Non-coding RNAs as Prognostic and Diagnostic Markers in Prostate Cancer

非编码 RNA 作为前列腺癌的预后和诊断标志物

• 批准号: 8763262
• 负责人: Stefan Ambs
• 金额: $ 8.33万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8763262
• 关键词: Actins; Adhesions; Affect; Androgen Analogues; Androgens; Apoptotic; Base Pairing; Binding; Biological Assay; Cancer Biology; Cell Adhesion; Cell Culture Techniques; Cell Cycle Progression; Cell Proliferation; Cells; Code; Collaborations; Confidence Intervals; DNA biosynthesis; Data; Data Set; Development; Diagnostic; Disease; Disease Outcome; Distant Metastasis; Epigenetic Process; Extraprostatic; F-Actin; Functional RNA; Genes; Genetic Transcription; Genomic Segment; Gleason Grade for Prostate Cancer; Goals; Growth; Histone Deacetylase Inhibitor; Human; In Vitro; Inhibition of Apoptosis; Investigation; Malignant Neoplasms; Malignant neoplasm of prostate; Mediating; Messenger RNA; Metastatic Lesion; MicroRNAs; Mitosis; Modeling; Neoplasm Metastasis; Ohio; Oncogenic; Pathogenesis; Pathway interactions; Patients; Pattern; Pharmaceutical Preparations; Pharmacotherapy; Phenotype; Primary Neoplasm; Process; Prognostic Marker; Property; Prostate; Prostatic Neoplasms; Proteins; RNA; Recurrence; Reporter; Reporting; Role; Ru-1881; Testing; Time; Tissues; Transcript; Tumor Cell Invasion; Tumor Suppressor Proteins; Universities; Untranslated Regions; Up-Regulation; Xenograft Model; base; caspase-7; cell motility; follow-up; gene repression; hazard; member; novel; overexpression; prognostic; prostate cancer cell; protein expression; repaired; research study; tumor; tumor progression

We previously examined expression of 329 human microRNAs and 13,000 protein-coding genes in primary human prostate tumors in collaboration with Carlo Croce at Ohio State University. This collaboration generated several of the earliest reports that showed altered microRNA expression in prostate cancer. Tumor microRNAs were both up- and down-regulated when compared with non-cancerous tissue. Notably, prostate tumors tended to express all members of the miR-106b-25 cluster at significantly higher levels than the non-cancerous prostate, which is consistent with miR-106b-25 having oncogenic properties in prostate cancer biology. In contrast, the expression of the miR-1-133 cluster was consistently lower in tumors than in the non-cancerous prostate, indicating that this microRNA cluster may act as a tumor suppressor. In two follow-up studies, we now showed that both up-regulation of miR-106b-25 expression and suppression of miR-1-133 expression are key steps in the progression of human prostate cancer. To further define the oncogenic role of the miR-106b-25 cluster in prostate cancer progression, we analyzed a large public dataset consisting of primary tumors, disease metastases, and disease recurrence status. Concordant with our previous findings, all miR-106-25-encoded microRNAs were significantly up-regulated in primary tumors. Expression of these microRNAs further increased in metastatic lesions, and specifically the expression of miR-106b was associated with early disease recurrence. To identify yet unknown oncogenic functions of miR-106b, we overexpressed this microRNA in human prostate cancer cells. The approach revealed that miR-106b suppressed the expression of pro-apoptotic caspase 7. Additional investigations made the novel observation that caspase 7 is a tumor suppressor and is associated with prostate cancer-specific survival. Most importantly, however, the combination of high miR-106b and low caspase-7 expression in primary tumors was found to be an independent predictor of early disease recurrence (adjusted hazard ratio=4.1; 95% confidence interval: 1.6-12.3). We also showed that phenotypes induced by miR-106b-25 expression in human prostate cancer cells, e.g., inhibition of apoptosis and altered adhesion properties, did not develop when caspase 7 expression was inhibited. Our data indicate a prominent role of miR-106b-25 in prostate cancer progression and disease outcome by altering survival- and cell adhesion-related pathways. We used a similar approach when we investigated the functions of the miR-1-133 cluster in prostate cancer biology. Here, we found that miR-1 expression is further reduced in distant metastasis, leading to early disease recurrence among patients with low miR-1 expression in their tumors. Moreover, we performed in vitro experiments to explore the tumor suppressor function of miR-1. Cell-based assays showed that miR-1 is epigenetically silenced in human prostate cancer. Overexpression of miR-1 in these cells led to growth inhibition and down-regulation of genes in pathways regulating cell cycle progression, mitosis, DNA replication/repair and actin dynamics. This observation was further corroborated with protein expression analysis and 3'-UTR-based reporter assays, indicating that genes in these pathways are either direct or indirect targets of miR-1. A gene set enrichment analysis revealed that the miR-1-mediated tumor suppressor effects are globally similar to those of histone deacetylase inhibitors. Lastly, we obtained preliminary evidence that miR-1 alters the cellular organization of F-actin and inhibits tumor cell invasion and filipodia formation. In conclusion, our findings showed, for the first time, that miR-1 acts as a tumor suppressor in prostate cancer by influencing multiple cancer-related processes and by inhibiting cell proliferation and motility. More recently, the Croce group reported that RNA expression from ultraconserved regions is altered in human cancer. Ultraconserved regions (UCR) are genomic segments of more than 200 base pairs that are absolutely conserved among mammalian species. This conservation suggests an important regulatory function that is encoded by these sequences. Thus, we hypothesized that UCR-encoded transcripts may have unidentified roles in the pathogenesis of human prostate cancer. Using microarrays representing 481 UCR-derived transcripts in sense and antisense direction, we discovered novel expression patterns for these transcripts that were associated with prostate cancer development, Gleason score, and extraprostatic extension. To search for possible functional interactions of ucRNAs as non-coding RNAs, RNA loop-loop interactions were computationally modeled to discover ucRNA:mRNA binding pairs. This approach yielded novel candidate interactions between ucRNAs and mRNAs. We also tested whether androgen exposure or epigenetic drug therapy may affect ucRNA transcript expression. These studies identified several ucRNAs that were responsive to treatment with either epigenetic drugs or a synthetic androgen, R1881. Lastly, we compared expression of selected ucRNAs with tumor mRNA and microRNA expression patterns and found global relationships between them. This first study of ucRNA expression in human prostate cancer indicates a dysregulated expression of these RNAs in the disease.

