K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas

Abstract

Pediatric glioblastomas (GBM) including diffuse intrinsic pontine gliomas (DIPG) are devastating brain tumors with no effective therapy. Here, we investigated clinical and biological impacts of histone H3.3 mutations. Forty-two DIPGs were tested for H3.3 mutations. Wild-type versus mutated (K27M-H3.3) subgroups were compared for HIST1H3B, IDH, ATRX and TP53 mutations, copy number alterations and clinical outcome. K27M-H3.3 occurred in 71 %, TP53 mutations in 77 % and ATRX mutations in 9 % of DIPGs. ATRX mutations were more frequent in older children (p < 0.0001). No G34V/R-H3.3, IDH1/2 or H3.1 mutations were identified. K27M-H3.3 DIPGs showed specific copy number changes, including all gains/amplifications of PDGFRA and MYC/PVT1 loci. Notably, all long-term survivors were H3.3 wild type and this group of patients had better overall survival. K27M-H3.3 mutation defines clinically and biologically distinct subgroups and is prevalent in DIPG, which will impact future therapeutic trial design. K27M- and G34V-H3.3 have location-based incidence (brainstem/cortex) and potentially play distinct roles in pediatric GBM pathogenesis. K27M-H3.3 is universally associated with short survival in DIPG, while patients wild-type for H3.3 show improved survival. Based on prognostic and therapeutic implications, our findings argue for H3.3-mutation testing at diagnosis, which should be rapidly integrated into the clinical decision-making algorithm, particularly in atypical DIPG.

Fig. 1

K27M-H3.3 is associated with worse overall survival and higher age of diagnosis in DIPG. a Kaplan–Meier curve of overall survival for all DIPG patients (n = 39). b DIPG patients carrying K27M-H3.3 mutation have worse overall survival compared to patients wild-type for this histone as determined by Kaplan–Meier analysis (Log-rank, p = 0.0027). Notably, all long term survivors were wild-type for H3F3A. c Age distribution of DIPG patients based on K27M-H3.3 mutational status. DIPG patients mutated for K27M-H3.3 have a higher age of diagnosis 8.13 years (±3.75) as compared to wild-type patients [4.57 years (±4.07), p = 0.010]

Fig. 2

K27M-H3.3 is prevalent in DIPG and is associated with ATRX mutations mainly in older children. a Distribution of DIPG and supratentorial GBM based on H3.3 mutations suggests prevalence of K27M-H3.3 in DIPG. ATRX mutations in DIPG (b) and all location pediatric GBM (c) are significantly more prevalent in tumors from older children (mean ages 11.82 (±1.18) years and 16.91 ± 2.11, respectively) as compared to children with no ATRX mutation (mean ages of 5.20 (±0.81) years and 8.00 ± 0.69, respectively) (p = 0.02 and p < 0.0001, respectively)

Fig. 3

Whole chromosome view of copy number alterations (CNA) in K27M-H3.3 mutants and wild-type DIPG samples. a Similarities in CNA between both groups included loss of 10q, 11p, 13q and 14q as well as gains of 1q and 19q. However, major differences in copy number were identified with samples wild-type for K27M-H3.3 exhibiting gains of chromosome 2p and 7p as well as losses of chromosome 9p and 12q while samples mutants for K27M-H3.3 commonly exhibited loss of chromosome 5q, 6q, 17p and 21q. b Focal recurrent amplifications determined by GISTIC 2.0 analysis (q ≤ 0.05) show significant differences in focal gains between samples carrying K27M-H3.3 and samples wild type for H3.3. This included PDGFRA (4q12), MYV/PVT1 locus (8q24.21) gains and amplifications, which were exclusively identified in K27M-H3.3 mutants and ASAP2 (2p25.1) and MYCN (2p24.3) gains and amplifications which were exclusively identified in wild-type patients