Combined DNA methylation and gene expression profiling in gastrointestinal stromal tumors reveals hypomethylation of SPP1 as an independent prognostic factor

Gastrointestinal stromal tumors (GISTs) have distinct gene expression patterns according to localization, genotype and aggressiveness. DNA methylation at CpG dinucleotides is an important mechanism for regulation of gene expression. We performed targeted DNA methylation analysis of 1.505 CpG loci in 807 cancer-related genes in a cohort of 76 GISTs, combined with genome-wide mRNA expression analysis in 22 GISTs, to identify signatures associated with clinicopathological parameters and prognosis. Principal component analysis revealed distinct DNA methylation patterns associated with anatomical localization, genotype, mitotic counts and clinical follow-up. Methylation of a single CpG dinucleotide in the non-CpG island promoter of SPP1 was significantly correlated with shorter disease-free survival. Hypomethylation of this CpG was an independent prognostic parameter in a multivariate analysis compared to anatomical localization, genotype, tumor size and mitotic counts in a cohort of 141 GISTs with clinical follow-up. The epigenetic regulation of SPP1 was confirmed in vitro, and the functional impact of SPP1 protein on tumorigenesis-related signaling pathways was demonstrated. In summary, SPP1 promoter methylation is a novel and independent prognostic parameter in GISTs, and might be helpful in estimating the aggressiveness of GISTs from the intermediate-risk category. What's new? Variations in the clinical behavior of gastrointestinal stromal tumors (GISTs) are associated with underlying variations in gene expression. But the mechanisms regulating gene expression in GIST and how they influence tumor progression remain unclear. A mechanism implicated in the present study is epigenetic dysregulation, specifically of secreted phosphoprotein 1 (SPP1), based on targeted DNA methylation profiling and genome-wide mRNA expression analysis in a cohort of GISTs. In vitro experiments indicate that SPP1 raises oncogenic potential by influencing the activation of major intracellular regulators. The findings suggest that SPP1 hypermethylation is an independent prognostic marker in GIST.