Homo sapiens strain:Susa
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB18216 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Young and old breast skin, normal fibroblast cell line, senescent fibroblast cell line RNA seq data
2023-03-30 | GSE191055 | GEO
Project description:The polyphenol resveratrol has anti-inflammatory effects in various cells, tissues, animals and human settings of low-grade inflammation. Psoriasis is a disease of both localized and systemic low-grade inflammation. The Sirtuin1 enzyme thought to mediate the effects of resveratrol is present in skin and resveratrol is known to downregulate NF-κB; a major contributor in the development of psoriasis. Consequently we investigated whether resveratrol has an effect on an Imiquimod induced psoriasis-like skin inflammation in mice and sought to identify candidate genes, pathways and interleukins mediating the observed effects. The study consisted of three treatment groups: A control group, an Imiquimod group and an Imiquimod+resveratrol group. Psoriasis severity was assessed using elements of the Psoriasis Area Severity Index, actual skin thickness measurements, and histological examination. We performed an RNA microarray from lesional skin and afterwards Ingenuity pathway analysis to identify affected signalling pathways. Our microarray was compared to a previously deposited microarray to determine if gene changes were psoriasis-like, and to a human microarray to determine if findings could be relevant in a human setting. Imiquimod treatment induced a psoriasis-like skin inflammation. Resveratrol significantly diminished the severity of the psoriasis-like skin inflammation. The RNA microarray revealed a psoriasis-like gene expression-profile in the Imiquimod treated group, and highlighted several resveratrol dependent changes in relevant genes, such as increased expression of genes associated with retinoic acid stimulation and reduced expression of genes involved in IL-17 dependent pathways (e.g.IL-17A, IL-17F,IL-23p19 ). Quantitative PCR confirmed a resveratrol dependent decrease in mRNA levels of IL-17A and IL-19; both central in developing psoriasis. In conclusion, resveratrol ameliorates psoriasis, and changes in expression of retinoic acid stimulated genes, IL-17 signalling pathways, IL-17A and IL-19 mRNA levels in a beneficial manner suggests it might have a role in the treatment of psoriasis and should be explored further in a human setting.
2015-11-17 | GSE63684 | GEO
Project description:Young and old breast skin, and fibroblast cell line RNA seq data
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Project description:RNA-seq of human fibroblast cell cultures treated with resveratrol against DMSO treated controls, with and without siRNA treatment targeting SIRT1
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Project description:Keloid radiotherapy is clinically effective but has an incomplete underlying molecular mechanism and limited accessibility; we used X-ray exposure to identify effector pathways replicating its antifibrotic benefits without further radiation. After collecting patient keloid samples, primary human keloid fibroblasts and normal skin fibroblasts, non-targeted metabolomics and RNA-seq were performed, identifying phytosphingosine (PHS) and KIF20A as key mediators of fibrosis and cell death in keloid radiotherapy. X-ray irradiation increased PHS release in keloid fibroblasts; exogenous PHS and X-ray irradiation independently induced cell death and reduced fibrosis, their combination exerted radiosensitization by boosting G2/M arrest and apoptosis while lowering fibrosis progression, and both PHS and irradiation reduced KIF20A whose loss induced cell cycle arrest and apoptosis. Our findings reveal that X-ray irradiation enhances keloid fibroblast PHS secretion that downregulates KIF20A to exert keloid therapeutic effects, and topical PHS or KIF20A-targeting agents are immediately translatable alternatives for radiotherapy-ineligible patients.
2026-06-06 | MTBLS14461 | MetaboLights
Project description:Genome wide DNA methylation profiling of lowly invasive MCF10CA1h human breast cancer cell line treated with vehicle control (ethanol) and with 15uM RSV (resveratrol, 4-day treatment). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in the human cell line exposed to described treatments. Samples included biological triplicate of MCF10CA1h control (ethanol treated) and biological triplicate of MCF10CA1h treated with RSV.
2021-01-31 | GSE132670 | GEO
Project description:Kilian2024 - Immune cell dynamics in Cue-Induced Extended Human Colitis Model
Single-cell technologies such as scRNA-seq and flow cytometry provide critical insights into immune cell behavior in inflammatory bowel disease (IBD). However, integrating these datasets into computational models for dynamic analysis remains challenging. Here, Kilian et al., (2024) developed a deterministic ODE-based model that incorporates these technologies to study immune cell population changes in murine colitis. The model parameters were optimized to fit experimental data, ensuring an accurate representation of immune cell behavior over time. It was then validated by comparing simulations with experimental data using Pearson’s correlation and further tested on independent datasets to confirm its robustness. Additionally, the model was applied to clinical bulk RNA-seq data from human IBD patients, providing valuable insights into immune system dynamics and potential therapeutic strategies.
Figure 4c, obtained from the simulation of human colitis model is highlighted here.
This model is described in the article:
Kilian, C., Ulrich, H., Zouboulis, V.A. et al. Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease. npj Syst Biol Appl 10, 69 (2024). https://doi.org/10.1038/s41540-024-00395-9
Abstract:
Single-cell-based methods such as flow cytometry or single-cell mRNA sequencing (scRNA-seq) allow deep molecular and cellular profiling of immunological processes. Despite their high throughput, however, these measurements represent only a snapshot in time. Here, we explore how longitudinal single-cell-based datasets can be used for deterministic ordinary differential equation (ODE)-based modelling to mechanistically describe immune dynamics. We derived longitudinal changes in cell numbers of colonic cell types during inflammatory bowel disease (IBD) from flow cytometry and scRNA-seq data of murine colitis using ODE-based models. Our mathematical model generalised well across different protocols and experimental techniques, and we hypothesised that the estimated model parameters reflect biological processes. We validated this prediction of cellular turnover rates with KI-67 staining and with gene expression information from the scRNA-seq data not used for model fitting. Finally, we tested the translational relevance of the mathematical model by deconvolution of longitudinal bulk mRNA-sequencing data from a cohort of human IBD patients treated with olamkicept. We found that neutrophil depletion may contribute to IBD patients entering remission. The predictive power of IBD deterministic modelling highlights its potential to advance our understanding of immune dynamics in health and disease.
This model was curated during the Hackathon hosted by BioMed X GmbH in 2024.
2025-03-07 | MODEL2502180001 | BioModels
Project description:Genome wide DNA methylation profiling of human mammary epithelial MCF10A cell line treated with vehicle control (ethanol) and with RSV (resveratrol). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human cell lines exposed to described treatments. Samples included biological triplicate of MCF10A control (ethanol treated), biological triplicate of MCF10A treated with RSV.
2022-01-31 | GSE113299 | GEO