Identification and validation of putative target genes regulated by miR-34 in cervical cancer

Abstract

The emergence of large-scale transcriptomic data provides the opportunity for identifying novel putative targets of microRNAs (miRNAs). In this study, we followed a computational pipeline to predict the candidate gene targets of the miR-34 family. This approach integrates the expressions of miR-34 with genes of heterogeneous primary cervical epithelial squamous cell carcinomas (CESC). Integration of miR-34b and epithelial-mesenchymal transition (EMT) regulated genes has also been focussed, EMT being a reversible process that fuels cancer metastasis. An in-silico approach involving three processes was carried out with CESC datasets of the cancer atlas genome (TCGA), which includes correlation analysis, target prediction database lookup, functional enrichment, network analysis, survival analysis, and EMT score derivation. The results indicate that the miR-34 family may regulate the candidate genes of the mTOR pathway, cell cycle (CCND2) and cell adhesion functions (FZD4). Further, the study reveals the possible regulation of EMT signature genes, namely BMP7, CAV1 and ID2by miR-34b. Further, these transcriptomic signatures were validated in a subset of CESC from the South Asian Indian population (n = 10) and in non-cancerous cervical tissues (n = 5). Upon stably expressing miR-34b in cervical cancer cells (C33A and HeLa), we found repression of these candidate genes and a low negative correlation (r² = -0.07) between miR-34b and EMT score indicating FN1 as its putative target. Together, these studies revealed the potential targets of the miR-34 family, especially miR-34b, with the hope that they would emerge as potential biomarkers and/or promising therapeutic targets in CESC.