Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA197502 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Detection of DNA hypermethylation has emerged as a novel molecular biomarker for the evaluation of prostate cancer diagnosis and prognosis, but the use of single gene hypermethylation could produce unspecific results. Defining the specific gene hypermethylation profile for prostate cancer could provide groups of genes that specifically discriminate the patients with indolent and aggressive tumors. To compare the methylation profile of normal and malignant prostate we performed Genome-wide methylation analysis on 83 tumor samples, that included all clinical stages of the disease, 10 normal prostate samples and LNCaP, DU145 and PC3 prostate cancer cell lines using the GoldenGate Methylation Cancer Panel I (Illumina, Inc.) that interrogate for 1505 CpGs. We found 41 genes significantly hypermethylated in more than 20% of the tumors analyzed (p<0.01). Of these we identified GSTM2 and PENK as novel hypermethylated genes in prostate cancer that were simultaneously methylated in 40.9% of the tumors analyzed. We also identified panels of genes more frequently methylated in tumor samples with clinico-pathological indicators of poor prognosis: high Gleason score, elevated Ki-67 or advanced disease. Of these, we found that simultaneous hypermethylation of CFTR and HTR1B is common in patients with high Gleason score and high ki-67 levels and might signal the population at higher risk of therapeutic failure. DNA hypermethylation profile was associated with cancer-specific mortality (log-rank, p=0.007) and biochemical recurrence-free survival (log-rank, p=0.0008). In conclusion, our data strongly indicate that epigenetic silencing of GSTM2 and PENK is a common event in prostate cancer that could be used as a molecular marker for prostate cancer diagnosis. In addition, simultaneous HTR1B and CFTR hypermethylation could help discriminate aggressive from indolent prostate tumors.A DNA hypermethylation profile associated with cancer-specific mortality and biochemical recurrence in patients receiving radical prostatectomy is presented. GST2 and PENK are new hipermethylated genes identified. Simultaneous hypermethylation of CFTR and HTR1B could help discriminate aggressive disease.
2014-12-31 | GSE46177 | GEO
Project description:Exosomal miRNAs play important roles in cancer progression and therapeutic resistance and have shown great potential as liquid biopsy biomarkers for cancer diagnosis/prognosis. We investigated for the first time plasma exosomal miRNAs for their association with and early detection potential of castration-resistant prostate cancer (CRPC). RNA-sequencing was performed to identify candidate exosomal miRNAs associated with development of CRPC in 24 treatment-naive prostate cancer (PCa) and 24 CRPC patients.
2021-01-07 | GSE136321 | GEO
Project description:Dyskeratosis congenita (DKC) is characterized by impaired telomere maintenance and reveals clinical features of premature aging. So far, diagnosis of DKC relies particularly on telomere length screening raising the need for additional biomarkers. In this study, we analysed global DNA methylation (DNAm) profiles of DKC patients. Age-associated DNAm changes were not generally accelerated in DKC. However, we observed significant hypermethylation in the gene for PR domain containing 8 (PRDM8). Notably, the same genomic region revealed hypermethylation in aplastic anemia (AA), and Down syndrome (DS), indicating that there might be an association with premature aging syndromes. Site-specific analysis of DNAm level in PRDM8 with pyrosequencing and MassArray validated aberrant hypermethylation in 14 DKC patients and 27 AA patients. Notably, telomere length was not directly correlated with DNAm in PRDM8, indicating that the two methods are complementary. In conclusion, DNAm at PRDM8 provides a new biomarker to support diagnosis of of AA and DKC.
2016-05-23 | GSE75310 | GEO
Project description:Single-cell analysis of castration-resistant prostate cancers to identify potential biomarkers for diagnosis and prognosis of neuroendocrine prostate cancer
| PRJNA1311495 | ENA
Project description:Differentially expressed noncoding RNAs as potential biomarkers for DIPG diagnosis and prognosis
| PRJNA575738 | ENA
Project description:Prostate cancer (PCa) is one of the most prevalent cancers among men and the fifth leading cause of cancer-related death in men. Currently, PCa suspicion is based on abnormal digital rectal examination and/or raised PSA serum levels, with prostate needle biopsy being required for a definitive diagnosis. Histopathological classification of tumours based on GS grading, cancer staging and PSA levels are used to predict the indolent or aggressive progression of the tumour as well as the likelihood of disease recurrence. These diagnosis and prognosis tools for PCa have revealed limited usefulness, especially PSA testing, which despite organ-specificity is not cancer-specific, being associated with low specificity. In this vein, new markers have been proposed in order to increase the accuracy of PCa detection, most of them proteins. Despite the significant efforts that have been undertaken for discovering other biomarkers for PCa management, few were translated into clinical practice. The simple and non-invasive nature of urine collection along with its proteome stability and storing many secreted proteins of prostate origin, makes the identification of PCa urinary biomarkers an attractive approach. With this in mind, we aimed to compare the urinary proteome profile of PCa patients with non-cancer patients in order to identify non-invasive candidate biomarkers for PCa prediction. To fulfil this task, we followed a shotgun LC-MS/MS approach using an Orbitrap instrument. A combination of two different software packages, MaxQuant and Proteome Discover was used to increase the robustness of analysis and enhance the search for new biomarkers. Proteins quantification was based on a label-free quantification approach (false discovery rate (FDR) 1%). The present dataset was used to disclosure potential markers in PCa management.
