Transcriptome-wide gene expression analysis of prostate cancer (PCa) needle biopsies
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA554132 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We assessed transcriptome-wide gene expression in needle biopsies of PCa patients prior to radical prostatectomy (RP) by next-generation sequencing (HiSeq 2500). We applied Cox proportional hazard models to the cohorts from different platforms and specimen types and combined the evidence from these by fixed effect meta-analysis to identify genes predictive for time to DoD (death of disease). Genes were combined by a weighted median approach into a prognostic score. Tumor cell content and GS from the biopsy cores were evaluated by pathologists. If applicable, the hospital provided tissue sections from the biopsy with the highest tumor cell content. If multiple biopsy cores were used for analysis, the average tumor cell content of all the samplings (typically 2 o 3 cores) was calculated. The primary clinical endpoint of the cohort was death of disease (DoD).
2020-07-21 | GSE134171 | GEO
Project description:Prostate cancer (PCa) is a common cancer and remains the second leading cause of cancer-associated mortality in men. To investigate the involvement of differentially expressing genes in PCa with deregulated pathways to allow earlier diagnosis of the disease, transcriptomic analyses of differential expression genes in Fine-Needle Aspiration (FNA) biopsies were for discrimination of PCa from benign prostatic hyperplasia (BPH). The RNA samples were extracted from four PCa biopsy samples and four BPH biopsy controls for microarray profiling and performed in Affymetrix Human U133 Plus 2 arrays for gene expression profiling analysis. Microarray data were analyzed using GeneSpring GX 10 (Agilent).On average, we detected expression of 47,000 transcripts.Under the criteria fold change > 2 or < 0.5, we obtained 1819 differential expressed genes(DEGs).Hierarchy cluster analysis also indicated that the 8 samples were distributed into two clusters, 4 PCa samples in one cluster and 4 BPH samples in another cluster.Then,qRT-PCR validation of the DEGs in PCa tissue and prostate cancer cells.The results revealed that grouping was reasonable and the data can be directly applied to further analysis.
2017-10-11 | GSE104749 | GEO
Project description:Clinical manifestation of PCa is highly variable. Aggressive tumors require radical treatment, while clinically non-significant ones may be suitable for active surveillance. We have previously developed the prognostic ProstaTrend signature mainly on prostatectomy specimens by application of transcriptome‐wide microarray and RNA-sequencing (RNA-Seq) analyses. We used a cohort of 185 tumor specimens obtained from FFPE biopsies for RNA-Seq to facilitate the application of ProstaTrend at the beginning of routine PCa diagnostic. All patients of the FFPE biopsy cohort were treated by radical prostatectomy (RPx) and median follow-up for biochemical recurrence (BCR) was 9 years. Based on the transcriptome data of the FFPE biopsies, we filtered ProstaTrend for genes susceptible to FFPE-associated degradation via regression analysis. ProstaTrend was additionally restricted to genes with concordant prognostic effects in the RNA-Seq TCGA prostate adenocarcinoma (PRAD) cohort to ensure robust and broad applicability. The prognostic relevance of the refined Transcriptomic Risk Score (TRS) was analyzed by Kaplan-Meier curves, Cox-regression models in our FFPE-biopsy cohort and 9 other public datasets from PCa patients with BCR as primary endpoint. The TRS based on the revised ProstaTrend signature, which included 204 genes, was significantly associated with BCR in the FFPE biopsy cohort (Cox-regression p-value <0.001). The TRS retained prognostic relevance when adjusted for Gleason Score (GS). We confirmed a significant association with BCR in 9 independent cohorts with a total of 1109 PCa patients. Comparison of the prognostic performance of the TRS with 17 other prognostically relevant PCa panels revealed that the revised ProstaTrend was among the best-ranked panels.
2023-09-08 | GSE220095 | GEO
Project description:Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed and paraffin-embedded (FFPE) biopsies has many unique challenges. Here we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers from diagnostic prostate needle core biopsies. 158 samples from diagnostic needle core biopsies (Bx) and radical prostatectomies (RP) were collected from 33 patients at three hospitals, each patient provided up to 6 tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the Bx and RP samples.
2016-03-09 | GSE72220 | GEO
Project description:Transcriptome-wide gene expression analysis of Formalin-Fixed Paraffin-Embedded (FFPE) biopsies of prostate cancer (PCa)
| PRJNA908792 | ENA
Project description:Comparison of miRNA expression profiles in a small set of prostate needle core biopsies or fine needle aspirates. Keywords: Expression profiling of prostate needle core biopsies
2006-04-05 | GSE4574 | GEO
Project description:Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes
2011-10-31 | GSE32518 | GEO
Project description:Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed and paraffin-embedded (FFPE) biopsies has many unique challenges. Here we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers from diagnostic prostate needle core biopsies. 158 samples from diagnostic needle core biopsies (Bx) and radical prostatectomies (RP) were collected from 33 patients at three hospitals, each patient provided up to 6 tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the Bx and RP samples. For 23 patients from UCSF and CSMC, six prostate tissue samples were obtained from each patient: tumor biopsy, tumor RP, benign adjacent biopsy, benign adjacent RP, and benign contralateral biopsy, and benign contralateral RP. For the 10 UHN patients only tumor biopsy and tumor RP samples were obtained. A total of 147 samples passed RNA, cDNA, and microarray quality control.
2016-03-09 | E-GEOD-72220 | biostudies-arrayexpress
Project description:Molecular analyses of prostate tumors for diagnosis of malignancy on Fine-Needle Aspiration biopsies
| PRJNA413754 | ENA
Project description:Nonaggressive prostate cancer (NAG-PCa) with Gleason score of 6 is considered as a low-risk disease and does not require clinical interventions. However, current assessment of aggressiveness of PCa is invasive using needle biopsies. Urine is an appealing biospecimen for noninvasive detection of aggressive PCa. Using urine, particularly from easily obtainable from pre-DRE urine specimens, to identify AG-PCa-associated molecular markers is critical for clinical risk stratification. Herein, we acquired quantitative mass spectrometry data for glycoproteins from pre-DRE and post-DRE urine specimens from patients underwent PCa diagnosis with biopsies. Compared with urinary glycoproteins identified from post-DRE urine samples, we confirmed that three previously reported AG-PCa-associated glycoproteins identified in post-DRE urine specimens were also found to be significantly associated with AG disease in pre-DRE urine samples. In addition, new AG-PCa-associated glycoproteins were identified in pre-DRE urine specimens. Our study provides a foundation for further studies of AG-PCa biomarkers using pre-DRE urine specimens.
2023-07-20 | PXD036468 | Pride