Integrative Transcriptomic Network Analysis of Butyrate Treated Colorectal Cancer Cells

Abstract

Simple Summary High-fiber diets are known to protect against colorectal cancer (CRC), largely through the influence of butyrate, which is generated by the colonic microbiota. To better understand how dietary butyrate prevents colorectal cancer, a systems biology approach was used to define the transcriptomic responses of butyrate-treated CRC cells. Butyrate altered the expression and/or splicing of thousands of genes. Through the integration of microRNA and mRNA datasets, molecular interaction networks were generated that identified key components of the butyrate response and facilitated bioinformatic predictions of butyrate-induced changes in cellular activity. Moreover, two butyrate-regulated microRNAs identified through this analysis were shown to enhance the effect of butyrate on cellular proliferation and apoptosis. These results help create a framework for identifying novel drug targets that may act in concert with histone deacetylase inhibitors, such as butyrate, to prevent or treat cancers. Abstract Diet-derived histone deacetylase inhibitor (HDACi), butyrate, alters global acetylation and consequently global gene expression in colorectal cancer (CRC) cells to exert its anticancer effects. Aberrant microRNA (miRNA) expression contributes to CRC development and progression. Butyrate-mediated modulation of microRNA (miRNA) expression remains under-investigated. This study employed a systems biology approach to gain a comprehensive understanding of the complex miRNA-mRNA interactions contributing to the butyrate response in CRC cells. Next-generation sequencing, gene ontology (GO) and pathway enrichment analyses were utilized to reveal the extent of butyrate-mediated gene regulation in CRC cells. Changes in cell proliferation, apoptosis, the cell cycle and gene expression induced by miRNAs and target gene knockdown in CRC cells were assessed. Butyrate induced differential expression of 113 miRNAs and 2447 protein-coding genes in HCT116 cells. Butyrate also altered transcript splicing of 1589 protein-coding genes. GO, and pathway enrichment analyses revealed the cell cycle to be a central target of the butyrate response. Two butyrate-induced miRNAs, miR-139 and miR-542, acted cooperatively with butyrate to induce apoptosis and reduce CRC cell proliferation by regulating target genes, including cell cycle-related EIF4G2 and BIRC5. EIF4G2 RNA interference mimicked the miR-139-mediated reduction in cell proliferation. The cell cycle is a critical pathway involved in the butyrate response of CRC cells. These findings reveal novel roles for miRNAs in the cell cycle-related, anticancer effects of butyrate in CRC cells.