GEMINI (Gastric Encyclopedia of Molecular Interactions and Nodes for Intervention) : 37 unique Gastric cancer cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Patrick Tan
PROVIDER: E-GEOD-22183 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Genome-wide mRNA expression profiles of 37 unique gastric cancer cell lines (GCCLs). Keywords: gastric cancer, cell culture
2010-06-08 | GSE22183 | GEO
Project description:The biological behavior and clinical outcome of gastric cancers are variable considerably according to anatomic location, such as proximal gastric cancer (PGC) and distal gastric cancer (DGC). Therefore, identification of the biomarkers used for recognizing the biological behavior and predicting clinical outcome has been a major goal in gastric cancer researches.
2013-03-27 | E-MTAB-1307 | biostudies-arrayexpress
Project description:DNA methylation is a key contributor to normal mammalian development, although, abnormal CpG islands methylation has been described to have a role in carcinogenesis. In gastric cancer, it is observed a global hypomethylation within the bulk genome and local hypermethylation at specific tumor suppressor genes. Conversely, the absence of DNA methylation may be an important step in stable transcriptional activation of oncogenes, contributing to tumor development. The screening of genes modulated by DNA methylation in gastric cancer may contribute to the identification of tumor suppressor genes and/or oncogenes modulated by DNA methylation never described in this neoplasia. In this experiment we aimed to identify differentially expressed genes by comparing 5-Aza-2’-deoxycytidine (5-AZAdC)-treated and non-treated gastric cancer cell lines. 5-AZAdC is a demethylation agent and has received FDA approval for the treatment of myelodysplastic syndromes. This drug has also showed capacity to treat solid tumors with low dose. The ACP02 and ACP03 gastric cancer cell lines used in this experiment were previously established by our research group from primary gastric adenocarcinomas classified as diffuse and intestinal types, respectively. Both cell lines present chromosome 8 trisomy, MYC amplification, and TP53 loss of copy. Moreover, ACP03 is able to start a tumorigenesis process in Cebus apellas.
2019-04-30 | E-MTAB-7880 | biostudies-arrayexpress
Project description:Genome-wide mRNA expression profiles of 25 unique gastric cancer cell lines (GCCLs). Gastric cancer (GC) is the second leading cause of global cancer mortality, with individual gastric tumors displaying significant heterogeneity in their deregulation of various oncogenic pathways. We aim to identify major oncogenic pathways in GC that robustly impact patient survival and treatment response. We used an in silico strategy based on gene expression signatures and connectivity analytics to map patterns of oncogenic pathway activation in 25 unique GCCLs, and in 301 primary gastric cancers from three independent patient cohorts. Of 11 oncogenic pathways previously implicated in GC, we identified three predominant pathways (proliferation/stem cell, NF-kB, and Wnt/b-catenin) deregulated in the majority (>70%) of gastric tumors. Using a variety of proliferative, Wnt, and NF-kB-related assays, we experimentally validated the pathway predictions in multiple GC cell lines showing similar pathway activation patterns in vitro. Patients stratified at the level of individual pathways did not exhibit consistent differences in clinical outcome. However, patients grouped by oncogenic pathway combinations demonstrated robust and significant survival differences (e.g., high proliferation/high NF-kB vs. low proliferation/low NF-kB), suggesting that tumor behavior in GC is likely influenced by the combined effects of multiple oncogenic pathways. Our results demonstrate that GCs can be successfully taxonomized by oncogenic pathway activity into biologically and clinically relevant subgroups. Keywords: gastric cancer, cell culture Profiling of 25 unique Gastric Cancer Cell Lines on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Replicates are included for a total of 33 arrays.
2009-10-06 | E-GEOD-15455 | biostudies-arrayexpress
Project description:Genome-wide mRNA expression profiles of 25 unique gastric cancer cell lines (GCCLs). Gastric cancer (GC) is the second leading cause of global cancer mortality, with individual gastric tumors displaying significant heterogeneity in their deregulation of various oncogenic pathways. We aim to identify major oncogenic pathways in GC that robustly impact patient survival and treatment response. We used an in silico strategy based on gene expression signatures and connectivity analytics to map patterns of oncogenic pathway activation in 25 unique GCCLs, and in 301 primary gastric cancers from three independent patient cohorts. Of 11 oncogenic pathways previously implicated in GC, we identified three predominant pathways (proliferation/stem cell, NF-kB, and Wnt/b-catenin) deregulated in the majority (>70%) of gastric tumors. Using a variety of proliferative, Wnt, and NF-kB-related assays, we experimentally validated the pathway predictions in multiple GC cell lines showing similar pathway activation patterns in vitro. Patients stratified at the level of individual pathways did not exhibit consistent differences in clinical outcome. However, patients grouped by oncogenic pathway combinations demonstrated robust and significant survival differences (e.g., high proliferation/high NF-kB vs. low proliferation/low NF-kB), suggesting that tumor behavior in GC is likely influenced by the combined effects of multiple oncogenic pathways. Our results demonstrate that GCs can be successfully taxonomized by oncogenic pathway activity into biologically and clinically relevant subgroups. Keywords: gastric cancer, cell culture
2009-10-06 | GSE15455 | GEO
Project description:Selected genes within the 1 Mb minimal amplified region on 20q13.3 driven by ADRM1 in gastric cancer cell line AGS were analyzed by Gene expression Microarray. Gene Expression of ADRM1, HRH3, MTG2, LAMA5 and OSBPL2 were then compared in 16 Gastric cancer cell lines to a reference composed of mixed gastric cancer cell lines.
