Identification of Alternative Splicing Events Regulated by the Oncogenic Factor SRSF1 in Lung Cancer
Identification of Alternative Splicing Events Regulated by the Oncogenic Factor SRSF1 in Lung Cancer
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DOI：
10.1158/0008-5472.can-13-1481
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发表时间：
2014-02-15
期刊：
影响因子：
11.2
通讯作者：
Pio, Ruben
中科院分区：
文献类型：
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作者：
de Miguel, Fernando J.;Sharma, Ravi D.;Pio, Ruben
异常的选择性剪接与癌症有关。全基因组微阵列可用于检测差异剪接事件。在这项研究中，我们开发了ExonPointer，一种使用外显子和连接探针的数据来识别注释的盒式外显子的算法。我们使用该算法来分析肺腺癌A549细胞中致癌的富含丝氨酸/丝氨酸的剪接因子1（SRSF1）下调后的差异剪接事件。使用两种不同的微阵列平台生成数据。前20位基因的PCR验证率分别为60%和100%。功能富集分析发现了大量的剪接事件的基因与RNA代谢。这些分析还确定了与癌症、发育和遗传性疾病以及细胞分裂、凋亡和增殖等生物过程相关的基因。排名前20位的基因中的大多数在其他腺癌和鳞状细胞肺癌细胞中得到验证，验证率分别为80%至95%和70%至75%。此外，该分析使我们能够鉴定四种基因，ATP 11C、IQCB 1、TUBD 1和富含脯氨酸的卷曲螺旋2C（PRRC 2C），与正常肺组织相比，它们在原发性非小细胞肺肿瘤中具有显著不同的选择性剪接模式。在PRRC2C的情况下，SRSF1下调导致原发性肺肿瘤中过表达的外显子跳跃。含有外显子的变体的特异性siRNA下调显著降低了细胞生长。总之，使用一种新的分析工具，我们已经确定了肺癌中致癌剪接因子SRSF1调控的新剪接事件。（C）2013年AACR。
Abnormal alternative splicing has been associated with cancer. Genome-wide microarrays can be used to detect differential splicing events. In this study, we have developed ExonPointer, an algorithm that uses data from exon and junction probes to identify annotated cassette exons. We used the algorithm to profile differential splicing events in lung adenocarcinoma A549 cells after downregulation of the oncogenic serine/arginine-rich splicing factor 1 (SRSF1). Data were generated using two different microarray platforms. The PCR-based validation rate of the top 20 ranked genes was 60% and 100%. Functional enrichment analyses found a substantial number of splicing events in genes related to RNA metabolism. These analyses also identified genes associated with cancer and developmental and hereditary disorders, as well as biologic processes such as cell division, apoptosis, and proliferation. Most of the top 20 ranked genes were validated in other adenocarcinoma and squamous cell lung cancer cells, with validation rates of 80% to 95% and 70% to 75%, respectively. Moreover, the analysis allowed us to identify four genes, ATP11C, IQCB1, TUBD1, and proline- rich coiled-coil 2C (PRRC2C), with a significantly different pattern of alternative splicing in primary non-small cell lung tumors compared with normal lung tissue. In the case of PRRC2C, SRSF1 downregulation led to the skipping of an exon overexpressed in primary lung tumors. Specific siRNA downregulation of the exon-containing variant significantly reduced cell growth. In conclusion, using a novel analytical tool, we have identified new splicing events regulated by the oncogenic splicing factor SRSF1 in lung cancer. (C)2013 AACR.