GEO DataSets

(Submitter supplied) Purpose: Patients with locally advanced prostate cancer after radical prostatectomy are candidates for secondary therapy. However, this higher risk population is heterogeneous. Many cases do not metastasize even when conservatively managed. Given the limited specificity of pathological features to predict metastasis, newer risk prediction models are needed. We report a validation study of a genomic classifier that predicts metastasis after radical prostatectomy in a high risk population. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

235 Samples

Download data: CEL

(Submitter supplied) To test the hypothesis that a genomic classifier (GC) would predict biochemical failure (BF) and distant metastasis (DM) in men receiving radiation therapy (RT) after radical prostatectomy (RP).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

139 Samples

Download data: CEL

(Submitter supplied) To determine whether adding Decipher to standard risk stratification tools (CAPRA-S and Stephenson nomogram) improves accuracy in prediction of metastatic disease within 5 years after surgery in men with adverse pathologic features after RP.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

182 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Expression profiling by array

Platforms:

GPL14550 GPL10152

20 Samples

Download data: TXT

(Submitter supplied) Neuroendocrine prostate cancer (NEPC) is proliferative, invasive, and untreatable. Its molecular pathogenesis remains poorly understood but appears to require TP53 and RB1 aberration. In this study we modeled the development of NEPC from conventional prostatic adenocarcinoma using a unique patient-derived xenograft and identified up-regulation of the placental gene PEG10. We found that the androgen receptor and the E2F/RB pathway dynamically regulate distinct post-transcriptional and post-translational isoforms of PEG10 at different stages of NEPC development. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10152

6 Samples

Download data: TXT

(Submitter supplied) Neuroendocrine prostate cancer (NEPC) is proliferative, invasive, and untreatable. Its molecular pathogenesis remains poorly understood but appears to require TP53 and RB1 aberration. In this study we modeled the development of NEPC from conventional prostatic adenocarcinoma using a unique patient-derived xenograft and identified up-regulation of the placental gene PEG10. We found that the androgen receptor and the E2F/RB pathway dynamically regulate distinct post-transcriptional and post-translational isoforms of PEG10 at different stages of NEPC development. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

14 Samples

Download data: TXT

(Submitter supplied) Purpose: Clinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer. We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis. Methods: A nested case-control design was used to select 639 patients from the Mayo Clinic tumor registry that underwent radical prostatectomy between 1987 and 2001. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

545 Samples

Download data: CEL, TXT

(Submitter supplied) Radical prostatectomy (RP) is a primary treatment option for men with intermediate- and high-risk prostate cancer. Although many are effectively cured with local therapy alone, these men are by definition at higher risk of adverse pathologic features. It has been shown previously that genomic data can be used to predict tumor aggressiveness. Our objective was to evaluate genomic data and it's relationship to pathological stage and grade in a cohort of men that received no treatment other than radical prostatectomy surgery.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

260 Samples

Download data: CEL, CSV

(Submitter supplied) Treatment-emergent neuroendocrine prostate cancer (t-NEPC) is a lethal subtype of advanced prostate cancer that develops via NE transdifferentiation of prostate adenocarcinomas in response to androgen receptor (AR)-inhibition therapy. Study of t-NEPC has been hampered by a lack of clinically relevant models. We previously established a unique and first-in-field patient-derived xenograft (PDX) model of adenocarcinoma (LTL331)-to-NEPC (LTL331R) transdifferentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Due to their varied outcomes, men with biochemical recurrence (BCR) following radical prostatectomy (RP) present a management dilemma. Here, we evaluate Decipher, a genomic classifier (GC), for its ability to predict metastasis following BCR. METHODS: The study population included 85 clinically high-risk patients who developed BCR after RP. Time-dependent receiver operating characteristic (ROC) curves, weighted Cox proportional hazard models, and decision curves were used to compare GC scores to Gleason score (GS), PSA doubling time (PSAdT), time to BCR (ttBCR), the Stephenson nomogram, and CAPRA-S for predicting metastatic disease progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

85 Samples

Download data: CEL

(Submitter supplied) To test whether a genomic classifier (GC) predicts development of metastatic disease in patients treated with salvage radiation therapy (SRT) after radical prostatectomy (RP).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

70 Samples

Download data: CEL

(Submitter supplied) Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer (PCa) with hyperchromatic nuclei being a distinguishing histopathological feature. Here we show that, underlying this distinct nuclear structure, heterochromatin related genes are significantly enriched in NEPC. Among them, heterochromatin protein 1α (HP1α) expression is increased early in NE transdifferentiation and is consistently elevated in clinical NEPC samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

13 Samples

Download data: TXT

(Submitter supplied) To determine the underlying mechanism of ONECUT2 in prostate cancer hypoxia, we conducted a series of RNA-Seq and ChIP-Seq experiments in LNCaP and PC3 cells under normoxia and hypoxia conditions. We did RNA-Seq in LNCaP cells with or without OC2 overexpression and in PC3 cells with or without OC2 knockdown. We used anti-Flag antibody to perform the ChIP-Seq experiment in PC3 cells with Flag and OC2 fusion protein overexpression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL11154

28 Samples

Download data: BW, TXT

(Submitter supplied) Neuroendocrine prostate cancer (NEPC) is rare historically but may be increasingin prevalence as patients potentially develop resistance to contemporary anti-androgen treatment through a neuroendocrine phenotype. Diagnosis can be straightforward when classic morphological features are accompanied by a prototypical immunohistochemistry profile, however there is increasing recognition of disease heterogeneity and hybrid phenotypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

33 Samples

Download data: CEL

(Submitter supplied) Investigation of miRNA expression profiles of prostate cancer (PCa) and normal prostatic samples

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL13264

48 Samples

Download data: TXT

(Submitter supplied) Organotypic slice cultures from prostate cancer patients were generated and treated with or without 17b-estradiol or DHT to study estrogen and androgen signalling pathways.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

2 Samples

Download data: TXT

(Submitter supplied) Serine Peptidase Inhibitor, Kazal type 1 (SPINK1) overexpression represents the second-largest prostate cancer (PCa) subtype associated with increased risk of biochemical recurrence and poor prognosis. To determine the pathways regulated by SPINK1 in 22RV1 prostate cancer cells, we performed shRNA mediated knockdown of SPINK1 using lentiviral constructs. Scrambled shRNA was used as a control. pGIPZ constructs against SPINK1 (shSPINK1-1, shSPINK1-2, shSPINK1-3) and control shScrambled construct were purchased from Dharmacon.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL25978

3 Samples

Download data: TXT

(Submitter supplied) As part of functional characterization of neuroblastoma associated lncRNA HOXD-AS1, we performed its knock-down in neuroblastoma cell line SH-SY5Y, which resulted in modulation of expression levels of a set of genes involved in angiogenesis and inflammation, the hallmarks of metastatic cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) We profiled the epigenomes of neuroendocrine prostate cancer and prostate adenocarcinoma patient-derived xenografts using ChIP-seq for transcription factors and histone modifications.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

104 Samples

Download data: BED, BW

(Submitter supplied) Prostate adenocarcinoma (AdPC) cells can undergo lineage switching to neuroendocrine cells and develop into therapy-resistant neuroendocrine prostate cancer (NEPC). While genomic/epigenetic alterations are shown to induce neuroendocrine differentiation via an intermediate stem-like state, RNA splicing factor SRRM4 can transform AdPC cells into NEPC xenografts through a direct neuroendocrine transdifferentiation mechanism. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

6 Samples

Download data: TXT