Epigenetic biomarkers to track differentiation of pluripotent stem cells [methylation array]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA853572 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Epigenetic biomarkers to track differentiation of pluripotent stem cells
| PRJNA853755 | ENA
Project description:Epigenetic biomarkers to track differentiation of pluripotent stem cells [RNA-Seq]
| PRJNA853758 | ENA
Project description:Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that may be indicative for differentiation capacity, as well as lineage-specific differentiation scores to monitor either directed differentiation, or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.
2022-12-06 | GSE207076 | GEO
Project description:Epigenetic biomarkers for EZH2 inhibitor sensitivity in neuroblastoma [array]
| PRJNA680480 | ENA
Project description:Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that may be indicative for differentiation capacity, as well as lineage-specific differentiation scores to monitor either directed differentiation, or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.
2022-12-06 | GSE207118 | GEO
Project description:Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that tracks reprogramming and may indicate differentiation capacity, as well as lineage-specific scores to monitor either directed differentiation or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.
| S-EPMC9860076 | biostudies-literature
Project description:Epigenetic Biomarkers of Aging
| PRJNA875201 | ENA
Project description:Epigenetic Biomarkers of Aging
| PRJNA875202 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-12-06 | GSE207119 | GEO
Project description:EZH2 is a H3K27 methylase and a target of cancer epigenetic treatments. We recently reported the oncogenic roles and NTRK1 (TRKA) epigenetic regulation by EZH2 in the MYCN-amplified aggressive neuroblastomas (NB) (L. Here, we investigated the effects and function of small molecule EZH2 inhibitor (EZH2i) on aggressive NB model cell lines. We examined the antitumor effects of EZH2i using WST assay and colony formation assay. By EZH2i treatments, suppression of proliferation, G0/G1 cell cycle arrest, and apoptosis were observed in sensitive NB cells dose-dependently, whereas they were not observed in resistant NB cells. Transcriptome analysis and GSEA indicated significant changes were observed in the gene set related to differentiation and cell cycle arrest in the sensitive cells. We selected genes induced at mRNA level by EZH2i only in the sensitive cells and confirmed tumor suppressor function in NB cells. Almost of the EZH2i-induced gene promoters were marked by H3K27me3 in the sensitive NB cell line. Interestingly, a part of the EZH2i-induced gene promoters have CpG islands and methylated in NB tumor samples registered in databases and the EZH2i-resistant NB cells. Further, combination of EPZ-6438 and 5-aza-deoxycitide, resulted in effective suppression of proliferation in the EPZ-6438-resistant 3 NB cell lines. Transcriptome/methylome analysis of the EPZ-6438 and 5-aza-deoxycitide-treated NB cells revealed the combinational epigenetic regulation of the tumor suppressors and oncogene expression. Finally, we found that methylome analysis of the promoter regions, e.g. VSTM2L, GPNMB, and TIMP3 CpG islands can be biomarkers of EPZ-6438-registancy in unfavorable NB patients. These responsible CpG island methylation appears to be biomarkers for the application of EZH2i/DNMTi combination therapy.
2020-11-25 | GSE162058 | GEO