Human oropharyngeal metagenome
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ABSTRACT:
PROVIDER: PRJNA428766 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Oropharyngeal cancers have 2 main etiologies : High risk HPV (human papilloma virus) and tobacco/alcohol. The aim of this work is to find a miRNA signature specific to HPV induced oropharyngeal cancers
2015-05-12 | E-MTAB-3410 | biostudies-arrayexpress
Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.
2020-01-20 | GSE124464 | GEO
Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium MethylationEPIC BeadChip Kit was used to obtain DNA methylation profiles across more than 850,000 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.
2020-01-20 | GSE124632 | GEO
Project description:Background: The incidence of human papillomavirus (HPV) associated oropharyngeal carcinomas has increased rapidly over the last thirty years. These tumours behave as a distinct biological entity when compared to classical smoking- and alcohol-related disease. To gain more information regarding the pathway through pre-malignancy in HPV positive/HPV negative oropharyngeal carcinoma (OSCC), we investigated genomewide expression profiles in histopathologically confirmed tumour samples with site-matched normal epithelial controls. Methods: Twenty-four patients with primary oropharyngeal squamous cell carcinoma (4 with stage III and 20 with stage IV disease) were included in this prospective clinical trial (UKCRN11945). The tumour tissues were each assessed by a histopathologist with HPV status and typing by p16INK4A, consensus PGMY PCR, type-specific HPV16 DNA & RNA PCR and DNA sequencing. Fresh tissue samples were subjected to whole transcriptome analysis using the Illumina Bead Array (~47,000 transcripts) and the results validated with quantitative Real Time-PCR (qRT-PCR). In a separate cohort of twelve OSCC patients, laser capture micro-dissection of formalin fixed paraffin embedded (FFPE) tissue allowed RNA extraction from regions of in situ malignant change (with matched normal and invasive SCC samples). Results: The majority of OSCC patients (28/36) displayed evidence of high risk HPV positivity. Predictable fold changes of RNA expression in HPV-associated disease included multiple transcripts within the p53 oncogenic pathway (e.g. CDKN2A/CCND1). Other candidate transcripts found to have altered levels of expression in this study have not previously been established in HPV16 associated oropharyngeal cancer. These were involved in cell differentiation, proliferation and invasion and demonstrated considerable overlap with expression analysis data in other oncogenic pathways (SFRP1/CRCT1/DLG2/SYCP2/CRNN). SYCP2 showed the highest consistent fold change from baseline in both fresh frozen and FFPE tissue (qRT-PCR fresh frozen tissue [P<0.04]; FFPE tissue pre-invasive [P<0.01]; FFPE tissue invasive [P<0.01]), and aberrant expression of this meiosis-specific protein may contribute to genetic instability during HPV-associated cancer development. Conclusion: Investigation of differentially expressed genes in HPV-positive tumours may reveal unique pathways that can explain their different natural history and biological properties. The data from this study reveal SYCP2 (amongst others) as a potential biomarker in HPV positive oropharyngeal carcinoma, and if corroborated on a larger scale, may facilitate the development of a non-invasive screening tool. Twenty four samples (12 matched invasive oropharyngeal carcinoma and normal epithelial controls).
2015-11-01 | E-GEOD-56142 | biostudies-arrayexpress
Project description:Microbiome analysis of oropharyngeal and nasopharyngeal samples of SARS-CoV-2 infected patients
2021-02-06 | GSE166281 | GEO
Project description:mRNA sequencing was performed on oropharyngeal cancer cell lines including 4 HPV-positive and 4 HPV-negative lines. Two lines (CUOP2 and CUOP3) were newly derived from HPV-positive tonsil cancers (derivation is described in "Sensitivity to inhibition of DNA repair by Olaparib in novel oropharyngeal cancer cell lines infected with Human Papillomavirus" by Pirotte et al. This work was undertaken with the aims of quantifying levels of HPV gene transcription and identifying human:viral fusion transcripts arising from integrated viral sequences. We also wished to compare expression of genes involved in DNA damage responses between HPV positive and negative cell lines. The published analyses showed expression of HPV encoded genes in all of the HPV-positive cell lines, and the presence of fusion transcripts derived from integrated virus. We did not identify any obvious correlation between expression of DNA repair genes and HPV status.
2018-11-28 | GSE123029 | GEO
Project description:A detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and individuals infected with SARS-CoV-2 involving high throughput quantitative (iTRAQ) proteomics analysis.
