Investigation of health benefits of cocoa in human colorectal cancer cell line, HT-29 through interactome analysis

This bioinformatics study aims to identify the potential key genes influenced by cocoa extraction treatment on colon cancer cell line HT-29 after 24h. Cocoa consumption has been claimed to have a beneficial effect on cancer. The microarray dataset (GSE94154) from GEO, was the source for differentially expressed genes (DEGs) extraction through GEO2R analysis. The comparison was between 3 controls of colorectal cell line HT-29 and 3 ones incubated with cocoa extraction after 24 h. Afterwards, the top significant DEGs were assigned for protein-protein interaction network construction and analysis by Cytoscape v 3.7.0. and the related applications. The findings indicate that there are 222 up-regulated and 28 down-regulated genes among 250 top-ranked DEGs. What is more, centrality analysis of the DEGs network identified 10 hub-bottlenecks that ISG15, MX 1, and STAT1 were among the significant differential expression genes with the contribution in type 1 interferon signaling pathway, positive regulation of erythrocyte differentiation, and negative regulation of viral genome replication.  In conclusion, the underlying mechanisms of cocoa treatment could be clarified by its up-regulatory and modulatory effect on prominent genes of tumor suppressor family. In other words, valuable clues for future clinical studies of cocoa health benefits are highlighted in this study once validation studies are carried out.