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ABSTRACT: Transcriptomic Analysis of Contralateral Healthy Mucosa in Oropharyngeal Squamous Cell Carcinoma (OPSCC) Patients

PROVIDER: PRJNA1069986 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27753390.fastq.gz	Fastqsanger.gz
	SRR27753391.fastq.gz	Fastqsanger.gz
	SRR27753392.fastq.gz	Fastqsanger.gz
	SRR27753393.fastq.gz	Fastqsanger.gz
	SRR27753394.fastq.gz	Fastqsanger.gz

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DNA methylation analysis in oropharyngeal cancer [450K array]

Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.

2020-01-20 | GSE124464 | GEO

DNA methylation analysis in oropharyngeal cancer [EPIC array]

Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium MethylationEPIC BeadChip Kit was used to obtain DNA methylation profiles across more than 850,000 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.

2020-01-20 | GSE124632 | GEO

DNA methylation analysis in head and neck cancer cells

Project description:DNA methylation analysis in oropharyngeal squamous carcinoma(OPSCC) samples, oropharyngeal non-cancerous mucosa samples and head and neck cancer cell lines, FaDu and UMSCC47 before and after 5-aza'2-deoxycytidine(Aza)/trichostatin A(TSA) treatment. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 13 OPSCC samples, 4 non-cancerous mucosa samples and 2 FaDu with and without Aza/TSA treatment and 2 UMSCC47 with and without Aza/TSA treatment.

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Expression profiling of HPV+ Patient Derived Xenografts (PDXs) by high throughput sequencing

Project description:The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased in recent years. RNAseq was performed for systems-based analysis of cellular pathways involved in HPV+ve OPSCCs.

2025-01-10 | GSE193388 | GEO

The HLA-ligandome of oropharyngeal squamous cell carcinomas reveals shared tumor-exclusive peptides for semi-personalized vaccination

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

A proteomic signature for human papillomavirus-associated oropharyngeal squamous cell carcinoma predicts patients at high risk of recurrence

Project description:The incidence of human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) is increasing and effective treatment for targeting the subset of patients at high risk for recurrence remains a significant clinical challenge. In this study, pre-treatment tumour biopsies were used for proteomic analysis by data-independent acquisition mass spectrometry (DIA-MS) to identify protein and peptide biomarker signatures able to stratify patients at low, intermediate, or high-risk of recurrence. For further details, refer to the publication that accompanies this data deposition.

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Patients with early stage oropharyngeal squamous cell carcinoma can be identified with label-free serum proteomics

Project description:Increased incidence of oropharyngeal squamous cell carcinoma (OPSCC) is mainly related to Human Papilloma Virus (HPV) infection. As OPSCCs are often diagnosed at an advanced stage, mortality and morbidity remain high. There are no diagnostic biomarkers for early stage detection of OPSCC. Serum from 25 patients with stage I-II OPSCC and 12 disease- individuals were studied with quantitative label-free proteomics using ultra-definition MSE. Statistical analyses were performed to identify proteins most reliably distinguishing early stage OPSCCs from controls. P16 was used as a surrogate marker for HPV. P16-positive and -negative tumours were also analysed separately. With two or more unique proteins per identification, 176 proteins were quantified. A clear separation between patients with early-stage tumours and controls was seen in principal component analysis. Latent structures discriminant analysis identified 96 proteins most reliably differentiating OPSCC patients from controls, with 13 upregulated and 83 downregulated in study cases. The set of proteins was studied further with network, pathway and protein-protein interaction analyses, and found to participate in e.g. lipid metabolism. We identified patients with early stage OPSCC from controls based on their serum proteome, and suggest a protein set for further evaluation as a diagnostic biomarker panel for OPSCC.

2018-07-11 | PXD008445 | Pride

The HLA-ligandome of oropharyngeal squamous cell carcinomas reveals shared tumor-exclusive peptides for semi-personalized vaccination

2025-11-18 | MSV000099949 | MassIVE

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Project description:Human papillomavirus (HPV)-related multiphenotypic sinonasal carcinoma (HMSC) is a recently described rare tumor that is morphologically similar to high grade adenoid cystic carcinoma (ACC), but clinically distinct. We utilized single-cell RNA sequencing (scRNA-seq) to characterize transcriptional heterogeneity in a human HMSC tumor and compared it to published ACC and oropharyngeal squamous cell carcinoma (OPSCC) scRNA-seq datasets.

2025-10-22 | GSE293187 | GEO

A Prognostic Gene Expression Signature for Oropharyngeal Squamous Cell Carcinoma

Project description:Background: Robust prognostic stratification of patients with oropharyngeal squamous cell carcinoma (OPSCC) is important for developing individualized treatment plans. This study was conducted to develop and validate a clinically feasible prognostic classifier based on transcriptome-wide gene expression profiles. Methods: Tumor tissues were collected from 208 OPSCC patients treated at Washington University in St. Louis and 115 OPSCC patients treated at Vanderbilt University, used for model training and validation, respectively. OPSCC patients (n = 70) from the TCGA cohort were also included for independent validation. Based on RNA-seq profiling data, Cox proportional hazards regression analysis was performed to identify genes associated with disease outcomes. Then, Lasso-penalized multivariate survival models were constructed to identify biomarker genes for developing a prognostic gene signature. Findings: A 60-gene signature was identified by RNA-seq profiling analysis. Computed risk score of the gene signature was significantly predictive of 5-year overall survival of the training cohort (Hazard ratio (HR) 28.32, P = 4.3E-41). Subgroup analysis stratified by HPV status revealed that the signature was prognostic in HPV-positive OPSCC patients (HR 30.55, P = 7.0E-37) and was independent of clinical features. Importantly, the gene signature was validated in two independent patient cohorts, including the TCGA cohort (HR 3.94, P = 0.0018) and the Vanderbilt cohort (HR 8.50, P = 5.7E-09) for overall survival. Conclusions: The prognostic gene signature is a robust tool for risk stratification of OPSCC patients. The signature remains prognostic among HPV-positive OPSCC patients.

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