Identification a novel set of 6 differential expressed genes in prostate cancer that can potentially predict biochemical recurrence after curative surgery
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Approximately, 30% patients after radical prostatectomy (RP) will undergo post-operative biochemical recurrence (BCR). Present stratification method by TNM staging and Gleason score was not adequate to screen high-risk patients. In this study, we intended to identify a novel set of differentially expressed gene (DEG) signature that can predict BCR after RP.
358 patients after RP with follow-up data were extracted from The Cancer Genome Atlas (TCGA), among which 61 patients had undergone BCR. Key DEGs were confirmed by the intersection of GSE35988 and TCGA_PCa dataset, and their gene expression data were also extracted from TCGA_PCa dataset. Kaplan–Meier plot and Cox proportion hazard regression model were applied to assess the relationship between risk score and survival outcome (BCR).
310 DEGs were confirmed in two prostate cancer dataset. 6 DEGs (SMIM22, NINL, NRG2, TOP2A, REPS2, and TPCN2) were selected to construct a risk score formula. The risk score was a powerful predictive factor independent of TNM stage (HR 3.045, 95% CI 1.655–5.602, p < 0.001).
In this study, a novel 6-gene signature with robust predictive ability on post-operative BCR was constructed and 4 genes (SMIM22, NRG2, NINL and TPCN2) in the 6-gene signature were not reported to be associated with prostate cancer.
KeywordsBiomarker Recurrence Gene expression Prognosis Prostatic neoplasms
This research was based on public database: TCGA, GEO and GEPIA, and we are grateful for the extraordinary works of these project groups. We thank Bioinformatics Engineer Rang-Fei Zhu for his excellent pretreatment of TCGA-PCa data.
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
The patients’ information involved in our research was obtained from The Cancer Genome Atlas (TCGA). All the patients and treatments were complied with the principles laid down in the Declaration of Helsinki in 1964 and its later amendments or comparable ethical standards.
Informed consent was confirmed by all the patients participated in the TCGA-Prostate adenocarcinoma project.
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