Human papillomavirus strain:genus
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB15907 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR472266.fastq.gz | Fastqsanger.gz | |||
| DRR472266_1.fastq.gz | Fastqsanger.gz | |||
| DRR472266_2.fastq.gz | Fastqsanger.gz | |||
| DRR472267.fastq.gz | Fastqsanger.gz | |||
| DRR472267_1.fastq.gz | Fastqsanger.gz |
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Project description:Integration of human papillomavirus (HPV) DNA into the host genome is a critical aetiological event in the progression from normal cervix to intraepithelial neoplasm, and finally to invasive cervical cancer. In this study, we want to know how HPV DNA physical status relates to treatment outcome for cervical carcinomas. Cervical cancer samples were compared with normal sample. And also, we divided 39 cervical cancer patients into four groups according to HPV DNA physical status and investigated differentially expressed gene profiles in these groups using Agilent two-color experiment.
2013-07-28 | E-GEOD-49288 | biostudies-arrayexpress
Project description:Integration of human papillomavirus (HPV) DNA into the host genome is a critical aetiological event in the progression from normal cervix to intraepithelial neoplasm, and finally to invasive cervical cancer. In this study, we want to know how HPV DNA physical status relates to treatment outcome for cervical carcinomas.
2013-07-28 | GSE49288 | GEO
Project description:HPV genotype and integration sites in patients at different stages of cervical lesions using nanopore technology Raw sequence reads
| PRJNA944395 | ENA
Project description:Human papillomavirus (HPV) is the etiological agent of cervical cancer. Three viral proteins, E5, E6 and E7 have been implicated in cell transformation. Increased expression of sialic acid and sialylated antigens have been reported during cervix transformation, these results agree with the increased mRNA levels of the sialyltransferases genes ST6GAL1 and ST3GAL3 reported in premalignant and malignant tissue of the cervix. E6 and E7 HPV oncoproteins modify the expression of some glycogenes. The role of E5 HPV oncoprotein in the glycogene expression changes in premalignant and malignant cervical tissue has not been reported. The objective of this work was to identify glycogenes that modify their expression by E5 HPV oncoprotein in HaCaT cell line. A gene expression microarray was performed on HaCaT cells that stably expressed the HPV16 E5 oncogene. Analysis revealed alteration in some glycogenes including upregulation of ST6GAL1 and ST3GAL3. The increased mRNA levels of both genes were confirmed by qRT-PCR. In addition, an in-silico analysis was performed to identify glycosylation networks altered in presence of E5 oncoprotein. The analysis showed that E5 could modify the sialic acid expression, keratan sulfate synthesis, N-glycosylation and biosynthesis of glycosaminoglycans. This is the first report of the role of HPV16 E5 oncoprotein on glycogenes expression changes. Moreover, our results suggest that the increase of the sialyltransferases genes reported in premalignant and malignant cervical tissue, could be the result of the expression of E5 oncoprotein. These results provide information of the possible role of HPV infection on the sialylation changes in the cervical epithelium identified in premalignant lesions and cancer.
2018-08-21 | GSE118776 | GEO
Project description:Oncogenic human papillomavirus (HPV) genomes are often integrated into host chromosomes in HPV-associated cancers. HPV genomes are integrated either as a single copy, or as tandem repeats of viral DNA interspersed with, or without, host DNA. Integration occurs frequently in common fragile sites susceptible to tandem repeat formation, and the flanking or interspersed host DNA often contains transcriptional enhancer elements. When co-amplified with the viral genome, these enhancers can form super-enhancer-like elements that drive high viral oncogene expression. Here, we compiled highly curated datasets of HPV integration sites in cervical (CESC) and head and neck squamous cell carcinoma (HNSCC) cancers and assessed the number of breakpoints, viral transcriptional activity, and host genome copy number at each insertion site. Tumors frequently contained multiple distinct HPV integration sites, but often only one “driver” site that expressed viral RNA. Since common fragile sites and active enhancer elements are cell-type specific, we mapped these regions in cervical cell lines using FANCD2 and Brd4/H3K27ac ChIP-seq, respectively. Large enhancer clusters, or super-enhancers, were also defined using the Brd4/H3K27ac ChIP-seq dataset. HPV integration breakpoints were enriched at both FANCD2-associated fragile sites, and enhancer-rich regions, and frequently showed adjacent focal DNA amplification in CESC samples. We identified recurrent integration “hotspots” that were enriched for super-enhancers, some of which function as regulatory hubs for cell-identity genes. We propose that during persistent infection, extrachromosomal HPV minichromosomes associate with these transcriptional epicenters, and accidental integration could promote viral oncogene expression and carcinogenesis.
