MRNA expression profiles of 7 gastric cancer cell lines and primary cancer cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE172196 | GEO | 2023/04/01
REPOSITORIES: GEO
Similar Datasets
Project description:Establishment and molecular characterization of 49 peritoneally-metastatic gastric cancer cell lines from 18 patients’ ascites. We performed comprehensive transcriptome analyses using microarrays of our established gastric cancer cell lines.
2023-04-01 | GSE172197 | GEO
Project description:Establishment and molecular characterization of 239 peritoneally-metastatic cancer cell lines from 170 patients’ ascites in 11 kinds of cancers mainly consisted of gastric, pancreatic, and ovarian cancer. We performed comparative transcriptome analyses using microarrays between our established cancer cell lines and cell-bank derived cancer cell lines
2023-02-21 | GSE172159 | GEO
Project description:Gastric cancer is one of the most lethal malignancies with high mortality and gastric cancer-specific biomarker is need due to the lack of specific method for early screening, diagnosis, and prognosis of the patients with gastric cancer. Ascites is known for an important source for conducing biomarker discovery because it contains the secreted proteins from malignant cells, growth factors, and cytokines. In this study, we have conducted a comprehensive proteome study using ascites of patients with inflammatory diseases and gastric cancer. In the discovery stage, we have identified 2761 ascites-specific proteins, where 234 proteins were quantitated using the label free quantitation method, the normalized spectral abundance factor (NSAF); 152 and 82 proteins showed up and down-regulated pattern, respectively. Our ascites proteome can be used as baseline data for the discovery of novel biomarkers of the gastric cancer.
2018-04-16 | PXD002213 | Pride
Project description:To define the cellular characteristics of malignant ascites of advanced gastric cancer patients and search for therapeutic strategies, we applied single cell RNA sequencing to cancer cells and tumor associated macrophages (TAM), present in large numbers in malignant ascites. We analyzed 180 cells from 4 malignant ascites and 1 cerebrospinal fluid metastasis. The results indicate that the anti-inflammatory characteristics of the tumor associated macrophages are concocted by the tumor cells. By constructing reference transcriptomes for M1 and M2 type macrophages, we found a strong non-inflammatory property of macrophages recovered from the malignant ascites of gastric cancer.
2020-12-10 | GSE140182 | GEO
Project description:Histone deacetylation is involved in epigenetically mediated tumor suppressor genes silencing. The screen of genes modulated by histone acetylation in gastric cancer maycontribute to the identification of potential therapeutic targets. In this experiment we aimed to identify differentially expressed genes by comparing Trichostatin A (TSA)-treated and non-treated gastric cancer cell lines. TrichostatinA (TSA) belongs to the hydroxamic acid chemical class histone deacetylaseinhibitors, which selectively inhibit the class I and II mammalian histonedeacetylase families. As expected, TSA acetylates promoter regions, or disables corepressors, resulting in increased gene expression. 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.
2016-10-21 | E-MTAB-4736 | biostudies-arrayexpress
Project description:Regions of recurrent genomic amplification and deletion are frequently observed in primary gastric cancers (GC). However, identifying specific oncogenes and tumor suppressor genes within these regions can be challenging, as they often cover tens to hundreds of genes. Here, we combined high-resolution array-based comparative genomic hybridization (aCGH) with gene expression profiling to target genes lying within focal high-level amplifications in GC cell lines, and identified RAB23 as an amplified and overexpressed Chr 6p11p12 gene in Hs746T cells. High RAB23 protein expression was also observed in some lines lacking RAB23 amplification, suggesting additional mechanisms besides gene amplification for up-regulating RAB23. siRNA silencing of RAB23 reduced the invasive potential of both amplified and nonamplified GC cell lines. RAB23 gene amplifications were observed in 13% of primary gastric carcinomas. In two independent patient cohorts, RAB23 transcript and protein expression was significantly associated with diffuse-type gastric cancer (dGC) compared to intestinal-type gastric cancer (iGC), providing further evidence that dGC and iGC likely represent two molecularly distinct tumor types. Our study demonstrates that investigating focal chromosomal amplifications by combining highresolution aCGH with expression profiling is a powerful general strategy for identifying novel cancer genes in recurrent regions of chromosomal aberration. Keywords: gastric cancer cell lines, comparative genomic hybridization, gene expression profiling Affy 100K SNP profiling and 32K BAC Array profiling for 7 Gastric Cancer Cell Lines
