Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA170824 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Biliary tract cancers (BTCs) are aggressive malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we report integrative analysis of 63 BTC cell lines via multi-omics and genome-scale CRISPR screens. We identify widespread EGFR dependency in BTC, alongside dependencies selective to anatomic subtypes. Additionally, we delineate strategies to overcome therapeutic resistance, with combined EGFR inhibition potentiating targeting of KRAS-mutant and FGFR2-fusion-driven models, and SHP2 inhibition effective in the latter context. Clustering RNA/protein expression and dependencies data revealed functional relationships transcending single-gene alterations, with biliary, squamous, or dual biliary/hepatocyte lineage signatures stratifying BTC models. These subtypes exhibit distinct dependency profiles— including cell fate transcription factors GRHL2, TP63, and HNF1B, respectively— and demonstrate prognostic significance in patient samples. Potential subtype-specific targetable vulnerabilities include Integrin-a3 and the detoxification enzyme UXS1. This cell line atlas reveals therapeutic targets in molecularly-defined BTCs, unveils disease subtypes, and provides a resource for therapeutic development.
2025-04-30 | GSE295371 | GEO
Project description:Recently, expression profiling of breast carcinomas has revealed gene signatures that predict clinical outcome, and discerned prognostically relevant breast cancer subtypes. Measurement of the degree of genomic instability provides a very similar stratification of prognostic groups. We therefore hypothesized that these features are linked. We used gene expression profiling of 48 breast cancer specimens that profoundly differed in their degree of genomic instability and identified a set of 12 genes that defines the two groups. The biological and prognostic significance of this gene set was established through survival prediction in published datasets from patients with breast cancer. Of note, the gene expression signatures that define specific prognostic subtypes in other breast cancer datasets predicted genomic instability in our samples. This remarkable congruence suggests a biological dependency of poor-prognosis gene signatures, breast cancer subtypes, genomic instability, and clinical outcome. Keywords: disease state analysis 44 samples
2009-11-30 | E-GEOD-11901 | biostudies-arrayexpress
Project description:Recently, expression profiling of breast carcinomas has revealed gene signatures that predict clinical outcome, and discerned prognostically relevant breast cancer subtypes. Measurement of the degree of genomic instability provides a very similar stratification of prognostic groups. We therefore hypothesized that these features are linked. We used gene expression profiling of 48 breast cancer specimens that profoundly differed in their degree of genomic instability and identified a set of 12 genes that defines the two groups. The biological and prognostic significance of this gene set was established through survival prediction in published datasets from patients with breast cancer. Of note, the gene expression signatures that define specific prognostic subtypes in other breast cancer datasets predicted genomic instability in our samples. This remarkable congruence suggests a biological dependency of poor-prognosis gene signatures, breast cancer subtypes, genomic instability, and clinical outcome. Keywords: disease state analysis
2009-12-01 | GSE11901 | GEO
Project description:Adenocarcinomas of the ampulla of Vater are classified as biliary cancers, though the exact epithelium of origin for these cancers is not known. We sought to molecularly classify ampullary adenocarcinomas in comparison to known adenocarcinomas of the pancreas, extrahepatic bile duct, and duodenum by gene expression analysis. We analyzed 32 fresh-frozen resected, untreated periampullary adenocarcinomas (8 pancreatic, 2 extrahepatic biliary, 8 duodenal, and 14 ampullary) using the Affymetrix U133 Plus 2.0 genome array.
2013-01-01 | E-GEOD-39409 | biostudies-arrayexpress
Project description:Introduction: Ampullary cancer is a relatively rare entity and usually treated by pancreatoduodenectomy followed by adjuvant therapy. The intestinal subtype is associated with markedly improved prognosis after resection. Only few cell lines are available for in vitro studies of ampullary cancer and they have not been collectively characterized. Methods: We characterized available ampullary cancer cell lines by subtype maker expression, epithelial-mesenchymal transition (EMT) features, growth and invasion, drug sensitivity and response to cancer-associated fibroblast conditioned medium (CAF-CM). Results: On the basis of EMT features, subtype marker expression, growth, invasion and drug sensitivity three types of cell lines could be distinguished: mesenchymal-like, pancreatobiliary-like and intestinal-like. In response to CAF-CM, enhanced growth, EMT induction as well as suppression of intestinal differentiation markers were observed, but in a heterogenous pattern. Also proteomic analysis of the CAF response distinguished intestinal-like from other cell lines. Discussion: Most of the available AMPAC cell lines seem to reflect a poorly differentiated pancreatobiliary or mesenchymal-like phenotype, consistent with their origin. We suggest that the best cell line model for intestinal-like AMPAC is the SNU869 cell line, while others seem to reflect aggressive AMPAC subtypes.
2016-03-14 | PXD002657 | Pride
Project description:Clinical heterogeneity of gastric cancer reflected in unequal outcome of treatment is poorly defined in molecular level, and molecular subtypes and their associated biomarkers have not been established to improve prognostification and treatment of gastric cancer. Using microarray technologies, we analyzed gene expression profiling data from patients with advanced gastric cancer and uncovered potential prognostic subtypes and identify gene expression signature associated with prognosis. Using microarray technologies, we analyzed gene expression profiling data from patients with advanced gastric cancer and uncovered potential prognostic subtypes and identify gene expression signature associated with prognosis.
2012-04-29 | E-GEOD-28541 | biostudies-arrayexpress
Project description:Gene expression profiling classifies lung squamous cell carcinomas with N1 positive lymph nodes
| PRJNA97219 | ENA
Project description:Adenocarcinomas of the ampulla of Vater are classified as biliary cancers, though the exact epithelium of origin for these cancers is not known. We sought to molecularly classify ampullary adenocarcinomas in comparison to known adenocarcinomas of the pancreas, extrahepatic bile duct, and duodenum by gene expression analysis.
2013-01-01 | GSE39409 | GEO
Project description:Introduction: Ampullary cancer is a relatively rare entity and usually treated by pancreatoduodenectomy followed by adjuvant therapy. The intestinal subtype is associated with markedly improved prognosis after resection. Only few cell lines are available for in vitro studies of ampullary cancer and they have not been collectively characterized. Methods: We characterized available ampullary cancer cell lines by subtype maker expression, epithelial-mesenchymal transition (EMT) features, growth and invasion, drug sensitivity and response to cancer-associated fibroblast conditioned medium (CAF-CM). Results: On the basis of EMT features, subtype marker expression, growth, invasion and drug sensitivity three types of cell lines could be distinguished: mesenchymal-like, pancreatobiliary-like and intestinal-like. In response to CAF-CM, enhanced growth, EMT induction as well as suppression of intestinal differentiation markers were observed, but in a heterogenous pattern. Also proteomic analysis of the CAF response distinguished intestinal-like from other cell lines. Discussion: Most of the available AMPAC cell lines seem to reflect a poorly differentiated pancreatobiliary or mesenchymal-like phenotype, consistent with their origin. We suggest that the best cell line model for intestinal-like AMPAC is the SNU869 cell line, while others seem to reflect aggressive AMPAC subtypes.
2017-03-29 | MSV000080802 | MassIVE
Project description:Staging of biliary atresia at diagnosis by molecular profiling of the liver
2025-01-24 | E-GEOD-15235 | ExpressionAtlas