DNA methylome profiling of invasive pituitary macroadenomas reveals deregulation in enhancer regions involved in pituitary morphogenesis and developmental pathways
Asmaro K, Mosella M, Sabedot T, Malta T, Felicella M, Aho T, Poisson T, Decarvalho A, Noushmehr H, Rock J, and Castro A. Dna methylome profiling of invasive pituitary macroadenomas reveals deregulation in enhancer regions involved in pituitary morphogenesis and developmental pathways. J Neurol Surg Part B Skull Base 2019; 80.
J Neurol Surg Part B Skull Base
Pituitary tumors (PT) are the second most common central nervous system tumors. Pituitary macroadenomas (≥10 mm; MacroPT) may exhibit invasive behavior, potentially impeding a complete surgical resection which may lead to progression or recurrence. Few somatic mutations or genetic alterations have been reported and the role of DNA methylation in sporadic PT remains elusive. Herein, we profiled the DNA methylome of 14 formalin-fixed paraffin-embedded pituitary specimens (5 nontumoral; 9 MacroPT; 25 ± 10 mm average size; 6 nonfunctioning) from 14 patients (54 ± 16-year-old, white, 67% male) using the Human Illumina EPIC (HM850K) array platform. Nonparametric Wilcoxon's rank-sum was performed between invasive (InvPTs; n = 6) and noninvasive PTs (nonInvPTs; n = 3) and differentially methylated probes (DMPs) were selected. DMPs were integrated with publicly available data related to gene ontology (GO; Metascape), enhancer information (GeneHancer) and DNA motif analyses (Homer). We found 295 differentially methylated CpG probes in InvPT compared with nonInvPTs, mainly located in distal/open sea genomic regions (OpS) (72%). The majority of CpG sites were hypermethylated (87%) in InvPTs, and hypomethylated in nonInvPTs. GO analysis showed that the nearest gene associated with CGI/Sh DMPs was enriched for embryonic limb morphogenesis, protein homoligomerization, and gland development. DMPs regions overlapped with 135 predicted enhancers, mostly located in OpS regions. In InvPT, hypermethylated enhancers were enriched for basic helix-loop-helix (bHLH) motifs, predictive of binding sites for the recombination signal binding protein for Immunoglobulin Kappa I region (RBPJ) and Achaete-Scute Family bHLD (ASCL1) transcription factors (p < 0.05), related to Notch signaling and for basic leucine Zipper (bZIP) domain motifs, binding site for Jun-B AP-1 subunit's transcription factor, both related to proliferation (p < 0.05). Our results showed distinct DNA methylation pattern in invasive MacroPTs, especially related with pathways involved in pituitary morphogenesis and development. These preliminary findings suggest a novel epigenetic deregulation mechanism involving distal regions of genome that may contribute to the invasive behavior of MacroPT. Understanding the molecular mechanisms involved in the invasive behavior of these tumors may offer opportunities to the discovery of therapeutic targets, which is currently limited.