Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Mol Cancer. 2013 Feb 14;12:13. doi: 10.1186/1476-4598-12-13.
Ultraconserved regions (UCR) are genomic segments of more than 200 base pairs that are evolutionarily conserved among mammalian species. They are thought to have functions as transcriptional enhancers and regulators of alternative splicing. Recently, it was shown that numerous RNAs are transcribed from these regions. These UCR-encoded transcripts (ucRNAs) were found to be expressed in a tissue- and disease-specific manner and may interfere with the function of other RNAs through RNA: RNA interactions. We hypothesized that ucRNAs have unidentified roles in the pathogenesis of human prostate cancer. In a pilot study, we examined ucRNA expression profiles in human prostate tumors.
Using a custom microarray with 962 probesets representing sense and antisense sequences for the 481 human UCRs, we examined ucRNA expression in resected, fresh-frozen human prostate tissues (57 tumors, 7 non-cancerous prostate tissues) and in cultured prostate cancer cells treated with either epigenetic drugs (the hypomethylating agent, 5-Aza 2'deoxycytidine, and the histone deacetylase inhibitor, trichostatin A) or a synthetic androgen, R1881. Expression of selected ucRNAs was also assessed by qRT-PCR and NanoString®-based assays. Because ucRNAs may function as RNAs that target protein-coding genes through direct and inhibitory RNA: RNA interactions, computational analyses were applied to identify candidate ucRNA:mRNA binding pairs.
We observed altered ucRNA expression in prostate cancer (e.g., uc.106+, uc.477+, uc.363 + A, uc.454 + A) and found that these ucRNAs were associated with cancer development, Gleason score, and extraprostatic extension after controlling for false discovery (false discovery rate < 5% for many of the transcripts). We also identified several ucRNAs that were responsive to treatment with either epigenetic drugs or androgen (R1881). For example, experiments with LNCaP human prostate cancer cells showed that uc.287+ is induced by R1881 (P < 0.05) whereas uc.283 + A was up-regulated following treatment with combined 5-Aza 2'deoxycytidine and trichostatin A (P < 0.05). Additional computational analyses predicted RNA loop-loop interactions of 302 different sense and antisense ucRNAs with 1058 different mRNAs, inferring possible functions of ucRNAs via direct interactions with mRNAs.
This first study of ucRNA expression in human prostate cancer indicates an altered transcript expression in the disease.
超保守区域（UCR）是指长度超过 200 个碱基对的基因组片段，在哺乳动物物种之间具有进化上的保守性。它们被认为具有转录增强子和可变剪接调节剂的功能。最近，研究表明许多 RNA 是从这些区域转录而来的。这些 UCR 编码的转录本（ucRNA）在组织和疾病特异性表达，并且可能通过 RNA：RNA 相互作用干扰其他 RNA 的功能。我们假设 ucRNA 在人类前列腺癌的发病机制中具有未被识别的作用。在一项初步研究中，我们检查了人前列腺肿瘤中的 ucRNA 表达谱。
使用具有 962 个探针的定制微阵列，代表 481 个人类 UCR 的正义和反义序列，我们检查了切除的新鲜冷冻人前列腺组织（57 个肿瘤，7 个非癌前列腺组织）和培养的前列腺癌细胞中 ucRNA 的表达，这些细胞用表观遗传药物（去甲基化剂 5-Aza 2'-脱氧胞苷和组蛋白脱乙酰酶抑制剂曲古抑菌素 A）或合成雄激素 R1881 处理。通过 qRT-PCR 和 NanoString®-based 测定法评估选定的 ucRNA 的表达。由于 ucRNA 可能作为通过直接和抑制性 RNA：RNA 相互作用靶向蛋白质编码基因的 RNA 发挥作用，因此应用计算分析来鉴定候选 ucRNA：mRNA 结合对。
我们观察到前列腺癌中 ucRNA 表达的改变（例如，uc.106+，uc.477+，uc.363+A，uc.454+A），并发现这些 ucRNA 与癌症发展，Gleason 评分和前列腺外延伸有关，在控制假发现率后（对于许多转录物，假发现率<5％）。我们还鉴定了一些对表观遗传药物或雄激素（R1881）治疗有反应的 ucRNA。例如，用 LNCaP 人前列腺癌细胞进行的实验表明，uc.287+由 R1881 诱导（P<0.05），而 uc.283+A 在联合使用 5-Aza 2'-脱氧胞苷和曲古抑菌素 A 治疗后上调（P<0.05）。其他计算分析预测了 302 个不同的正义和反义 ucRNA 与 1058 个不同 mRNA 之间的 RNA 环loop 相互作用，通过与 mRNA 的直接相互作用推断出 ucRNA 的可能功能。
这是第一项人类前列腺癌中 ucRNA 表达的研究，表明该疾病中存在转录本表达的改变。
