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| Status |
Public on Oct 12, 2019 |
| Title |
Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
20 biliary tract cancer cell lines were profiled by RNA-seq analysis.
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| Contributor(s) |
Lau DK, Mouradov D, Wasenang W, Luk I, Scott CM, Williams D, Yeung Y, Limpaiboon T, Iatropoulos G, Jenkins L, Reehorst CM, Chionh F, Nikfarjam M, Croagh D, Dhillon AS, Weickhardt AJ, Tebbutt NC, Sieber OM, Mariadason JM |
| Citation(s) |
31731200 |
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| Submission date |
Oct 11, 2019 |
| Last update date |
Jan 20, 2020 |
| Contact name |
John M Mariadason |
| E-mail(s) |
john.mariadason@onjcri.org.au
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| Phone |
+613 9496 3068
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| Organization name |
Olivia Newton-John Cancer Research Institute
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| Department |
Gastrointestinal Cancers
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| Lab |
Oncogenic Transcritpion
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| Street address |
Austin Health, 145 Studyley Road
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| City |
Heidelberg |
| State/province |
Victoria |
| ZIP/Postal code |
3084 |
| Country |
Australia |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA577107 |
| SRA |
SRP225209 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE138772_BTC_gene_counts.txt.gz |
639.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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