Identification and characterization of novel transcribed ultraconserved regions as long non-coding RNAs in medulloblastoma

University Of Virginia, Charlottesville VA

Investigators

Abstract

PROJECT SUMMARY/ABSTRACT Medulloblastoma (MB) is the most common malignant pediatric brain tumor. MB accounts for over 60% of all embryonal tumors in US children aged 0-19 with nearly 300 cases of this cerebellar tumor diagnosed in the US per year. While the 5-year survival rate for pediatric MB patients is just over 70%, children who undergo standard of care treatments frequently experience permanent neurological deficits such as reduced motor and cognitive functions. Additionally, all medulloblastoma subgroups lack approved targeted therapies. This application proposes to investigate in MB the role of “Transcribed Ultra-Conserved Regions” (TUCRs) about which there is no published literature. TUCRs represent a distinct group of 481 transcripts that are 100% conserved across human, mouse, and rat genomes. A large fraction of TUCRs likely consist of long non-coding RNAs. Since their discovery, TUCRs have only been correlated to a handful of cancers and remain exceedingly underexamined within cancer research. I performed the first analysis of TUCRs in MB. I performed differential gene expression analysis of RNA-sequencing data from MB tumors and normal cerebellum samples and identified a multitude of differentially expressed TUCRs. Using Kaplan-Meir survival analyses, I identified numerous TUCRs whose expression was significantly correlated with overall survival. I generated a multifaceted, computational ranked scoring and prioritization system, which identified the top TUCRs in MB. Utilizing well established MB human cell lines and siRNA knockdown technology, I discovered top scoring TUCRs such as uc.242 and uc.115 significantly promote MB cell invasion. I propose to study the expression, functions and mechanisms of action of TUCRs in three aims: Aim 1 will identify and prioritize dysregulated TUCRs in MB and its subgroups by conducting analysis on tumors from two multi-institutional research programs. Completion of differential expression analysis, survival analysis, and prioritization scoring as performed in the preliminary analysis will produce the top TUCRs in MB. Aim 2 will determine the functional effects of the top four TUCRs in MB through the implementation of in vitro cell proliferation, invasion, migration, and death assays and in vivo tumor formation and survival analysis (Subaim 2.1). TUCR function and mechanisms will be investigated with WGCNA on all TUCRs in MB (Subaim 2.2). Completion of this work will elucidate the oncogenic and tumor suppressive nature of the top TUCRs in MB. Altogether, this proposal investigates the oncogenic and tumor suppressive nature of TUCRs in MB. It represents the first study of TUCRs in MB and will significantly advance the basic understanding of this highly understudied class of molecules. Not only is the proposed work impactful, innovative, and feasible, it incorporates a strong training plan designed to significantly advance the investigator as a cancer researcher. UVA provides a robust training environment with multiple experimental cores, accredited classes, and renowned mentorship.