Inorganic Ions Activate Lineage-Specific Gene Regulatory Networks to Drive Stem Cells Differentiation
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE234727 | GEO | 2024/06/10
REPOSITORIES: GEO
Similar Datasets
Project description:Bioactive materials harness the body’s innate regenerative potential by directing endogenous progenitor cells to facilitate tissue repair. Dissolution products of inorganic biomaterials provide unique biomolecular signaling for tissue-specific differentiation. We demonstrate the role of the inorganic biomaterial synthetic two-dimensional (2D) nanosilicates, and its ionic dissolution products on human mesenchymal stem cell differentiation. We utilize whole transcriptome sequencing (RNA-seq), to characterize the contribution of nanosilicates and its ionic dissolution products on endochondral differentiation. Our study highlights the modulatory role of ions in stem cell transcriptome dynamics by regulating lineage-specific gene expression patterns.
2022-05-04 | GSE193172 | GEO
Project description:Exposure to ambient particulate matter (PM) is associated with adverse health effects. Yet, due to the complexity of its chemical composition, the molecular effects of PM exposure and the mechanism of PM-mediated toxicity remain largely unknown. Here, we show that water-soluble inorganics such as nitrate and sulfate ions, rather than PM themselves, are responsible for perturbing gene expression in the lungs by rapidly penetrating the lung surfactant barrier to the alveolar region. Furthermore, from high-throughput sequencing of lung adenocarcinoma cells, we find that exposure to nitrate and sulfate ions activates the cholesterol biosynthetic metabolism and induces the expression of genes related to tumorigenesis and inflammatory response, particularly interferon-gamma. Transcriptome analysis of mouse lungs exposed to nitrate/sulfate aerosols further supports our findings. Notably, we find that exposure to nitrate/sulfate mixture leads to a unique gene expression pattern that is not observed when nitrate or sulfate is treated alone. Our work suggests the water-soluble ions as a potential source of PM-mediated toxicity and provides a roadmap to unveil the working mechanism of health hazards of PM exposure.
2023-11-01 | GSE182629 | GEO
Project description:We investigate cellular responses to traditional bioactive mineral-based nanomaterials, such as hydroxyapatite (nHA), whitlockite (nWH), silicon-dioxide (nSiO2), and the emerging synthetic 2D nanosilicates (nSi), on human mesenchymal stem cells (hMSCs). Specifically, using next-generation transcriptome sequencing (RNA-seq), we uncover key signaling pathways and transcriptome dynamics due to exposure to these inorganic nanomaterials. Whole-transcriptome sequencing identified a stabilized skeletal progenitor state in stem cells treated with nanosilicates that suggests endochondral differentiation of hMSCs, resulting in increased deposition of matrix mineralization compared with control or other treatment groups.
2024-06-01 | GSE193173 | GEO
Project description:Little is known about molecular mechanism for its effectiveness of C-ions in melanomas. In this study, we examined the cytotoxic effects of C-ions on 6 human malignant melanoma cell lines, and gene expression profiles and cell cycle progression were also examined to reveal the mechanism of the therapeutic effectiveness of C-ions. Equivalent doses of the C-ions were more effective at reducing the survival rates than X-rays, and the relative biological effectiveness (RBE) was > 2.0 in all cell lines. In unsupervised 2D clustering performed for C-ions irradiated groups at 1 h after irradiation, many of the probes were down-regulated among 6 cell lines. We identified probes, such as XKRY, ELA3A, T-STAR, SCN9A, ELA2A, CRK7, CCNA2, CROP, CYR61, SDFR1, and SMAD4 differentially responded to C-ions and X-rays among 4 cell lines. CCNA2 was down-regulated by C-ions more than X-rays at 3 h after irradiation, and C-ions induced G2/M arrest more than X-rays in three cell lines at 30 h. Many of p53 target genes, such as ATF3, BTG2, CDKN1A, GADD45A, SESN1, and TNFRSF6 were up-regulated by C-ions at 3 h. The expressions of p53 target genes were not changed in HMV-I and MeWo. In MeWo, APG3L, RPL26 and PCNA were down-regulated or E2F2 and LIMS3 were up-regulated, and in HMV-I, ATF3, FOS, and CYR61 were up-regulated at 1 h after C-ions. In conclusion, C-ions affected p53-dependent and p53-independent pathways of cell death and cell cycle. Individual mechanism in activating of cell death was observed in each cell line of 6 melanomas. Keywords: Specific gene expression prfiles after carbon ion irradiation
2008-06-01 | GSE6630 | GEO
Project description:This study aims at investigating the link between internalized inorganic or methyl Hg and the global expression of genes, obtained by high-throughput sequencing (RNA-Seq), in the microalga Chlamydomonas reinhardtii. Algal cells were exposed two hours in a simplified artificial medium spiked with series of inorganic Hg concentrations (0.1, 1, 100 nM Hg) or series of methyl Hg concentrations (0.05, 0.5, 5, 50 nM CH3Hg).
