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

Gloria Ravegnini, César Serrano, Vittorio Simeon, Giulia Sammarini, Margherita Nannini, Erica Roversi, Milena Urbini, Fabrizio Ferrè, Riccardo Ricci, Giuseppe Tarantino, Maria A Pantaleo, Patrizia Hrelia, Sabrina Angelini

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Abstract

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.

Original languageEnglish
Pages (from-to)545-557
Number of pages13
JournalEpigenetics
Volume14
Issue number6
DOIs
Publication statusPublished - Jun 2019

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Ravegnini, G., Serrano, C., Simeon, V., Sammarini, G., Nannini, M., Roversi, E., Urbini, M., Ferrè, F., Ricci, R., Tarantino, G., Pantaleo, M. A., Hrelia, P., & Angelini, S. (2019). 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. Epigenetics, 14(6), 545-557. https://doi.org/10.1080/15592294.2019.1595997