2022-12-22 | PXD032150 | Pride
Project description:Background: The incidence of human papillomavirus (HPV) associated oropharyngeal carcinomas has increased rapidly over the last thirty years. These tumours behave as a distinct biological entity when compared to classical smoking- and alcohol-related disease. To gain more information regarding the pathway through pre-malignancy in HPV positive/HPV negative oropharyngeal carcinoma (OSCC), we investigated genomewide expression profiles in histopathologically confirmed tumour samples with site-matched normal epithelial controls. Methods: Twenty-four patients with primary oropharyngeal squamous cell carcinoma (4 with stage III and 20 with stage IV disease) were included in this prospective clinical trial (UKCRN11945). The tumour tissues were each assessed by a histopathologist with HPV status and typing by p16INK4A, consensus PGMY PCR, type-specific HPV16 DNA & RNA PCR and DNA sequencing. Fresh tissue samples were subjected to whole transcriptome analysis using the Illumina Bead Array (~47,000 transcripts) and the results validated with quantitative Real Time-PCR (qRT-PCR). In a separate cohort of twelve OSCC patients, laser capture micro-dissection of formalin fixed paraffin embedded (FFPE) tissue allowed RNA extraction from regions of in situ malignant change (with matched normal and invasive SCC samples). Results: The majority of OSCC patients (28/36) displayed evidence of high risk HPV positivity. Predictable fold changes of RNA expression in HPV-associated disease included multiple transcripts within the p53 oncogenic pathway (e.g. CDKN2A/CCND1). Other candidate transcripts found to have altered levels of expression in this study have not previously been established in HPV16 associated oropharyngeal cancer. These were involved in cell differentiation, proliferation and invasion and demonstrated considerable overlap with expression analysis data in other oncogenic pathways (SFRP1/CRCT1/DLG2/SYCP2/CRNN). SYCP2 showed the highest consistent fold change from baseline in both fresh frozen and FFPE tissue (qRT-PCR fresh frozen tissue [P<0.04]; FFPE tissue pre-invasive [P<0.01]; FFPE tissue invasive [P<0.01]), and aberrant expression of this meiosis-specific protein may contribute to genetic instability during HPV-associated cancer development. Conclusion: Investigation of differentially expressed genes in HPV-positive tumours may reveal unique pathways that can explain their different natural history and biological properties. The data from this study reveal SYCP2 (amongst others) as a potential biomarker in HPV positive oropharyngeal carcinoma, and if corroborated on a larger scale, may facilitate the development of a non-invasive screening tool.
2015-11-01 | GSE56142 | GEO
Project description:Methylation of CpG Islands within promoter regions of genes has been associated with gene silencing, suggesting loss of tumor suppressor function and tumorigenesis. The northeastern states of India are leaders in the country for cancers of several sites. Almost no reports are available of any DNA methylation biomarker for oropharyngeal cancers of the northeastern states. The present study aimed to identify targets of CpG hypermethylation and hypomethylation in oropharyngeal cancer prevalent in northeast India. Using Illumina Infinium Human Methylation 450K microarray platform a genome wide screening has been done for differentially methylated genes, including genes not previously implicated in carcinogenesis. Differential gene expression correlated to their methylation status was elaborated using transcriptome profiling. The new genes identified may be used to develop promising panels of DNA Methylation biomarkers for oropharyngeal screening and detection at a very early stage.
2020-09-25 | GSE136704 | GEO
Project description:The ability to taste is critical for animal nutrition and toxin deterrence. The majority of research on taste bud development and regeneration is in mice, where taste buds are located within specialized papillae on the tongue. However, taste buds in fish and amphibians, such as axolotls (Ambystoma mexicanum), are not housed in papillae, rather they are within the pharyngeal epithelium. This simplified tissue level organization, along with the ability of cultured oropharyngeal explants from early embryos to produce taste buds on the same time-line as embryos, make the axolotl an excellent model to identify molecules specifically involved in taste bud cell differentiation. In this study, we performed de novo transcriptomic analysis on RNA sequences from three different stages of oropharyngeal explants: stages 37/38, 39, and 41. RNA-seq data from 17 total samples representing these stages were pooled to generate de novo assemblie(s) of the transcriptome using a Trinity pipeline. Raw reads and the assembly were uploaded to Mendeley (doi:10.17632/tvxh3jm83m.1). From 27.9Gb of raw sequences, we identified 21,244 transcripts. To our knowledge, this study provides the first published assembly of axolotl oropharyngeal endoderm explants. This RNA-seq data and transcriptome assembly provide information on genes expressed in the oropharyngeal endoderm and will be valuable in the identification of taste bud development genes.
2020-06-02 | GSE151535 | GEO