ABSTRACT: Genome and transcriptome sequence data from a tongue squamous cell carcinoma (head and neck) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
Project description:DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 83 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array.
Project description:DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 83 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array. 83 FFPE primary OTSCC tumour samples were analysed in one experimental run.
Project description:Aim Treatment options for patients with recurrent or metastatic head and neck squamous cell carcinoma (R/M-HNSCC) are limited. Therefore, prognostic and predictive biomarkers for the application of personalized therapies are urgently needed.
Project description:The head and neck / oral squamous cell carcinoma (HNOSCC) is a diverse group of cancers, which develop from many different anatomic sites and are associated with different risk factors and genetic characteristics. The oral tongue squamous cell carcinoma (OTSCC) is one of the most common types of HNOSCC. It is significantly more aggressive than other forms of HNOSCC, in terms of local invasion and spread. In this study, we aim to identify specific transcriptomic signatures that associated with OTSCC. Keywords: Disease/Control analysis
Project description:Head and neck squamous cell carcinoma (HNSCC) constitutes 90% of head and neck cancers. HNSCC development is linked to chronic inflammation through mechanisms that are not fully understood. The cytosolic double-stranded DNA sensor Absent in Melanoma 2 (AIM2) is an inflammasome-forming protein that also has inflammasome-distinct roles in restricting tumorigenesis. We performed bulk RNA sequencing on tongue tissue from wild type (WT) and Aim2-/- mice treated with the carcinogen 4NQO in drinking water as a model of experimental HNSCC to uncover gene signatures regulated by AIM2 during HNSCC development.
Project description:The head and neck / oral squamous cell carcinoma (HNOSCC) is a diverse group of cancers, which develop from many different anatomic sites and are associated with different risk factors and genetic characteristics. The oral tongue squamous cell carcinoma (OTSCC) is one of the most common types of HNOSCC. It is significantly more aggressive than other forms of HNOSCC, in terms of local invasion and spread. In this study, we aim to identify specific transcriptomic signatures that associated with OTSCC. Experiment Overall Design: 26 OTSCC samples and 12 control samples were analyzed using Affymetrix U133 Plus 2.0 array.
Project description:Sage performed on microdissection of Head and Neck tumor, and Head and Neck normal tissue comparative analysis of gene expression profiles of head and neck squamous cell carcinoma and Head and Neck normal tissue
Project description:This data was used to detect good biomarkers for head and neck squamous cell carcinoma and was integrated with transcriptome and miRNome data aiming to elucidate role of epigenetics on gene expression in head and neck squamous cell carcinoma.
Project description:To investigate the molecular mechanisms driving neoplastic evolution in head and neck squamous cell carcinoma, we established genetically defined mouse tongue organoid models harboring key driver mutations: control (Ctrl), Trp53/Cdkn2a dual-knockout with a control vector (DKOC), and Trp53/Cdkn2a dual-knockout with the PIK3CA E545K mutation (DKOP), and performed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform on these organoid lines.
Project description:Microarrays were used to examine gene expression differences between human head and neck squamous cell carcinoma cell lines (FaDu, UTSCC8, UTSCC42a) grown in culture in comparison to a normal oral epithelial cell line. Gene expression data was integrated with global protein expression of head and neck squamous cell carcinoma cell lines and conditioned media to identify secreted protein markers up-regulated at the mRNA level in cancer cells versus the normal cell line. Total RNA obtained from head and neck squamous cell carcinoma cell lines and a normal oral epithelial cell line
