Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA318810 | ENA |
REPOSITORIES: ENA
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Project description:SUMMARY of the associated publication: Many adult epithelial stem cells cannot undergo prolonged expansion. This may be due to a cell autonomous limitation or a lack of necessary culture conditions. Thus far, the long-term culture of adult stem cells has required the use of Matrigel organoid culture or feeder co-culture systems. We demonstrate that the TGFbetaBMP/SMAD signaling pathway is highly active in the luminal cells of diverse p63+ basal cell-containing epithelia. Indeed, the activation of SMAD signaling in airway stem cells causes their differentiation, while conversely, inhibition of SMAD signaling leads to stem cell hyperplasia and compromised differentiation. Consistently, TGFbetaBMP/SMAD signaling activation prevents mature cell dedifferentiation. Using pharmacologic dual SMAD inhibition, we developed a feeder-free culture system that allows the cloning of single airway basal stem cells and the expansion of airway stem cells from clinical non-invasively obtained samples with high efficiency. Furthermore, the expansion protocols are applicable not only to human cells but also to those of mouse, ferret, and pig. When differentiated epithelia are produced from expanded cells, they exhibit proper epithelial physiology, and respond to clinically relevant pharmacologic agents. Most remarkably, a very wide variety of functional adult epithelial basal stem cells can be expanded despite their differing origins. The goal of this microarray analysis: It has been shown that inhibition of TGFbeta signaling leads to tumorigenesis (e.g. Guasch et al., 2007, and others). It will be important to show whether the dual inhibited population assumes a tumorigenic status in the same or different manner compared to directly isolated progenitor cells. To address this concern, we have done comprehensive transcriptome analysis comparing gene expression signature of airway stem cells at their early and late passages. We do not find tumor-associated gene signatures during stem cell expansion.
2016-04-19 | GSE80408 | GEO
Project description:Discovery of therapies that are able to correct defective CFTR requires patient derived in vitro pre-clinical cell models to be developed. Two main approaches exist to expand bronchial and nasal cultures, such as conditionally reprogrammed cells (CRC) and feeder free dual SMAD inhibition (SMADi) to overcome senescence, low cell count, and increase passages. To mimic airway epithelium the expanded cells are differentiated at air liquid Interface (ALI). This project focused to compare the global proteome of ALI differentiated CRC and SMADi expanded HNECs both treated and untreated with CFTR corrector VX-809.
2021-12-05 | PXD018386 | Pride
Project description:Dual SMAD inhibitors (TGF-beta inhibitor A-8301 and BMP inhibitor DMH-1) were previously reported to promote long-term expansion of basal cells. Since UK-5099 showed a comparable effect to dual SMAD inhibitors in promoting basal cells expansion, we performed RNA-seq to determine if cells expanded by these two methods exhibit a similar transcriptional profile. The Pierson correlation test indicated that cells expanded by UK5099 displayed a transcriptional profile similar to those expanded with dual-SMAD inhibitors. The expression levels of canonical basal cell marker genes, such as Krt5 and p63, were comparable in cells expanded using both methods, as well as genes related to the TCA cycle and glycolysis. Interestingly, despite the similarity in the expression of canonical basal cell markers, cells expanded via UK-5099 exhibited higher activity in differentiation-related signaling pathways, such as the Hippo and TGF-β signaling pathways.This observation suggests that mitochondrial pyruvate transport is a critical metabolic checkpoint for basal cell differentiation.
2025-01-08 | GSE240499 | GEO
Project description:Underdeveloped lungs are a primary cause of morbidity and mortality in premature infants, but our ability to help these patients by speeding up lung development are hindered by a lack of understanding of human lung developmental biology. Here, we performed single cell RNA sequencing of the human fetal lung from samples spanning from 11.5 weeks gestation to 21 weeks gestation from the distal lung, middle airways, and the tracheal epithelium. The primary goal of this experiment was to define fetal cell states to serve as a gold standard for pluripotent stem cell-derived lung cells and tissues, and to identify potential signaling pathways that drive differentiation of lung progenitor cells to mature cell types. Additionally, we generated bud tip progenitor organoids from 12 week human fetal lung bud tip progenitors. We show that treatment of bud tip progenitor organoids with a short pulse of dual SMAD activation (BMP4+TGFb1) led to the upregulation of lung basal cell markers, a cell type that serves as a critical stem cell for the adult airway, and that further treatment with dual SMAD inhibition leads to the generation of airway-like organoids containing differentiated cell types of the adult airway, including basal stem cells.
