Transcriptomic Dissection of Tongue Squamous Cell Carcinoma
ABSTRACT: 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 Overall design: 26 OTSCC samples and 12 control samples were analyzed using Affymetrix U133 Plus 2.0 array.
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:Gene expression profiles of oral tongue squamous cell carcinoma tissues. Keywords: human tongue cancer, brachytherapy, biopsy sample, primary tissues Overall design: For investigations of oral squamous cell carcinoma, pre-therapeutic biopsy sample tissues were taken from the patients suffering with tongue cancer. All the patients was treated by brachytherapy using 137Cs, 192Ir or 198Au source. Oligonucleotide microarray analysis-duplicate hybridization was carried out to total RNA of these samples.
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:Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of aggressive tumors in the head and neck region, with a rising incidence among younger population. The role of altered DNA methylation in OTSCC and its link with clinical parameters has not been fully assessed yet. We performed genome-wide methylation analysis of oral tongue primary tumors (n = 52) using 485, 512 probes and correlated altered methylation with differences in gene expression. We used an ensemble machine-learning algorithm to identify differentially methylated probes and regions predictive of survival, risk habits, nodal status, tumor stage, and HPV infection followed by validation using data from the cancer genome atlas (TCGA) project on oral tongue (n = 24) and tumors from all subsites of head and neck region (n = 50). Bisulphite converted DNA from the 52 tumor:matched control sample pairs were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:The study aimed to resolve the mechanisms of protective actions of MMP-8 in oral tongue squamous cell carcinoma. The experiment compares the gene expression levels of control and MMP-8 overexpressing human oral tongue squamous cell carcinoma cells (HSC-3) in stationary and migrating phenotype. Overall design: 90 000 HSC-3 cells were cultured in 6-well plates (three replicates) with and without wounding the cell layer. The RNA samples from three different plates of each cell lines (wounded +/-) were pooled and the changes in gene expressions were analyzed.
Project description:Tumor microenvironment (TME) is an active player in malignant growth and spread. Changes in the composition and structure of TME and extracellular matrix can result in either suppression or facilitation of malignant tumor growth. Carcinoma‐associated fibroblasts, bone marrow-derived multipotent mesenchymal stromal cells (BMMSCs), tumor associated macrophages and other inflammatory cells all affect the composition of TME, proliferation and survival of cancer cells, angiogenesis, invasion and metastasis. The objective of this work was to investigate the effect of the interaction between bone marrow-derived BMMSCs and human oral tongue squamous cell carcinoma (OTSCC) cells in the processes of invasion and gene expression. Co-cultures of OTSCC cancer cells and BMMSCs in 3D organotypic invasion assay were used in addition to cell culture, immunological, microarray, and RNA interference techniques. Total number of 4 samples were analyzed. 2 replicates of cultured human oral tongue squamous cell carcinoma (OTSCC) cells, and 2 replicates of OTSCC cells co-cultured with bone marrow-derived multipotent mesenchymal stromal cells
Project description:Tongue squamous cell carcinoma is a tumour type with rather low five year survival, around 60%. The poor survival rate has been ascribed to late detection, a high frequency of locoregional recurrence, the occurrence of secondary primary tumours and death due to comorbidity. One reason for development of recurrence is thought to be the existence of transformed cells in areas adjacent to the primary tumour, cancerization field effect. The aim of this study was to map the changes in the tumour free tongue tissue adjacent to tongue tumours compared with healthy control tongue tissue to better understand the cancerization field effect. Tissue biopsies were collected from tumour (T) and tumour free tissue adjacent to the tumour (TF) from patients with tongue squamous cell carcinoma. Control tissue was collected from latter border of the tongue of tumour free healthy volunteers (C). All samples were homogenized and RNA was extracted. The RNA was biotin labelled and run on Illumina HT-12 bead chip array.
Project description:We hypothesized that the expression of many genes are dysregulated during oral cancer carcinogenesis. We examined genome-wide transcript levels in normal mouse tongues and the tongue squamous cell carcinomas induced by 4-NQO. The results will provide important information for the diagnosis, prevention, and treatment of human oral cancers, including tongue cancer. Total RNA obtained from normal tongues (not treated with 4-NQO) and tongue squamous cell carcinomas induced by 4-NQO.
Project description:41% of all oral carcinomas have been found to localize at tongue, where they were characterized as being aggressive and having capacity to locally invade and relapse frequently. Despite considerable enhancements in the cancer diagnosis and treatment techniques, tongue squamous cell carcinoma (TSCC) still remains to be one of the most common and lethal cancer types in the head and neck region. In this study, we aimed to identify a signature of saliva-specific microRNAs (miRNAs) expression in TSCC patients. To explore putative diagnostic biomarkers, we compared the miRNA profiles of saliva samples obtained from 3 TSCC patients and 4 healthy control individual using Agilent miRNA microarray (V19). Three of the differentially expressed miRNAs were selected for further validation with quantitative reverse-transcription PCR (qRT-PCR) using saliva samples of 25 TSCC patients and 25 healthy control individuals. Microarray analysis demonstrated that 428 miRNA probes were deregulated in TSCC patients when compared to control group and qRT-PCR results validated the reduced expression of miR-139-5p in TSCC saliva. Further analysis of post-operative saliva samples of TSCC patients revealed that miR-139-5p level elevated to normal level after surgery, pointing its diagnostic and prognostic power. As a conclusion, we propose saliva as a feasible source in routine patient examination for early diagnosis of TSCC patients, and our results suggest saliva miR-139-5p as a novel potential diagnostic marker. Overall design: We compared the miRNA profiles of saliva samples obtained from 3 TSCC patients and 4 healthy control individual using Agilent miRNA microarray (V19). Two group comparison
Project description:In order to identify aberrantly expressed microRNAs in oral squamous cell carcinomas (OSCCs), we have employed microRNA microarray profile using healthy tongue samples as control. All seventeen human OSCCs and three normal tongue tissues were collected from the Tissue Bank at the Moffitt Cancer Center and approved by the University of Florida institutional review board. Majority (15 out of 17) of the OSCCs were derived from tongue cancers. The tumor samples contained greater than 80% of cancerous cells, confirmed by microscopic examination by a head and neck pathologist. The normal tongues were taken from a non-cancerous region. Tissues were snap-frozen and stored at -80°C until further use. Total RNAs were isolated from human tissues using mirVana miRNA Isolation kit (Ambion/Applied Biosystems, Austin, TX) according to the manufacturer’s instruction. NanoDrop® ND-100 spectrophotometer (Thermo Scientific, Wilmington, DE) was used to quantify the isolated RNA. The Agilent 2100 Bioanalyzer from the Interdisciplinary Center for Biotechnology Research at the University of Florida was used to detect the size distribution of total RNA and to determine the quality as well. Expression of microRNAs from this signature was quantified in the same RNA samples by real-time PCR, confirming the expression pattern. Human tissues of oral squamous cell carcinoma and healthy normal tongues were used for microRNA microarray profile to identify aberrantly expressed microRNAs in oral squamous cell carcinomas.