MicroRNA sequencing of growing teratoma tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE251975 | GEO | 2024/04/28
REPOSITORIES: GEO
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Project description:MicroRNA sequencing of growing teratoma tissues
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Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of 12 different growing teratoma tissues. Samples were subgrouped based on growth speed into GTSslow to GTSrapid (see corresponding publication).
2024-04-28 | GSE240091 | GEO
Project description:In this study, we aimed to identify a miRNA expression signature that could be used to distinguish PCa from BPH. We have shown for the first time in the literature the presence of miRNAs in the PSS. We suggest PSS as a powerful non-invasive source for evaluation of prognosis in PCa, since prostate massages can be easily applied during routine examination. Our results showed that certain differentially expressed miRNAs in PSS could be used as diagnostics markers. Prostate secretion samples (PSS) from 23 PCa and 25 benign prostate hyperplasia (BPH) patients were obtained from Urology Department of Bagcilar Educational and Research Hospital (Istanbul). MicroRNA (miRNA) profiling of eight PSS (four from BPH, four from PCa patients) were performed using microarray. Four of significantly deregulated miRNAs were further confirmed using quantitative reverse-transcription PCR (qRT-PCR). Statistical analysis was performed using Student’s t-test. ROC curves were plotted with SPSS-15.0.
2013-09-27 | E-GEOD-49298 | biostudies-arrayexpress
Project description:Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues
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Project description:Mature teratomas are usually benign tumors that rarely undergo malignant transformation. We report an advanced neuroblastoma arising in a mature teratoma of the ovary. Whole-exome sequencing identified extensive copy-neutral LOH in both neuroblastoma and teratoma elements, suggesting that the neuroblastoma evolved from the teratoma.
| EGAS00001005116 | EGA
Project description:expression analysis of teratoma, grown from mouse embryonic stem cells that are Evi/Wls knockout cells and comparison with wildtype (control) tumors
2014-12-10 | E-MTAB-2927 | biostudies-arrayexpress
Project description:We collected the Superficial temporal artery (STA) tissues from patients with Moyamoya disease who underwent combined direct and indirect bypass surgery and patients with brain trauma requiring craniotomy in the Department of Neurosurgery, First Affiliated Hospital of USTC (Anhui Provincial Hospital). One part was fixed in 10% neutral formalin solution, and the other part was stored in a refrigerator at -80 ℃. All protocols using human specimens were approved by the ethics committee of the First Affiliated Hospital of USTC (Anhui Provincial Hospital). Written informed consent was obtained from all patients. All protocols were approved by the Institutional Review Board of the First Affiliated Hospital of USTC (Anhui Provincial Hospital).Total RNA was extracted from the STA tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. The integrity and concentration of RNA were detected using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, Calif., USA), enriched and purified with Oligo (dT) -bearing magnetic beads. RNA sequencing was performed by Anoroad (Beijing, China).
2024-08-28 | GSE249254 | GEO
Project description:Human induced pluripotent stem (iPS) cells are capable of differentiating into derivatives of the three embryonic germ layers both in vitro and in vivo. To date the the molecular differences between teratoma-forming cells and non-teratoma-forming cells has not been analysed. A cell line, B1, bears typical ES cell-like morphology, expression of pluripotency-associated genes, and in vitro pluripotency capacity, but fails to form teratomas after subcutaneously injected into immune-deficient mice based on histological analysis. Besides histological analysis, we characterized the tumors derived from line B1, and teratomas derived from bona fida iPS and ES (line H1) cells respectively, using microarray-based gene expression analysis. The expression levels of pluripotency-associated markers in B1 cells were comparable to that in iPS and ES cells, while the complexity of tissue expression commitment was decreased upon spontaneous differentiation of B1 cells as compared to iPS and ES cells. Total RNA obtained from HFF1 (human foreskin fibroblast) cells, line B1, iPS-A4, iPS-B4 and ES (line H1) cells, and their derived tumors in immune-deficient mice.
2012-04-29 | E-GEOD-31970 | biostudies-arrayexpress
Project description:Studying early human developmental processes requires access to a model system that is easy to perturb, either genetically or chemically, genetically tractable and recapitulates key features of organogenesis. We propose that the teratoma, a recognized standardused for for validating pluripotency in stem cells, could be a promising platform for modeling human development. Teratomas differentiate to all germ layers, have regions of complex tissue-like organization with internal vasculature, and are relatively easy to generate and thus accessible, especially in comparison to human fetal tissue. Teratomas, however, have not been characterized rigorously to determine their suitability to model human developmental processes the diversity and identities of the cell types present, and their level of maturity in comparison to human developmental cell types. We thus systematically analyzed, perturbed, and engineered human pluripotent stem cell (PSC)-derived teratomas. Usingused histology, RNA in situ hybridization, and single cell RNA-seq (scRNA-seq) of 179,632 cells across 23 teratomas generated from 4 cell lines, we observed to find that teratomas reproducibly contain approximatelyat least 20 cell types across all three germ layers, and the cell type heterogeneity between teratomas was comparable to that found in organoid systems. We found that a significant fraction of injected PSCs engrafted, suggestingused lentiviral barcoding to determine there is minimalno bottlenecking during teratoma formation. Additionally, we mapped our teratoma data to published human fetal data and showed that the teratoma gut and brain cell types correspond well to existing fetal gut and brain scRNA-seq datasetscells. We then performed a CRISPR-Cas9 knockout screen in teratomas targeting key genes known to be embryonic lethal, and found that TWIST1, RUNX1, ASCL1, CDX2, and KLF6 knockouts resulted in assessed shifts in lineage abundance. using scRNA-seq. We found that TWIST1, RUNX1, ASCL1, CDX2, and KLF6 knockouts resulted in reproducible shifts in lineage abundance consistent with known biology. All of these These knockouts had effects on cell types from multiple germ layers, showing that the teratoma can serve as a platform to studymodel all major human lineages of human development simultaneously. Additionally, we ran a CRISPR-Cas9 screen targetingWe also knocked out the genes underlying Rett, Pitt-Hopkins, and L1 Syndromes and identified cell type specific shifts in gene expression. Finally, we engineered a novel miRNA-regulated suicide gene circuit that enriches for tissues in the teratoma that express a specific miRNA that selectively depletes cells that do not express a tissue-specific endogenous miRNA, allowing us to enrich for desired lineages in the teratoma, which we demonstrated using miR-124 to enrich for neuro-ectoderm. Specifically, we used miR-124 to successfully enrich for neuro-ectoderm. Taken together, we believe the teratoma is a promising platform for modeling multi-lineage human development, functional genetic screening, and cellular engineering
2020-11-04 | GSE156170 | GEO