2021-09-01 | GSE183048 | GEO
Project description:Our previous study implied a correlation of inhibitors of differentiation-1 (Id-1) to cervical cancer development. However, how Id-1 contributes to cervical carcinogenesis is unknown. In the present study, we investigated the role of Id-1 in transforming cervical cells with an in vitro transformation model. The human papillomavirus (HPV) immortalized cervical epithelial cells (H8) were successfully transformed by exposure to the carcinogen N-nitrosopyrrolidine (NPYR). The results showed that both Id-1 RNA and protein expression were significantly increased in transformed H8 cells, suggesting a possible role of Id-1 in cervical cell transformation. Ectopic expression of Id-1 in H8 cells potentiated NPYR-induced cell transformation. In contrast, silencing of Id-1 suppressed NPYR-induced H8 cell transformation. A cDNA microarray assay was performed, which identified suggested potential cell signaling pathways for NPYR-induced H8 cell transformation. The results suggest that Id-1 plays an oncogenic role in the cervix, which sheds light on cervical cancer development and implies potential target for cervical cancer prevention and therapy.
2013-05-11 | GSE46842 | GEO
Project description:Hypermutated human papillomavirus16 genome in cervical cancer
| PRJDB3394 | ENA
Project description:Human papillomavirus (HPV) infection related malignancy remains a severe public health problem worldwide, although HPV prophylactic vaccine has been introduced 15 years ago . HPV-associated cancers comprise 29.1% of all 2.2 million infection-related cancers, including nearly 100% of cervical cancers1 and some head and neck cancers . Cervical cancers are the 3rd most common cancer in women worldwide, HPV16 and 18 account for about 70% of cervical cancers. Moreover, high-risk HPV infection, especially HPV16 infection, is related to a proportion of head and neck epithelial carcinoma in both developed and undeveloped countries. HPV related cancers are most severe in developing countries where HPV prophylactic vaccination rates are low.In this project, we use iTRAQ8plex-labelling proteomics to comparatively study the protein contents in the tumour tissues of early and late stage cervical cancer patietns.
2023-01-26 | PXD029103 | Pride
Project description:Interventions: Brief name: anal swab
Kidney transplant recipients attending routine review appointments will be approached to participate. They will be provided a participant information and consent form (PICF) detailing the purpose, methods and risks and benefits of the study. The study will include adults willing and able to give informed consent in English. Consented participants will complete an initial coded demographic and behavioural questionnaire. Trained staff will then take an anal swab taken using a moistened Dacron swab for subsequent HPV testing. The Dacron swab will be vigorously eluded into a ThinPrep (Hologic) vial containing PreservCyt fixative medium. Any participant with either a significant cytological abnormality, or in whom high risk HPV is detected, will be referred for further investigation at a specialist clinic. A letter will be sent to participants with negative or low-risk results as well as their nominated GP.
This pilot study will evaluate the feasibility of collecting potentially sensitive behavioural data, taking anal swab specimens and performing rectal examinations, in order to identify those at high risk of serious disease.
Primary outcome(s): Prevalence of type-specific anal human papilloma virus (HPV) infection in renal transplant recipients, using PCR amplification of target DNA, and hybridization with a reverse line blot system.[ Anal swab will be performed within 14 days after completion of baseline questionnaire. Genotyping will be performed in batches, for every 20 participant samples.];Prevalence and type of anal cytological abnormalities in renal transplant recipients, using ThinPrep (Hologic) standard procedure.
[ Anal swab will be performed within 14 days after completion of baseline questionnaire. Cytology testing will be performed within 7 days of sample collection.];Feasibility of use of anal swabs as a screening tool for the detection of HPV infection and abnormal cytological abnormalities. This will be assessed through enrolment rates from all eligible approached participants and also feedback given in the baseline questionnaires.[ Feasibility will be assessed after all participants have been tested, and followed up if needed.]
Study Design: Purpose: Diagnosis; Allocation: Non-randomised trial; Masking: Open (masking not used);Assignment: Single group;Type of endpoint: Efficacy
| 2464549 | ecrin-mdr-crc