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Comprehensive analysis of the gene expression profiles in human gastric cancer cell lines

ABSTRACT: Gastric adenocarcinoma is one of the major malignancies worldwide. Gastric cell lines have been widely used as the model to study the genetics, pharmacology and biochemistry of gastric cancers. Here we describe a comprehensive survey of the gene expression profiles of 12 gastric carcinoma cell lines, using cDNA microarray with 43 000 clones. For comparison, we also explored the gene expression patterns of 15 cell lines derived from lymphoid, endothelial, stromal and other epithelial cancers. Expression levels of specific genes were validated through comparison to protein expression by immunohistochemistry using cell block arrays. We found sets of genes whose expression corresponds to the molecular signature of each cell type. In the gastric cancer cell lines, apart from genes that are highly expressed corresponding to their common epithelial origin from the gastrointestinal tract, we found marked heterogeneity among the gene expression patterns of these cell lines. Some of the heterogeneity may reflect their underlying molecular characteristics or specific differentiation program. Two putative gastric carcinoma cell lines were found to be B-cell lymphoma, and another one had no epithelial specific gene expression and hence was of doubtful epithelial origin. These cell lines should no longer be used in gastric carcinoma research. In conclusion, our gene expression database can serve as a powerful resource for the study of gastric cancer using these cell lines Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

ORGANISM(S): Homo sapiens

PROVIDER: GSE3547 | GEO | 2005/11/03

SECONDARY ACCESSION(S): PRJNA93615

REPOSITORIES: GEO

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Comprehensive analysis of the gene expression profiles in human gastric cancer cell lines

Project description:Gastric adenocarcinoma is one of the major malignancies worldwide. Gastric cell lines have been widely used as the model to study the genetics, pharmacology and biochemistry of gastric cancers. Here we describe a comprehensive survey of the gene expression profiles of 12 gastric carcinoma cell lines, using cDNA microarray with 43 000 clones. For comparison, we also explored the gene expression patterns of 15 cell lines derived from lymphoid, endothelial, stromal and other epithelial cancers. Expression levels of specific genes were validated through comparison to protein expression by immunohistochemistry using cell block arrays. We found sets of genes whose expression corresponds to the molecular signature of each cell type. In the gastric cancer cell lines, apart from genes that are highly expressed corresponding to their common epithelial origin from the gastrointestinal tract, we found marked heterogeneity among the gene expression patterns of these cell lines. Some of the heterogeneity may reflect their underlying molecular characteristics or specific differentiation program. Two putative gastric carcinoma cell lines were found to be B-cell lymphoma, and another one had no epithelial specific gene expression and hence was of doubtful epithelial origin. These cell lines should no longer be used in gastric carcinoma research. In conclusion, our gene expression database can serve as a powerful resource for the study of gastric cancer using these cell lines Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Using regression correlation

2005-11-02 | E-GEOD-3547 | biostudies-arrayexpress

Expression profiling of PBMC from patients with hepatocellular carcinoma

2013-08-03 | GSE49515 | GEO

Gene expression analysis of TGF-beta signaling-disrupting gastric cancer cell line 2MLN

Project description:Diffuse-type gastric carcinoma is a poor-prognostic cancer with high expression of transforming growth factor (TGF)-β and thick stromal fibrosis. However, detailed investigations on the roles of TGF-β signaling in diffuse-type gastric carcinoma have not been performed. We generated two diffuse-type gastric carcinoma cell lines, dominant-negative TGF-β type II receptor expressing cells (2MLN-dnTβRII) and GFP-expressing cells (2MLN-GFP). Cells were subcutaneously or orthotopically injected into nude mice. Although dnTβRII did not affect the growth of OCUM-2MLN in vitro, it accelerated the growth of subcutaneously or orthotopically transplanted tumors in vivo. By microarray analysis, we found gene expression of TSP-1, an angiogenic inhibitor, was down-regulated in dnTβRII tumors. This results suggested disruption of TGF-β signaling in diffuse-type gastric carcinoma cells leads to alteration of tumor microenvironment and acceleration of tumor growth. We generated two OCUM-2MLN-derived gastric carcinoma cell lines; 2MLN-dnTβRII, which expresses dominant negative form of TβRII, and control 2MLN-GFP, which expresses GFP. The transplanted tumors of these cell lines were subjected to gene expression analysis with Affymetrix U133 plus2 arrays.

