IDH-mutant astrocytomas with primitive neuronal component have a distinct methylation profile and a higher risk of leptomeningeal spread

Abstract

IDH-mutant astrocytomas are diffuse gliomas that are defined by characteristic mutations in IDH1 or IDH2 and do not have complete 1p/19q co-deletion. The established grading criteria include histological features of brisk mitotic activity (grade 3) and necrosis and/or microvascular proliferation (grade 4). In addition, homozygous deletion of the CDKN2A/B locus has recently been implemented as a molecular marker for grade 4 IDH-mutant astrocytomas. Here, we describe a subgroup of high-grade IDH-mutant astrocytomas characterised by a primitive neuronal component based on histology and a distinct DNA methylation profile (n = 51, ASTRO PNC). Misinterpretation as carcinoma metastasis was common, since GFAP expression was absent in the primitive neuronal component, whereas TTF-1 expression was detected in 15/19 cases (79%) based on immunohistochemistry. Apart from mutations in IDH1, TP53, and ATRX, we observed enrichment for alterations in RB1 (n = 19/51, 37%) and MYCN (n = 14/51, 27%). Homozygous CDKN2A/B deletion (n = 1/51, 2%) and CDK4 amplification (n = 3/51, 6%) were relatively rare events. Clinical (n = 31 patients) and survival data (n = 23 patients) indicate a clinical behaviour similar to other CNS WHO grade 4 IDH-mutant astrocytomas, however with an increased risk for leptomeningeal (n = 7) and extra-axial (n = 2) spread. Taken together, ASTRO PNC is defined by a distinct molecular and histological appearance that can mimic metastatic disease and typically follows an aggressive clinical course.

Keywords: MYCN; RB1; Astrocytoma; DNA methylation; IDH-mutant; Primitive neuronal component.

Fig. 1

a The index case presents itself with a small blue round cell morphology with mitotic figures and occasional cell wrapping. b TTF-1 immunohistochemistry is expressed in the tumour cells. c High-molecular-weight cytokeratins were not expressed. d Synaptophysin is expressed. Scale bar denotes 200 µm

Fig. 2

Methylation data: in a tSNE analysis with selected reference entities from our database (n = 310), astrocytoma, IDH-mutant, PNC separates clearly from the other entities. PMMRDIA, primary mismatch-repair-deficient IDH-mutant astrocytoma; MB SHH IDH, medulloblastoma, SHH-activated, IDH-mutant; GBM PNC, glioblastoma, IDH-wildtype, with primitive neuronal component. The methylation class astrocytoma, IDH-mutant, high grade consists of 28 grade 4 tumours and 3 grade 3 tumours. The methylation class astrocytoma, IDH-mutant, low grade consists of 2 grade 4 tumours, 13 grade 3 tumours and 17 grade 2 tumours

Fig. 3

a All cases investigated by histology harbour a primitive neuronal component with small blue round tumour cells. In addition, in this case, cell wrapping (arrow) can be observed. b In most cases, a sharp demarcation of the primitive neuronal component and the astrocytic component can be found. c Presence of tumour growth inside the lumina of two vessels (asterisks). Despite reported extra-axial spread in this tumour entity, this case does not have reported metastases: d some cases present themselves with rosettes (arrows). Scale bar denotes 60 µm in a, b and d. Scale bar denotes 600 µm in c

Fig. 4

a TTF-1: the primitive neuronal component expresses TTF-1 (using TTF-1 clone EP229). In a subset of cases, the expression is limited to a small number of cells. b IDH1 R132H: most tumour cases strongly express IDH1 R132H. c ATRX: nuclear ATRX expression is lost in most of the cases with blood vessels suited as positive internal controls. d GFAP: GFAP expression is lost in the primitive neuronal component. e Olig2: a subset of the primitive tumour cells expresses Olig2. f AE1/3: the tumours do not express high-molecular-weight cytokeratins stained with AE1 and/or AE3. g Ki-67: the proliferation index is high in the primitive neuronal component, whilst in most cases, the glial component does not show an elevated proliferation index. h p53: p53 is strongly expressed in the primitive tumour cells. i Synaptophysin: synaptophysin is expressed in the primitive tumour cells. Scale bar denotes 300 µm

Fig. 5

a Oncoprint of 21 samples for which DNA targeted panel sequencing was performed, including genetic mutations, immunohistochemistry (IHC) and copy number variations calculated from the DNA methylation array. b The copy number summary plot (n = 42) reveals a focal deletion at the RB1 locus in addition to several chromosomal gains and losses

Fig. 6

a Left side: the most common site of origin for primary diagnoses of ASTRO PNC is the frontal lobe followed by the temporal lobe. Right side: for recurrent ASTRO PNC cases, the most common site is the temporal lobe. b The tumours show a predisposition for the male sex. c Age distribution in ASTRO PNC (n = 30, median age = 38). d Kaplan–Meier estimate indicates no significant difference to IDH-mutant astrocytomas WHO grade 4 (p = 0.24). In contrast, there is a significant difference to IDH-mutant astrocytomas WHO grade 2 and 3 (p(A2) = < 0.0001; p(A3) = < 0.0001)