VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription

The Vitamin D Receptor (VDR) is a member of the nuclear receptor superfamily and is of therapeutic interest in cancer and other settings. Regulation of microRNA (miRNA) by the VDR appears to be important to mediate its actions, for example, to control cell growth. To identify if and to what extent VDR-regulated miRNA patterns change in prostate cancer progression, we undertook miRNA microarray analyses in 7 cell models representing non-malignant and malignant prostate cells (RWPE-1, RWPE-2, HPr1, HPr1AR, LNCaP, LNCaP-C4–2, and PC-3). To focus on primary VDR regulatory events, we undertook expression analyses after 30 minutes treatment with 1α,25(OH)₂D₃. Across all models, 111 miRNAs were significantly modulated by 1α,25(OH)₂D₃ treatment. Of these, only 5 miRNAs were modulated in more than one cell model, and of these, only 3 miRNAs were modulated in the same direction. The patterns of miRNA regulation, and the networks they targeted, significantly distinguished the different cell types. Integration of 1α,25(OH)₂D₃-regulated miRNAs with published VDR ChIP-seq data showed significant enrichment of VDR peaks in flanking regions of miRNAs. Furthermore, mRNA and miRNA expression analyses in non-malignant RWPE-1 cells revealed patterns of miRNA and mRNA co-regulation; specifically, 13 significant reciprocal patterns were identified and these patterns were also observed in TCGA prostate cancer data. Lastly, motif search analysis revealed differential motif enrichment within VDR peaks flanking mRNA compared to miRNA genes. Together, this study revealed that miRNAs are rapidly regulated in a highly cell-type specific manner, and are significantly co-integrated with mRNA regulation.

维生素D受体（Vitamin D Receptor, VDR）是核受体超家族成员，在癌症及其他领域具备治疗研究价值。VDR对微小RNA（microRNA, miRNA）的调控似乎是其介导生物学功能的关键途径，例如调控细胞生长。为明确VDR调控的miRNA模式在前列腺癌进展中是否发生改变及改变程度，我们针对7种分别代表非恶性与恶性前列腺细胞的模型（RWPE-1、RWPE-2、HPr1、HPr1AR、LNCaP、LNCaP-C4–2及PC-3）开展了miRNA微阵列分析。为聚焦于原发性VDR调控事件，我们在经1α,25(OH)₂D₃处理30分钟后开展了基因表达分析。在所有细胞模型中，共有111种miRNA经1α,25(OH)₂D₃处理后发生显著表达调控。其中仅5种miRNA在多种细胞模型中被调控，且仅3种miRNA的调控方向保持一致。miRNA的调控模式及其靶向的调控网络可显著区分不同细胞类型。将1α,25(OH)₂D₃调控的miRNA与已发表的VDR染色质免疫共沉淀测序（ChIP-seq）数据整合分析后发现，VDR结合峰在miRNA侧翼区域存在显著富集。此外，对非恶性RWPE-1细胞的mRNA与miRNA表达分析显示二者存在共调控模式；具体而言，我们鉴定出13种显著的相互调控模式，且该模式在癌症基因组图谱（The Cancer Genome Atlas, TCGA）的前列腺癌数据中同样被观测到。基序搜索分析显示，相较于miRNA基因，VDR结合峰侧翼区域的基序富集情况存在显著差异。综上，本研究表明miRNA可通过高度细胞类型特异性的方式被快速调控，且其与mRNA的调控存在显著的共整合关联。