DNA-Methylation Analysis as a Tool for Thymoma Classification

Abstract

Background: Thymomas are malignant thymic epithelial tumors that are difficult to diagnose due to their rarity and complex diagnostic criteria. They represent a morphologically heterogeneous class of tumors mainly defined by “organo-typical” architectural features and cellular composition. The diagnosis of thymoma is burdened with a high level of inter-observer variability and the problem that some type-specific morphological alterations are more on the continuum than clear-cut. Methylation pattern-based classification may help to increase diagnostic precision, particularly in borderline cases. Methods and Results: We applied array-based DNA methylation analysis to a set of 113 thymomas with stringent histological annotation. Unsupervised clustering and t-SNE analysis of DNA methylation data clearly segregated thymoma samples mainly according to the current WHO classification into A, AB, B1, B2, B2/B3, B3, and micronodular thymoma with lymphoid stroma. However, methylation analyses separated the histological subgroups AB and B2 into two methylation classes: mono-/bi-phasic AB-thymomas and conventional/“B1-like” B2-thymomas. Copy number variation analysis demonstrated methylation class-specific patterns of chromosomal alterations. Interpretation: Our study demonstrates that the current WHO classification is generally well reflected at the methylation level but suggests that B2- and AB-thymomas are (epi)genetically heterogeneous. Methylation-based classifications could help to refine diagnostic criteria for thymoma classification, improve reproducibility, and may affect treatment decisions.

Non-Mutational Key Features in the Biology of Thymomas

“…Most of the available literature has focused on the potential use of DNA methylation markers to discriminate between different histologic subtypes or between THs with and without myasthenia gravis or as a prognostic indicator. Studies analyzing global methylation patterns in TETs have found substantial hyper- or hypomethylation of CpG sites with significant correlations with the TH histologic subtype [ 4 , 63 , 64 , 65 ], GTF2I or HRAS mutation status, and mRNA and miRNA expression patterns [ 4 ]. Previous studies using a candidate gene approach revealed the hypomethylation of several tumor suppressor genes (e.g., APC1A , CDKN2A , E-cad , FHIT , hMLH1 , MGMT , RARβ , RASSF1A ) or hypermethylation of DNMT1 , DNMT3a , and DNMT3b [ 66 ] in early stage THs compared to more aggressive or late stage THs and TCs (reviewed in [ 61 , 62 ]).…”

The Molecular Landscape of Thymic Epithelial Tumors: A Comprehensive Review

“…The methylation analysis could also be employed for diagnostic purposes for the distinction of the various WHO subtypes [48]. To improve precision, particularly in morphological borderline cases, Gaiser et al explored a methylation pattern-based classification [48]. In their study, an array-based DNA methylation analysis of 113 thymomas with detailed histological annotation was conducted.…”

“…However, methylation analyses revealed a nuanced distinction within histological subgroups AB and B2, yielding two methylation classes: mono-/bi-phasic AB-thymomas and conventional/"B1-like" B2-thymomas. This emphasizes the potential of methylation-based classifications to refine diagnostic criteria, improve reproducibility, and impact treatment decisions [48].…”

Histogenetic and disease‐relevant phenotypes in thymic epithelial tumors (TETs): The potential significance for future TET classification

“…Genetic and epigenetic signatures are essential for understanding and rationally classifying tumors, 117 and TETs are no exception. 55,118 The biggest discovery in TET genetics was made by Petrini et al in 2014. 59 They were the first to report that significant proportions of thymomas, especially type A and AB thymomas, harbored a hot spot mutation in general transcription factor II-I (GTF2I), namely, GTF2I L424H.…”

“…Genetic and epigenetic signatures are essential for understanding and rationally classifying tumors, 117 and TETs are no exception 55,118 . The biggest discovery in TET genetics was made by Petrini et al in 2014 59 .…”