Abstract A34: Regulation of pancreatic cells by isomiRs

Abstract

Abstract Pancreatic ductal adenocarcinoma (PDAC) is currently the 4th leading cause of cancer related deaths in the U.S. and expected to become the 2nd leading cause behind only lung cancer over the next decade. MicroRNAs (miRNAs) are short non-coding RNAs, with a length of ~22 nucleotides (nts), that play key roles in post-transcriptional gene regulation. Their dysregulation has been implicated in many cancers including PDAC. Alternative processing of miRNA precursors can result in the formation of isomiRs that differ by a few bps in either the 5′ and/or 3′ ends of the miRNAs. These seemingly slight differences can potentially alter the set of genes that are targeted by a particular miRNAs thereby resulting in differences in the post-transcriptional regulation program. To examine the role of isomiRs in PDAC, we performed next-generation sequencing of the short RNA transcriptome in two pancreatic cell lines, HPNE and MIA PaCa-2. Using next-generation sequencing. Over 1,000 isomiRs, arising from 500 distinct miRNA loci, were identified as being statistically significantly expressed in the cell lines. Of these isomiRs, we identified over 200 that were differentially expressed between the HPNE and MIA PaCa-2 cell lines. Interestingly, 44 miRNA loci gave rise to a differentially expressed isomiR that differed from the one currently listed in miRBase v.20. This suggests that distinct isomiRs from the same miRNA locus can exhibit differences in their expression patterns. In addition to being expressed in the HPNE and MIA PaCa-2 cell lines, we were able to confirm the presence of many of these isomiRs in the short RNA sequences of PDAC primary tissues from The Cancer Genome Atlas (TCGA) project. To further explore the functional role of these isomiRs, we sought potential targets for them among the deep-sequenced data that we obtained from the HPNE and MIA PaCa-2 cell lines after UV-crosslinking followed by Immunoprecipitation with the Argonaute antibody (Ago-CLIP-seq). Indeed, we find that isomiRs from similar miRNA loci do exhibit differences in their preferences for mRNA targets. Furthermore, Gene Ontology (GO) analysis of the genes targeted by isomiRs reveals an enrichment for pathways involved in the regulation of cell death in the HPNE cell lines. Analogously, isomiR targets in the MiaPaCa-2 cell lines exhibit an enrichment for cell motility pathways. In summary, we find that isomiRs of specific miRNA loci exhibit differences in their expression levels, have distinct mRNA target preferences in two model cell lines, and are specifically involved in the post-transcriptional events regulating gene expression. Citation Format: Eric R. Londin, Phillipe Loher, Kevin Quann, Kathleen Delgrosso, Paolo Fortina, Jonathan Brody, Isidore Rigoutsos. Regulation of pancreatic cells by isomiRs. [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 A34.