Deep Sequencing of Small Regulatory RNAs in Diffuse Large B cell Lymphoma

描述（由申请人提供）：本申请涉及广泛的挑战领域（08）基因组学和特定的挑战主题，08-CA-103：癌症中的MicroRNA。 小调控RNA由其有限的大小（20-30个核苷酸）及其与Argonaute（Ago）家族蛋白的关联来定义。 基于它们的生物发生机制和与它们相关的Ago蛋白的类型，小调控RNA可以被细分为至少三类：microRNA（miRNAs）、Piwi相互作用RNA（piRNAs）和内源性小干扰RNA（endo-siRNA）。 小分子调控RNA是近年来出现的一类重要的反式调节因子，其功能包括异染色质形成、mRNA降解和翻译调控等。 通过基因组和转录组的广泛巡逻，小的调控RNA参与了几乎所有的生物过程，包括细胞分化，细胞增殖和细胞死亡。 许多小的调节RNA在淋巴细胞发育和淋巴瘤细胞中表现出高度差异的表达模式。 在某些淋巴瘤类型中特异性表达的小调控RNA被鉴定，遗传学研究表明它们在淋巴瘤发生过程中起重要作用。 然而，在淋巴瘤细胞中表达的小调控RNA及其个体功能的完整列表仍然缺乏。 现在有机会利用深度测序技术的最新进展和弥漫性大B细胞淋巴瘤（DLBCL）财团病例的独特集合来解决以下挑战：开发DLBCL中小调控RNA表达谱的全面知识，并发现具有诊断和/或预后价值的小调控RNA。 我们的长期目标是了解在淋巴瘤发生中起重要作用的小调控RNA的身份、功能和分子作用机制。 这一目标将在以下具体目标中得到解决：（1）通过深度测序鉴定DCBCL中小调控RNA的表达谱。 将对长度为18-35个核苷酸的小RNA进行凝胶分级，并进行最新的Illumina深度测序技术，以鉴定其组成和相对丰度。(2)通过对深度测序数据进行生物信息学和生物统计学分析，结合临床结局和同一系列DLBCL病例的其他分子分析结果，鉴定具有诊断和/或预后价值的小调控RNA。 拟议研究的初步影响将是建立一个大系列DLBCL中小调控RNA表达谱的全面视图，并发现具有诊断和/或预后价值的小调控RNA。 从长远来看，这项研究将促进我们对淋巴瘤发生过程中小调控RNA功能的理解。 如果开发出能够调节特定小调控RNA功能的技术，则可以利用此处获得的知识来设计具有更好定义的靶点和更清楚理解的下游效应的适当疗法。 公共卫生相关性：在短期内，拟议的研究将确定具有诊断和/或预后价值的小调控RNA。 从长远来看，它应该促进我们对淋巴瘤发生过程中小调控RNA功能的理解，并且可以进一步利用这里获得的知识来开发更好的淋巴瘤诊断和治疗方案。

DESCRIPTION (provided by applicant): This application addresses broad challenge area (08) Genomics and specific challenge topic, 08-CA-103: MicroRNAs in Cancer. Small regulatory RNAs are defined by their limited size (20-30 nucleotides) and their association with Argonaute (Ago)-family proteins. Based on their biogenesis mechanisms and the type of Ago proteins with which they are associated, small regulatory RNAs can be subdivided into at least three classes: microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), and endogenous small interfering RNAs (endo-siRNAs). Small regulatory RNAs recently emerged as a major class of trans-regulators, with functions ranging from heterochromatin formation to mRNA degradation and translational control. Through such extensive patrolling of the genome and transcriptome, small regulatory RNAs are involved in almost every biological process, including cell differentiation, cell proliferation, and cell death. Many small regulatory RNAs exhibit highly differential expression patterns during lymphocyte development and in lymphoma cells. Small regulatory RNAs specifically expressed in certain lymphoma types were identified and genetic studies have demonstrated that they play important roles during lymphomagenesis. However, a complete list of small regulatory RNAs expressed in lymphoma cells and their individual functions is still lacking. The opportunity now exists to take advantage of recent advances in deep sequencing technology and a unique collection of diffuse large B cell lymphoma (DLBCL) consortium cases to address the following challenge: to develop a comprehensive knowledge of small regulatory RNA expression profiles in DLBCL, and to discover small regulatory RNAs that have diagnostic and/or prognostic values. Our long-term goal is to understand the identities, functions, and molecular mechanisms of action of small regulatory RNAs that play important roles in lymphomagenesis. This goal will be addressed in the following specific aims: (1) identify an expression profile of small regulatory RNAs in DCBCL by deep sequencing. Small RNAs of 18-35 nucleotides in length will be gel fractionated and subjected to the latest Illumina deep sequencing technology to identify their composition and relative abundances. (2) Identify small regulatory RNAs with diagnostic and/or prognostic value by bioinformatic and biostatistical analyses of the deep sequencing data, in combination with clinical outcome and results from other molecular analyses of the same series of DLBCL cases. The initial impact of the proposed research will be to establish a comprehensive view of small regulatory RNA expression profiles in a large series of DLBCL and to discover small regulatory RNAs with diagnostic and/or prognostic values. In the long run, the proposed study should advance our understanding of the functions of small regulatory RNAs during lymphomagenesis. Should technologies be developed capable of modulating the functions of specific small regulatory RNAs, the knowledge gained here could be exploited to design appropriate therapies with better defined targets and more clearly understood downstream effects. PUBLIC HEALTH RELEVANCE: In the short-term, the proposed research will identify small regulatory RNAs with diagnostic and/or prognostic values. In the long run, it should advance our understanding of the functions of small regulatory RNAs during lymphomagenesis, and the knowledge gained here can be further exploited to develop better diagnostic and therapeutic protocols for lymphoma.