挪威科学家新揭示DNA甲基化和拷贝数改变对microRNA表达影响

发表日期：2013-11-26 12:53AM 阅览次数：

一项新研究揭示DNA甲基化和拷贝数改变对micrornA表达的影响，这是挪威奥斯陆大学等机构的研究人员通过对对乳腺癌队列人群进行分析所得。这一项研究有望于揭示乳腺癌中miRNA失调背后的机制。相关文章发表于2013年11月20日的《Genome Biology》杂志上。

microRNA(miRNA)是一类小的非编码rna分子，它通过控制mRNA稳定性和翻译而在转录后水平上调控基因表达。之前的研究发现，miRNA在癌症中往往异常表达。在乳腺癌中，miRNA表达的改变与雌激素受体(ER)信号通路、增殖和转移相关联。然而，miRNA表达异常的潜在机制还不太清楚，可能的原因有DNA拷贝数改变、突变、表观遗传改变等。

为了了解乳腺癌中拷贝数和甲基化对miRNA表达的影响，奥斯陆大学K.G. Jebsen乳腺癌研究中心的Vessela N Kristensen领导的研究小组整合了全基因组的DNA甲基化、拷贝数和miRNA表达，以鉴定miRNA失调背后的遗传机制。

研究人员利用安捷伦的8x15k miRNA芯片，开展了89个原发性乳腺癌样本的miRNA表达谱分析。DNA甲基化分析使用的是Illumina的Infinium HumanMethylation450 BeadChip芯片，而DNA拷贝数分析则用的是Illumina Human-1 109k BeadChip SNP芯片。

通过这一系列分析，他们鉴定出70个miRNA，其表达与拷贝数或甲基化的改变相关，或与两者都相关。这些miRNA代表了5个miRNA家族。有趣的是，这些家族的成员编码在不同的染色体上，在甲基化不足或甲基化过度时互补改变。

在随后的验证研究中，研究人员分析了另123名乳腺癌患者的miRNA表达和拷贝数数据。他们发现，在这70个miRNA中，41个的表达变化模式经过确认。之后，研究人员在三个乳腺癌细胞系中开展了体外功能实验，用miRNA模拟物来评估其功能意义。他们发现了4个miRNA(miR-21-3p、miR-148b-3p、miR-151a-5p和let-7e-3p)，其中let-7e-3p在肿瘤中与甲基化不足相关，它诱导凋亡并降低细胞活力，而let-7e-3p低表达与预后不良有关。其他三个miRNA的过表达与拷贝数增加相关，会增加乳腺癌细胞系的增殖。此外，miR-151a-5p提高了磷酸化AKT蛋白的水平。

作者认为，他们的数据为乳腺癌中mirna失调背后的机制提供了新证据。这项研究加深了人们对甲基化和拷贝数改变如何影响miRNA表达的了解。而miRNA家族成员的冗余编码增添了复杂性，在研究miRNA功能时应当考虑。

原文摘要：

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

Miriam Ragle Aure, Suvi-Katri Leivonen, Thomas Fleischer, Qian Zhu, Jens Overgaard,Jan Alsner, Trine Tramm, Riku Louhimo, Grethe I Alnæs, Merja Perälä, Florence Busato, Nizar Touleimat, Jörg Tost, Anne-Lise Børresen-Dale, Sampsa Hautaniemi,Olga G Troyanskaya, Ole Christian Lingjærde, Kristine Kleivi Sahlberg and Vessela N Kristensen

Background

The global effect of copy number and epigenetic alterations on miRNA expression in cancer is poorly understood. In the present study, we integrate genome-wide DNA methylation, copy number and miRNA expression and identify genetic mechanisms underlying miRNA dysregulation in breast cancer.

Results

We identify 70 miRNAs whose expression was associated with alterations in copy number or methylation, or both. Among these, five miRNA families are represented. Interestingly, the members of these families are encoded on different chromosomes and are complementarily altered by gain or hypomethylation across the patients. In an independent breast cancer cohort of 123 patients, 41 of the 70 miRNAs were confirmed with respect to aberration pattern and association to expression. In vitro functional experiments were performed in breast cancer cell lines with miRNA mimics to evaluate the phenotype of the replicated miRNAs. let-7e-3p, which in tumors is found associated with hypermethylation, is shown to induce apoptosis and reduce cell viability, and low let-7e-3p expression is associated with poorer prognosis. The overexpression of three other miRNAs associated with copy number gain, miR-21-3p, miR-148b-3p and miR-151a-5p, increases proliferation of breast cancer cell lines. In addition, miR-151a-5p enhances the levels of phosphorylated AKT protein.

Conclusions

Our data provide novel evidence of the mechanisms behind miRNA dysregulation in breast cancer. The study contributes to the understanding of how methylation and copy number alterations influence miRNA expression, emphasizing miRNA functionality through redundant encoding, and suggests novel miRNAs important in breast cancer.

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