EGAS00001002939-sc-2024-03-11T15:15:07Z - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001015352 | EGA |
REPOSITORIES: EGA
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Project description:The landscapes of somatic mutation in normal cells inform on the processes of mutation and selection operative throughout life, permitting insight into embryogenesis, normal ageing and the earliest stages of cancer development. Here, by whole-genome sequencing and targeted panel sequencing of microdissections from 30 individuals, including 18 with gastric cancer, we elucidate the developmental trajectories of normal and malignant gastric epithelium.
| EGAD00001015351 | EGA
Project description:The aim of this study was to determine differences in microRNA expression profiles of gastric cancer and adjacent healthy gastric mucosa. Both types of tissue samples were collected during operative procedures of 20 patients. microRNA expression was determined by miRNA microarrays.
2017-01-12 | GSE93415 | GEO
Project description:Mutation accumulation over time in normal somatic cells contributes to cancer development and is proposed as a cause of ageing. DNA polymerases POLE and POLD1 replicate DNA with high fidelity during normal cell divisions. However, in some cancers defective proofreading due to acquired mutations in the exonuclease domains of POLE or POLD1 causes markedly elevated somatic mutation burdens with distinctive mutational signatures. POLE and POLD1 exonuclease domain mutations also cause familial cancer predisposition when inherited through the germline. Here, we sequenced normal tissue DNA from individuals with germline POLE or POLD1 exonuclease domain mutations. Increased mutation burdens with characteristic mutational signatures were found to varying extents in all normal adult somatic cell types examined, during early embryogenesis and in sperm. Mutation burdens were further markedly elevated in neoplasms from these individuals. Thus human physiology is able to tolerate ubiquitously elevated mutation burdens. Indeed, with the exception of early onset cancer, individuals with germline POLE and POLD1 exonuclease domain mutations are not reported to show abnormal phenotypic features, including those of premature ageing. The results, therefore, do not support a simple model in which all features of ageing are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.
| EGAD00001006212 | EGA
Project description:The objective of my study was to identify the genes differentially expressed in gastric adenocarcinoma associated with prevalent risk factor such as tobacco use (Meiziol, Tuibur etc) in high-risk Indian population. The Tumor tissue and matched normal tissue distant to the tumor were collected during endoscopy in RNA later, Snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical report, operative notes and pathologic report. Institutional Human ethics committee approved the study.
2010-03-23 | GSE20143 | GEO
Project description:HGPS is a rare premature ageing disease, caused by a mutation in the LMNA gene, which activates a cryptic splice site, resulting in the production of a mutant lamin A isoform, called progerin. Sporadic usage of the same cryptic splice site has been observed with normal physiological aging. As it is unknown how HGPS causes premature ageing defects, we set out to determine the gene signature of both young healthy individuals, old healthy individuals, as well as HGPS patients.
2015-05-30 | GSE69391 | GEO
Project description:There are a total of 73 CSF proteomic data, including 37 samples from pre-operative iNPH, 16 samples from normal elderly controls, and 20 samples from inter-operative and post-operative iNPH. This study aims to identify biomarkers for shunt prognosis by CSF proteomic profiling.
2025-01-14 | PXD059796 |
Project description:During the maternal-to-zygotic transition (MZT), which encompasses the earliest stages of animal embryogenesis, a subset of maternally supplied gene products is cleared, thus permitting activation of zygotic gene expression. In the Drosophila melanogaster embryo, the RNA-binding protein Smaug plays an essential role in progression through the MZT by regulating the translational repression and degradation of a large number of maternal mRNA species. The Smaug protein itself is rapidly cleared at the end of the MZT by the Skp/Cullin/F-box (SCF) E3-ligase complex; clearance of Smaug requires zygotic transcription. Here, we show that an F-box protein, which we name Bard (encoded by CG14317), is required for degradation of Smaug. Bard is expressed zygotically and physically interacts with Smaug at the end of the MZT, coincident with binding of the maternal SCF proteins, SkpA and Cullin1, and with degradation of Smaug. We show that shRNA-mediated knock-down of Bard or deletion of the bard gene in the early embryo results in stabilization of Smaug protein, a phenotype that is rescued by transgenes expressing Bard .
