The genomic landscape of dysembryoplastic neuroepithelial tumours and a comprehensive analysis of recurrent cases

Abstract

Aims: Dysembryoplastic neuroepithelial tumour (DNT) is a glioneuronal tumour that is challenging to diagnose, with a wide spectrum of histological features. Three histopathological patterns have been described: specific DNTs (both the simple form and the complex form) comprising the specific glioneuronal element, and also the non-specific/diffuse form which lacks it, and has unclear phenotype-genotype correlations with numerous differential diagnoses.

Methods: We used targeted methods (immunohistochemistry, fluorescence in situ hybridisation and targeted sequencing) and large-scale genomic methodologies including DNA methylation profiling to perform an integrative analysis to better characterise a large retrospective cohort of 82 DNTs, enriched for tumours that showed progression on imaging.

Results: We confirmed that specific DNTs are characterised by a single driver event with a high frequency of FGFR1 variants. However, a subset of DNA methylation-confirmed DNTs harbour alternative genomic alterations to FGFR1 duplication/mutation. We also demonstrated that a subset of DNTs sharing the same FGFR1 alterations can show in situ progression. In contrast to the specific forms, "non-specific/diffuse DNTs" corresponded to a heterogeneous molecular group encompassing diverse, newly-described, molecularly distinct entities.

Conclusions: Specific DNT is a homogeneous group of tumours sharing characteristics of paediatric low-grade gliomas: a quiet genome with a recurrent genomic alteration in the RAS-MAPK signalling pathway, a distinct DNA methylation profile and a good prognosis but showing progression in some cases. The "non-specific/diffuse DNTs" subgroup encompasses various recently described histomolecular entities, such as PLNTY and diffuse astrocytoma, MYB or MYBL1 altered.

Keywords: DNA methylation profiling; FGFR1; dysembryoplastic neuroepithelial tumours; glioneuronal tumours; molecular pathology; paediatric low-grade gliomas.

FIGURE 1

(A) Classification of 51 DNTs in the paediatric tumour DNA methylation landscape. The 51 DNTs with DNA methylation data available were compared with 244 reference low‐grade gliomas samples cohort belonging to 9 methylation classes and 74 control samples from the German Cancer Research Center (DKFZ) [32]. The 51 cases of this study are indicated as dark purple dots. (B) Genomic alterations identified in the 58 DNTs of the cohort

FIGURE 2

Histopathological and copy number changes at progression in a DNT with FGFR1 duplication . (top panel) Characteristics of the tumour at diagnosis: axial T1‐weighted pre‐operative MR image showing a hypointense signal without contrast enhancement (A), HES showing typical complex DNT (B), copy‐number profile showing no copy number alteration (C); (bottom panel) Characteristics of the tumour at relapse: axial T1‐weighted pre‐operative MR image showing mass arising in the operative cavity with contrast enhancement (D), HES showing cytonuclear atypia (E), copy‐number profile showing gain of chromosomes 6, 7, 10, 11, 16 and 20 (F). Magnification X200 (Figure 2B, E)

FIGURE 3

(A) Unsupervised hierarchical clustering based on 51 DNT methylation profiles . Unsupervised hierarchical clustering revealed two main clusters named 1 and 2. Histopathologic and genetic correlates are shown and colour coded. The heatmap (red increase methylation, blue decreased methylation) showed distinct CpG methylation level. Cluster 1 was broadly enriched in progressive DNTs. (B) Survival analysis. Kaplan–Meier estimates of the progression‐free survival (PFS) stratified by DNA methylation Cluster 1 or Cluster 2. DNTs from Cluster 1 are associated with a higher risk of progression than DNTs from Cluster 2

FIGURE 4

Methylation‐based t‐SNE distribution of 23 “non‐specific” DNTs. The 23 “non‐specific” DNTs with DNA methylation data available were compared with 244 reference low‐grade gliomas samples cohort belonging to 9 methylation classes and 74 control samples from the German Cancer Research Center (DKFZ) [32]. The 51 cases of this study are indicated as black dots

FIGURE 5

Final data integration results in 24 “non‐specific” DNTs . The integration of data from DNA methylation array to the histopathological diagnosis and molecular data helped establishing final diagnoses showing that the WHO tumour group “non‐specific” DNTs encompassed several morphomolecular entities. LGG = low‐grade glioma; GG = ganglioglioma; PLNTY = polymorphous low‐grade neuroepithelial tumour of the young; NEC = not elsewhere classified; wt = wild type