Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.
Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.
Neuroendocrinology. 2024;114(1):51-63. doi: 10.1159/000533692. Epub 2023 Sep 12.
Growth hormone secretion by sporadic somatotroph neuroendocrine pituitary tumors (PitNETs) is a major cause of acromegaly. These tumors are relatively heterogenous in terms of histopathological and molecular features. Our previous transcriptomic profiling of somatotroph tumors revealed three distinct molecular subtypes. This study aimed to investigate the difference in DNA methylation patterns in subtypes of somatotroph PitNETs and its role in distinctive gene expression.
Genome-wide DNA methylation was investigated in 48 somatotroph PitNETs with EPIC microarrays. Gene expression was assessed with RNAseq. Bisulfite pyrosequencing and qRT-PCR were used for verifying the results of DNA methylation and gene expression.
Clustering tumor samples based on methylation data reflected the transcriptome-related classification. Subtype 1 tumors are densely granulated without GNAS mutation, characterized by high expression of NR5A1 (SF-1) and GIPR. The expression of both genes is correlated with specific methylation of the gene body and promoter. This subtype has a lower methylation level of 5' gene regions and CpG islands than the remaining tumors. Subtype 2 PitNETs are densely granulated and frequently GNAS-mutated, while those in subtype 3 are mainly sparsely granulated. Methylation/expression analysis indicates that ∼50% genes located in differentially methylated regions are those differentially expressed between tumor subtypes. Correlation analysis revealed DNA methylation-controlled genes, including CDKN1B, CCND2, EBF3, CDH4, CDH12, MGMT, STAT5A, PLXND1, PTPRE, and MMP16, and genes encoding ion channels and semaphorins.
DNA methylation profiling confirmed the existence of three molecular subtypes of somatotroph PitNETs. High expression of NR5A1 and GIPR in subtype 1 tumors is correlated with specific methylation of both genes.
散发性生长激素细胞瘤（PitNETs）的生长激素分泌是肢端肥大症的主要原因。这些肿瘤在组织病理学和分子特征方面相对具有异质性。我们之前对生长激素细胞瘤的转录组分析显示了三种不同的分子亚型。本研究旨在研究生长激素细胞瘤亚型之间 DNA 甲基化模式的差异及其在独特基因表达中的作用。
使用 EPIC 微阵列对 48 例生长激素细胞瘤进行全基因组 DNA 甲基化分析。使用 RNAseq 评估基因表达。使用亚硫酸氢盐焦磷酸测序和 qRT-PCR 验证 DNA 甲基化和基因表达的结果。
基于甲基化数据对肿瘤样本进行聚类反映了与转录组相关的分类。亚型 1 肿瘤颗粒密集且无 GNAS 突变，其特征是 NR5A1（SF-1）和 GIPR 的高表达。这两个基因的表达与基因体和启动子的特定甲基化相关。该亚型的 5'基因区域和 CpG 岛的甲基化水平低于其余肿瘤。亚型 2 生长激素细胞瘤颗粒密集且经常 GNAS 突变，而亚型 3 主要为稀疏颗粒。甲基化/表达分析表明，位于差异甲基化区域的约 50%基因是肿瘤亚型之间差异表达的基因。相关性分析显示，受 DNA 甲基化控制的基因包括 CDKN1B、CCND2、EBF3、CDH4、CDH12、MGMT、STAT5A、PLXND1、PTPRE 和 MMP16，以及编码离子通道和 semaphorins 的基因。
DNA 甲基化分析证实了生长激素细胞瘤存在三种分子亚型。亚型 1 肿瘤中 NR5A1 和 GIPR 的高表达与这两个基因的特定甲基化相关。
