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

Koichi Nishimura,1,2,* Jinichi Mori,1– 3,* Takahiro Sawada,1,2 Shuhei Nomura,1,4 Alexander Kouzmenko,1 Kaori Yamashita,5 Yoshiaki Kanemoto,1,2 Tomohiro Kurokawa,1,2 Akira Hayakawa,1 Suguru Tokiwa,5 Michihisa Ochi,5 Hiroaki Shimmura,5 Shigeaki Kato1,2 1Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Japan; 2Graduate School of Life Science and Engineering, Iryo Sosei University, Iwaki, Japan; 3Department of Hematology, Jyoban Hospital, Iwaki, Japan; 4Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; 5Department of Urology, Jyoban Hospital, Iwaki, Japan*These authors contributed equally to this workCorrespondence: Shigeaki Kato Email uskato0525@gmail.comIntroduction: 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.Keywords: enhancer RNA, prostate cancer, androgen receptor, PSA, non-coding RNA, epigenetic modification