Profiling of Androgen-Dependent Enhancer RNAs Expression in Human Prostate Tumors: Search for Malignancy Transition Markers

Abstract

Introduction Although the ability of androgens to promote prostate cancer development has been known for decades, the molecular mechanisms of androgen receptor (AR) signaling in the tumorigenesis remain unclear. Enhancer RNAs (eRNAs) transcribed from strong enhancers, or super-enhancers (SEs), have recently emerged as a novel class of regulatory non-coding RNAs (ncRNAs) that facilitate transcription, including that of androgen target genes, through chromatin looping to position enhancers proximate to the promoters. The aim of this study was to assess androgen-dependent transcription in prostate tumors of eRNAs (designated as KLK3eRNAs) from the SE of the KLK3 gene encoding the prostate-specific antigen (PSA) protein, a clinical marker of prostate carcinogenesis. Materials and Methods The androgen-induced KLK3eRNAs were identified in the LNCaP human prostate cancer cell line. The expressions of these KLK3eRNAs together with KLK3 and AR mRNA transcripts were assessed by qRT-PCR in prostate tumor samples from five prostate cancer patients. Results Androgen-induced KLK3eRNAs have been identified in the LNCaP cells, and their expression was further analyzed in tumors of prostate cancer patients. Transcripts of the tested KLK3eRNAs have been detected in all clinical samples, but their expression patterns differed between individual tumor specimens. We found a statistically significant correlation between the levels of the KLK3 and AR mRNAs with those of the previously reported KLK3eRNAs, while such correlation was not observed for novel KLK3eRNAs described in our recent report. Conclusion Presented data suggest that prostate tumor development may associate with epigenetic reorganization in the KLK3 genomic regulatory elements reflected by changes of the KLK3eRNA expression. Our findings support a potential of eRNAs profiling to be used as diagnostic marker.

A long non-coding RNA as a direct vitamin D target transcribed from the antisense strand of the human HSD17B2 locus

“…Enhancer RNAs serve as transcriptional and epigenetic regulators by dynamic reconfiguration of the chromatin environment [ 34 , 35 ]. Consistent with our previous reports [ 21 , 22 ], we recently detected candidate VD-induced eRNAs in the VD-responsive gene promoter of CYP24A in HaCaT cells [ 19 ]. The present results suggest that certain lncRNAs other than eRNAs are regulated by VD [ 33 , 34 ].…”

“…We characterized the 91 non-coding RNAs obtained by in silico data mining [ 21 , 22 ] as direct VD targets if they were found to be transcriptionally regulated by VD-bound VDR. Of these, 28 non-coding RNAs, including two miRNAs and 11 lncRNAs, with greater than twofold up-regulated expression, were selected.…”

“…VDR-KO HaCaT cells were a kind gift from Dr. S. Sawatsubashi (Tokushima, Japan) [ 18 ]. Human prostate cancer cell lines were cultured in RPMI1640 medium (PC3, LNCaP, and CWR22 cells) or DMEM (DU-145 cells) [ 20 , 21 ]. All cells were cultured at 37°C under 5% CO 2 .…”

Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in Cancer

“…Accumulated evidence supported that prostate tumor expansion may correlate with epigenetic reorganization in the KLK3 genomic regulatory elements reproduced by alterations of the KLK3 eRNA expression. Thus, the KLK3 eRNAs levels were indicated to be dissimilar in distinct tumor specimens and, furthermore, varied between normal and cancerous parts from the same tissue specimens [ 111 ].…”