Ena-DATASET-GARVAN-29-10-2015-06:17:06:937-61 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001001660 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:High-risk human papillomavirus (hr-HPV) has been implicated in a subset of patients with esophageal adenocarcinoma (EAC). We therefore hypothesized that HPV associated EAC may have distinct genomic aberrations compared with viral negative esophageal cancer as shown in Head and Neck cancer and cervical cancer. Whole exome sequencing (WES) was performed to explore the mutational landscape and potential molecular signature of HPV positive versus HPV negative EAC, which includes four hr-HPV-positive and 8 HPV-negative treatment naive fresh-frozen EAC tissue specimens and matched normal tissues.
| EGAS00001001340 | EGA
Project description:To further explore the expression profile of lncRNAs and mRNAs in cervical cancer, six cases of HPV-positive cervical cancer tissues (including three HPV16 and three HPV18 positive patients) and three HPV-negative normal cervical tissues were collected randomly that were confirmed by histopathological. These patients did not accept any local or systemic treatment.
2023-05-25 | GSE228568 | GEO
Project description:Metagenomic profiling in hr-HPV positive women
| PRJEB59411 | ENA
Project description:Purpose: We aim to identify irradiation-induced transciptional changes in HPV-positive and HPV-negative HNSCC cell lines in vitro. Methods: Cells were seeded to tissue culture flasks and irradiated after adherence, with 0 Gy or 4 Gy carbon ions or 4 Gy photons or 8 Gy photons. Analysis was performed 4h and 48h and 72h after irradiation Results: Analysis of the data reveals a clear difference between irradiated and unirradiated samples, as well as between HPV-positive and HPV-negative HNSCC cells Conclusion: Transcriptomic changes are dependent on HPV Status and irradiation, but independent from the type of irradiation.
2022-05-11 | GSE198100 | GEO
Project description:Human papillomaviruses (HPVs) are associated with nearly all cervical cancers (CCs), 20-30% of head and neck cancers (HNCs), and other cancers. Because HNCs also arise in HPV-negative patients, this type of cancer provides unique opportunities to define similarities and differences of HPV-positive versus HPV-negative cancers arising in the same tissue. Here, we describe genome-wide expression profiling of 84 HNCs, CCs and site-matched normal epithelial samples in which we used laser capture microdissection to enrich samples for tumor-derived versus normal epithelial cells. This analysis revealed that HPV+HNCs and CCs differed in their patterns of gene expression yet shared many changes compared to HPV-HNCs. Some of these shared changes were predicted, but many others were not. Notably, HPV+HNCs and CCs were found to be upregulated in their expression of a distinct and larger subset of cell cycle genes than observed in HPV-HNC. Moreover, HPV+ cancers over-expressed testis-specific genes that are normally expressed only in meiotic cells. Many, though not all, of the hallmark differences between HPV+HNC and HPV-HNC were a direct consequence of HPV and in particular the viral E6 and E7 oncogenes. This included a novel association of HPV oncogenes with testes specific gene expression. These findings in primary human tumors provide novel biomarkers for early detection of HPV+ and HPV- cancers, and emphasize the potential value of targeting E6 and E7 function, alone or combined with radiation and/or traditional chemotherapy, in the treatment of HPV+ cancers. Keywords: Gene expression ptofiles of primary cancers
2007-05-15 | GSE6791 | GEO
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:mRNA sequencing was performed on 10 oropharyngeal cancer cell lines (5 HPV-positive and 5 HPV-negative cell lines) for this project. Two cell lines (CU-OP-17 and CU-OP-20) were newly derived from HPV-negative and HPV-positive tonsil cancers, respectively (described in " Sensitivity of human papillomavirus-positive and -negative oropharyngeal cancer cell lines to ionizing irradiation" by Holzhauser et al. This study was performed with the goal to identify differences in gene expression between irradiated and non-irradiated cell line samples. Additionally, the aim was to identify possible changes in genes, involved in DNA repair or DNA damage response of the HPV-positive and HPV-negative cell lines. The data published showed an increase of HPV integration sites after irradiation. Additionally, all HPV-positive cell lines in this study showed expression of HPV encoded genes. However, no direct correlation of changes or expression of DNA repair genes was identified.
2020-07-08 | GSE153966 | GEO
Project description:Genome wide DNA methylation profiling of HPV positive and HPV negative head and neck squamous cell cancer (HNSCC) samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across approximately 485577 CpGs in 4 HPV positive and 4 HPV negative HNSCC tumors
2015-03-21 | GSE67114 | GEO
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.
2014-03-05 | GSE55549 | GEO