Authors' Affiliations: Division of Oncology, Center for Applied Medical Research (CIMA); Departments of Histology and Pathology and Biochemistry and Genetics, Schools of Science and Medicine, University of Navarra, Pamplona; and CEIT and TECNUN, University of Navarra, San Sebastian, Spain.
Cancer Res. 2014 Feb 15;74(4):1105-15. doi: 10.1158/0008-5472.CAN-13-1481. Epub 2013 Dec 26.
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.
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，这是一种算法，它使用外显子和连接探针的数据来识别注释的盒式外显子。我们使用该算法在致癌丝氨酸/精氨酸丰富的剪接因子 1（SRSF1）下调后，对肺腺癌 A549 细胞中的差异剪接事件进行了分析。使用两种不同的微阵列平台生成了数据。排名前 20 的基因的基于 PCR 的验证率为 60%和 100%。功能富集分析发现，大量的剪接事件发生在与 RNA 代谢相关的基因中。这些分析还确定了与癌症以及发育和遗传疾病相关的基因，以及细胞分裂、细胞凋亡和增殖等生物学过程相关的基因。排名前 20 的基因中有大多数在其他腺癌和鳞状细胞肺癌细胞中得到了验证，验证率分别为 80%至 95%和 70%至 75%。此外，该分析使我们能够识别出四个基因，ATP11C、IQCB1、TUBD1 和富含脯氨酸的卷曲螺旋 2C（PRRC2C），与正常肺组织相比，这些基因在原发性非小细胞肺癌肿瘤中的选择性剪接模式存在显著差异。对于 PRRC2C，SRSF1 下调导致在原发性肺肿瘤中过表达的外显子跳过。包含外显子的变异体的特异性 siRNA 下调显著降低了细胞生长。总之，使用一种新的分析工具，我们已经确定了由致癌剪接因子 SRSF1 在肺癌中调控的新的剪接事件。