2021-10-06 | MSV000088199 | MassIVE
Project description:MPSS analysis of signatures from microdissections of mouse inner ear tissues. Keywords: other
2006-10-01 | GSE4965 | GEO
Project description:Nuclear lamins orchestrate the nuclear envelope architecture to maintain nuclear homeostasis, such as nuclear integrity and chromatin organization. The LMNA mutations lead to a variety of laminopathies, including progeroid syndrome. Other than typical Hutchinson-Gilford progeria syndrome (HGPS), the mechanism of LMNA mutation associated atypical progeria remains largely unexplored. We used patient-specific induced pluripotent stem cells (iPSCs) and their derivatives to remodel an LMNA (c.1579 C>T, p.R527C) mutation that causes Mandibuloacral dysplasia type A (MAD). Vascular lineages, including vascular smooth muscle cells (VSMCs) and endothelial cells (VECs), exhibited premature ageing phenotypes, such as genome instability and nuclear deformations, whereas neural lineages showed no obvious defects. Based on the observation that MAD-iPSCs derived mesenchymal stem cells (MSCs) also recapitulated accelerated senescence, an integrated multi-omics approach was adapted to reveal the underlying mechanisms of stem cells ageing. We found that among available human MSCs ageing models, MAD-MSCs had the highest transcriptional similarity to normal ageing hMSCs. The nuclear lamina-chromatin interaction was dramatically altered for both A and B type lamin-associating domains (LADs) as well as non-LADs binding sites, resulting in ageing-associated gene dysregulations. Chromatin state analysis further showed increased chromatin accessibility, enhancer remodelling, global chromatin compartments loss, topologically associating domains (TADs) and TAD boundaries reorganization in MAD-MSCs. These hierarchical chromatin reorganizations, coupled with gene dysregulation as consequences, expedited the MAD-MSCs ageing. Collectively, this study revealed a multilevel chromatin dysregulation contributed to ageing significantly in a laminopathy-mediated atypical progeroid syndrome.
2024-10-24 | GSE193694 | GEO
Project description:Despite continual efforts to establish pre-operative prognostic model of gastric cancer by using clinical and pathological parameters, a staging system that reliably separates patients with early and advanced gastric cancer into homogeneous groups with respect to prognosis does not exist. With use of microarray and quantitative RT-PCR technologies, we exploited series of experiments in combination with complementary data analyses on tumor specimens from 161 gastric cancer patients. Various statistical analyses were applied to gene expression data to uncover subgroups of gastric cancer, to identify potential biomarkers associated with prognosis, and to construct molecular predictor of risk from identified prognostic biomarkers.Two subgroups of gastric cancer with strong association with prognosis were uncovered. The robustness of prognostic gene expression signature was validated in independent patient cohort with use of support vector machines prediction model. For easy translation of our finding to clinics, we develop scoring system based on expression of six genes that can predict the likelihood of recurrence after curative resection of tumors. In multivariate analysis, our novel risk score was an independent predictor of recurrence (P=0.004) in cohort of 96 patients, and its robustness was validated in two other independent cohorts. We identified novel prognostic subgroups of gastric cancer that are distinctive in gene expression patterns. Six-gene signature and risk score derived from them has been validated for predicting the likelihood of survival at diagnosis. 65 primary gastric adenocarcinoma, 6 GIST and 19 surrounding normal fresh frozen tissues were used for microarray. All the tissues were obtained after curative resection after pathologic confirm at Yonsei cancer center(Seoul, Korea). Microarray experiment and data analysis were done at Dept. of systems biology, MDACC DNA microarray (Illumina human V3)
2011-07-18 | E-GEOD-13861 | biostudies-arrayexpress