2022-05-19 | PXD017902 | Pride
Project description:The early diagnosis of diabetic nephropathy (DN) is essential to improve the prognosis and manage patients affected by this disease. Standard biomarkers, including albuminuria and glomerular filtration rate, are limited to give a precise result. New molecular biomarkers are needed to identify better and predict DN disease evolution. Characteristic DN biomarkers can be identified using transcriptomic analysis. Blood samples were used to isolate RNA for microarray expression using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays, we evaluated the transcriptomic profile of controls , prediabetes, type-2 diabetes mellitus, and DN.
2022-09-16 | E-MTAB-12135 | biostudies-arrayexpress
Project description:DNA methylation analysis of paired prostate tumor and noncancerous tissues was perform in order to identify potential DNA methylation biomarkers for prostate cancer diagnostics and prognosis. Based on comparison of tumors versus noncancerous tissues and cases with and without biochemical disease recurrence (BCR), several gene targets were selected for more detailed analysis. Differences in methylation were further confirmed by means of methylation-specific PCR and significantly correlated with gene expression. Survival analysis indicated various combinations of DNA methylation biomarkers as significant prognosticaters of time to BCR, therefore, showing their potential clinical significance.
2017-04-30 | GSE89243 | GEO
Project description:Purpose: Available tools for prostate cancer (PC) diagnosis and prognosis are suboptimal and novel biomarkers are urgently needed. Here, we investigated the regulation and biomarker potential of the GABRE~miR-452~miR-224 genomic locus. Experimental design: GABRE/miR-452/miR-224 transcriptional expression was quantified in 80 non-malignant and 281 PC tissue samples. GABRE promoter methylation was determined by methylation-specific qPCR (MethyLight) in 35 non-malignant, 293 PC (radical prostatectomy (RP) cohort 1) and 198 PC tissue samples (RP cohort 2). Diagnostic/prognostic biomarker potential of GABRE methylation was evaluated by ROC, Kaplan-Meier, uni- and multivariate Cox regression analyses. Functional roles of miR-224 and miR-452 were investigated in PC3 and DU145 cells by viability, migration, and invasion assays and gene-set enrichment analysis (GSEA) of post-transfection transcriptional profiling data. Results: GABRE~miR-452~miR-224 was significantly downregulated in PC compared to non-malignant prostate tissue and had highly cancer-specific aberrant promoter hypermethylation (AUC=0.98). Functional studies and GSEA suggested that miR-224 and miR-452 inhibit proliferation, migration, and invasion of PC3 and DU145 cells by direct/indirect regulation of pathways related to the cell cycle and cellular motility. Finally, in uni- and multivariate analyses, high GABRE promoter methylation was significantly associated with biochemical recurrence in RP cohort 1, which was successfully validated in RP cohort 2. Conclusion: The GABRE~miR-452~miR-224 locus is downregulated and hypermethylated in PC and is a new promising epigenetic candidate biomarker for PC diagnosis and prognosis. Tumor suppressive functions of the intronic miR-224 and miR-452 were demonstrated in two PC cell lines, suggesting that epigenetic silencing of GABRE~miR-452~miR-224 may be selected for in PC. Affymetrix GeneChip Human Gene 1.0 ST Arrays were used for whole-genome transcriptional profiling of DU145 and PC3 cells at 48 hours post-transfection with either miR-224, miR-452, or scrambled miRNA mimics, or untransfected. All experiments were performed in duplicate. Transcript expression levels were determined after RMA16 normalization in GeneSpringGX 11.0 software (Agilent). PC3 and DU145 arrays were normalized separately. DU145 48 t Scr2a were excluded from the study because of bad performance of this microarray.
2013-12-11 | E-GEOD-51053 | biostudies-arrayexpress