The rs17084733 variant in the KIT 3' UTR disrupts a miR-221/222 binding site in gastrointestinal stromal tumour: a sponge-like mechanism conferring disease susceptibility

• Published in: Epigenetics Vol. 14; no. 6; pp. 545 - 557
• Main Authors: Ravegnini, Gloria, Serrano, César, Simeon, Vittorio, Sammarini, Giulia, Nannini, Margherita, Roversi, Erica, Urbini, Milena, Ferrè, Fabrizio, Ricci, Riccardo, Tarantino, Giuseppe, Pantaleo, Maria A., Hrelia, Patrizia, Angelini, Sabrina
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 03.06.2019; Taylor & Francis Group
• Subjects: 3' Untranslated Regions - genetics; Adult; Aged; Aged, 80 and over; Apoptosis; Binding Sites; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Case-Control Studies; Cell Proliferation; Disease Susceptibility; epigenetics; Female; Follow-Up Studies; Gastrointestinal Neoplasms - genetics; Gastrointestinal Neoplasms - metabolism; Gastrointestinal Neoplasms - pathology; gastrointestinal stromal tumor; Gastrointestinal Stromal Tumors - genetics; Gastrointestinal Stromal Tumors - metabolism; Gastrointestinal Stromal Tumors - pathology; Gene Expression Regulation, Neoplastic; GIST; Humans; imatinib; Male; MicroRNAs - genetics; MicroRNAs - metabolism; Middle Aged; miR-221/222; miRNA sponge; miRSNP; Polymorphism, Single Nucleotide; Prognosis; Proto-Oncogene Proteins c-kit - genetics; Proto-Oncogene Proteins c-kit - metabolism; Research Paper; Retrospective Studies; SNP; Survival Rate; Tumor Cells, Cultured; Young Adult; miRNA sponge; miRSNP; GIST; SNP; gastrointestinal stromal tumor; KIT; imatinib; epigenetics; miR-221/222
• ISSN: 1559-2294; 1559-2308; 1559-2308
• DOI: 10.1080/15592294.2019.1595997

Several miRNAs are dysregulated in gastrointestinal stromal tumours (GIST), and miR-221/222 appear to have a prominent role in GIST biology. Therefore, we investigated the role of DNA variants located in miR-221/222 precursor sequences and their target KIT 3'UTR. Ninety-five polymorphisms were analysed in 115 GIST cases and 88 healthy controls. KIT 3'UTR rs17084733 and pri-miR-222 rs75246947 were found significantly associated with GIST susceptibility. Specifically, KIT rs17084733 A allele was more common in GIST, particularly in KIT wild-type (WT) patients (Padj = 0.017). rs17084733 variant is located within one of the three miR-221/222 binding sites in the KIT 3'UTR, resulting in a mismatch in this seed region. Conversely, KIT mRNA levels were lower in patients carrying the variant allele, except for KIT mutant GIST. Luciferase assay data in GIST cells, generated using a construct containing all the three miR-221/222 binding sites, are consistent with KIT mRNA levels in GIST patients. Reporter assay data, generated using a construct containing only the site encompassing rs17084733, confirmed that this is a functional variant disrupting the miR-221/222 binding site. In conclusion, this is the first study investigating the role of SNPs on miR-221/222 precursor sequences and their binding region on KIT 3'UTR in GIST. We identified the KIT variant rs17084733 as a possible novel genetic biomarker for risk of developing KIT-WT GIST. Moreover, our findings suggest the role of one of the three miR-221/222 binding sites on KIT 3'UTR as endogenous sponge, soaking up and subtracting miR-221/222 to the other two sites characterized by a higher affinity.