Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis.
Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis.
复制标题
揭示 microRNA/lncRNA 在表征乳腺癌亚型和预后中的作用
DOI：
10.1186/s12859-021-04215-3
复制
发表时间：
2021-06-04
影响因子：
3
通讯作者：
Le TD
中科院分区：
文献类型：
--
作者：
Li X;Truong B;Xu T;Liu L;Li J;Le TD
准确的预后和在分子水平上识别癌症亚型是实现乳腺癌有效和个性化治疗的重要步骤。为此，已经开发了许多计算方法来使用基因(MRNA)表达数据来进行乳腺癌的亚型和预后。同时，在过去的20年里，人们对微小RNAs(MiRNAs)和长非编码RNAs(LncRNAs)进行了广泛的研究，并证实了它们与乳腺癌亚型和预后的关系。然而，目前尚不清楚使用miRNA和/或LncRNA表达数据是否有助于改善基于基因表达的亚型和预后方法的性能，这就提出了如何以及何时在实践中使用这些数据和方法的挑战。在本文中，我们在19个独立的乳腺癌数据集上对35种方法进行了比较研究，其中包括12种乳腺癌亚型方法和23种乳腺癌预后方法。我们的目的是从系统的比较中揭示miRNAs和lncRNAs在乳腺癌亚型和预后中的作用。此外，我们创建了一个R包，CancerSubtyesPrognosis，包括所有35种方法，以促进方法的重复性和简化评估。实验结果表明，整合miRNA表达数据有助于提高基于mRNA的癌症亚型方法的性能。然而，miRNA信号不如信使核糖核酸信号对乳腺癌预后的影响。总的来说，lncRNA表达数据无助于改进基于mRNA的方法在癌症亚型和癌症预后中的作用。这些结果表明，miRNA/lncRNA信号在改善乳腺癌预后方面的预后作用有待进一步验证。网上版载有补充材料，可在10.1186/s12859-021-04215-3查阅。
Accurate prognosis and identification of cancer subtypes at molecular level are important steps towards effective and personalised treatments of breast cancer. To this end, many computational methods have been developed to use gene (mRNA) expression data for breast cancer subtyping and prognosis. Meanwhile, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been extensively studied in the last 2 decades and their associations with breast cancer subtypes and prognosis have been evidenced. However, it is not clear whether using miRNA and/or lncRNA expression data helps improve the performance of gene expression based subtyping and prognosis methods, and this raises challenges as to how and when to use these data and methods in practice. In this paper, we conduct a comparative study of 35 methods, including 12 breast cancer subtyping methods and 23 breast cancer prognosis methods, on a collection of 19 independent breast cancer datasets. We aim to uncover the roles of miRNAs and lncRNAs in breast cancer subtyping and prognosis from the systematic comparison. In addition, we created an R package, CancerSubtypesPrognosis, including all the 35 methods to facilitate the reproducibility of the methods and streamline the evaluation. The experimental results show that integrating miRNA expression data helps improve the performance of the mRNA-based cancer subtyping methods. However, miRNA signatures are not as good as mRNA signatures for breast cancer prognosis. In general, lncRNA expression data does not help improve the mRNA-based methods in both cancer subtyping and cancer prognosis. These results suggest that the prognostic roles of miRNA/lncRNA signatures in the improvement of breast cancer prognosis needs to be further verified. The online version contains supplementary material available at 10.1186/s12859-021-04215-3.
登录
查看更多内容
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
3.7
作者：
Enerly E;Steinfeld I;Kleivi K;Leivonen SK;Aure MR;Russnes HG;Rønneberg JA;Johnsen H;Navon R;Rødland E;Mäkelä R;Naume B;Perälä M;Kallioniemi O;Kristensen VN;Yakhini Z;Børresen-Dale AL
通讯作者：
Børresen-Dale AL
影响因子：
3.7
作者：
BIRNBAUM, A
通讯作者：
BIRNBAUM, A
影响因子：
64.8
作者：
Curtis, Christina;Shah, Sohrab P.;Chin, Suet-Feung;Turashvili, Gulisa;Rueda, Oscar M.;Dunning, Mark J.;Speed, Doug;Lynch, Andy G.;Samarajiwa, Shamith;Yuan, Yinyin;Graef, Stefan;Ha, Gavin;Haffari, Gholamreza;Bashashati, Ali;Russell, Roslin;McKinney, Steven;Langerod, Anita;Green, Andrew;Provenzano, Elena;Wishart, Gordon;Pinder, Sarah;Watson, Peter;Markowetz, Florian;Murphy, Leigh;Ellis, Ian;Purushotham, Arnie;Borresen-Dale, Anne-Lise;Brenton, James D.;Tavare, Simon;Caldas, Carlos;Aparicio, Samuel
通讯作者：
Aparicio, Samuel
影响因子：
3.7
作者：
Chalise P;Fridley BL
通讯作者：
Fridley BL