Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer

Sudhanshu Shukla, Xiang Zhang, Yashar S. Niknafs, Lanbo Xiao, Rohit Mehra, Marcin Cieślik, Ashley Ross, Edward Schaeffer, Bhavna Malik, Shuling Guo, Susan M. Freier, Huynh Hoa Bui, Javed Siddiqui, Xiaojun Jing, Xuhong Cao, Saravana M. Dhanasekaran, Felix Y. Feng, Arul M. Chinnaiyan, Rohit Malik

Research output: Contribution to journalArticle

Abstract

Rapid advances in the discovery of long noncoding RNAs (lncRNAs) have identified lineage- and cancer-specific biomarkers that may be relevant in the clinical management of prostate cancer (PCa). Here we assembled and analyzed a large RNA-seq dataset, from 585 patient samples, including benign prostate tissue and both localized and metastatic PCa to discover and validate differentially expressed genes associated with disease aggressiveness. We performed Sample Set Enrichment Analysis (SSEA) and identified genes associated with low versus high Gleason score in the RNA-seq database. Comparing Gleason 6 versus 9+ PCa samples, we identified 99 differentially expressed genes with variable association to Gleason grade as well as robust expression in prostate cancer. The top-ranked novel lncRNA PCAT14, exhibits both cancer and lineage specificity. On multivariate analysis, low PCAT14 expression independently predicts for BPFS (P = .00126), PSS (P = .0385), and MFS (P = .000609), with trends for OS as well (P = .056). An RNA in-situ hybridization (ISH) assay for PCAT14 distinguished benign vs malignant cases, as well as high vs low Gleason disease. PCAT14 is transcriptionally regulated by AR, and endogenous PCAT14 overexpression suppresses cell invasion. Thus, Using RNA-sequencing data we identify PCAT14, a novel prostate cancer and lineage-specific lncRNA. PCAT14 is highly expressed in low grade disease and loss of PCAT14 predicts for disease aggressiveness and recurrence.

Original languageEnglish (US)
Pages (from-to)489-499
Number of pages11
JournalNeoplasia (United States)
Volume18
Issue number8
DOIs
Publication statusPublished - Aug 1 2016

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ASJC Scopus subject areas

  • Cancer Research

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Shukla, S., Zhang, X., Niknafs, Y. S., Xiao, L., Mehra, R., Cieślik, M., ... Malik, R. (2016). Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer. Neoplasia (United States), 18(8), 489-499. https://doi.org/10.1016/j.neo.2016.07.001