Genetic Overview of Brainstem and Thalamic Gliomas

Until recently, very little was known about the genetic alterations involved in brainstem gliomas, perhaps mainly due to their inaccessible location and the difficulty of acquiring sufficient tissue for genetic analysis.

On June 1, 2014, an unprecendentedly detailed overview of the genetic alterations involved in adult and childhood brainstem and thalamic gliomas was published online, and later in the July 2014 edition of Nature Genetics (1). The study, called Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas was a collaborative effort involving researchers mainly located in Beijing China and Duke University in the USA. Somatic mutations and copy number alterations were detected by whole-exome sequencing in 14 brainstem and 12 thalamic gliomas. Targeted Sanger sequencing of the IDH1, TP53, H3F3A, and PPM1D genes was then performed on an additional 24 brainstem and thalamic gliomas. In total, 33 brainstem and 17 thalamic gliomas were investigated.

A major new discovery of this study was the detection of PPM1D mutations in a significant fraction of brainstem gliomas. This mutation always co-occurred with the H3F3A mutation. Nearly all H3F3A mutated brainstem and thalamic gliomas were also mutated in either TP53 (brainstem and thalamic cases) or PPM1D (only in brainstem cases). Another major disovery is that IDH1 mutations are not at all rare in adult brainstem gliomas, though many of these are alternative mutants, such as R132C and R132L, which will not be detected by immunohistochemistry using R132H antibodies.

Mutation statistics

Adult brainstem glioma

The brainstem consists of the midbrain, pons, and medulla. Though in the main study no information is given on patient age of the samples, tables in the Supplementary Infomation show the ages of all the patients involved in the study and complete mutational profiles of the 26 whole-exomed sequenced gliomas are listed.

While previously it was thought that IDH1 mutations were rare in brainstem gliomas, this study shows that in adult cases, IDH1 mutations are not at all rare. It must be remembered that alternative IDH1 mutations other than R132H can only be detected by DNA sequencing, and not by immunostaining with R132H antibodies.

In all, 13 adult brainstem gliomas were whole-exome sequenced. The ages of these patients ranged from 20 to 53. Of these 13 cases:

  • 5 (38%) were IDH1 mutated. There were three IDH1 R132H mutations, one R132C, and one R132L mutation. All of these cases also had mutant TP53, and four of the cases had mutant ATRX. Genetically, this group resembles classic IDH1 mutant cerebral astrocytomas, which also usually harbour mutations in the TP53 and ATRX genes. Mean age of these five patients was 40 and the predominant tumour location was in the pons, with all five having a pontine location, four of which were located both in the pons and medulla. Histopathology was oligoastrocytoma grade 2 or 3 in four cases and GBM in one.
  • 7/13 (54%) were H3F3A mutated. This mutation was always a K27M mutation, which is very commonly found in gliomas of childhood. Each of these seven cases additionally harboured a mutation in either TP53 (four cases) or PPM1D (3 cases). One of these cases carried a mutation in PDGFRA (in addition to PPM1D). One had a mutation in NF1 (in addition to PPM1D). Mean age of these adult patients was 29, and the predominant location was in the medulla (four cases) and midbrain (2 cases). Two of the cases had dual location in the medulla and pons. Notably, while all the IDH1 mutant cases had a pontine location, only 2/7 of the H3F3A mutant cases had a pontine location, and the H3F3A mutant cases tended to be younger on average. Histopathology in this group was oligoastrocytoma (two cases), astrocytoma (two cases), oligodendroglioma (one case), and glioblastoma (two cases).
  • Only one of the 13 adult brainstem gliomas (8%) had neither an IDH1 mutation, nor a H3F3A mutation. This was a 53 year old woman with a grade 2 oligoastrocytoma of the thalamus and midbrain. This case was found to have a mutation in NF1, CDKN2A and FGFR1.
  • Based on this detailed evidence, if an adult brainstem glioma patient has a biopsy which does not stain positive for IDH1 R132H, DNA sequencing should be done on the IDH1 gene (to test for alternative IDH1 R132 mutations) and the H3F3A gene, if sufficient tissue is available for testing. These two mutations will stratify the majority of adult brainstem gliomas into one of two groups. Remarkably, IDH1 mutations lead to DNA hypermethylation throughout the genome, while H3F3A mutant tumours are associated with DNA hypomethylation. So while both of these tumour types have a significant epigenetic basis, opposite strategies will be required to target the opposite DNA methylation status of these two groups. Looking at all 50 cases included in this study (childhood, adult, brainstem and thalamic gliomas), the IDH1-mutant cases had a significantly better median survival than the IDH1 wild-type cases.

    Adult thalamic gliomas

    Unlike adult brainstem gliomas, which are frequently IDH1 mutant, adult thalamic gliomas do not show mutations in IDH1, but usually have H3F3A K27M mutations. Looking at two different studies (1, 2), there were ten adult thalamic gliomas, median age 25.5 years (range 22-53). Eight of ten (80%) had H3F3A K27M mutations. Of those eight, all had also TP53 mutations. Of the two patients without an H3F3A mutation, one was a 53 year old woman (described above in the adult brainstem section) with an oligoastrocytoma grade 2 of the thalamus and midbrain. The other was a 41 year old whose glioblastoma had mutations in TP53, cyclin D3, the RB1 tumour suppressor, and PTEN (another tumour suppressor). The median age of the eight patients with mutant H3F3A was 24 (range 22-48), while the two patients without mutant H3F3A were aged 41 and 53.

    Childhood thalamic gliomas

    Reviewing the same two studies (1, 2) the mutational status of thalamic gliomas of childhood is surprisingly uniform. Of ten cases, all had the same H3F3A K27M mutation. Seven cases also had a TP53 mutation. Mean age of these 10 young patients was 10.6 years (range 6-15). The 15 year-old thalamic astrocytoma grade 2 also had a mutation of the PDGFRA gene, likely leading to increased proliferative PDGF signaling. As discussed above, mutations in H3F3A are associated with DNA hypomethylation, unlike mutations in IDH1 which lead to hypermethylation.

    An genetic overview of childhood brainstem glioma (usually diffuse intrinsic pontine glioma) will be added upon request.

    1. Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas. Zhang et al. 2014.
      READ ABSTRACT Email me for a PDF copy of the study and Supplementary Information
    2. Hotspot Mutations in H3F3A and IDH1 Define Distinct Epigenetic and Biological Subgroups of Glioblastoma. Sturm et al. 2012.