RT Journal Article SR Electronic T1 Identification and validation of putative target genes regulated by miR-34 in cervical cancer JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.09.02.458804 DO 10.1101/2021.09.02.458804 A1 Venkatesan, Nalini A1 Xavier, Ashley A1 Sindhu, K.J. A1 Sinha, Himanshu A1 Devarajan, Karunagaran YR 2021 UL http://biorxiv.org/content/early/2021/09/03/2021.09.02.458804.abstract AB 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.Brief Description A combined analysis of miR-34 and gene expression in heterogeneous primary CESC, along with the integration of miR-34b and EMT regulated genes, was used to predict the candidate gene targets of the miR-34 family. The results show that the miR-34 family may regulate the mTOR pathway, cell cycle, and cell adhesion functions. Further, we showed that EMT signature genes (BMP7, CAV1, ID2, FN1) were regulated by miR-34b in CESC and cervical cancer cells.Competing Interest StatementThe authors have declared no competing interest.APIApplication Programming InterfaceCESCCervical Epithelial Squamous cell CarcinomaCPMCounts Per MillionCtCycle thresholddbEMTDatabase for EMT genesDMEMDulbecco’s Modified Eagle’s MediumECMEpithelial Cell MigrationEMTEpithelial-Mesenchymal TransitionFDRFalse Discovery RateFBSFoetal Bovine SerumFPKMFragments Per Kilo-base of exon per Million mappedFIGOInternational Federation of Gynaecology and ObstetricsGOGene ontologyGDCGenomic Data CommonsGFPGreen Fluorescence ProteinIDIdentitymRNAMessenger Ribonucleic AcidmiRNAMicro Ribonucleic AcidMREmiRNA Response ElementOVOvarian cancerqPCRquantitative Polymerase Chain ReactionTCGAThe Cancer Genome AtlasUCECUterine Corpus Endometrial Carcinoma3’UTR3’ Untranslated Regions