Typing the Transcriptome in Cancer Using Splicing Array

描述（由申请人提供）： 选择性剪接是高等真核细胞的一个永久性特征，了解选择性剪接如何改变蛋白质组的组成和功能是后基因组时代的一个重大挑战。对于癌症研究，独特的mRNA亚型可以为诊断和预后提供一组强大的生物标志物，并且癌症特异性mRNA亚型可以作为有效治疗干预的鉴别靶标。此外，了解剪接选择如何在发育和疾病中进行和调节是癌细胞生物学中的一个基本问题。mRNA异构体敏感的微阵列技术将是理想的，及时地适合于解决广泛的临床和机制的问题，关于选择性剪接。 在过去的IMAT资助期间，我们开发了一个独特而新颖的技术平台来解决拼接问题。经过数据库建设和实验开发的系统和大量的努力，该技术现已成熟，其在各种条件下可重复测量mRNA异构体的优越性已被证明。剪接阵列的独特之处在于需要逐步扩大数据库以准确注释mRNA同种型并制备相应的寡核苷酸组用于测量。因此，我们正在寻求IMAT的支持，将技术投入实际使用，让研究界利用技术发展。 我们有三个具体的目标，为下一阶段应用新兴技术的分子分析癌症。(1)我们计划使用该技术来识别与前列腺癌相关的独特mRNA亚型。我们将调查现有的前列腺癌细胞系未经治疗或治疗与雄激素和雌激素以及癌症组织在不同的恶性阶段，以确定肿瘤特异性和激素调节的选择性剪接。(2)我们建议将该技术应用于通过在敲低和敲除细胞中识别大量剪接调节因子的直接靶点来解决剪接调节机制。(3)沿着所提出的技术应用，我们将随着技术的发展逐步扩大高质量的数据库，并通过增加新的特性和功能来继续改进和扩大数据库，并开发用于拼接阵列数据分析的链接软件。

DESCRIPTION (provided by applicant): Alternative splicing is a permanent feature in higher eukaryotic cells and understanding of how alternative splicing alters the composition and function of the proteome represents a major challenge in the post-genome era. For cancer research, unique mRNA isoforms may provide a robust set of biomarkers for diagnosis and prognosis, and cancer-specific mRNA isoforms may serve as discriminating targets for effective therapeutic interventions. Furthermore, understanding of how splice choice is made and regulated in development and disease is a fundamental issue in cancer cell biology. An mRNA isoform-sensitive microarray technology would be ideally and timely suited for addressing a wide range of clinical and mechanistic questions regarding alternative splicing. In the past IMAT funding period, we have developed a unique and novel technology platform to attack the splicing problem. After a systematic and substantial effort in database construction and experimental development, the technology is now matured, and its superiority in reproducible measurement of mRNA isoforms under a variety of conditions has been demonstrated. Unique to the splicing array is the need to progressively enlarge the database for accurately annotated mRNA isoforms and preparation of corresponding oligo sets for measurement. We are therefore seeking IMAT support to put the technology in practical use and let the research community to take advantage of the technology development. We have three specific goals for the next phase in applying the emerging technology for molecular analysis of cancer. (1) We plan to use the technology to identify unique mRNA isoforms associated with prostate cancer. We will survey existing prostate cancer cell lines untreated or treated with androgen and estrogen as well as cancer tissues at different malignant stages to identify tumor-specific and hormonal regulated alternative splicing. (2) We propose to apply the technology to address mechanisms of splicing regulation by identifying direct targets for a large number of splicing regulators in knockdown and knockout cells. (3) Along with the proposed technology applications, we will progressively enlarge the high quantity databases coupled with the technology development and continue to improve and enlarge the database by adding new features and functions and develop linked software for splicing array data analysis.