Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets

ABSTRACT: Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets

PROVIDER: PRJNA1254299 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR33263876_1.fastq.gz	Fastqsanger.gz
	SRR33263876_2.fastq.gz	Fastqsanger.gz
	SRR33263877_1.fastq.gz	Fastqsanger.gz
	SRR33263877_2.fastq.gz	Fastqsanger.gz
	SRR33263878_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets

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

Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets

Project description:Biliary tract cancers (BTCs) are lethal malignancies, including intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Through multi-omics profiling and CRISPR screens of 63 BTC cell lines, we identify widespread EGFR dependency and subtype-specific vulnerabilities with predictive markers. Strategies to overcome targeted therapy resistance include EGFR inhibition potentiating mutant-KRAS and FGFR inhibition, while SHP2 inhibition counters FGFR inhibitor resistance. Clustering by gene/protein expression and dependencies reveals functional subtypes ductal, squamous, and bi-lineage each with distinct survival dependencies. Transcriptional analysis of patient samples highlights the prognostic value of this classification. This BTC cell line atlas uncovers therapeutic targets, defines disease subtypes, and serves as a critical resource for BTC research. Multiplexed proteomics was performed using TMT tags (TMT1 to TMT12) and TMTpro tags (TMT13 to TMT17) and the SPS3 method on an Orbitrap Fusion Lumos instrument. The sample key is provided as an excel file as a metadata file.

2025-03-07 | MSV000097266 | MassIVE

Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets

Project description:Purpose: Biliary tract cancers (BTCs) carry a very poor prognosis and have no approved targeted therapies. Recent genomic profiling of primary BTCs identified a number of potentially actionable drug targets, however accurate model systems to evaluate these targets are currently lacking. The purpose of this study was to compare the genomic landscape of commonly used BTC cell lines to primary BTCs, and to utilize these models for drug target evaluation. Design: Twenty BTC cell lines were profiled by RNA-seq analysis. Results: Transcriptomic profiling of BTC cell lines identified two subtypes, enriched for epithelial and mesenchymal genes respectively, which were also identified in primary BTC. Conclusions: Cell lines harbor similar genomic alterations to primary BTCs. Integration of cell line and primary cancer data identify novel molecular subsets, and highlight specific molecular vulnerabilities in BTC.

2019-10-12 | GSE138772 | GEO

MicroRNA markers for the diagnosis of pancreatic and biliary tract cancers

Project description:MicroRNAs from serum samples could detect pancreatic and biliary tract cancer patients more accurately than other traditional markers. Prospective miRNA markers for pancreatic/biliary tract cancer were selected in the training cohort. Using these miRNAs, discriminant analysis was performed, and the diagnostic accuracy, sensitivity and specificity were calculated in the test cohort.

2015-03-01 | E-GEOD-59856 | biostudies-arrayexpress

Sphere cultured biliary tract cancer cell lines SNU245 and SNU1196

Project description:We analyzed sphere cultured biliary tract cancer cell lines and analysed cancer stem cells asociated-differentially expressed genes by microarray analysis. biliary tract cancer stem cells(CSCs) associated DEG

2024-03-27 | GSE233893 | GEO

Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets

Project description:Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets

| PRJNA577107 | ENA

Project description:Tumour and adjacent components from human resected biliary tract cancers were characterised for the expression of immunorelated transcripts

2018-02-14 | GSE90698 | GEO

Project description:Adjacent components from human resected biliary tract cancers were characterised for the expression of immunorelated transcripts

2018-02-14 | GSE90699 | GEO

MicroRNA markers for the diagnosis of pancreatic and biliary tract cancers

Project description:MicroRNAs from serum samples could detect pancreatic and biliary tract cancer patients more accurately than other traditional markers.

2015-03-01 | GSE59856 | GEO

Differences in the biliary microbiome between biliary tract cancer and benign biliary disease

Project description:Differences in the biliary microbiome between biliary tract cancer and benign biliary disease

| PRJEB96013 | ENA