Abstract A78: Profiling of miRNA interactions in pancreatic adenocarcinoma by Argonaute CLIP-seq suggests a highly dynamic repertoire of targets

Abstract

Abstract MicroRNAs (miRNAs) are primary post-transcriptional regulators of gene expression which operate by degrading or otherwise repressing translation of target transcripts containing a corresponding miRNA recognition element (MRE). MiRNAs exert their effects through recruitment of the Argonaute (Ago) silencing complex to MRE sites. Although disruption of miRNA expression profiles is characteristic of many disease states, the inherent biological complexity of these regulatory networks has limited the ability to exhaustively catalog miRNA target repertoires and their associated functional phenotypes for a given tissue or cell type. To address these issues in the context of pancreatic adenocarcinoma, we performed next generation sequencing of both short and long RNA species to profile expression levels of both miRNAs and potential target transcripts, respectively, in hTERT-HPNE and MIA PaCa-2 cell lines. Additionally, we deep-sequenced Argonaute-bound RNAs (Ago CLIP-seq). Our results indicate that although the transcriptional profiles of both cell lines are stable across replicates, the subset of MREs that are engaged at any time with miRNAs is highly dynamic and not necessarily commensurate with relative transcript abundance. Additionally, we found that most MREs are located in intergenic and intronic regions. Moreover, of the MREs that are in protein-coding transcripts, the majority exist outside the 3′ untranslated regions (3′UTRs), in the coding regions and the 5′UTRs. These results further suggest that standard models for miRNA interactions that are commonly utilized may not adequately capture the interactions that are at work in pancreatic cells. Taken together, these results highlight a newfound complexity of miRNA regulatory networks and suggest their functional relevance in a model of pancreatic adenocarcinoma. Citation Format: Kevin Quann, Phillipe Loher, Peter Clark, Kathleen Delgrosso, Paolo Fortina, Yi Jing, Jonathan Brody, Isidore Rigoutsos. Profiling of miRNA interactions in pancreatic adenocarcinoma by Argonaute CLIP-seq suggests a highly dynamic repertoire of targets. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr A78.