Gong Shasha, Song Zhijian, Spezia-Lindner David, Meng Feilong, Ruan Tingting, Ying Guangzhi, Lai Changhong, Wu Qianqian, Liang Yong
Institute of Cancer Research, Department of Basic Medicine, School of Medicine, Taizhou University, Taizhou, China.
Precision Medicine Center, Taizhou University Hospital, Taizhou University, Taizhou, China.
Front Genet. 2020 Jun 11;11:534. doi: 10.3389/fgene.2020.00534. eCollection 2020.
Alternative splicing (AS) is important in the regulation of gene expression and aberrant AS is emerging as a major factor in the pathogenesis of human conditions, including cancer. Triple-negative breast cancer (TNBC) is the most challenging subtype of breast cancer with strong invasion, high rate of metastasis, and poor prognosis. Here we report a systematic profiling of aberrant AS in TNBC.
The percent spliced in (PSI) values for AS events in 151 TNBC patients were obtained from The Cancer Genome Atlas (TCGA) SpliceSeq database. Univariate Cox and stepwise Multivariate Cox regression analyses were conducted to find the best prognostic AS model. Splicing regulatory networks were constructed by prognosis-related spliceosome and aberrant AS events. Additionally, pathway enrichment and gene set enrichment analysis (GSEA) were further employed to reveal the significant pathways for prognosis-related AS genes. Finally, splicing regulatory networks were constructed via Spearman's rank correlation coefficients between prognosis-related AS events and splicing factor expressions.
A total of 1,397 prognosis-associated AS events were identified in TNBC. The majority of the parent genes of prognostic AS events exhibited direct interactions to each other in the STRING gene network. Pathways of focal adhesion ( < 0.001), RNA splicing ( = 0.007), homologous recombination ( = 0.042) and ECM-receptor interaction ( = 0.046) were found to be significantly enriched for prognosis-related AS. Additionally, the area under curve (AUC) of the best AS prognostic predictor model reached 0.949, showing a powerful capability to predict outcomes. The Exon Skip (ES) type of AS events displayed more robust and efficient capacity in predicting performance than any other specific AS events type in terms of prognosis. The ES AS signature might confer a strong oncogenic phenotype in the high-risk group with elevated activities in cell cycle and SUMOylating pathways of tumorigenesis, while programmed cell death and metabolism pathways were found to be enriched in the low-risk group of TNBC. The splicing correlation network also revealed a regulatory mode of prognostic splicing factors (SFs) in TNBC.
Our analysis of AS events in TNBC could not only contribute to elucidating the tumorigenesis mechanism of AS but also provide clues to uncovering underlying prognostic biomarkers and therapeutic targets for further study.
可变剪接（AS）在基因表达调控中起重要作用，异常的AS正成为包括癌症在内的人类疾病发病机制中的一个主要因素。三阴性乳腺癌（TNBC）是最具挑战性的乳腺癌亚型，具有较强的侵袭性、高转移率和较差的预后。在此，我们报告了TNBC中异常AS的系统分析。
从癌症基因组图谱（TCGA）SpliceSeq数据库中获取151例TNBC患者AS事件的剪接百分率（PSI）值。进行单变量Cox和逐步多变量Cox回归分析以找到最佳的预后AS模型。通过与预后相关的剪接体和异常AS事件构建剪接调控网络。此外，进一步采用通路富集和基因集富集分析（GSEA）来揭示与预后相关的AS基因的重要通路。最后，通过预后相关AS事件与剪接因子表达之间的Spearman等级相关系数构建剪接调控网络。
在TNBC中总共鉴定出1397个与预后相关的AS事件。预后AS事件的大多数亲本基因在STRING基因网络中彼此表现出直接相互作用。发现粘着斑（<0.001）、RNA剪接（=0.007）、同源重组（=0.042）和细胞外基质受体相互作用（=0.046）通路与预后相关的AS显著富集。此外，最佳AS预后预测模型的曲线下面积（AUC）达到0.949，显示出强大的预测结果的能力。就预后而言，外显子跳跃（ES）类型的AS事件在预测性能方面比任何其他特定AS事件类型表现出更强健和有效的能力。ES AS特征可能在高风险组中赋予强烈的致癌表型，在肿瘤发生的细胞周期和SUMO化途径中活性升高，而程序性细胞死亡和代谢途径在TNBC的低风险组中富集。剪接相关网络还揭示了TNBC中预后剪接因子（SFs）的调控模式。
我们对TNBC中AS事件的分析不仅有助于阐明AS的肿瘤发生机制，还为进一步研究揭示潜在的预后生物标志物和治疗靶点提供线索。