2015-01-01 | E-GEOD-64604 | biostudies-arrayexpress
Project description:To identify the lncRNA profiles of gastric cancer samples, we performed microarray analysis using tumor samples and paired normal samples. 66 lncRNAs were statistically dysregulated more than 2-fold. The samples were divided into two groups, paired normal samples (negative control group_Rep10) and tumor samplea (Experiment group_Rep10).
2016-07-26 | E-GEOD-84787 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of gastric cancer cell lines. The Illumina Goldengate DNA methylation Beadchip was used to obtain DNA methylation profiles across 1,505 CpG CpGs in 20 gastric cancer cell lines. Bisulphite converted DNA from the 20 gastric cancer cell lines were hybridised to the Illumina Goldengate Methylation Beadchip
2012-05-02 | E-GEOD-29499 | biostudies-arrayexpress
Project description:The abundance of noncanonical open reading frames present in long noncoding RNAs (lncRNAs) indicates the potential for translational capacity, thereby enabling the generation of multiple functional peptides or proteins. Nevertheless, the existence of peptide or protein products derived from lncRNAs and their specific roles in gastric cancer remain largely unexplored. In this study, we identified HOXA10-HOXA9-derived small protein (HDSP) in gastric cancer by conducting a comprehensive analysis and experimental validation with mass spectrometry and western blotting. HDSP is highly expressed and has oncogenic roles in gastric cancer. Mechanistically, HDSP blocked TRIM25-mediated ubiquitination and degradation by interacting with MECOM. This led to the accumulation of MECOM, which further enhanced the transcription of SPINK1, a gene that promotes cancer through the EGFR signaling pathway. In addition, MECOM promoted the transcription of HOXA10-HOXA9, creating a feedback regulatory loop that activated downstream SPINK1-EGFR signaling. Finally, we found that HDSP knockdown inhibited tumor growth in a patient-derived xenograft (PDX) model, and the infusion of an artificially synthesized HDSP peptide as a neoantigen improved the anti-tumor efficacy of immune cells against gastric cancer in vitro and in vivo. Our findings provide a potential therapeutic target or neoantigen candidate for the treatment of gastric cancer.
2024-05-07 | PXD043737 | Pride
Project description:Genome-wide mRNA expression profiles of normal skin fibroblasts, used as one of the (normal) references in the study. Gastric cancer (GC) is the second leading cause of global cancer mortality, with individual gastric tumors displaying significant heterogeneity in their deregulation of various oncogenic pathways. We aim to identify major oncogenic pathways in GC that robustly impact patient survival and treatment response. We used an in silico strategy based on gene expression signatures and connectivity analytics to map patterns of oncogenic pathway activation in 301 primary gastric cancers from three independent patient cohorts. Of 11 oncogenic pathways previously implicated in GC, we identified three predominant pathways (proliferation/stem cell, NF-kB, and Wnt/b-catenin) deregulated in the majority (>70%) of gastric tumors. Using a variety of proliferative, Wnt, and NF-kB-related assays, we experimentally validated the pathway predictions in multiple GC cell lines showing similar pathway activation patterns in vitro. Patients stratified at the level of individual pathways did not exhibit consistent differences in clinical outcome. However, patients grouped by oncogenic pathway combinations demonstrated robust and significant survival differences (e.g., high proliferation/high NF-kB vs. low proliferation/low NF-kB), suggesting that tumor behavior in GC is likely influenced by the combined effects of multiple oncogenic pathways. Our results demonstrate that GCs can be successfully taxonomized by oncogenic pathway activity into biologically and clinically relevant subgroups. Keywords: normal skin fibroblasts, cell culture
2009-10-06 | GSE15537 | GEO