Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison between HPV+ / p16+ versus the HPV-/p16- from HNSCC patients

ABSTRACT: Head and neck squamous cell carcinomas are heterogeneous neoplasms that show clinical and biological differences in association with the human papillomavirus (HPV). To provide adequate therapeutic strategies, biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico, thus in the present study, we analyze 414 cases of HNSCC, including those of the oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC). We determined the presence of HPV and p16 expression. Global expression profiles were analyzed with Affymetrix HTA 2.0 microarray in 25 selected cases HPV+/p16+ versus HPV-/p16-. In our study we analyze 25 samples derived from HNSCC patients. 18 samples were HPV-/p16- and 7 HPV+/p16+. We compared the HPV-/p16- versus the HPV+/p16+ and identified differentially expressed RNAs with a fold change greater than 1.5 or less than -1.5. These data were used to obtain 98 genes that are differentially expressed in absence of HPV. The present study offers information regarding clinical and molecular characteristics of HNSCC, both associated and unassociated with HPV, in Mexican patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE181805 | GEO | 2021/12/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comparison between HPV+ / p16+ versus the HPV-/p16- from HNSCC patients

Project description:Comparison between HPV+ / p16+ versus the HPV-/p16- from HNSCC patients

| PRJNA753515 | ENA

Methylome Analysis of FF HPV+ and HPV- HNSCC samples

Project description:The analysis of the 6 methylomes by MeDIP-Seq comprise 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples Analysis of the 6 methylomes, comprising 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-01 | E-GEOD-38263 | biostudies-arrayexpress

450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples

Project description:The methylation analysis of 21 FFPE HPV+ HNSCC samples and 21 FPPE HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip Analysis of 42 450k methylation profiles, comprising 21 HPV+ HNSCC samples and 21 HPV- HNSCC samples

2012-11-30 | E-GEOD-38266 | biostudies-arrayexpress

Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours.

Project description:Purpose: Human papilloma virus (HPV) associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than HPV(-) negative cancer. This may be due, in part, to the higher number of tumour infiltrating lymphocytes (TIL) in HPV(+) tumours. We used RNAseq to evaluate whether these differences in clinical behaviour could be explained simply by a numerical difference in TILs or whether there was a fundamental difference between TILs in these two settings. Patients and methods: Twenty-three consecutive HNSCC cases with high and moderate TIL density were subjected to RNAseq analysis. Differentially expressed genes (DEG) between 10 HPV(+) and 13 HPV(-) tumours were identified with EdgeR. Immune subset analysis was performed using, FAIME (Functional Analysis of Individual Microarray Expression) and Immune gene transcript count analysis. Results: 1634 genes were differentially expressed. There was a dominant immune signature in HPV(+) tumours. After normalizing expression profiles for numerical differences in T cells and B cells, 437 significantly DEGs still remained. A B-cell associated signature emerged, which segregated HPV(+) from HPV(-) cancers and included CD200, STAG3, GGA2, SPIB and ADAM28. Differential expression of these genes was confirmed by real-time quantitative PCR and immunohistochemistry. Conclusion: In our dataset, the difference associated with T-cells between patients with HPV(+) and (-) HNSCC was predominantly numerical. However, when TIL numbers are corrected, a distinct differential B-cell signature was revealed. mRNA profiles of 10 HPV driven (HPV+) and 13 HPV independant (HPV-) head and neck squamous cell carcinoma (HNSCC) tumours were generated by RNA-Seq, using Illumina HiSeq 2000.

2016-09-01 | E-GEOD-72536 | biostudies-arrayexpress

450k Analysis of 3 FF HPV+ and 3 FF HPV- HNSCC samples

Project description:The methylation analysis of 3 FF HPV+ HNSCC samples and 21 FP HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip Analysis of 6 450k methylation profiles, comprising 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-30 | E-GEOD-38268 | biostudies-arrayexpress

Integration of p16/HPV DNA status with a 24-miRNA-defined molecular phenotype improves clinically relevant stratification of head and neck cancer patients

Project description:Head and neck squamous cell carcinomas (HNSCC) driven by human papillomavirus (HPV) generally have a more favourable prognosis. We hypothesized that HPV-positive HNSCC may be identified based on a miRNA signature according to their specific molecular pathogenesis and are characterized by a unique transcriptome compared to HPV-negative HNSCC. We characterized the miRNA-expression patterns of the tumors from 229 head and neck squamous cell carcinoma patients by Agilent miRNA microarrays in order to define a HPV-predicting miRNA signature.

2023-05-10 | GSE175509 | GEO

Methylome Analysis of FF HPV+ and HPV- HNSCC samples

Project description:The analysis of the 6 methylomes by MeDIP-Seq comprise 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-01 | GSE38263 | GEO

450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples

Project description:The methylation analysis of 21 FFPE HPV+ HNSCC samples and 21 FPPE HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

2012-11-30 | GSE38266 | GEO

450k Analysis of 3 FF HPV+ and 3 FF HPV- HNSCC samples

Project description:The methylation analysis of 3 FF HPV+ HNSCC samples and 21 FP HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

2012-11-30 | GSE38268 | GEO

Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours.

2016-09-01 | GSE72536 | GEO