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Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)

ABSTRACT: We report the first RNA-Seq experiments profiling the effects of DEK loss in HNSCC. Our data also incorporates HPV+ and HPV- tumors to idenfity HPV-dependent and -independent gene signatures. RNA-Seq of DEK-dependent gene signatures in HNSCC cell lines

ORGANISM(S): Homo sapiens

SUBMITTER: Susanne Wells

PROVIDER: E-GEOD-70462 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival.

Adams Allie K AK Bolanos Lyndsey C LC Dexheimer Phillip J PJ Karns Rebekah A RA Aronow Bruce J BJ Komurov Kakajan K Jegga Anil G AG Casper Keith A KA Patil Yash J YJ Wilson Keith M KM Starczynowski Daniel T DT Wells Susanne I SI

Oncotarget 20151201 41

The chromatin-binding DEK protein was recently reported to promote the growth of HPV+ and HPV- head and neck squamous cell carcinomas (HNSCCs). Relevant cellular and molecular mechanism(s) controlled by DEK in HNSCC remain poorly understood. While DEK is known to regulate specific transcriptional targets, global DEK-dependent gene networks in HNSCC are unknown. To identify DEK transcriptional signatures we performed RNA-Sequencing (RNA-Seq) in HNSCC cell lines that were either proficient or defi ...[more]

PMID: 26527316

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Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)

Project description:We report the first RNA-Seq experiments profiling the effects of DEK loss in HNSCC. Our data also incorporates HPV+ and HPV- tumors to idenfity HPV-dependent and -independent gene signatures.

2016-02-05 | GSE70462 | GEO

Methylome Analysis of FF HPV+ and HPV- HNSCC samples

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Comparison between HPV+ / p16+ versus the HPV-/p16- from HNSCC patients

Project description:Head and neck squamous cell carcinomas are heterogeneous neoplasms that show clinical and biological differences in association with the human papillomavirus (HPV). To provide adequate therapeutic strategies, biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico, thus in the present study, we analyze 414 cases of HNSCC, including those of the oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC). We determined the presence of HPV and p16 expression. Global expression profiles were analyzed with Affymetrix HTA 2.0 microarray in 25 selected cases HPV+/p16+ versus HPV-/p16-. In our study we analyze 25 samples derived from HNSCC patients. 18 samples were HPV-/p16- and 7 HPV+/p16+. We compared the HPV-/p16- versus the HPV+/p16+ and identified differentially expressed RNAs with a fold change greater than 1.5 or less than -1.5. These data were used to obtain 98 genes that are differentially expressed in absence of HPV. The present study offers information regarding clinical and molecular characteristics of HNSCC, both associated and unassociated with HPV, in Mexican patients.

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Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours.

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2016-09-01 | E-GEOD-72536 | biostudies-arrayexpress

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| PRJNA753515 | ENA