2011-12-30 | E-GEOD-12336 | biostudies-arrayexpress

Expression profiling of PBMC from patients with hepatocellular carcinoma

Project description:Aberrant gene expression analysis between peripheral blood mononuclear cell (PBMC) samples from healthy individuals and patients with pancreatic carcinoma, gastric carcinoma and hepatocellular carcinoma (HCC) were identified using Affymetrix gene arrays. Peripheral blood mononuclear cell (PBMC) from healthy individuals, patients with pancreatic carcinoma, gastric carcinoma and HCC were isolated and total RNA was extracted for Affymetrix gene microarray analysis.

2013-08-03 | E-GEOD-49515 | biostudies-arrayexpress

Prediction of drug sensitivity

Project description:Tumor cell lines and drug-resistant counterparts. These data support the publication Gyorffy et al, Oncogene 2005 (July), Prediction of doxorubicin sensitivity in breast tumors based on gene expression profiles of drug-resistant cell lines correlates with patient survival. We contrasted the expression profiles of 13 different human tumor cell lines of gastric (EPG85-257), pancreatic (EPP85-181), colon (HT29) and breast (MCF7 and MDA-MB-231) origin and their counterparts resistant to the topoisomerase inhibitors daunorubicin, doxorubicin or mitoxantrone. We interrogated cDNA arrays with 43 000 cDNA clones ( approximately 30 000 unique genes) to study the expression pattern of these cell lines. A cell type comparison design experiment design type compares cells of different type for example different cell lines. Keywords: cell_type_comparison_design

2005-07-30 | GSE3034 | GEO

Protein profiling reveals the characteristic changes of complement cascade pathway in the tissues of gastric signet ring cell carcinoma

Project description:Signet ring cell carcinoma (SRCC) is a histological subtype of gastric cancer with distinct features in multiple aspects compared to adenocarcinomas (ACs). Lacking of systematically molecular overview to this disease made a slow progress in its clinical practice. In the present proteomics study, gastric tissues were collected from tumor and adjacency including 14 SRCCs and 34 ACs, and laser capture microdissection (LCM) was employed to eradicate cellular heterogeneity of the tissues. Proteome of tissues were profiled by data independent acquisition (DIA) mass spectrometry (MS). Based on the over 6 000 proteins quantified. Univariate analysis and pathway enrichment revealed that some proteins and pathways bared the differences between SRCC and ACs. Importantly, the up regulation for a majority of complement-related proteins were iconic for SRCC but not for AC. A hypothesis, based on the proteomics evidence, was proposed that the complement cascade was evoked in the SRCC microenvironment upon infiltration, while the SRCC cells survived the complement cytotoxicity by secreting endogenous negative regulators. Moreover, an attempt was made to seek appropriate cell models for gastric SRCC, through proteomic comparison of the 15 gastric cell lines and the gastric tumors. The prediction of supervised classifier suggested none of these gastric cell lines qualified in mimicking SRCC. This study discovered that complement cascade is activated at a higher level in gastric SRCC than AC.

2021-02-25 | PXD022952 | Pride

Protein profiling reveals the characteristic changes of complement cascade pathway in the tissues of gastric signet ring cell carcinoma

2021-02-25 | PXD022627 | Pride

Protein profiling reveals the characteristic changes of complement cascade pathway in the tissues of gastric signet ring cell carcinoma

2021-02-25 | PXD022405 | Pride

Single-cell sequencing of Epstein-Barr virus infected cells reveals constitutive lytic gene expression in latent cell populations

Project description:Single-cell RNA sequencing using the 10X Genomics 3' platform was performed to determine patterns of gene expression in EBV-positive lymphoma and gastric carcinoma cell lines.

2023-06-27 | GSE101561 | GEO

Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Illumina mRNA expression array data]

Project description:Background: Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries. Methods: Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays and Illumina mRNA expression arrays as well as Illumina sequencing of the coding regions of 384 genes belonging to various pathways known to be altered in other cancers. Results: Genetic alterations were observed in the WNT, Hedgehog, cell cycle, DNA damage and epithelial-to-mesenchymal-transition pathways. Conclusions: The data suggests targeted therapies approved or in clinical development for gastric carcinoma would be of benefit to ~22% of the patients studied. In addition, the novel mutations detected here, are likely to influence clinical response and suggest new targets for drug discovery.

2012-10-25 | GSE29998 | GEO

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