Transcriptome sequencing analysis of FFPE prostate tissue
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB43878 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5532313.fastq.gz | Fastqsanger.gz | |||
| ERR5532314.fastq.gz | Fastqsanger.gz | |||
| ERR5532315.fastq.gz | Fastqsanger.gz | |||
| ERR5532316.fastq.gz | Fastqsanger.gz |
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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.
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