我们先前与俄亥俄州立大学的卡洛·克罗斯（Carlo Croce）合作研究了原发性前列腺肿瘤中329个人类microRNA和13,000个蛋白质编码基因的表达。这项合作产生了一些最早的报告，这些报告显示了前列腺癌中microRNA表达改变。与非癌组织相比，肿瘤microRNA都会上调和下调。值得注意的是，前列腺肿瘤倾向于以明显高于非癌性前列腺水平来表达miR-106b-25簇的所有成员，这与前列腺癌生物学中具有致癌特性的miR-106b-25一致。相反，肿瘤中miR-133簇的表达始终低于非癌性前列腺，表明该microRNA簇可以充当肿瘤抑制器。在两项后续研究中，我们现在表明miR-106b-25表达的上调和miR-133表达的抑制是人类前列腺癌进展的关键步骤。为了进一步定义miR-106B-25簇在前列腺癌进展中的致癌作用，我们分析了一个大型公共数据集，该数据集由原发性肿瘤，疾病转移和疾病复发状态组成。与我们以前的发现一致，所有miR-106-25编码的microRNA在原发性肿瘤中均显着上调。这些microRNA的表达在转移性病变中进一步增加，特别是miR-106b的表达与早期疾病复发有关。为了鉴定miR-106b的尚未知道的致癌功能，我们在人类前列腺癌细胞中过度表达了该microRNA。该方法表明，miR-106b抑制了促凋亡caspase 7的表达。其他研究使新的研究表明，caspase 7是肿瘤抑制因子，与前列腺癌特异性生存有关。然而，最重要的是，发现原发性肿瘤中高miR-106b和低caspase-7表达的组合是早期疾病复发的独立预测指标（调整后危险比= 4.1; 95％置信区间：1.6-12.3）。我们还表明，当抑制caspase 7表达时，没有发展为人类前列腺癌细胞中miR-106b-25表达诱导的表型，例如抑制凋亡和粘附特性。我们的数据表明，通过改变与生存和细胞粘附相关的途径，miR-106b-25在前列腺癌进展和疾病预后的重要作用。当我们研究了miR-1-133簇在前列腺癌生物学中的功能时，我们使用了类似的方法。在这里，我们发现在远处转移中，miR-1表达进一步降低，导致肿瘤中miR-1表达低的患者的早期疾病复发。此外，我们进行了体外实验，以探索miR-1的肿瘤抑制功能。基于细胞的测定表明，在人前列腺癌中，miR-1表观遗传沉默。这些细胞中miR-1的过表达导致在调节细胞周期进程，有丝分裂，DNA复制/修复和肌动蛋白动力学的途径中的基因抑制和下调。通过蛋白质表达分析和基于3'-UTR的报告基因测定，该观察结果进一步证实，表明这些途径中的基因是miR-1的直接或间接靶标。基因集富集分析表明，miR-1介导的肿瘤抑制作用在全球范围内与组蛋白脱乙酰基酶抑制剂相似。最后，我们获得了miR-1的初步证据，表明miR-1改变了F-肌动蛋白的细胞组织并抑制肿瘤细胞侵袭和菲律宾形成。总之，我们的发现首次表明，miR-1通过影响多个与癌症相关的过程并抑制细胞增殖和运动性来充当前列腺癌中的肿瘤抑制因子。最近，Croce组报告说，超保守区域的RNA表达在人类癌症中发生了改变。超保守区域（UCR）是哺乳动物物种中绝对保守的200多个碱基对的基因组段。这种保护表明，这些序列编码的重要调节功能。因此，我们假设UCR编码的转录本可能在人类前列腺癌的发病机理中具有不明的作用。使用代表481个UCR衍生的转录本的微阵列，我们发现了这些转录本的新型表达模式，这些模式与前列腺癌的发展，Gleason Score和Proprofostatic延伸相关。为了搜索UCRNA作为非编码RNA的可能功能相互作用，对RNA Loop-loop相互作用进行了计算建模以发现UCRNA：mRNA结合对。这种方法产生了UCRNA和mRNA之间的新型候选相互作用。我们还测试了雄激素暴露或表观遗传药物治疗是否可能影响UCRNA转录本的表达。这些研究确定了几种对用表观遗传药物或合成雄激素治疗的UCRNA，R1881。最后，我们比较了选定的UCRNA与肿瘤mRNA和microRNA表达模式的表达，并发现了它们之间的全球关系。对人类前列腺癌中UCRNA表达的首次研究表明，这些RNA在该疾病中的表达失调。