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Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers (mRNA)

ABSTRACT: Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO

ORGANISM(S): Homo sapiens

PROVIDER: GSE41116 | GEO | 2013/01/01

SECONDARY ACCESSION(S): PRJNA175839

REPOSITORIES: GEO

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Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers (microRNA)

Project description:Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO We measured microRNA expression of 43 OSCC cases with Agilent Human miRNA microarray rel12.0

2013-01-01 | E-GEOD-41115 | biostudies-arrayexpress

Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers (mRNA)

Project description:Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO We measured gene expression of 43 OSCC cases with the Affymetrix Human Exon 1.0 ST Array

2013-01-01 | E-GEOD-41116 | biostudies-arrayexpress

Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers (methylation)

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Gene Expression Profiling of Oral Squamous Cell Carcinoma

Project description:Gene Expression Profiling of Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate genes clusters with potential to distinguish normal and tumor tissue from oral cavity. All tissue samples were collected after obtaining written informed consent. The RNA profile of 27 OSCC patients was compared with 4 independent controls and 1 pooled control oral cavity tissue from healthy donors. Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

2011-10-29 | E-GEOD-23558 | biostudies-arrayexpress

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Identification of salivary biomarkers for oral cancer with quantitative proteomics and two-phase verifying approaches

Project description:Oral cavity cancer is one of the most common cancer worldwide and oral cavity squamous cell carcinoma (OSCC) accounts for up to 90 percent of oral cancers. In Taiwan, OSCC is the fifth most common malignancy of male and causes more than 250 deaths per year. The poor outcome of OSCC patients is principally ascribed to the fact that this disease is often advanced at the time of diagnosis, suggesting that early detection and prevention of OSCC are urgently needed to reduce the cancer burden. Analysis of cancer-related body fluids is one of promising approaches to identify cancer-related molecules and biomarker candidates. To identify salivary biomarkers of OSCC, salivary samples of OSCC patients, individuals with oral potentially malignant disorders (OPMD), and healthy volunteers were collected. With isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry (MS) analysis, 1838 proteins were identified. The levels of 102 proteins are found to be elevated in the saliva samples of OSCC patients compared to that of OPMD and healthy groups. To improve the feasibility of biomarkers, we used a two-phase verification to measure these candidates. Among them, salivary levels of AHSG, CFH, FGA, and SERPINA1 were determined to be significantly higher in the OSCC patients than in the healthy or in the OPMD group with both of MRM-MS and ELISA. Furthermore, the levels of these proteins were highly related to tumor size, lymph-node metastasis, and cancer stages. The results of this study not only provides a powerful strategy for verification of biomarker candidates, but also suggested that AHSG, CFH, FGA, and SERPINA1 could act as salivary biomarkers for OSCC detection.

2019-08-15 | PXD008655 | Pride

Protein markers in Oral Squamous Cell Carcinoma (OSCC)

Project description:Oral squamous cell carcinoma (OSCC) is a main reason of oral cancer mortality and morbidity. Cancer of oral cavity in central south Asia, ranks among third most common kinds of cancer. The discovery of candidate markers to differentiate normal from malignant cells in clinical diagnosis of OSCC would be of critical importance because this malignancy has poor prognosis. To improve the clinical outcome in OSCC patients, the present study was aimed at identifying robust candidate biomarkers for early OSCC diagnosis and to enhance understanding of the mechanisms of disease progression and pathogenesis. Of particular interest are proteins that can be found in tissue lysates of OSCC tumor vs normal adjacent mucosa samples and secreted in cell line Secretomes of HNSCC for non-invasive detection. We analysed 17 paired human malignant OSCC tissues and normal adjacent tissue in addition to secretomes of 9 HNSCC cell lines. The proteome dataset of OSCC and normal tissues consisted of 5,123 protein groups, including 299 proteins with strong differential expression (p-value <0.01, fold change barrier to ˃+2 and <-2, 205 upregulated and 94 down regulated) and 134 common proteins were also found out of total dataset of 4473 identified proteins of HNSCC cell line secretomes. Functional data analysis revealed that these differential proteins were significantly associated with multiple biological processes. Myogenesis, Fatty Acid Metabolism and KRAS Signaling DN were associated with the proteins downregulated in cancer tissues, while Protein Secretion, Unfolded Protein Response, Spliceosomal complex assembly, Protein localization to endosome and Interferon Gamma Response were enriched in the set of upregulated proteins and these regulated proteins may be classically or non-classically secreted. Furthermore, we found differential enrichment of Creb3L1, ESRRA, YY, ELF2, STAT1 and XBP transcription factors potentially regulating these major pathways.

2022-04-04 | PXD025701 | Pride

Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer.

Project description:Head and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco- and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ~65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome towards PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage.

2023-08-07 | GSE227919 | GEO

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