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Global gene expression analysis of primary head and neck cancer cases

ABSTRACT: Global gene expression analysis of primary head and neck cancer cases

PROVIDER: PRJNA483879 | ENA |

REPOSITORIES: ENA

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Global gene expression analysis of primary head and neck cancer cases

Project description:This study addressed the assumption that in addition to somatic mutations epigenetic silencing of cancer-related genes by promoter hyper-methylation is a common event in head and neck cancer. A multi-scale omics approach based on whole-exome sequencing, global DNA methylation and gene expression profiling data derived from tumor samples of the HIPO-HNC cohort was conducted and new findings were confirmed with data from TCGA-HNC. Results provide experimental evidence that the ryanodine receptor 2 (RYR2) exhibits variable promoter methylation and expression in both tumor samples and HNSCC cell lines. Moreover, immunohistochemical staining of tissue sections unraveled a gradual loss of RYR2 expression from normal mucosa via dysplastic lesions to cancer, and indicated that reduced RYR2 expression in adjacent tissue and precancer lesions might serve as a risk factor for unfavorable prognosis and upcoming malignant conversion.

2020-06-19 | GSE117973 | GEO

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer

Project description:This SuperSeries is composed of the following subset Series: GSE25083: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue GSE25089: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: HNSCC GSE25091: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: blood controls Refer to individual Series

2011-10-27 | E-GEOD-25093 | biostudies-arrayexpress

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue

Project description:Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas. The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples. Bisulphite-converted DNA from the 18 normal head and neck samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

2011-10-27 | E-GEOD-25083 | biostudies-arrayexpress

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue

2011-10-28 | GSE25083 | GEO

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: HNSCC

Project description:Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas (HNSCCs). The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples. Bisulphite-converted DNA from the 91 head and neck squamous cell carcinoma samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

2011-10-27 | E-GEOD-25089 | biostudies-arrayexpress

Transcription profiling of matching human primary head and neck squamous cell carcinomas and cervical lymph node metastases.

Project description:An experiment was performed to investigate the perservation of gene expression upon metastasis of primary head and neck squamous cell carcinomas to the cervical lymph node.

2006-10-23 | E-TABM-114 | biostudies-arrayexpress

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

Gene expression profiles of head and neck squamous cell carcinoma

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

2008-09-30 | E-GEOD-11986 | biostudies-arrayexpress

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: HNSCC

2011-10-28 | GSE25089 | 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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