Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from prostate cancer samples

ABSTRACT: Although many genes have been proposed to be involved in prostate carcinogenesis, no single gene or gene profile has shown to have prognostic value. The main challenge for clinical management is to distinguish slowly growing tumors from those that will relapse. In this study, we compared expression profiles of 18 prostate samples (7 with Gleason 6, 8 with Gleason 7 and 3 with Gleason score equal or higher than 8) and 5 non-neoplastic prostate samples, using the GeneChip® Human Exon Array 1.0 ST of Affymetrix. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason score 6, 7 and 8. In addition, mRNA expression of 29 selected genes was analyzed by qRT-PCR with microfluidic cards in an extended series of 30 prostate tumors. From these, 29 were selected to be validated and the differential expression of 18 of them (62%) was independently confirmed by quantitative real-time RT-PCR (14 upregulated and 4 downregulated in higher Gleason scores) in the extended series. This list was further narrowed down to 12 genes that were differentially expressed in tumors with Gleason score of 6-7 vs 8. Finally, the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) were additionally validated by immunohistochemistry. Strong protein levels of both genes were correlated with Gleason score, stage, and PSA progression. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

ORGANISM(S): Homo sapiens

PROVIDER: GSE30521 | GEO | 2012/10/25

SECONDARY ACCESSION(S): PRJNA143295

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from prostate cancer samples

Project description:Although many genes have been proposed to be involved in prostate carcinogenesis, no single gene or gene profile has shown to have prognostic value. The main challenge for clinical management is to distinguish slowly growing tumors from those that will relapse. In this study, we compared expression profiles of 18 prostate samples (7 with Gleason 6, 8 with Gleason 7 and 3 with Gleason score equal or higher than 8) and 5 non-neoplastic prostate samples, using the GeneChipÂ® Human Exon Array 1.0 ST of Affymetrix. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason score 6, 7 and 8. In addition, mRNA expression of 29 selected genes was analyzed by qRT-PCR with microfluidic cards in an extended series of 30 prostate tumors. From these, 29 were selected to be validated and the differential expression of 18 of them (62%) was independently confirmed by quantitative real-time RT-PCR (14 upregulated and 4 downregulated in higher Gleason scores) in the extended series. This list was further narrowed down to 12 genes that were differentially expressed in tumors with Gleason score of 6-7 vs 8. Finally, the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) were additionally validated by immunohistochemistry. Strong protein levels of both genes were correlated with Gleason score, stage, and PSA progression. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. 23 Samples were analyzed.

2012-10-25 | E-GEOD-30521 | biostudies-arrayexpress

Homo sapiens

Project description:Prostate Cancer Gleason Score

| PRJNA115927 | ENA

Prostate Cancer Gleason Score

Project description:Screening of differentially expressed genes between benign and prostate tumors with respect to different prostate cancer gleason score 6 and 8 Keywords: disease subtype analysis

2010-03-31 | GSE15484 | GEO

Discovery of novel hypermethylated gene loci in prostate cancer using genome wide coverage CpG island microarrays

2009-03-27 | GSE15298 | GEO

Proteomic-based computational stratification of intermediate-risk prostate cancer patients.

Project description:Gleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in Gleason Grade Groups (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or over-treatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign samples from 278 patients. Three proteins (F5, TMEM126B and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomise prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management.

2023-11-30 | PXD041005 | Pride

An mRNA Expression Signature of Gleason Grade Predicts Lethal Prostate Cancer

Project description:PSA screening has led to enormous overtreatment of prostate cancer, due to the inability to distinguish potentially lethal disease at diagnosis. We reasoned that by identifying an mRNA signature of Gleason grade, the best predictor of prognosis, we could improve prediction of lethal disease among men with moderate Gleason 7 tumors, the most common grade, and most indeterminate in terms of prognosis. Using the complementary DNA (cDNA)–mediated annealing, selection, extension, and ligation assay, we measured the mRNA expression of 6,100 genes in prostate tumor tissue in the Swedish Watchful Waiting cohort (N=358) and Physicians’ Health Study (PHS; N=109). We developed an mRNA signature of Gleason comparing individuals with Gleason ≤6 to those with Gleason ≥8 tumors, and applied the model among Gleason 7 cases to discriminate lethal cases. We built a157-gene signature using the Swedish data that predicted Gleason with low misclassification (AUC=0.91); when this signature was tested in the PHS validation set, the discriminatory ability remained high (AUC=0.94). In men with Gleason 7 tumors, who were excluded from the model building, the signature significantly improved the prediction of lethal disease beyond knowing whether the Gleason score was 4+3 or 3+4 (p=0.006). Our expression signature and the genes identified may improve our understanding of the de-differentiation process of prostate tumors. Additionally, the signature may have clinical applications among men with Gleason 7, by further estimating their risk of lethal prostate cancer and thereby guiding therapy decisions to improve outcomes and reduce overtreatment.

