Genomic characterization of head and neck cancer cell lines
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PROVIDER: PRJNA453456 | ENA |
REPOSITORIES: ENA
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Project description:Genomic characterization of head and neck cancer cell lines
| PRJNA453457 | ENA
Project description:To provide full characterization of genome changes in six commonly used head and neck cancer cell lines. These data will serve as an excellent resource when designing future experiments that attempt to model HNSCC behaviour. Six commonly used ATCC head and neck cancer cell lines are analyzed.
2010-06-25 | E-GEOD-16872 | biostudies-arrayexpress
Project description:<p>Head and neck squamous cell carcinoma (HNSCC) is the sixth leading cancer by incidence worldwide(1). Various chemical carcinogens (tobacco, alcohol and betel nut), human papillomavirus (HPV) infection, and genetic predisposition contribute to the etiology of HNSCC, and to the complex genetic alterations in tumor subsets that differ in prognosis and response to therapies (2).</p> <p>Recently, a comprehensive landscape of genomic and transcriptomic alterations in HNSCC tumors has emerged from The Cancer Genome Atlas (TCGA) Network (3). TCGA revealed novel and previously recognized gene and chromosomal region copy number alterations (CNAs), mutations, and expression clusters, and defined their frequency, co-occurrence, and relationship to common and rare subtypes of HPV(-) and (+) tumors that vary in prognosis. To identify cell line models for determining the functional role and therapeutic importance of these alterations, we are performing whole exome and RNA sequencing and bioinformatic analysis of an expanded panel of 15 HPV(-) and 11 HPV(+) HNSCC cell lines and primary oral keratinocytes.</p> <p>We find that the recurrent genomic alterations in cell lines are remarkably consistent with those found in more aggressive tumors, from which cell lines have traditionally been most readily adapted to culture (4). Genome-wide correlation of CN (copy number) with expression identified a suite of potential drivers or modifier genes that differ by HPV status, and are of potential biologic and therapeutic relevance. Further, our findings elucidate and validate genomic alterations underpinning numerous discoveries made with these widely-used and recently derived HNSCC lines, and provide a roadmap for their potential use as models for future studies of tumor subtypes with worse prognosis.</p> <p>References</p> <p> <ol> <li>Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. CA Cancer J Clin. 2015;65(2):87-108.</li> <li>Van Waes C, Musbahi O. Genomics and advances towards precision medicine for head and neck squamous cell carcinoma. Laryngoscope Investig Otolaryngol. 2017;2(5):310-9.</li> <li>Cancer Genome Atlas N. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015;517(7536):576-82.</li> <li>White JS, Weissfeld JL, Ragin CC, Rossie KM, Martin CL, Shuster M, et al. The influence of clinical and demographic risk factors on the establishment of head and neck squamous cell carcinoma cell lines. Oral Oncol. 2007;43(7):701-12.</li> </ol> </p>
| phs001581 | dbGaP
Project description:To provide full characterization of genome changes in six commonly used head and neck cancer cell lines. These data will serve as an excellent resource when designing future experiments that attempt to model HNSCC behaviour.
2010-06-26 | GSE16872 | GEO
Project description:Two HPV(+) head and neck cancer cell lines (UPCI-SCC-090, UM-SCC-104), one HPV(–) head and neck cancer cell line (FaDu) and one nasopharyngeal epithelial cell line (NP69SV40T) were subjected to RNA-seq analysis.
2023-01-06 | GSE211322 | GEO
Project description:Genomic Sequencing of Head and Neck Cancer
| PRJNA74917 | ENA
Project description:Genomic Analysis of Head and Neck Cancers
| PRJNA476029 | ENA
Project description:Genomic Analysis of Head and Neck Cancers
| PRJNA476030 | ENA
Project description:Transcriptome analysis in head and neck cancer cell lines, FaDu and UMSCC47 with and without 5-aza'2-deoxycytidine(Aza)/trichostatin A(TSA) treatment.
2018-05-10 | GSE98805 | GEO
Project description:This study investigated the use of three different established cell sorting strategies to isolate and characterize stem cells from head and neck cancer cell lines. Five low passage cell lines were subjected to cell sorting based on Hoechst side population, Aldefluor and CD44 expression. Isolated cell populations were studied for gene expression, radiosensitivity and chemosensitivity to cis-platin and paclitaxel Each sorting method identified a different set of genes associated with different Gene Ontology categories with mitosis being the only common category. CD44 associated gene changes were almost exclusively associated with cell cycle and in particular mitosis. There were no significant differences in radiosensitivity or cis-platin sensitivity of stem or non-stem cells but CD44 isolated stem cells were more resistant to paclitaxel Five head and neck cell lines were used to isolate cancer stem cells by 3 isolation methods. For each isolation method, cancer stem cell enriched populations (n=5) were compared to cancer stem cell depleted populations (n=5). The resulting gene expression patterns were compared among the 3 isolation methods.
2014-03-02 | E-GEOD-55487 | biostudies-arrayexpress