title: In silico dissection of miRNA targetome polymorphisms and their role in regulating miRNA-mediated gene expression in esophageal cancer.
abstract: Esophageal cancer is the eighth most common cancer worldwide. Also middle-aged obese adults with higher body mass index during childhood have a greater risk to develop esophageal cancer. The contribution of microRNAs to esophageal cancer has been extensively studied and it became clear that these noncoding RNAs may play crucial roles in pathogenesis, diagnosis and prognosis of the disease. Increasing evidences have suggested that polymorphisms perturbing microRNA targetome (i.e., the compendium of all microRNA target sites) are associated with cancers including esophageal cancer. However, the extent to which such variants contribute to esophageal cancer is still unclear. In this study, we applied an in silico approach to systematically identify polymorphisms perturbing microRNA targetome in esophageal cancer and performed various analyses to predict the functional consequences of the occurrence of these variants. The computational results were integrated to provide a prioritized list of the most potentially disrupting esophageal cancer-implicated microRNA targetome polymorphisms along with the in silico insight into the mechanisms with which such variations may modulate microRNA-mediated regulation. The results of this study will be valuable for future functional experiments aimed at dissecting the roles of microRNA targetome polymorphisms in the onset and progression of esophageal cancer.
authors: Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
authors: Ziba
authors: Z
authors: Nariman-Saleh-Fam
authors: Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
authors: Milad
authors: M
authors: Bastami
authors: Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
authors: Mohammad Hossein
authors: MH
authors: Somi
authors: Faculty of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.|Department of Biochemistry and Medical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
authors: Naser
authors: N
authors: Samadi
authors: Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, 9196773117, Iran.
authors: Mohammad Reza
authors: MR
authors: Abbaszadegan
authors: Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
authors: Farkhondeh
authors: F
authors: Behjati
authors: Medical Genetics Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
authors: Hamid
authors: H
authors: Ghaedi
authors: Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. tavakkolybazzazj@tums.ac.ir.
authors: Javad
authors: J
authors: Tavakkoly-Bazzaz
authors: Bambino Gesù Children's Hospital-IRCCS, Gene Expression - Microarrays Laboratory, Viale di San Paolo 15, Rome, 00146, Italy. andrea.masotti@opbg.net.
authors: Andrea
authors: A
authors: Masotti
mesh_terms: D020413:3' Untranslated Regions; D019295:Computational Biology; D030541:Databases, Genetic; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D015870:Gene Expression; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Bioinformatics; Esophageal Cancer; MicroRNAs; Polymorphism; miRNA target sites