title: Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer.
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.
authors: Dept. of Urology, Erasmus MC, Rotterdam, The Netherlands.|Dept. of Bioinformatics, Technical University of Applied Sciences Wildau, Wildau, Germany.
authors: René
authors: R
authors: Böttcher
authors: Dept. of Pathology, Erasmus MC, Rotterdam, The Netherlands.
authors: A Marije
authors: AM
authors: Hoogland
authors: Dept. of Urology, Erasmus MC, Rotterdam, The Netherlands.
authors: Natasja
authors: N
authors: Dits
authors: Dept. of Pathology, Erasmus MC, Rotterdam, The Netherlands.
authors: Esther I
authors: EI
authors: Verhoef
authors: Dept. of Pathology, Erasmus MC, Rotterdam, The Netherlands.
authors: Charlotte
authors: C
authors: Kweldam
authors: Dept. of Urology, Erasmus MC, Rotterdam, The Netherlands.
authors: Piotr
authors: P
authors: Waranecki
authors: Dept. of Urology, Erasmus MC, Rotterdam, The Netherlands.
authors: Chris H
authors: CH
authors: Bangma
authors: Dept. of Pathology, Erasmus MC, Rotterdam, The Netherlands.
authors: Geert J L H
authors: GJ
authors: van Leenders
authors: Dept. of Urology, Erasmus MC, Rotterdam, The Netherlands.
authors: Guido
authors: G
authors: Jenster
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis* / Q000235:genetics; D045744:Cell Line, Tumor; D005091:Exons; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D006801:Humans; D017403:In Situ Hybridization; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D011471:Prostatic Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000378:metabolism; D064129:Prostatic Neoplasms, Castration-Resistant / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000032:analysis* / Q000235:genetics; D046888:Tissue Array Analysis
chemical_list: D014408:Biomarkers, Tumor; D062085:RNA, Long Noncoding