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Series GSE55545 Query DataSets for GSE55545
Status Public on Mar 05, 2014
Title Gene expression profiling of HPV-inactive and HPV-negative oropharyngeal cancers
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Head and neck cancer (HNC) is the fifth most common malignancy worldwide with an annual mortality rate of 200,000. About 90% of HNC can be classified as head and neck squamous cell carcinomas (HNSCC), of which approximately 75% are attributed to alcohol and tobacco consumption and 25 are associated with human papillomavirus (HPV), predominantly HPV16. HPV-associated OPC have better prognosis and a more favorable response to therapy as compared to HPV-negative tumors. Viral oncoproteins are capable of transforming primary human keratinocytes from either genital or oral epithelia in vitro and most likely play the same role in vivo, by disrupting cell-cycle regulatory pathways leading to a genetic progression to ano-genital cancer and OPC. However, the precise mechanisms by which HPV mediates malignant transformation of keratinocytes in the upper digestive tract epithelia are not entirely clear. HPV E7-mediated inactivation of pRb results in overexpression of p16INK4A, which is commonly used as a clinical surrogate marker for HPV positivity/activity. However, high p16INK4A alone has insufficient sensitivity and specificity as a biomarker of HPV positivity in different mucosal sub-sites of HNC. Therefore, increasing emphasis is being placed on the assessment of viral load and E7 oncogene expression, resulting in further classification of HPV positive OPC as HPV-active and HPV-inactive. Differences in risk factors, age of presentation, clinical behavior and gene expression profiles indicate that HPV-positive and HPV-negative tumors develop via different molecular mechanisms and are biologically distinct. This study aimed to compare the gene expression profiles of HPV-negative and HPV-inactive OPCs from both African American and European American patients, and determine their biological and racial differences.
Overall design ANALYSIS 4: Four-condition, one-color experiment: African American (AA) HPV-inactive, African American (AA) HPV-negative, European American (EA) HPV-inactive, European American (EA) HPV-negative oropharyngeal tumor samples. Biological replicates: 4 AA HPV Inactive samples, 8 AA HPV Negative samples, 4 EA HPV Inactive samples and 8 EA HPV Negative samples,
Contributor(s) Tomar S, Altomare D, Kowli S, Kassler S, Sutkowski N, Gillespie MB, Creek KE, Pirisi L
Citation(s) 25899179
Submission date Mar 04, 2014
Last update date Apr 23, 2018
Contact name Diego Altomare
Organization name University of South Carolina
Department Department of Drug Discovery and Biomedical Sciences
Lab Functional Genomics Core
Street address 715 Sumter Street, Room 617
City Columbia
State/province SC
ZIP/Postal code 29208
Country USA
Platforms (1)
GPL17077 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)
Samples (24)
GSM1339005 Analysis 4: AA - HPV Inactive - Biological replicate 1
GSM1339006 Analysis 4: AA - HPV Inactive - Biological replicate 2
GSM1339007 Analysis 4: AA - HPV Inactive - Biological replicate 3
This SubSeries is part of SuperSeries:
GSE55550 Gene expression profiles of oral and oropharyngeal cancers from European American and African American patients
BioProject PRJNA240001

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE55545_RAW.tar 73.1 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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