Integrated microRNA and mRNA expression profiling in a rat colon carcinogenesis model: Effect of a chemoprotective diet Academic Article uri icon


  • Abstract Recent studies have demonstrated that nutritional bioactives (fish oil and pectin) modulate microRNA molecular switches in the early stages of colon cancer. However, an integrated analysis of microRNA and mRNA target expression at an early stage of colon cancer development is lacking. We hypothesized that microRNAs altered by diet and carcinogen co-treatment modulate their gene targets, in part, by differentially binding to total mRNA or actively translated (polysome) mRNA. Sprague Dawley rats were fed diets containing corn oil or fish oil, with either pectin or cellulose and injected with azoxymethane (AOM, a colon-specific carcinogen). Colonic mucosa was assayed at an early stage of cancer development (10 wk post AOM injection). We examined microRNAs significantly altered by diet and carcinogen treatment with respect to their putative post-transcriptionally regulated mRNA targets, i.e., both total mRNAs and actively translated mRNA transcripts (in polyribosome complexes). Five complementary computational approaches were utilized to test the hypothesis. Specifically, gene set enrichment (GSEA) and Ingenuity (IPA) pathway analyses were used to identify those microRNAs significantly enriched by the change in expression of their putative target genes. In addition, coherent analysis was performed wherein microRNAs inversely related with their putative targets were examined, and cumulative distribution function (CDF) plots were used to evaluate the impact of diet and carcinogen combination on mRNA levels induced via microRNA alterations. Finally, linear discriminant analysis (LDA) was used to identify the best single, two and three-microRNA combinations for classifying dietary effects and colon tumor development. From a diet/carcinogen perspective, these complementary approaches were instrumental in demonstrating that chemoprotective fish oil + pectin feeding as compared to corn oil + cellulose feeding up regulated microRNAs -miR-16, miR-18a, miR-19b, miR-26b, miR-27b and miR-93, which coherently modulate several significantly down regulated putative targets; total RNA (ATP2B1, COL1A1, PDE4B, LAT and IGF1R) and polysomal RNA (MAPK6, LAT, ATP2B1). These changes reflect perturbations in pathways related to colorectal cancer, e.g., ERK-MAPK, IGF1R signaling, c-AMP mediated signaling, calcium signaling, PI3K/AKT signaling and apoptosis. We conclude that polysomal profiling is tightly related to microRNA changes when compared with total mRNA profiling. To our knowledge, this represents the first integrated analysis of microRNA and mRNA expression at an early stage of colon cancer development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1160. doi:10.1158/1538-7445.AM2011-1160

published proceedings


author list (cited authors)

  • Shah, M. S., Schwartz, S. L., Zhao, C., Davidson, L. A., Zhou, B., Lupton, J. R., Ivanov, I., & Chapkin, R. S.

citation count

  • 0

complete list of authors

  • Shah, Manasvi S||Schwartz, Scott L||Zhao, Chen||Davidson, Laurie A||Zhou, Beiyan||Lupton, Joanne R||Ivanov, Ivan||Chapkin, Robert S

publication date

  • April 2011