2012-05-01 | GSE37663 | GEO

An mRNA Expression Signature of Gleason Grade Predicts Lethal Prostate Cancer

Project description:PSA screening has led to enormous overtreatment of prostate cancer, due to the inability to distinguish potentially lethal disease at diagnosis. We reasoned that by identifying an mRNA signature of Gleason grade, the best predictor of prognosis, we could improve prediction of lethal disease among men with moderate Gleason 7 tumors, the most common grade, and most indeterminate in terms of prognosis. Using the complementary DNA (cDNA)M-bM-^@M-^Smediated annealing, selection, extension, and ligation assay, we measured the mRNA expression of 6,100 genes in prostate tumor tissue in the Swedish Watchful Waiting cohort (N=358) and PhysiciansM-bM-^@M-^Y Health Study (PHS; N=109). We developed an mRNA signature of Gleason comparing individuals with Gleason M-bM-^IM-$6 to those with Gleason M-bM-^IM-%8 tumors, and applied the model among Gleason 7 cases to discriminate lethal cases. We built a157-gene signature using the Swedish data that predicted Gleason with low misclassification (AUC=0.91); when this signature was tested in the PHS validation set, the discriminatory ability remained high (AUC=0.94). In men with Gleason 7 tumors, who were excluded from the model building, the signature significantly improved the prediction of lethal disease beyond knowing whether the Gleason score was 4+3 or 3+4 (p=0.006). Our expression signature and the genes identified may improve our understanding of the de-differentiation process of prostate tumors. Additionally, the signature may have clinical applications among men with Gleason 7, by further estimating their risk of lethal prostate cancer and thereby guiding therapy decisions to improve outcomes and reduce overtreatment. 198 cases from the population-based Swedish-Watchful Waiting cohort. The cohort consists of men with localized prostate cancer (clinical stage T1-T2, Mx, N0); expression profiles from tumors with Gleason M-bM-^IM-%8 (N=89) were compared to those from tumors with Gleason M-bM-^IM-$6 (N=109)

2012-04-30 | E-GEOD-37663 | biostudies-arrayexpress

Discovery of novel hypermethylated gene loci in prostate cancer using genome wide coverage CpG island microarrays

Project description:In order to identify methylation changes in prostate cancer, we performed a genome-wide analysis of DNA methylation using Agilent human CpG island arrays. We then chose specific genes to validate methylation both in the same cases as were hybridized to the array (using quantitative EpiTYPER analysis) and in an independent series of prostate cancer samples (using MethyLight quantitative methylation specific PCR). We specifically chose low grade (Gleason score 6 cases) and high grade (Gleason score 8 cases) to discover methylated genes/loci that may be involved in the progression to a higher grade of prostate cancer. We collected 20 specimens consisting of 10 Gleason 6 and 10 Gleason 8 prostate cancers, and compared these to a reference lymphocyte pool (6 age matched, healthy men) to determine cancer associated methylation changes as well as disease progression associated methylation changes. We performed the differential methylation hybridization procedure as described by Yan et al. (Methods, 2002) on each case to enrich for methylated DNA. Each specimen in the reference pool underwent the same enrichment with amplicons being pooled at the end of the procedure. Each prostate cancer case was subsequently co-hybridized to the microarray with the reference pool.

2009-03-26 | E-GEOD-15298 | biostudies-arrayexpress

[miRNA Training Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

Project description:To identify biomarkers predictive of biochemical recurrence, we isolated the RNA from 70 formalin-fixed paraffin-embedded (FFPE) radical prostatectomy specimens with known long term outcome to perform DASL expression profiling with a custom-designed panel of 522 prostate cancer relevant genes that we designed. We identified a panel of ten protein-coding genes and two miRNA genes that could be used to separate patients with and without biochemical recurrence (p < 0.001), as well as for the subset of 42 Gleason score 7 patients (p < 0.001). We performed an independent validation analysis on 40 samples and found that the biomarker panel was also significant at prediction of recurrence for all cases (p = 0.013) and for a subset of 19 Gleason score 7 cases (p = 0.010), both of which were adjusted for relevant clinical information including T-stage, PSA and Gleason score. Importantly, these biomarkers could significantly predict clinical recurrence for Gleason 7 patients. These biomarkers may increase the accuracy of prognostication following radical prostatectomy using formalin-fixed specimens. Total RNA prepared from FFPE cores from prostatectomy samples of 70 patients were used for the training phase (29 with biochemical recurrence and 41 controls). All samples were analyzed by both custom Prostate DASL of 522 genes and by Illumina miRNA microarray. Subsequently in the validation phase, samples from 40 patients were used on the same platforms (13 with biochemical recurrence and 27 controls). For the training set, 45 cases were from Sunnybrook Health Science Center (Toronto, ON), and 25 patients from Emory University. For the validation set, all samples were from Emory University. Relevant clinical metadata included are PSA, T-stage, and Gleason Score.

2011-06-01 | E-GEOD-26245 | biostudies-arrayexpress

[miRNA Validation Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

2011-06-01 | E-GEOD-26247 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data