Molecular and clinicopathologic features of gliomas harboring NTRK fusions

Abstract

Fusions involving neurotrophic tyrosine receptor kinase (NTRK) genes are detected in ≤2% of gliomas and can promote gliomagenesis. The remarkable therapeutic efficacy of TRK inhibitors, which are among the first Food and Drug Administration-approved targeted therapies for NTRK-fused gliomas, has generated significant clinical interest in characterizing these tumors. In this multi-institutional retrospective study of 42 gliomas with NTRK fusions, next generation DNA sequencing (n = 41), next generation RNA sequencing (n = 1), RNA-sequencing fusion panel (n = 16), methylation profile analysis (n = 18), and histologic evaluation (n = 42) were performed. All infantile NTRK-fused gliomas (n = 7) had high-grade histology and, with one exception, no other significant genetic alterations. Pediatric NTRK-fused gliomas (n = 13) typically involved NTRK2, ranged from low- to high-histologic grade, and demonstrated histologic overlap with desmoplastic infantile ganglioglioma, pilocytic astrocytoma, ganglioglioma, and glioblastoma, among other entities, but they rarely matched with high confidence to known methylation class families or with each other; alterations involving ATRX, PTEN, and CDKN2A/2B were present in a subset of cases. Adult NTRK-fused gliomas (n = 22) typically involved NTRK1 and had predominantly high-grade histology; genetic alterations involving IDH1, ATRX, TP53, PTEN, TERT promoter, RB1, CDKN2A/2B, NF1, and polysomy 7 were common. Unsupervised principal component analysis of methylation profiles demonstrated no obvious grouping by histologic grade, NTRK gene involved, or age group. KEGG pathway analysis detected methylation differences in genes involved in PI3K/AKT, MAPK, and other pathways. In summary, the study highlights the clinical, histologic, and molecular heterogeneity of NTRK-fused gliomas, particularly when stratified by age group.

Keywords: Glioma; Methylation; NGS sequencing; NTRK.

Fig. 1

Anatomic distribution of NTRK-fused gliomas: NTRK-fused gliomas are primarily hemispheric, particularly in infant and adult patients. NTRK-fused gliomas in pediatric patients are more diverse in anatomic location. *Includes case involving septum pellicidum

Fig. 2

Representative T1 postcontrast MRI images of a pediatric NTRK-fused glioma treated with targeted TRK inhibitor therapy. (a) Recurrent/residual tumor along the patient’s resection cavity (arrow) demonstrated (b) radiologic response to larotrectinib (arrow)

Fig. 3

NTRK fusions: (Top) Circos plot showing NTRK fusions from all 42 cases in the study cohort. There were a total of 29 unique fusion partners, with several recurrent fusions (BCAN-NTRK1, TPM3-NTRK1, ETV6-NTRK3, ARHGEF2-NTRK1, LMNA-NTRK1, BCR-NTRK2, and TRIM24-NTRK2). (Bottom): The frequencies of NTRK genes involved in the rearrangements varied by age group

Fig. 4

(Top-left) The histologic spectrum of NTRK-fused gliomas can include (a) glioblastoma (GBM), (b) infiltrative low-grade glioma, (c) glioma with anaplastic features and uncertain WHO grade, (d) pilocytic astrocytoma, (e) pleomorphic xanthoastrocytoma, and (f) ganglioglioma. (Top right) Histologic grades of NTRK-fused gliomas: most NTRK-fused gliomas demonstrate high-grade histology, particularly in tumors diagnosed in infant and adult patients. In contrast, the vast majority of NTRK-fused gliomas diagnosed in pediatric patients are of low-grade histology or of uncertain WHO grade. (Bottom) Histologic diagnoses of NTRK-fused gliomas: there were 12 unique histologic diagnoses assigned to NTRK-fused glioma in the study. Slightly less than half of all cases were diagnosed as GBM. Within the infantile and adult age cohorts, the majority of cases were diagnosed as GBM. A more diverse spectrum of tumors was diagnosed in the pediatric age cohort for which there was no single predominant histologic diagnosis

Fig. 5

Oncoprint detailing common molecular alterations in NTRK-fused gliomas and patient clinical characteristics

Fig. 6

Methylation clustering analysis t-distributed stochastic neighbor embedding (tSNE) plots: of the 18 NTRK-fused gliomas with methylation profiling data, only two matched with high confidence to known methylation class families. (a) Case 3 (histologic diagnosis: high-grade glioma with features of pleomorphic xanthoastrocytoma (PXA)) matched to methylation class PXA, and (b) case 14 (histologic diagnosis: glioblastoma) matched to methylation class infantile hemispheric glioma (IHG). LGG, GG, low grade glioma, ganglioglioma; LGG, PA/GG ST, low grade glioma, pilocytic astrocytoma ganglioglioma spectrum in supratentorial compartment

Fig. 7

(a) Heatmap of the top 10,000 differentially methylated genes/probes by NTRK gene involved (blue indicates hypomethylation, and red indicates hypermethylation). (b) KEGG pathway analysis reveals several pathways enriched in the top differentially methylated gene/probes. The dot plots represent the ratio of genes (x-axis) involved in each signaling pathway (y-axis). The size of the dots shows the gene counts, and the color denotes the significance level