Exon-level microarray analyses identify alternative splicing programs in breast cancer.
Exon-level microarray analyses identify alternative splicing programs in breast cancer.
复制标题
DOI：
10.1158/1541-7786.mcr-09-0528
复制
发表时间：
2010-07
期刊：
影响因子：
--
通讯作者：
Gray JW
中科院分区：
文献类型：
--
作者：
Lapuk A;Marr H;Jakkula L;Pedro H;Bhattacharya S;Purdom E;Hu Z;Simpson K;Pachter L;Durinck S;Wang N;Parvin B;Fontenay G;Speed T;Garbe J;Stampfer M;Bayandorian H;Dorton S;Clark TA;Schweitzer A;Wyrobek A;Feiler H;Spellman P;Conboy J;Gray JW
许多基因的选择性剪接（AS）产生的蛋白质亚型与癌症发生和进展的几个方面有关。这些观察激发了乳腺癌中AS的全基因组评估。我们通过使用Affyscore人类连接阵列（HJAY）测量31个乳腺癌和代表管腔型、基底型和低密蛋白乳腺癌亚型的非恶性永生化细胞系中的外显子水平表达来实现这一点。我们使用专门设计用于以低假阳性率检测AS的计算管道分析了这些数据。这确定了代表156个基因的181个剪接事件作为AS的候选者。预测AS事件的一个子集的RT-PCR验证证实了90%。大约一半的AS事件与基底、管腔或低密蛋白乳腺癌亚型相关。参与紧密连接蛋白低亚型特异性AS的外显子与组织特异性Fox 2剪接因子的进化保守结合基序的存在显著相关。Fox 2的siRNA敲低证实了这种剪接因子参与亚型特异性AS。本研究中检测到的亚型特异性AS可能反映了肿瘤发生的乳腺癌祖细胞中的剪接模式，并表明了Fox介导的AS测定在癌症亚型定义和早期检测中的实用性。这些数据还表明，通过靶向限制正常组织中不存在的蛋白质异构体来降低蛋白质靶向乳腺癌治疗的毒性的可能性。
Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects of cancer genesis and progression. These observations motivated a genome-wide assessment of AS in breast cancer. We accomplished this by measuring exon level expression in 31 breast cancer and nonmalignant immortalized cell lines representing luminal, basal and claudin-low breast cancer subtypes using Affymetrix Human Junction Arrays (HJAY). We analyzed these data using a computational pipeline specifically designed to detect AS with a low false positive rate. This identified 181 splice events representing 156 genes as candidates for AS. RT-PCR validation of a subset of predicted AS events confirmed 90%. Approximately half of the AS events were associated with basal, luminal or claudin-low breast cancer subtypes. Exons involved in claudin-low subtype-specific AS were significantly associated with the presence of evolutionarily conserved binding motifs for the tissue-specific Fox2 splicing factor. siRNA knockdown of Fox2 confirmed the involvement of this splicing factor in subtype specific AS. The subtype specific AS detected in this study likely reflects the splicing pattern in the breast cancer progenitor cells in which the tumor arose and suggests the utility of assays for Fox-mediated AS in cancer subtype definition and early detection. These data also suggest the possibility of reducing the toxicity of protein-targeted breast cancer treatments by targeting protein isoforms that are not present in limiting normal tissues.