Alternate Splicing and Alcohol Exposure: TransExpress Hematome 1.0

描述（由申请人提供）：尽管迫切需要酒精暴露的生物标志物，但高通量基因组学技术在该领域的应用文献却异常稀少。关于酒精暴露的生物标志物的有限报道主要局限于小鼠或大鼠大脑中对乙醇反应的生物标志物。由于无法获得人类受试者的大脑样本，因此无法将其转化为临床应用。目前迫切需要一种积极的方法，用于酒精研究中的高通量应用，以便在临床环境中进行测试。全基因组微阵列血液高通量实验只能监测15-20%的基因，而缺失了大多数功能多样的mRNA剪接产物。考虑到交替剪接作为后生动物使用的一种机制的进化意义，从与基因复制平行的少数基因中创造功能多样性，基因微阵列的局限性在生物标志物研究中非常有限。在这里，我们利用Jivan公司开发的全血剪接微阵列技术，Hematome 1.0，提出了一个研究计划，弥合了基因组研究和临床应用之间的差距。此外，通过允许测量受调节的剪接，Hematome 1.0为血液中酒精暴露提供了3到4倍的生物标志物。Jivan专有的TransExpress(tm) Hematome 1.0微阵列平台能够同时发现和测量基因的剪接调节。TransExpress（tm）的发现对这一努力至关重要，因为血液中大多数人类基因的剪接变体尚未被表征。该项目的关键人员将是Subha Srinivasan博士（首席研究员）和Jonathan Bingham，他们在基因组学、微阵列技术和生物信息学方面拥有丰富的行业经验。SBIR一期项目的具体目标是编制一份全面的候选基因清单，这些候选基因在猴子血液中对酒精暴露的反应中显示出受调节的剪接。使用猴子模型既可以使我们的发现尽可能与人类相关，又可以避免人类样本在自我报告酒精/食物/药物消费时产生偏差。5只动物在酒精暴露前后的不同时间点的剪接调节将在I期中对候选基因进行分析。在第二阶段，这些候选基因将在数百个人类血液样本中验证其预测意义。

DESCRIPTION (provided by applicant): Despite a critical need for biomarkers for alcohol exposure, the literature is unusually sparse in the applications of high-throughput genomics technologies in this area. The limited reports on biomarkers of alcohol exposure mostly confined to biomarkers identified in mouse or rat brains in response to ethanol. The inaccessibility of brain samples from human subjects renders them untranslatable to clinical settings. There is a dire need for an aggressive approach for high-throughput applications in alcohol research that can be ready tested in clinical settings. High-throughput experiments with blood on genome-wide microarrays can only monitor 15-20% of genes while missing majority of the functionally diverse mRNA spliced products. Considering evolutionary implications of alternate splicing as a mechanism used by metazoans to create functional diversity from small number of genes parallel to gene duplication, the limitations of gene microarrays are very limiting in biomarker research. Here, by utilizing a blood-wide splice microarray technology developed by Jivan, Hematome 1.0, we propose a research plan that bridges the gap between genome research and clinical application. Furthermore, by allowing for measurement of regulated splicing, Hematome 1.0 provide 3 to 4 fold more biomarkers for alcohol exposure from blood. Jivan's proprietary TransExpress(tm) Hematome 1.0 microarray platform has the capability to simultaneously discover and measure splice regulation of genes. The discovery aspect of TransExpress(tm) is critical to this endeavor because a majority of splice variants of human genes in blood are yet uncharacterized. The key personnel on this project will be Dr. Subha Srinivasan (Principal Investigator) and Jonathan Bingham, both of whom have extensive industry experience in genomics, microarray technologies, and bioinformatics. The specific aim of the SBIR Phase I project is to compile a comprehensive list of candidate genes that display regulated splicing in monkey blood in response to alcohol exposure. The monkey model is used both to make our findings as relevant to humans as possible and to avoid bias in human samples from selfreporting alcohol/food/drug consumption. Splice regulation in blood from 5 animals at various time points before and after exposure to alcohol will be profiled in Phase I for candidate genes. In Phase II, these gene candidates will be validated for predictive significance in hundreds of human blood samples.