2010-05-14 | E-GEOD-10611 | biostudies-arrayexpress
Project description:Gastric cancer (GC) is a leading cause of cancer-induced mortality with poor prognosis with metastasis. However, the mechanism of gastric carcinoma lymph node metastasis remains unknown due to traditional bulk-leveled approaches mask roles of subpopulations. To answer questions from the gastric carcinoma intratumoral perspective in the metastasis, we performed single-cell level analysis on three gastric cancer patients with primary cancer and paired metastatic lymph node cancer tissues using scRNA-seq. Results showed distinct carcinoma profiles from each patient, and diverse microenvironmental subsets were shared by a different patient. Clustering data showed significant intratumoral heterogeneity. Results also revealed a subgroup of cells bridging the metastatic group and primary group, implying the transition state of cancer during the metastatic process. In the present study we obtained a more comprehensive picture over gastric cancer lymph node metastasis, and we discovered some GC lymph node metastasis marker genes (ERBB2, CLDN11 and CDK12), as well as potential gastric cancer evolutionary driving genes (FOS and JUN), which provide a basis for the treatment of heterogeneity.
2020-12-06 | GSE158631 | GEO
Project description:Regions of recurrent genomic amplification and deletion are frequently observed in primary gastric cancers (GC). However, identifying specific oncogenes and tumor suppressor genes within these regions can be challenging, as they often cover tens to hundreds of genes. Here, we combined high-resolution array-based comparative genomic hybridization (aCGH) with gene expression profiling to target genes lying within focal high-level amplifications in GC cell lines, and identified RAB23 as an amplified and overexpressed Chr 6p11p12 gene in Hs746T cells. High RAB23 protein expression was also observed in some lines lacking RAB23 amplification, suggesting additional mechanisms besides gene amplification for up-regulating RAB23. siRNA silencing of RAB23 reduced the invasive potential of both amplified and nonamplified GC cell lines. RAB23 gene amplifications were observed in 13% of primary gastric carcinomas. In two independent patient cohorts, RAB23 transcript and protein expression was significantly associated with diffuse-type gastric cancer (dGC) compared to intestinal-type gastric cancer (iGC), providing further evidence that dGC and iGC likely represent two molecularly distinct tumor types. Our study demonstrates that investigating focal chromosomal amplifications by combining highresolution aCGH with expression profiling is a powerful general strategy for identifying novel cancer genes in recurrent regions of chromosomal aberration. Keywords: gastric cancer cell lines, comparative genomic hybridization, gene expression profiling
2008-12-29 | GSE10611 | GEO
Project description:Methylation profiling in gastric cancer with malignant ascites.
| PRJNA714888 | ENA
Project description:Gastric cancer (GC) constitutes a significant cause of cancer-related mortality worldwide, with metastatic patterns including hematogenous, peritoneal, and ovarian routes. Although GC gene expression patterns have been extensively researched, the metastasis-specific gene expression landscape remains largely unexplored. This study undertook a whole transcriptome sequencing analysis of 66 paired primary and metastatic (hematogenous, peritoneal, or ovarian) GC tumors from 14 patients, leading to the identification of 122 unique metastasis-specific epithelial-mesenchymal transition (msEMT) genes. These genes demonstrated varying expression patterns depending on the metastatic route, suggesting route-specific molecular mechanisms in GC metastasis. High expression of msEMT genes in primary tumors was associated with more frequent CDH1 mutations, the genomically stable subtype, and poor prognosis in The Cancer Genome Atlas GC cohort. This association was further corroborated by poor prognosis and high predictive performance for peritoneal or ovarian recurrence in two independent cohorts (GSE66229; n=300, GSE84437; n=433). Single-cell RNA sequencing analysis of primary tumors (GSE167297) and four independent ascites samples from GC patients revealed that msEMT genes were predominantly expressed in diverse fibroblast sub-populations, rather than cancer cells. This study illuminates the route-specific mechanisms and underlines the significance of msEMT genes and cancer-associated fibroblasts in GC metastasis, highlighting potential directions for future research.
2024-07-01 | GSE237876 | GEO