Altered global histone-trimethylation code and H3F3A-ATRX mutation in pediatric GBM

Abstract

Mutations in H3.3-ATRX-DAXX chromatin remodeling pathway have been reported in pediatric GBMs. H3.3 (H3F3A) mutations may affect transcriptional regulation by altered global histone-methylation. Therefore, we analyzed yet partly understood global histone code (H3K-4/9/27/36) trimethylation pattern in H3F3A-ATRX mutants and wild-type. H3F3A, HIST1H3B, IDH1, ATRX, DAXX and Tp53 mutations were identified by sequencing/immunohistochemistry in 27 pediatric GBMs. Global histone-methylation H3K-4/9/27/36me3 and Polycomb-protein EZH2 expression were evaluated by immunohistochemistry. H3F3A-ATRX mutation was observed in 66.7 % (18/27) of pediatric GBMs. K27M and G34R-H3F3A mutations were found in 37 % (10/27) and 14.8 % (4/27) patients respectively. G34V-H3F3A, HIST1H3B and IDH1 mutations were absent. Notably, commonest global histone-methylation mark lost was H3K27me3 (17/25, 68 %) followed by H3K4me3 (45.5 %, 10/22) and H3K9me3 (18.2 %, 4/22). Global H3K36me3 showed no loss. Most significant observation was loss of one or more histone-trimethylation mark in 80 % (20/25) pediatric GBMs. Notably, simultaneous loss of H3K27me3 and H3K4me3 were present in 7/22 (31.8 %) of pediatric GBMs. Low expression of EZH2 was found in 12/24 (50 %) of cases. However no significant correlation of loss of histone-marks or EZH2 expression with H3F3A-ATRX mutants (loss of at least one histone-marks in 87.5 % (14/16) cases) versus wild-types (loss of at least one histone-marks in 75 % (6/8) cases) was seen. The present study highlights for the first time combinatorial loss of one or more histone-trimethylation marks associated with majority of pediatric GBMs and the finding suggests significant role of histone-code in the molecular biology that underlies pediatric GBMs. Hence therapies for patients with particular combinations of histone modifications present opportunity to design innovative patient-tailored treatment protocols.

The role of histone modifications and telomere alterations in the pathogenesis of diffuse gliomas in adults and children

“…ATRX or DAXX gene mutations have been reported to co-occur with K27M mutations, yet the frequency of co-occurrence is variable across studies with reported co-mutation rates of 30%–60% [1, 37]. Variability in the coexistence of ATRX and K27M mutations may be explained by location specific differences.…”

“…ATRX mutations frequently occur with G34R/V histone mutations, with reported co-mutation rates ranging from 75% to 100% [1, 37]. Diffuse gliomas arising in the cerebral hemispheres can alternatively harbor mutations in SETD2 , a methyltransferase specific to lysine-36 of the histone 3 tail, making the encoded SETD2 (SET domain containing 2) protein a histone code writer.…”

Mutant ATRX: uncovering a new therapeutic target for glioma

“…Mutations in IDH define a subgroup that is mostly comprised of young adults (median: 40 years, range 13–71 years) and tumors tend to arise in the cerebral hemispheres and frontal cortex [81, 82, 88]. In pediatric non-brainstem HGG (age ≤ 21 years), ATRX mutations are also common, with a frequency ranging between 14–48% [16, 85, 89, 90]. In general, ATRX mutations are found to be significantly associated with a mutation in the tail of the histone H3.3 (H3F3A gene), e.g.…”

“…H3.3G34R/V [16, 89], accounting for 9–15% of pediatric HGG [16, 89, 90, 91], as well as with mutations in TP53 [16, 81, 90] (Figure 3). However, K27M mutation in the H3F3A gene, another frequent genetic alteration in the pediatric landscape (15–33%) [16, 86, 90, 91] which also usually cooccurs with TP53 mutations [16, 81], overlaps less frequently with ATRX mutations (22–60 %) [16, 89] [90]. These two types of histone mutations define two separate groups in terms of their genetic, epigenetic and clinical characteristics [83].…”

Therapeutic Targeting of Histone Modifications in Adult and Pediatric High-Grade Glioma

“…Pathak et al further investigated mutations in the H3.3-ATRX-DAXX chromatin remodeling pathway in pediatric glioblastoma (36). They reported a global loss of histone methylation in 80% of cases, particularly a loss of trimethylation in histones H3K27 and H3K4 (36).…”