Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA239998 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression profiling of HPV-negative oropharyngeal cancers and Normal benign uvula, tonsil
| PRJNA240003 | ENA
Project description:Gene expression profiling of HPV-negative oropharyngeal cancers and Normal benign uvula, tonsil from European American patients
| PRJNA239999 | ENA
Project description:Gene expression profiling of HPV-inactive oropharyngeal cancers and normal benign tissue (uvula, tonsil) from European American patients
| PRJNA240000 | ENA
Project description: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. 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 oropharyngeal squamous cell carcinoma (OPC) and normal benign uvula/tonsil tissues and determine what biological processes and pathways are affected in HPV-negative OPCs. ANALYSIS 6: Two-condition, one-color experiment: HPV-negative oropharyngeal tumor samples and normal benign uvula/tonsil tissues. Biological replicates: 16 HPV negtive samples and 4 Normal samples.
2014-03-05 | E-GEOD-55547 | biostudies-arrayexpress
Project description: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-active OPCs and normal benign uvula/tonsil tissues and determine what biological processes and pathways are affected in HPV-active tumors. ANALYSIS 5: Two-condition, one-color experiment: HPV-active oropharyngeal tumor samples and normal benign uvula/tonsil tissues. Biological replicates: 12 HPV active samples and 4 Normal samples.
2014-03-05 | E-GEOD-55546 | biostudies-arrayexpress
Project description: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. This study aimed to compare the gene expression profiles of HPV-inactive oropharyngeal squamous cell carcinoma (OPC) and normal benign uvula/tonsil tissues from European American patients and determine what biological processes and pathways are affected in HPV-inactive OPCs in this ethnic group. ANALYSIS 7: Two-condition, one-color experiment: European American (EA) HPV-inactive oropharyngeal tumor samples and normal benign uvula/tonsil tissues. Biological replicates: 4 EA HPV inactive samples and 4 EA Normal samples.
2014-03-05 | E-GEOD-55548 | biostudies-arrayexpress
Project description: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. 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. HPV has been characterized as a risk factor for OPC based on race, life style and sexual behavior, impacting survival outcomes for both African American (AA) and European American (EA) patients. According to some reports, the rate of HPV-associated tumors is much lower in AA patients as compared to EA patients in United States. In general, however, AA males have a higher incidence of HNC than any other racial/gender group, and a mortality rate almost three-fold that observed in EA males. Overall, AA patients tend to present with more HPV-negative OPC and have worse prognosis as compared to both HPV-positive and HPV-negative EA patients. This study aimed to compare the gene expression profiles of HPV-negative oropharyngeal squamous cell carcinoma (OPC) and normal benign uvula/tonsil tissues from European American patients and determine what biological processes and pathways are affected in HPV-negative OPCs in EA patients. Additional datasets in this study explore gene expression differences in HNC from EA and AA patients. ANALYSIS 8: Two-condition, one-color experiment: European American (EA) HPV-negative oropharyngeal tumor samples and normal benign uvula/tonsil tissues. Biological replicates: 8 EA HPV active samples and 4 EA Normal samples.
2014-03-05 | E-GEOD-55549 | biostudies-arrayexpress
Project description:Gene expression profiling of European American HPV-active, HPV-inactive and HPV-negative oral and oropharyngeal cancers
| PRJNA240004 | ENA
Project description:Gene expression profiling of HPV-inactive and HPV-negative oropharyngeal cancers
| PRJNA240001 | ENA
Project description:Oropharyngeal squamous cell carcinoma (OPSCC) is diagnosed in 93,000 patients worldwide per year and 51,000 annual deaths can be attributed to this disease. OPSCCs are either human papillomavirus associated (HPV-positive) cancers or non-virally induced, primarily tobacco and alcohol associated (HPV-negative) cancers. MS analysis enabled the identification of naturally HLA-presented peptides in OPSCC tumor tissue. By comparative profiling against benign HLA ligandomic datasets, we demonstrated that tumor-associated peptides are HLA-presented on the cell surfaces of OPSCCs. The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi-) personalized strategies.
2023-02-27 | PXD033383 | Pride