Objectives: Somatotropinomas can be divided into three subgroups based on their distinct DNA methylation profiles1, one matching sparsely granulated (SG) and the other two matching densely granulated phenotypes (DG-A and DG-B). Sparsely granulated adenomas show fibrous body formation on cytokeratin immunohistochemistry, compared to diffuse staining in densely granulated adenomas. Methylation1 and gene expression data were analysed to identify (i) differentially methylated regions (DMRs) and genes between SG, DG-A and DG-B and normal pituitary (NP), and (ii) genes showing differential promoter methylation with differential expression.
Methods: We identified.
DMRs using bumphunter (minimum probes/ DMR=7, adjusted P<0.05),
differentially expressed genes from Affymetrix data (false discovery rate <0.05, fold change of ≥2),
gene sets using gene set enrichment analysis (Fishers exact test (P<0.05)),
interaction hotspots using EpiMod (P<0.05).
Results: All tumour subgroups showed predominant hypomethylation compared to normal, with striking profound hypomethylation observed in DG-B. Three genes showed promoter hypermethylation with decreased RNA expression, including IER3 (SG vs.NP), with a known pro-apoptotic role in cervical cancer. Twenty-one genes showed promoter hypomethylation with increased RNA expression, including TET1 (DG-B vs. NP), which is a demethylating agent and may cause the profound hypomethylation in DG-B tumours. ITPR2 and SFRP1 showed promoter hypermethylation with decreased expression in SG vs. DG-B tumours. ITPR2 mediates oncogene-induced senescence and SFRP1 inhibits Wnt signalling, both consistent with tumour suppressive roles. Subnetworks based around inflammatory mediators show predominant promoter hypo-methylation (DG-B vs. DG-A/ DG-B vsSG), suggesting a key role for inflammatory mediators in DG-B tumours.
Conclusions: Pathways involving apoptosis, demethylation and inflammation mediate different tumorigenic pathways in pituitary adenomas with different cytokeratin-staining patterns on immunohistochemistry.
Reference: 1. Capper, D. et al. DNA methylation-based classification of central nervous system tumours. Nature 555, 469474, doi:10.1038/nature26000 (2018).