Molecular characterization of malignant evolution of Gastrointestinal Stromal Tumors

Gastrointestinal stromal tumor (GIST) is the most common sarcoma of the gastrointestinal tract. Interstitial cell of Cajal is considered to be its precursor. In contrast to most sarcomas, which have no known premalignant lesions, preneoplastic counterparts of GIST, known as mini-GIST have been identified. Although malignant GIST are rare, mini-GIST are remarkably common, with an incidence of 20-30% in the elderly population. The vast majority of mini-GIST display benign nature, but a fraction of them further progress toward overt malignancy. The aim of this study was to decipher the molecular mechanisms underlying the malignant progression of mini-GIST to overt GIST, focusing on non-coding RNAs. In particular, this project investigated the role and significance of dysregulation of long non-coding RNAs. A series of 179 samples, including 63 mini-GIST and 116 over GIST, was molecularly profiled by whole transcriptome sequencing. We found that the long non-coding RNA Musculin Antisense-1 (MSC-AS1) is overexpressed in KIT-mutated overt malignant GIST compared to mini-GIST, suggesting its involvement in malignant progression. Cytoplasmic localization in GIST cell lines supported competitive endogenous RNA (ceRNA) as a mechanism of action. The interplay in the lncRNA-miRNA-mRNA interactions was further investigated in a subset of 109 samples, for which miRNA sequencing data was also available. In silico prediction of MSC-AS1 targets in conjunction with miRNA profiling and correlation analysis with transcript expression revealed that miR-490-3p, miR-195-5p, miR-497-5p, miR-1-3p, miR-9-5p, miR-561-5p and miR-20b-5p were MSC-AS1 potential interactors. As well, in silico prediction of mRNA targets of these miRNAs in conjunction with transcriptome profiling and correlation analysis, identified overexpressed genes involved in cell-cycle and DNA repair related pathways. A ceRNA network of lncRNA-miRNA-mRNA was constructed, which suggested that the overexpression of MSC-AS1, by capturing miRNAs that regulate cell proliferation and genomic instability, may contribute to GIST malignant progression.