Oncotarget

Research Papers:

Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer

René Böttcher _, A. Marije Hoogland, Natasja Dits, Esther I. Verhoef, Charlotte Kweldam, Piotr Waranecki, Chris H Bangma, Geert J.L.H. van Leenders and Guido Jenster

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Oncotarget. 2015; 6:4036-4050. https://doi.org/10.18632/oncotarget.2879

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Abstract

René Böttcher1,3, A. Marije Hoogland2, Natasja Dits1, Esther I. Verhoef2, Charlotte Kweldam2, Piotr Waranecki1, Chris H. Bangma1, Geert J.L.H. van Leenders2, Guido Jenster1

1Dept. of Urology, Erasmus MC, Rotterdam, The Netherlands

2Dept. of Pathology, Erasmus MC, Rotterdam, The Netherlands

3Dept. of Bioinformatics, Technical University of Applied Sciences Wildau, Wildau, Germany

Correspondence to:

Guido Jenster, e-mail: g.jenster@erasmusmc.nl

Keywords: Long non-coding RNA, prostate cancer, in situ hybridization, exon array, biomarkers

Received: August 22, 2014     Accepted: December 08, 2014     Published: January 22, 2015

ABSTRACT

Current prostate cancer (PCa) biomarkers such as PSA are not optimal in distinguishing cancer from benign prostate diseases and predicting disease outcome. To discover additional biomarkers, we investigated PCa-specific expression of novel unannotated transcripts. Using the unique probe design of Affymetrix Human Exon Arrays, we identified 334 candidates (EPCATs), of which 15 were validated by RT-PCR. Combined into a diagnostic panel, 11 EPCATs classified 80% of PCa samples correctly, while maintaining 100% specificity. High specificity was confirmed by in situ hybridization for EPCAT4R966 and EPCAT2F176 (SChLAP1) on extensive tissue microarrays. Besides being diagnostic, EPCAT2F176 and EPCAT4R966 showed significant association with pT-stage and were present in PIN lesions. We also found EPCAT2F176 and EPCAT2R709 to be associated with development of metastases and PCa-related death, and EPCAT2F176 to be enriched in lymph node metastases. Functional significance of expression of 9 EPCATs was investigated by siRNA transfection, revealing that knockdown of 5 different EPCATs impaired growth of LNCaP and 22RV1 PCa cells. Only the minority of EPCATs appear to be controlled by androgen receptor or ERG. Although the underlying transcriptional regulation is not fully understood, the novel PCa-associated transcripts are new diagnostic and prognostic markers with functional relevance to prostate cancer growth.


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