Claudins family as potential prognostic indicators in ovarian cancer by bioinformatics analysis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA838618 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19226900_1.fastq.gz | Fastqsanger.gz | |||
| SRR19226900_2.fastq.gz | Fastqsanger.gz | |||
| SRR19226893_1.fastq.gz | Fastqsanger.gz | |||
| SRR19226893_2.fastq.gz | Fastqsanger.gz | |||
| SRR19226894_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:In this paper, the expression and possible function of CLDNs in ovarian cancer were explored by bioinformatics analysis, and verified by mRNA high-throughput sequencing of ovarian cancer and cancer-free ovary.
2024-12-31 | GSE203130 | GEO
Project description:Hepatocellular carcinoma (HCC) exhibits widespread epigenetic aberrations; however, the underlying transcriptional regulatory landscape remains underexplored. Here, we performed integrated analyses with genome-wide profiles of the transcriptomes, histone modifications and DNA methylation from patient-derived HCC tumors and controls. We identified both global and focal epigenetic alterations including large-scale DNA methylation loss, and dysregulation of cis-regulatory elements (CREs) associated with genes involved in cell cycle control, immune responses, and extracellular matrix organization. Notably, we discovered that transcriptional upregulation of Glypican-3 (GPC3), a diagnostic biomarker and immunotherapeutic target for HCC, was linked to the reactivation of a fetal liver super-enhancer (SE). This SE, in concert with DNA hypomethylation of two CpG islands, modulated GPC3 expression. Global DNA hypomethylation also contributed to transcriptional dysregulation of retrotransposon-derived CREs. Specifically, we observed that patients with high expression of a HERVE-int-driven long non-coding RNA transcript showed poorer disease outcomes and specific molecular signatures associated with better response to immunotherapy. Our results highlight this and other retrotransposons as potential prognostic indicators and a predictive signature for immunotherapy response. Taken together, our findings provide insights into the role of epigenetic dysregulation of CREs and retrotransposons in hepatocarcinogenesis, which could benefit the clinical management of HCC.
2025-02-28 | GSE276133 | GEO
Project description:Hepatocellular carcinoma (HCC) exhibits widespread epigenetic aberrations; however, the underlying transcriptional regulatory landscape remains underexplored. Here, we performed integrated analyses with genome-wide profiles of the transcriptomes, histone modifications and DNA methylation from patient-derived HCC tumors and controls. We identified both global and focal epigenetic alterations including large-scale DNA methylation loss, and dysregulation of cis-regulatory elements (CREs) associated with genes involved in cell cycle control, immune responses, and extracellular matrix organization. Notably, we discovered that transcriptional upregulation of Glypican-3 (GPC3), a diagnostic biomarker and immunotherapeutic target for HCC, was linked to the reactivation of a fetal liver super-enhancer (SE). This SE, in concert with DNA hypomethylation of two CpG islands, modulated GPC3 expression. Global DNA hypomethylation also contributed to transcriptional dysregulation of retrotransposon-derived CREs. Specifically, we observed that patients with high expression of a HERVE-int-driven long non-coding RNA transcript showed poorer disease outcomes and specific molecular signatures associated with better response to immunotherapy. Our results highlight this and other retrotransposons as potential prognostic indicators and a predictive signature for immunotherapy response. Taken together, our findings provide insights into the role of epigenetic dysregulation of CREs and retrotransposons in hepatocarcinogenesis, which could benefit the clinical management of HCC.
2025-02-28 | GSE276132 | GEO
Project description:Integrative epigenomic profiling of hepatocellular carcinoma uncovers aberrant cis-regulatory changes and potential prognostic indicators [ChIP-seq]
| PRJNA1154966 | ENA
Project description:Integrative epigenomic profiling of hepatocellular carcinoma uncovers aberrant cis-regulatory changes and potential prognostic indicators [RNA-seq]
| PRJNA1154965 | ENA
Project description:proteomics identified potential prognostic markers in early ovarian
2020-11-09 | PXD022436 |
Project description:Serous ovarian cancer (SOC) accounts for >50% of all epithelial ovarian cancers. However, patients with SOC present with various degrees of response to platinum‑based chemotherapy and, thus, their survival may differ. The present study aimed to identify the candidate genes involved in the carcinogenesis and drug resistance of SOC by analyzing the microarray datasets GDS1381 and GDS3592. GDS1381 and GDS3592 were downloaded from the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/gds/). A total of 219 differentially expressed genes (DEGs) were identified. Potential genes that may predict the response to carboplatin and, thus, the prognosis of SOC were analyzed. The enriched functions and pathways of DEGs included extracellular region, extracellular space and extracellular exosome, among others. Upon screening the upregulated and downregulated genes on the connectivity map, 10 small‑molecule drugs were identified that may be helpful in improving drug sensitivity in patients with ovarian cancer. A total of 30 hub genes were screened for further analysis after constructing the protein‑to‑protein interaction network. Through survival analysis, comparison of genes across numerous analyses, and immunohistochemistry, GNAI1, non‑structural maintenance of chromosomes (non‑SMC) condensin I complex subunit H (NCAPH), matrix metallopeptidase 9 (MMP9), aurora kinase A (AURKA) and enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) were identified as the key molecules that may be involved in the carcinogenesis and carboplatin resistance of SOC. In conclusion, GNAI1, NCAPH, MMP9, AURKA and EZH2 should be examined in further studies for the possibility of their participation in the carcinogenesis and carboplatin response of SOC.
