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

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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.