HPV genome expression at invasive cervical carcinomas infected by multiple HPV genotypes
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ABSTRACT:
PROVIDER: PRJNA603319 | ENA |
REPOSITORIES: ENA
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Project description:Multiple HPV genotypes infection is frequently detected in HPV+ cervical lesions, however it is not well stablished how is the different viral interaction during the carcinogenic process. Here we carried out a comprehensive study to characterize the multiple HPV genome expression and integration by RNA-Seq analysis in 19 invasive cervical carcinomas with HPV coinfections. Analysis of tumoral DNA by a hybridization kit indicated multi-infection ranging from 2 to 6 different HPV genotypes, without a preferential species coinfection. The expression analysis showed that a single HPV genotype preferentially expressed its genome, might indicating a competition between the infecting virus. Finally, the search for HPV/human chimeric transcripts indicated integration from just one HPV in almost all samples, corroborating the expression findings.
2021-07-28 | GSE144293 | GEO
Project description:Cells located at the invasive front and in the tumor mass of mouse cervical squamous cell carcinomas were isolated by laser microdissection from hematoxylin-stained HPV/E2 sections. 7 months old HPV/E2 mice treated with oestrogen develop invasive cervical squamous cell carcinomas. This model recapitulates human invasive cervical neoplasias. We used microarrays to compare the transcriptome of cells located at the invasive front versus cells located in the tumor mass of mouse squamous cell carcinomas.
2018-02-01 | GSE108208 | GEO
Project description:10 normal squamous cervical epitheilia samples, 7 high grade squamous intraepithelial lesions, and 21 invasive squamous cell carcinomas of the cervix samples were obtained using laser capture miicrodissection. Two rounds of T7-based linear RNA amplification using the Arcturus RiboAmp kit were performed for each sample, and assayed using Affymetrix HG_U133A arrays. Keywords: disease state analysis
2007-12-11 | GSE7803 | GEO
Project description:10 normal squamous cervical epitheilia samples, 7 high grade squamous intraepithelial lesions, and 21 invasive squamous cell carcinomas of the cervix samples were obtained using laser capture miicrodissection. Two rounds of T7-based linear RNA amplification using the Arcturus RiboAmp kit were performed for each sample, and assayed using Affymetrix HG_U133A arrays. Experiment Overall Design: 10 normal squamous cervical epitheilia samples, 7 high grade squamous intraepithelial lesions, and 21 invasive squamous cell carcinomas of the cervix, each from different patients, were each assayed on single HG_U133A arrays. Three additional test samples were also assayed. Experiment Overall Design: The log-transformed probe-set values and the results of the statistical analysis for each probe-set, and the associated README file, are included as Supplementary files.
2008-06-15 | E-GEOD-7803 | biostudies-arrayexpress
Project description:Persistent infection by high-risk human papillomaviruses (HPVs) is associated with the development of cervical cancer and a subset of anogenital and head and neck squamous cell carcinomas. Abnormal expression of cellular microRNAs (miRNAs) plays an important role in the development of cancer, including HPV-related tumors. MiRNA expression profile was investigated by microrray analysis in the HPV-positive cervical cancer cell lines SiHa (HPV16-positive cell line derived from a cervical squamous cell carcinoma), CaSki (HPV16-positive cell line derived from a metastatic cervical epidermoid carcinoma), and HeLa (HPV18-positive cell line derived from a cervical adenocarcinoma) and compared with primary HFKs and C33a (HPV-negative cervical cell line).
2018-01-16 | E-MTAB-6361 | 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:Cervical cancer is the fourth most common type of cancer is women worldwide,and it is a major cause of cancer-related deaths in developing countries. Despite the marked reduction oberved in the rates of this disease as a result of screening programs, it is necessary to develop robust biomarkers that can detect the neoplastic early in HPV-related cervical leisons. We performed comparative mRNA seqeuncing from exfoliative cervical cytology from nine Korean women on the Illumina NovaSeq6000 platforms. The pathological tissues mathced to the corresponding cytological samples were simulanously confirmed and were considered to be endpoint diagnosis. The pathological dianoses consisted of three cases of chronic cervicitis, 2 high-grade squamous intraepithelial leisons(HSILs), 2squamous cell carcinomas in situ(CIS); and 2 invasive quamous cell carcinomas (SQCCs), respectively. Using bioinformatics analyses, differentially expressed genes (DEGs; absolute fold change >1; p<0.05) were applied for Gene Ontology (GO), Gene Set EnrichmentAnalysis (GSEA), and protein-protein interaction (PPI) networks.
2022-10-18 | GSE215744 | GEO
Project description:Cervical cancer develops from pre-cancerous high-grade cervical intraepithelial neoplasia (CIN) lesions harbouring a transforming infection with high-risk human papillomavirus (hrHPV), which is characterised by p16INK4a overexpression. Since it takes one or more decades for these pre-cancerous lesions to progress to invasive squamous cell carcinomas (SCCs), it is obvious that they are heterogeneous in terms of duration of existence and progression risk. We performed array-based comparative genomic hybridisation (array CGH) of 46 p16INK4a immuno-positive CIN2/3 lesions to determine whether this heterogeneity is reflected in their chromosomal profiles. Chromosomal profiles of CIN2/3 lesions were related to those of invasive cervical squamous cell carcinomas (SCCs) and promoter methylation of the CADM1 gene, a tumour suppressor gene known to be functionally involved in the tumorigenic phenotype of cervical cancer cells. Frequent alterations found in CIN2/3 lesions included gains located at chromosome 1, 3, 7 and 20 and losses located at 4, 11, 16, 17 and 19. Unsupervised hierarchical clustering identified two subsets of CIN2/3 lesions, chromosomal profiles of one of which closely resembled invasive SCCs. Gains of 1, 3q and 20 were characteristic for CIN2/3 lesions with chromosomal signatures resembling carcinomas. In addition, dense promoter methylation of the CADM1 gene was significantly more frequent in these CIN2/3 lesions (p=0.004). No chromosomal alterations were detected in one p16INK4a positive and five p16INK4a negative CIN1 lesions. These findings suggest that biomarkers associated with gains at chromosomes 1, 3q and 20 are potential hallmarks of advanced p16INK4a positive CIN2/3 lesions with a high short-term risk of progression.
2009-02-20 | GSE11573 | GEO
Project description:<p>Cervical cancer is responsible for 10-15% of cancer related deaths in women worldwide. The etiological role of infection with high-risk human papilloma viruses (HPV) in carcinomas of the cervix is well established. In general, the development of cervical carcinomas follows a progression from persistent HPV infection through precancerous lesions to invasive cancer. Previous studies have implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS as well as chromosome-arm level copy number alterations in the pathogenesis of cervical carcinomas. Here, we report whole exome sequencing analysis of 118 cervical carcinoma-normal paired samples from patients in Norway and Mexico, as well as transcriptome sequencing of 80 cases and whole genome sequencing of 13 tumor-normal pairs. Novel somatic mutations include recurrent E322K substitutions in the MAPK1 gene encoding the ERK2 kinase and inactivating mutations in the HLA-B gene. In addition, recurrent somatic mutations in FBXW7, EP300, and NFE2L2 are novel in the context of primary cervical carcinomas. Analysis of HPV integration sites revealed recurrent integration into the RAD51B locus as well as co-occurrence of HPV genome integration and copy number gains within several genomic loci. These findings shed new light on the pathogenesis of cervical carcinomas and suggest potential novel therapeutic targets.</p>
| phs000600 | dbGaP
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