Multiplexed Analysis of the Epitranscriptome

项目总结/摘要 表位转录组学是RNA修饰的研究，其中包括170多种天然存在的化学修饰。 对核苷酸的改变。在人类所有类型的RNA中发现了60多种：mRNA，tRNA，rRNA，lncRNA， 还有其他人这些修改是动态的;它们的整体数量在发展和期间发生变化 疾病进展。它们由写入酶安装，由读取蛋白读取，并由擦除器移除 它们具有改变RNA结构和动力学的内在能力。影响翻译 起始和终止、翻译保真度、可变剪接、细胞区室之间的运输，以及 调节RNA降解。RNA阅读器、写入器和擦除器蛋白是有前途的高电流药物靶点 对制药感兴趣。目前可用的分析方法要么不报告序列背景，要么提供 序列信息，但以多路复用能力为代价。尽管有这些限制，现在我们知道 修饰与癌症进展、耐药性、衰老和 病毒感染Alida Biosciences正在开发一种新的商业平台，用于检测，识别和绘图 多重和高灵敏度的RNA修饰-适用于临床样品（例如，针穿刺活检， FFPE样品），其中可获得少量RNA。在完成第一阶段里程碑之后， 该提案专注于创建新的多重检测和概念验证测试，旨在（1）完成 检测开发，优化灵敏度、特异性和稳健且用户友好的工作流程，（2）开发检测 自动化，和（3）进行试验验证，为商业投放做准备。这项技术将 重要的是，它将提供第一个能够分析和关联 在给定样品中的整个转录组中的多种RNA修饰类型。

Project Summary/Abstract Epitranscriptomics is the study of RNA modifications, which include more than 170 naturally occurring chemical alternations to the nucleotides. More than 60 are found in human RNA of all types: mRNA, tRNA, rRNA, lncRNA, and the others. These modifications are dynamic; their global quantities change in development and during disease progression. They are installed by writer enzymes, read by reader proteins and removed by eraser enzymes, and they have an intrinsic capacity to alter RNA structure and dynamics. They influence translation initiation and termination, translation fidelity, alternative splicing, trafficking between cellular compartments, and regulate RNA degradation. RNA reader, writer and eraser proteins are promising drug targets of high current interest to pharma. Currently available analytical methods either do not report on sequence context or provide sequence information but at the expense of multiplexing capability. Despite these limitations, it is now known that modifications are dynamically tied to phenotypic changes in cancer progression, drug resistance, aging, and viral infection. Alida Biosciences is developing a new commercial platform to detecting, identifying, and mapping RNA modifications in a multiplex and with high sensitivity—suitable for clinical samples (e.g. needle biopsies, FFPE samples) in which low quantities of RNA may be available. Following completion of our Phase I milestones focused on creating the new multiplexed assay and proof-of-concept testing, this proposal aims to (1) complete assay development, optimizing sensitivity, specificity, and a robust and user-friendly workflow, (2) develop assay automation, and (3) perform assay validation in preparation for commercial launch. This technology will be significant because it will provide the first commercial platform capable of profiling and correlating changes of multiple RNA modification types across the entire transcriptome in a given sample.