Abstract #556: Integrating microRNA and mRNA expression profiles identified a small set of unique genes up-regulated in malignant pleural mesothelioma (MPM)
Authors: Milind Suraokar, Alejandro Corvalan, Chi-wan Chow, Adi Gazdar, Cesar Moran, Gabriela Raso, Reza Mehran, Anne Tsao, Ignacio Wistuba
Journal: Cancer Research (2009)

MPM is a highly aggressive neoplasm with poor prognosis and needs discovery of newer and critical therapeutic targets. MicroRNA\#8217;s (miRNA9s) play an important role in many different types of cancer but there is lack of published reports detailing their role in MPM. We decided to employ a global profiling strategy using miRNA microarrays to search for miRNA\#8217;s involved in the pathogenesis of MPM. We analyzed miRNA profiles, using Agilent human miRNA microarray v1 slides, to find an up regulation of 44 versus down regulation of 29 miRNA9s in mesothelioma MSTO-211H cancer cells compared to HCT-4012 - a pleural telomerase-transformed control cell line. Whereas profiling of 16 MPM tissues (8 normal versus 8 tumor) revealed down regulation of 11 miRNA\#8217;s in tumor tissue. Along with addressing the discrepancy between cells and tissue with respect to miRNA profiles we needed to devise a method to screen the possible candidates in order to focus on the most relevant miRNA\#8217;s. One alternative is to choose miRNA9s that regulate genes known to be involved in the cause or progression of MPM. However search of miRNA targets using the online targetscan 4.2 program (http://www.targetscan.org) resulted in >1000 unique genes. This is expected since miRNA9s are thought to regulate hundreds of genes and multiple miRNA\#8217;s could regulate a common message. Therefore we decided to explore a novel screening strategy, which integrates miRNA with messenger RNA (cDNA) expression profiles to narrow down our list of miRNA\#8217;s. We obtained cDNA profiles on same cell lines and tissue samples using Affymetrix U133 plus 2.0 chips. Bioinformatic analysis using the MultiExperiment Viewer software (www.tm4.org/mev.html), involving data reduction techniques (Correspondance Analysis), hierarchical clustering methods and Serial Analysis for Microarray (SAM), proposed up regulation of ~300 genes in MPM compared to normal tissues. Next using a custom-designed search algorithm we computed the number of miRNA\#8217;s regulating a common or different set of genes. Of the ~300 mRNA\#8217;s up regulated in MPM only 32 are recognized by the 11 down regulated miRNA\#8217;s. Moreover most of the miRNA\#8217;s regulate single messages while ~20 % of the messages are regulated by more than 1 miRNA\#8217;s. Interestingly some of these targets include Ets variant 1 (ETV1) and Protein kinase C - epsilon (PRKCE), which has not been evaluated in MPM but implicated in other cancers. Our next step is to validate our profiling studies using real-time PCR and protein analysis methods. Therefore aside from selecting highly relevant miRNA\#8217;s our innovative approach will also enable discovery of novel genes based on their ability to be bound by single or multiple miRNA\#8217;s. Supported by Grant: DoD W81XWH-07-1-0306.  Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 556.