2020-04-17 | E-MTAB-8221 | biostudies-arrayexpress
Project description:Background: Human basal stem cells, with their self-renewal and multilineage differentiation capacity, are essential tools for modeling airway diseases and advancing regenerative medicine. However, existing culture systems often rely on undefined components like serum, bovine pituitary extract, or feeder cells, limiting reproducibility and clinical translation. To address this limitation, we developed a well-defined culture medium that enables the long-term expansion of human airway basal stem cells while preserving their proliferative and differentiation potential. Methods: We formulated a novel medium (sfBSC) comprising 14 defined components, including basal media, supplements, growth factors (EGF, FGF10), and signaling inhibitors (Y-27632, A-83-01, DAPT, DMH1). Human bronchial and small airway epithelial cells were cultured over multiple passages in sfBSC and assessed for morphology, population doublings, marker expression, and differentiation capacity via air-liquid interface and organoid cultures. RNA-seq was performed to explore molecular changes across passages. Results: Bronchial and small airway epithelial cells were expanded up to 17 and 24 passages, respectively, with stable morphology and consistent cell size (10-15 μm). Cells maintained expression of canonical BSC markers (TP63, KRT5, NGFR) throughout long-term culture. Differentiation assays confirmed the ability to generate ciliated, goblet, and club cells. Optimized concentrations of EGF (1 ng/mL) and FGF10 (0.4 ng/mL) were critical for sustained proliferation. RNA-seq revealed stable marker expression and metabolic changes over time.Conclusions: sfBSC medium offers a defined, reproducible, and scalable platform for basal stem cell culture, enabling applications in disease modeling, regenerative medicine, and clinical-grade cell production.
2025-12-10 | GSE304935 | GEO
Project description:Gene expression analysis of basal cells expanded with UK-5099 or dual SMAD inhibitors
| PRJNA1003919 | ENA
Project description:Cells in culture undergo replicative senescence and unequivocally stop proliferation after a limited number of cell divisions. In this study, we have expanded mesenchymal stem cells (MSC) from human adipose tissue and analyzed genetic and epigenetic sequels. The subpopulation of highly proliferative cells and the in vitro differentiation potential decayed already within early passages. Relevant chromosomal aberrations were not detected by karyotyping and SNP-microarrays. Comparison of early and late passage of five samples of mesenchymal stem cells from human adipose tissue.
2013-02-15 | E-GEOD-27135 | biostudies-arrayexpress
Project description:Platform: iPSC-derived airway plated on 2D-air liquid interface through basal cell intermediate. Purpose of experiment: To examine the role of mutant CFTR on IPSC-derived airway epithelium (ie. immune dysregulation; dysregulated calcium channel signaling etc). Description of samples:Typical phenotype CF F508del (1565) and syngeneic CFTR-corrected (1564) iPSCs- derived airway epithelium at D90 (D15 CD47hi/CD26lo; replated in 3DMG cultured in 210DCIY x 2 weeks, single-cell passaged and cultured in PNExPlus+dual smad media in 3D, s/p 2 NGFR sorts, cultured at air-liquid interface at 2D)
2023-03-02 | GSE203006 | GEO
Project description:Mesenchymal stromal cells (MSC) were isolated from human bone marrow. Here, we have compared gene expression profiles of MSC at early and late passages. Long-term culture associated gene expression changes were then correlated with DNA-methylation profiles. The goal of this study was to determine if senescence-associated DNA-methylation (SA-DNAm) changes are reflected by differential gene expression. Overall, genes with SA-DNAm changes (particularly with SA-hypomethylation) were detected at low level and seemed to be scarcely expressed at early and late passages. MSC were isolated from three different donors and culture expanded until replicative senescence. Gene expression profiles were compared at early and late passage using GeneChip Humang Gene 1.0 ST arrays (Affymetrix). Six hybridizations are included in this series.
2012-09-24 | E-GEOD-37065 | biostudies-arrayexpress
Project description:Transcription profiling of human umbilical cord blood derived Outgrowth Endothelial Cells (OECs) at early and late passages. Outgrowth endothelial cells were isolated from the mononuclear fraction of umbilical cord blood and cultured on collagen coated flasks. Once OEC colonies emerged they were expanded in culture to study cell growth kinetics. Total RNA was extracted from OECs at an early passage and OECs at a late passage which were becoming senescent . The purpose of this experiment was to were compared early and late passage OECs to determine how senescence affects the gene expression profile of OECs.
2013-03-16 | E-MTAB-1388 | biostudies-arrayexpress