Epigenetic-dysregulated lncRNAs in Prostate Cancer Based on Multi-omics Analysis

Abstract Background: The purpose of this study was to investigate the relationship between Long non-coding RNAs (lncRNAs) expression and epigenetic changes, and explore the prognostic value of these findings in patients with prostate cancer. Methods: In this study, we systematically compared the histone modification and methylation regions on lncRNAs promoter and enhancer elements by multiomics. We analyzed the distribution characteristics of histone modified apparent lncRNAs promoters and enhancers in the genome. Single sample Gene Set Enrichment Analysis (ssGSEA) and Kyoto Encyclopedia of Gene and Genomes (KEGG) were used to analyze the functional enrichment of epigenetic dysregulated lncRNAs. The prostate cancer associated lncRNAs were downloaded from lnc2cancer V3.0 and survival analysis was performed. Results: We found 1124 epigenetic-dysregulated lncRNAs (epi-lncRNAs) and 9734 epigenetic-dysregulated protein coding genes (epi-PCGs) in prostate cancer, and the abnormal frequency of lncRNAs was much lower than that of PCGs. H3K4me3, H3K4me1, H3K27ac and H3K27me3 abnormally modified histones accounted for a large proportion and were mainly concentrated in the promoter region. Epigenetic abnormal lncRNAs affects the biological specific molecular function of prostate cancer by changing the abnormal modification of histone. The abnormal expression of lncRNAs caused by abnormal modification of H3K36me3 may be an important factor in the occurrence of prostate cancer. Finally, based on lncRNAs analysis of the prognosis of prostate cancer samples, three lncRNAs (HAR1A, SNHG12 and SNHG17) were identified as prognostic markers of prostate cancer.Conclusions: These findings may help to better understand the abnormal epigenetic regulation of lncRNAs expression in prostate cancer.