula is a specialized, cone-rich region of the eye, critical for high-acuity vision, yet the pathways regulating its development remain poorly understood. RA-catabolizing enzyme CYP26A1 establishes the chick high-acuity area via upregulation of fibroblast growth factor 8 (FGF8). However, detailed analysis of this pathway and its functions has not been performed in early human fetal tissue. Fluorescent in situ hybridization revealed striking biphasic CYP26A1 expression but little FGF8 in the presumptive macula region between post-conception weeks (PCW) 6-17. Pharmacological retinoic acid (RA) signaling inhibition in human retinal organoids mimicking the two waves of CYP26A1 revealed early RA inhibition prompted early cell cycle exit and increased cone genesis, while late inhibition altered cone subtype specification. Conversely, recombinant FGF8 had no effect on photoreceptor fate. This work provides spatiotemporal examination of CYP26A1 across human macular development, as well as experimental evidence for the different roles of RA signaling inhibition in a human model of retinal development.

Human pluripotent stem cells (hPSCs) are valuable tools for studying placental biology, yet their differentiation into bona fide trophoblast stem cells (TSCs) remains challenging. In this study, we established and thoroughly compared naive and primed-derived TSC-like cells with primary human TSCs derived from pre-implantation blastocyst and first-trimester placenta. Comprehensive analyses confirmed expression of trophoblast lineage-specific genes and typical placental features. Detailed transcriptional analyses revealed that naive-derived TSC-like cells resembled embryo and placenta-derived cell lines and differentiated faster and more directly into TSC than primed-derived cells. We used these TSC-like models to study the role of ELF5, a transcription factor indispensable for maintenance and differentiation in mouse TSC. In contrast to the mouse, knockout and knockdown experiments revealed that ELF5 is dispensable for human TSC-like cells self-renewal and differentiation. Our study provides valuable transcriptional data and highlights the utility of hPSC-derived TSC-like cells for modeling the placenta and studying gene function.

Human pluripotent stem cells (PSCs) are known to harbor mutations in tumor-associated genes, and here we aim to examine the status of adult stem cells (ASCs). We thus identify cancer-related mutations in 18% of about 600 mesenchymal stem cell samples, and in 41% of about 200 neural stem cell (NSC) samples. We show a lineage-specific profile of cancer-related genes, demonstrating that TP53 is a central mutated gene in human PSCs but not in mesenchymal or NSCs. We suggest that the lineage-specificity of tumor-associated genes correlates with their expression levels and with tumor-specific mutations in patients. We also show the consequences of mutations in oncogenes and tumor suppressor genes on the transcriptome of each specific stem cell lineage. We therefore propose a categorization of these mutated samples for further appreciation of their severity and emphasize the importance of genetic screening in pluripotent and ASC lines.

The interaction between hepatic stellate cells (HSCs) and hepatocytes contributes to HSC activation and liver regeneration; however, the mechanisms in humans remain unclear, particularly the significance of their direct contact and the role of cell adhesion molecules. In this study, we established a novel contact co-culture organoids using induced pluripotent stem cell (iPSC)-derived hepatic stellate-like cells (iPS-HSCs) and hepatocyte-like cells (iPS-Heps), termed iPSC-derived hepatocyte-stellate cell surrounding organoids (iHSOs). The iHSOs exhibit a unique morphology with iPS-HSCs surrounding central iPS-Heps. The iHSO enabled the identification of ICAM-1-interleukin-1β (IL-1β)-mediated iPS-Hep proliferation supported by iPS-HSCs, which displayed a quiescent and cytokine-rich phenotype, whereas this proliferative support was not observed in primary liver cell-based co-culture organoids. Furthermore, iHSOs treated with acetaminophen allowed for the modeling of HSC activation induced by hepatocyte injury, demonstrating their application potential. Our study presents a valuable platform for studying the HSC behavior and complex interactions between HSCs and hepatocytes in humans.

Naturally occurring diseases in companion dogs are increasingly being recognized as valuable translational disease models. While induced pluripotent stem cell (iPSC) technology had revolutionized the field of human bio-medical research, canine iPSC (ciPSC) technology is still in its infancy, and robust canine-specific iPSC medium formulations and differentiation protocols are lacking. Here, we have established NANOG-reporter ciPSC lines and found that fibroblast growth factor (FGF), activin/transforming growth factor (TGF)-β, and WNT signals were critical for the robust maintenance of ciPSCs. Manipulating these signaling pathways stabilized the culture of ciPSC regardless of the cell line or basal medium. ciPSCs cultured in the optimized medium showed a homogenized global gene expression pattern. Furthermore, the ciPSCs cultured in this medium successfully differentiated into cardiomyocytes displaying homogenous contraction as well as sarcomere alignment. This robust culture condition provides a valuable resource to facilitate the utilization of ciPSCs for various studies, including human disease modeling.