| S-EPMC5983937 | biostudies-literature
Project description:Full title: Predictive Gene Signatures as Strong Prognostic Indicators of the Effectiveness of Bacillus Calmette–Guérin (BCG) Immunotherapy in Primary pT1 Bladder Cancers Intravesical BCG immunotherapy is effective in prevention of recurrence and progression in many cases of non-muscle invasive bladder cancer, but many patients fail to respond. This study identified predictive gene signatures in primary pT1 bladder cancer with BCG immunotherapy. Fourty-Eight patients with primary pT1 bladder cancer treated with BCG immunotherapy were used. Microarray gene expression analysis of the 48 primary bladder cancers was carried out. Predictive gene signatures were individually selected based on the recurrence and progression status. Among 43,148 unique genes, 424 and 287 candidate predictive genes that could predict recurrence and progression, respectively, were selected. Time to recurrence or progression was shorter for patients with poor-predictive gene signatures than good-predictive gene signatures (log-rank test, p <0.001, respectively). Validation of predictive gene signatures with RT-PCR was nearly identical to those of microarray (log-rank test, p <0.05, respectively). In multivariate regression analysis, predictive gene signatures were the only independent predictors of recurrence (HR 3.38, p = 0.048) or progression (HR 10.49, p = 0.048) in validation cohorts. Predictive gene signatures have strong diagnostic value for determining the response to intravesical BCG immunotherapy in primary pT1 bladder cancer. Keywords: Gene expression, Bladder cancer, BCG
2010-03-26 | GSE19423 | GEO
Project description:Microbial indicators for rehabilitation of post-minings substrate
| PRJEB10826 | ENA
Project description:Full title: Predictive Gene Signatures as Strong Prognostic Indicators of the Effectiveness of Bacillus Calmetteâ??Guérin (BCG) Immunotherapy in Primary pT1 Bladder Cancers Intravesical BCG immunotherapy is effective in prevention of recurrence and progression in many cases of non-muscle invasive bladder cancer, but many patients fail to respond. This study identified predictive gene signatures in primary pT1 bladder cancer with BCG immunotherapy. Fourty-Eight patients with primary pT1 bladder cancer treated with BCG immunotherapy were used. Microarray gene expression analysis of the 48 primary bladder cancers was carried out. Predictive gene signatures were individually selected based on the recurrence and progression status. Among 43,148 unique genes, 424 and 287 candidate predictive genes that could predict recurrence and progression, respectively, were selected. Time to recurrence or progression was shorter for patients with poor-predictive gene signatures than good-predictive gene signatures (log-rank test, p <0.001, respectively). Validation of predictive gene signatures with RT-PCR was nearly identical to those of microarray (log-rank test, p <0.05, respectively). In multivariate regression analysis, predictive gene signatures were the only independent predictors of recurrence (HR 3.38, p = 0.048) or progression (HR 10.49, p = 0.048) in validation cohorts. Predictive gene signatures have strong diagnostic value for determining the response to intravesical BCG immunotherapy in primary pT1 bladder cancer. Keywords: Gene expression, Bladder cancer, BCG Total RNA, extracted from the fresh frozen tissues of 48 pT1 bladder cancers, was isolated by TRIzol reagent (Life Technologies, NY, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Five-hundred nanograms of total RNA were used for labeling hybridization according to the manufacturerâ??s protocol (Illumina HumanWG-6 BeadChip, version 2, Illumina, Inc., San Diego, CA, USA). Arrays were scanned with an Illumina Bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc.) according to the manufacturer's instructions. Initial microarray gene expression data were obtained using Bead Studio software with gene expression analysis module (version 3.1.3, Illumina, Inc.).
2010-04-07 | E-GEOD-19423 | biostudies-arrayexpress