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A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation

ABSTRACT: OSCC is associated with substantial mortality and morbidity. In this study, we built on our previous molecular work to identify and validate a prognostic 13-gene signature that showed a higher ability than tumor stage in predicting survival for patients with HPV-negative oral squamous cell carcinoma (OSCC).

ORGANISM(S): Homo sapiens

PROVIDER: GSE41613 | GEO | 2013/03/07

SECONDARY ACCESSION(S): PRJNA177687

REPOSITORIES: GEO

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A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation

Project description:OSCC is associated with substantial mortality and morbidity. In this study, we built on our previous molecular work to identify and validate a prognostic 13-gene signature that showed a higher ability than tumor stage in predicting survival for patients with HPV-negative oral squamous cell carcinoma (OSCC). We previously reported 131 genes to be associated with survival in OSCC patients. In this study, we applied L1/L2-penalized Cox regression models to the Affymetrix array data from 97 HPV-negative OSCC patients on the 131 gene to identify a model for prediction of OSCC-specific survival. We then tested the model in an independent dataset and compared to tumor stage.

2013-03-07 | E-GEOD-41613 | biostudies-arrayexpress

A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation.

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A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation

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Genome-wide LOH and DNA copy number alteration in HPV-neg OSCC and their associations with disease-specific survival

Project description:Oral squamous cell carcinoma (OSCC) is associated with high case-fatality. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we examined paired DNA from peripheral blood and tumor cells to assess genome-wide LOH and DNA copy number alteration (CNA) and their associations with risk factors, tumor characteristics, and disease-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p, and 11q that seem to play an important role in oral cancer biology and survival from this disease. We used Affymetrix 6.0 SNP arrays to test paired DNA from peripheral blood and tumor cells isolated by laser capture microdissection from 75 patients with HPV-negative OSCC. Peripheral blood DNA is used as reference for CNA to LOH.

2016-03-23 | E-GEOD-68717 | biostudies-arrayexpress

Genome-wide LOH and DNA copy number alteration in HPV-neg OSCC and their associations with disease-specific survival

2016-03-23 | GSE68717 | GEO

Expression profiling of primary oral cavity squamous cell carcinoma (OSCC)

Project description:Gene expression profiling of 66 HPV-negative OSCC primary tumor was performed to identify gene expression that is related to lymph node metastasis and poor prognosis. These gene expression profiles were combined in silico with gene expression profiles of 84 OSCC primary tumors retrieved from GSE30788.

2017-08-10 | GSE85446 | GEO

MicroRNA sequencing and Novel HPV miRNA discovery in HPV cell lines and human tissue samples

Project description:Human papillomaviruses (HPV) preferentially infect keratinocytes of mucous membranes or skin and cause numerous benign and malignant lesions at different anatomical locations. A number of DNA viruses encode their own miRNAs as well. To date, no studies have been able to validate viral miRNAs in papillomavirus infected cells using standard sequencing or next generation sequencing techniques. We sequenced small RNA (sRNA) libraries of two HPV 16 immortalized cell lines, HPK IA and HPK II, and ten formalin fixed paraffin embedded (FFPE) tissue samples from HPV infected cervical epithelium by SOLiD 4 technology. We used the miRSeqNovel software, to predict novel miRNAs and their likely pre-miRNAs. We further validated (qRT-PCR, northern blotting and in situ hybridization) the candidate miRNAs in a number of tissue samples from HPV associated cervical disease and also in HPV 16 positive cell lines CaSki and SiHa. Altogether nine candidate microRNAs were identified. The expression of four out of five studied miRNAs was confirmed in human tissue or human epithelial cell lines harboring HPV 16. Small RNA (sRNA) libraries of two HPV 16 immortalized cell lines, HPK IA and HPK II, and ten formalin fixed paraffin embedded (FFPE) tissue samples from HPV infected cervical epithelium, were made according to SOLiD sequencing instructions.

2013-08-18 | E-GEOD-42380 | biostudies-arrayexpress

Genome wide DNA methylation in oral squamous cell carcinoma (OSCC) disease and adjacent normal tissue samples

Project description:Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

2017-03-09 | GSE87053 | GEO

Comparative gene expression profiling of tobacco-associated HPV-positive versus negative oral squamous carcinoma cell lines

Project description:HPV-positive oral squamous cell carcinomas (OSCCs) are specific biological and clinical entities, characterized by a more favorable prognosis compared to HPV-negative OSCCs and occurring generally in non-smoking and non-drinking younger individuals. However, poor information is available on the molecular and the clinical behavior of HPV-positive oral cancers occurring in smoking/drinking subjects. Thus, this study was designed to compare, at molecular level, two OSCC cell lines, both derived from drinking and smoking individuals and differing for presence/absence of HPV infection.

2019-12-01 | E-MTAB-6152 | biostudies-arrayexpress

MicroRNA sequencing and Novel HPV miRNA discovery in HPV cell lines and human tissue samples

2013-08-18 | GSE42380 | GEO

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