2017-06-27 | GSE65109 | GEO
Project description:Stable and commonly bioactive cysteine-rich peptides (CRPs) have are typically discovered via mass shift analysis. However, the accurate assessment of unique CRP species in a given botanical species is often challenged by same mass species, post-translational modifications or modifications derived from sample handling, and incomplete MS2 fragmentation. Mass spectral fingerprint ions can be leveraged to gain additional information about a mass species prior to full sequence characterization and with only poor quality MS2 spectra. Herein we identify sets of mass spectral fingerprint ions characteristic of the CRP cyclotide family, which may indicate a mass belongs to a specific cyclotide subfamily, and “tell-tale” ions that are of importance when discriminating putative cyclotide species, including common oxidation and over-alkylation ions observed experimentally. Cyclotide-containing V. communis material is used as proof-of-principle, where experimental cyclotide fingerprint ions are explored. Fingerprint ions derived from a third type of CRP, the trypsin inhibitors, are assessed in the gourd L. siceraria. Combining mass shift analysis with the identification of prominent MS2 fingerprint ions is then used to identify three novel CRPs. We demonstrate that abundant mass spectral fingerprint ions can be used to quickly discern masses of interest in complex matrices and masses that are already characterized, aiding prioritization of the most promising novel mass species in a natural product sample for characterization.
2020-09-04 | PXD019501 | Pride
Project description:This study aims at investigating the link between internalized inorganic or methyl Hg and the global expression of genes, obtained by high-throughput sequencing (RNA-Seq), in the microalga Chlamydomonas reinhardtii. Algal cells were exposed two hours in a simplified artificial medium spiked with series of inorganic Hg concentrations (0.1, 1, 100 nM Hg) or series of methyl Hg concentrations (0.05, 0.5, 5, 50 nM CH3Hg). Three biological replicates were assessed for each of the 8 tested conditions: Control, 3 Hg concentrations, 4 CH3Hg concentrations.
2017-06-27 | E-GEOD-65109 | biostudies-arrayexpress
Project description:Gold salts has been used in the treatment of rheumatoid arthritis but has been replaced by biologicals such as TNF-alpha inhibitors. The mechanisms behind the anti-inflammatory effect of metallic gold ions are still unknown, however, recent data showed that charged gold atoms are released from pure metallic gold implants by macrophages via a dissolucytosis membrane, and that gold ions are taken up by local macrophages, mast cells and to some extent fibroblasts. These current findings offer new treatment options for metallic gold and deeper understanding of the effect of metallic gold on key inflammatory cells as macrophages are essential. In the present study the impact of phagocytised gold ions on the global gene expression profile of the human monocytic cell line THP-1 was investigated, using microarray analysis comprising approximately 20,000 genes. The gene expression data was confirmed by measurement of three secreted proteins. A unique gene expression signature of dissolucytotic macrophages that had taken up gold ions was demonstrated. A large number of regulated genes were functionally related to immunomodulation/protection. Gold ion uptake into macrophages induced downregulation of central inflammatory cytokines as TNF-alpha, IL-32 and CD28. The data obtained in this study offer new insights into the mode of action of gold ions and suggest a future role of metallic gold as implants or topical applications in treating inflammation.
2012-12-31 | GSE37814 | GEO
Project description:Rice grown in paddy fields prefers to use ammonium ions as a major source of inorganic nitrogen. Glutamine synthetase (GS) catalyzes the conversion of ammonium ions to glutamine. In three cytosolic GS in rice, OsGS1;1 has the critical role for normal growth and grain filling. To understand a role of GS1;1, we performed transcriptional profiling of wild type Nipponbare and GS1;1 mutant plants in seedling using the Agilent Rice Oligo Microarray.
2010-03-01 | GSE15122 | GEO
Project description:To investigate the inhibition mechanism of copper ions on S. mutans-V. parvula dual biofilm.
2023-02-01 | GSE222218 | GEO