Genome-Scale Profiling of DNA Methylation in Sporadic Pituitary Macroadenomas: Association with Tumor Invasion and Histopathological Subtype

Abstract

Pituitary adenomas (PAs) are commonly-occurring neoplasms that cause a variety of neurological and endocrine effects. Although known causal contributors include heredity, hormonal influence and somatic mutations, the pathophysiologic mechanisms driving tumorigenesis and invasion of sporadic PAs remain unknown. We aimed to investigate whether variation in DNA methylation is associated with PA invasion and functional phenotype. Genome-wide DNA methylation profiles were assessed in 24 sporadic pituitary macroadenomas, according to histopathological subtype and Knosp invasion scores. Methylation data were analyzed using two tailed t-test and one-way ANOVA statistics. Two-way hierarchical clustering analysis was performed using Pearson's correlation and average linkage for the gene/sample tree. Although no significant differences in global methylation levels were observed between invasive and noninvasive PAs, two CpGs annotated as enhancers in invasion-associated genes (FLT1 and SLIT3) were significantly hypomethylated in invasive PAs. Compared with hormonally-active somatotroph adenomas, nonfunctional PAs displayed global hypermethylation across CpG sites (β-value 0.47 versus 0.42, p = 0.005). The most significant site of differential methylation was within the promoter region of the potassium voltage-gated channel, shaker-related subfamily, β member 2 (KCNAB2) (FDR = 5.11 × 10^-10). Pathway analysis in global promoter-associated CpGs showed that non-functional PAs are most closely associated with the ion channel activity signal pathway (FDR < 0.25). DNA methylation analysis may provide a clinically useful molecular correlate to standard PA immunostaining classification. Differential methylation of cell motility related genes (FLT1 and SLIT3) may be associated with PA invasion. Hypermethylation of KCNAB2 and downstream ion channel activity signal pathways may contribute to the endocrine-inactive status of non-functional PAs.