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Array comparative genomic hybridization in oral cavity (head and neck) squamous cell carcinoma

ABSTRACT: Genome wide high resolution assay of copy number in a series of frozen, microdissected head and neck cancers originating from the oral cavity. The objective was to characterize areas of amplification and deletion in head and neck cancers arising from the oral cavity subsite.

ORGANISM(S): Homo sapiens

PROVIDER: GSE33983 | GEO | 2012/04/01

SECONDARY ACCESSION(S): PRJNA150617

REPOSITORIES: GEO

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Array comparative genomic hybridization in oral cavity (head and neck) squamous cell carcinoma

Project description:Genome wide high resolution assay of copy number in a series of frozen, microdissected head and neck cancers originating from the oral cavity. The objective was to characterize areas of amplification and deletion in head and neck cancers arising from the oral cavity subsite. 31 tumors were snap frozen at the time of surgical resection, microdissected to >70% tumor content, and DNA extracted.

2012-03-31 | E-GEOD-33983 | biostudies-arrayexpress

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Whole exome sequencing and transcription profiling of a patient cohort of oral cavity squamous cell carcinomas

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Head and neck squamous cell carcinoma

Project description:Quantitative (iTRAQ 4-plex) proteomic analysis of progressive head and neck cancers

2022-03-01 | PXD001438 | Pride

Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma

Project description:These are the Visium spatial transcriptomic data (10x Genomics) from 9 patients with Head and Neck Squamous Cell Carcinoma (oral cavity) treated in Gustave Roussy. Patients are stratified by their tumoral density of multinucleated giant cells (MGC) : 6 patients have high MGC density (patients 1, 2, 3, 4, 5, 8) and 3 have low MGC density (patients 6, 7, 9). There is one data file for each patient, except for one patient that has 3 data files (patient 1). Accordingly, there are 9 patients but 11 samples. The source code of the is available on GitHub (https://github.com/AhmedAmineAnzali/MGC_Paper_Analysis). The results are published in the paper untitled : Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma (Gessain et al., 2024, Cancer Discovery). Please contact the corresponding author for more information.

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Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

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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

DNA methylation profiles of lymph node tissue of head and neck cancer of unknown primary

Project description:Background. The unknown tissue of origin in head and neck cancer of unknown primary (hnCUP) leads to invasive diagnostic procedures and unspecific and potentially inefficient treatment options for patients. The most common histological subtype, squamous cell carcinoma, can stem from various tumor primary sites, including the oral cavity, oropharynx, larynx, head and neck skin, lungs, and esophagus. DNA methylation profiles are highly tissue-specific and have been successfully used to classify tissue origin. We therefore developed a support vector machine (SVM) classifier trained with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n = 1,103) in order to identify the primary tissue of origin of our own cohort of squamous cell hnCUP patient’s samples (n = 28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. Results. The SVM algorithm achieved the highest overall accuracy of tested classifiers, with 87%. Squamous cell hnCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted cancer localization was the oral cavity in 11 cases (39%), followed by the oropharynx and larynx (both 7, 25%), skin (2, 7%), and esophagus (1, 4%). These frequencies concord with the expected distribution of lymph node metastases in epidemiological studies. Conclusions. On DNA methylation level, hnCUP is comparable to primary tumor tissue cancer types that commonly metastasize to cervical lymph nodes. Our SVM-based classifier can accurately predict these cancers’ tissues of origin and could significantly reduce the invasiveness of hnCUP diagnostics and enable a more precise therapy after clinical validation.

2024-03-04 | GSE256413 | GEO

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