Novel RNA biomarkers of prostate cancer revealed by RNA-seq analysis of formalin-fixed samples obtained from Russian patients

Novel RNA biomarkers of prostate cancer revealed by RNA-seq analysis of formalin-fixed samples obtained from Russian patients

Due to heterogeneous multifocal nature of prostate cancer (PCa), there is currently a lack of biomarkers that stably distinguish it from benign prostatic hyperplasia (BPH), predict clinical outcome and guide the choice of optimal treatment. In this study RNA-seq analysis was applied to formalin-fixe...

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Bibliographic Details
Published in:Oncotarget Vol. 8; no. 20; pp. 32990 - 33001
Main Authors: Nikitina, Anastasia S, Sharova, Elena I, Danilenko, Svetlana A, Butusova, Tatiana B, Vasiliev, Alexandr O, Govorov, Alexandr V, Prilepskaya, Elena A, Pushkar, Dmitry Y, Kostryukova, Elena S
Format: Journal Article
Language:English
Published: United States Impact Journals LLC 16-05-2017
Subjects:
Aged
Formaldehyde
Gene Expression Profiling - methods
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
Genetic Markers - genetics
Humans
Male
MicroRNAs - genetics
Middle Aged
Prostatic Hyperplasia - genetics
Prostatic Neoplasms - genetics
Research Paper
Russia
Sequence Analysis, RNA - methods
Tissue Fixation
Transcription Factors - genetics
prostate cancer
RNA biomarkers
FFPE
RNA-Seq
benign prostatic hyperplasia
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Summary:Due to heterogeneous multifocal nature of prostate cancer (PCa), there is currently a lack of biomarkers that stably distinguish it from benign prostatic hyperplasia (BPH), predict clinical outcome and guide the choice of optimal treatment. In this study RNA-seq analysis was applied to formalin-fixed paraffin-embedded (FFPE) tumor and matched normal tissue samples collected from Russian patients with PCa and BPH. We identified 3384 genes differentially expressed (DE) (FDR < 0.05) between tumor tissue of PCa patients and adjacent normal tissue as well as both tissue types from BPH patients. Overexpression of four of the discovered genes (ANKRD34B, NEK5, KCNG3, and PTPRT) was validated by RT-qPCR. Furthermore, the enrichment analysis of overrepresented microRNA and transcription factor (TF) recognition sites within DE genes revealed common regulatory elements of which 13 microRNAs and 53 TFs were thus linked to PCa for the first time. Moreover, 8 of these TFs (FOXJ2, GATA6, NFE2L1, NFIL3, PRRX2, TEF, EBF2 and ZBTB18) were found to be differentially expressed in this study making them not only candidate biomarkers of prostate cancer but also potential therapeutic targets.
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ISSN:1949-2553
1949-2553
DOI:10.18632/oncotarget.16518