Circulating microRNAs predict biochemical recurrence in prostate cancer patients
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE47125 | GEO | 2013/05/22
SECONDARY ACCESSION(S): PRJNA203690
REPOSITORIES: GEO
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Project description:Comparison of circulating miRNA levels in patients who experienced rapid biochemical recurrence or no recurrence following radical prostatectomy qRT-PCR miRNA expression profiling of patient serum
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Project description:Prostate tumors with the gene fusion TMPRSS2:ERG have been reported to have a significantly higher risk of recurrence compared with tumors lacking the fusion. Tumors from 139 patients who underwent radical prostatectomy were analyzed for the expression of 502 cancer-related genes to identify genes differentially regulated in TMPRSS2:ERG fusion tumors as well as identify biomarkers of biochemical recurrence. 139 prostate fresh-frozen tumors from radical prostatectomy surgery where profiled on the Illumina Human Cancer DASL Panel. 69 tumors were positive for the gene fusion TMPRSS2:ERG while 70 where not. 33 of the 139 patients experienced biochemical recurrence. Data was analyzed for differential genes in TMPRSS2:ERG fusion positive tumors as well as clinical and molecular biomarkers of recurrence.
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Project description:This SuperSeries is composed of the following subset Series: GSE26022: [Gene Expression Training Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy GSE26242: [Gene Expression Validation Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy GSE26245: [miRNA Training Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy GSE26247: [miRNA Validation Set] Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy Refer to individual Series
2011-06-01 | E-GEOD-26367 | biostudies-arrayexpress
Project description:Radical prostatectomy remains one of the more widely-used treatment options for men with prostate cancer. However, few molecular biomarkers have been established to predict patients who are at high risk of biochemical failure. To our knowledge, this is the first such report on miRNA profiling in radical prostatectomy tissue using Nanostring. In addition, this is the first report to look at the prognostic value of miRNAs in the setting of biochemical failure and salvage radiation therapy post-radical prostatectomy.
2015-01-23 | GSE65061 | GEO
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
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-26247 | biostudies-arrayexpress
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-26242 | biostudies-arrayexpress
Project description:Radical prostatectomy remains one of the more widely-used treatment options for men with prostate cancer. However, few molecular biomarkers have been established to predict patients who are at high risk of biochemical failure. To our knowledge, this is the first such report on miRNA profiling in radical prostatectomy tissue using Nanostring. In addition, this is the first report to look at the prognostic value of miRNAs in the setting of biochemical failure and salvage radiation therapy post-radical prostatectomy. RNA was extracted from tumor-enriched 1mm cores from 43 radical prostatectomy paraffin tissue blocks. 800 miRNAs were profiled using the NanoString nCounter human miRNA assay. mirNAs were then correlated to clinical outcomes.
2015-01-23 | E-GEOD-65061 | biostudies-arrayexpress
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. ***This submission represents the mRNA component of the study
2011-06-01 | E-GEOD-26022 | biostudies-arrayexpress