NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE65858 Query DataSets for GSE65858
Status Public on Jun 24, 2015
Title Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck cancer
Organism Homo sapiens
Experiment type Expression profiling by array
Summary A growing proportion of head and neck squamous cell carcinomas (HNSCC) is associated with the human papilloma virus (HPV), particularly HPV16. We compare tumors with different HPV16 DNA and RNA (E6*I) status from 290 consecutively recruited HNSCC patients by gene expression profiling and targeted sequencing of 50 genes. We confirm that the HPV16 DNA+ RNA+ tumors are molecularly distinct from the HPV-negative (DNA-) HNSCC and have elevated expression of cell cycle genes and rare TP53 mutations (3.6%, 1/28). We show that tumors with non-transcriptionally active HPV16 (DNA+ RNA-) are similar to HPV DNA- tumors regarding gene expression and frequency of TP53 mutations (47%, 8/17 and 43%, 72/167, respectively). Furthermore, we identify four gene expression clusters. They moderately but significantly differ in overall survival. One cluster exhibits high expression of immune response genes (IR) and contains most of the HPV16 DNA+ RNA+ patients. The IR cluster and disruptive TP53 mutations are associated with lymph node metastasis independent of HPV16 status and we validate each of these associations in another large data set. Consistent with earlier studies, disruptive TP53 mutations are prognostically unfavorable. Our findings underscore the importance of measuring the HPV16 RNA (E6*I) and TP53-mutation status for patient stratification and for the first time identify associations of an immune response-related gene expression cluster and TP53 mutations with lymph node metastasis in HNSCC.
 
Overall design A total of 300 samples were considered. Quality control procedures were applied to microarray probe-level intensity files. A total of 270 tumor arrays remained after removing low-quality arrays, duplicate arrays, and arrays from non-HNSCC samples. Expression values were log2-transformed and normalized using RSN.
 
Contributor(s) Wichmann G, Rosolowski M
Citation(s) 26095926
Submission date Feb 11, 2015
Last update date Aug 13, 2018
Contact name Maciej Rosolowski
E-mail(s) maciej.rosolowski@imise.uni-leipzig.de
Organization name Institute for Medical Informatics, Statistics and Epidemiology (IMISE)
Street address Härtelstr. 16-18
City Leipzig
ZIP/Postal code 04107
Country Germany
 
Platforms (1)
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Samples (270)
GSM1607684 GW_001 Head and neck squamous cell carcinoma Illumina HT12v4
GSM1607685 GW_003 Head and neck squamous cell carcinoma Illumina HT12v4
GSM1607686 GW_004 Head and neck squamous cell carcinoma Illumina HT12v4
Relations
BioProject PRJNA275235

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
GSE65858_Non-normalized_data.txt.gz 45.5 Mb (ftp)(http) TXT
GSE65858_RAW.tar 26.2 Mb (http)(custom) TAR
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap