Characterizing functional targets of a non-coding RNA oncogene, SNORA42

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DESCRIPTION (provided by applicant): snoRNAs are non-coding guide RNAs that direct site-specific post-transcriptional RNA modifications - either pseudouridylation or 2'-O-methylation - of their target RNAs. Although snoRNAs' biochemical functions are relatively well characterized, their biological roles are just beginning to be explored. Notably, dysregulation of specific snoRNAs is associated with increased risk for breast, prostate, lung, brain and colorectal cancers as well as leukemia and multiple myeloma. Most remarkably, one pseudouridylation-directing snoRNA, SNORA42, was recently identified as an oncogene in non-small cell lung carcinoma (NSCLC). Despite increasing awareness of the medical significance of snoRNA biology, the mechanisms by which altered snoRNA activities cause cancer remain mysterious. We have preliminary data supporting a new paradigm for snoRNA function, which we here propose to investigate in the context of increased NSCLC cell proliferation and metastasis. Using a novel technology (Pseudo-seq) that allows us to map the locations of pseudouridines (φ) genome-wide with single nucleotide resolution, we have demonstrated for the first time that endogenous human messenger RNAs (mRNAs) contain φ's at specific sites. Because previously known snoRNA targets were restricted to ribosomal RNAs, or less frequently, spliceosomal small RNAs, this breakthrough expands the number of potential cancer-relevant targets of SNORA42 more than 100-fold, and raises the possibility that amplification/over-expression of oncogenic SNORA42 causes tumorigenesis by perturbing modification of mRNA targets. Although the molecular consequences of endogenous mRNA pseudouridylation remain to be determined, recent work dramatically illustrates the potential significance of this post-transcriptional mRNA modification: artificial incorporation of φ's into model mRNAs changes the meaning of the genetic code! Building on these discoveries, we propose to conduct an exploratory research program (1) to investigate the molecular and cellular effects of site-specific mRNA pseudouridylation in non-small cell lung carcinoma; and (2) to comprehensively identify the pseudouridylated targets of the snoRNA oncogene SNORA42. Together, the proposed investigations will illuminate the mechanisms by which over-expression/genomic amplification of SNORA42 contributes to lung cancer with poor prognosis.