The Diagnostic Role and Clinical Relevance of Determination of BRAF Status in Brain Tumors

Marco Gessi; Torsten Pietsch


Personalized Medicine. 2013;10(4):405-412. 

In This Article

BRAF Alterations in Brain Tumors: Different Diagnostic Relevance of BRAFV600E & BRAF Fusions in Routine Neuropathology

BRAF mutations are common in a wide spectrum of brain tumors, including in gliomas and glioneuronal tumors.[15,16]BRAFV600E mutations have been found in approximately 10–15% of pilocytic astrocytoma (Figure 1A)[15–17] and in approximately 5–10% of pediatric diffusely infiltrating gliomas, including diffuse astrocytomas (WHO grade II), anaplastic astrocytomas (WHO grade III) and glioblastomas (WHO grade IV),[15–17] but in less than 2% of comparable adult gliomas.[4,18] Mutations have been also identified in gangliogliomas, as well as in pleomorphic xanthoastrocytomas (PXA). Among ganglioglioma, the incidence of BRAFV600E mutations varied from 30 to 60%[15–17] and the mutated protein seems to be predominantly localized to the neuronal compartment.[19] In PXA, the incidence of BRAF mutations is approximately 60%[20,21] and appears to be age related. In a recent study, BRAFV600E -activating mutations have also been revealed in a subgroup of dysembryoplastic neuroepithelial tumors.[22]

Figure 1.

BRAF alterations in the tumors of the CNS.
(A) Frequency of BRAFV600E mutations in HGG, GG, PXA and PA, respectively (left). In these tumors, BRAFV600E (GTG→GAG: Val→Glu) mutations can be identified using a pyrosequencing-based method as well as by immunohistochemistry with anti-BRAFV600E-mutated protein monoclonal Ab VE-1 (right). (B) Pilocytic astrocytomas frequently present BRAF–KIAA1549 fusion, as illustrated by FISH analysis (above), which shows overlapping signals indicative of fusion (yellow signal), as well as by real-time PCR and sequencing (below), corresponding to a KIAA1549–BRAF ex 16–ex 9 fusion.
Ab: Antibody; ex: Exon; GG: Ganglioglioma; HGG: High-grade glioma; PA: Pilocytic astrocytoma; PXA: Pleomorphic xanthoastrocytomas.
The sequence showing KIAA1549–BRAF ex 16–ex 9 fusion was kindly provided by M Badiali; the FISH image is reproduced with permission from[69] © Springer Science + Business Media.

Interestingly, primary melanocytic tumors of the CNS do not show BRAF mutations. Similar to eye melanomas, they present alternatively frequent GNAQ- and GNA11-activating mutations.[23]

Pilocytic astrocytomas, the most common glioma subtype in children and young adults, represent, among brain tumors, the neoplasms that more frequently show constitutive activation of the MAPK pathway,[24] which could result from NF1, RAF 1, BRAF and N-RAS mutations.[1,24–27]BRAF activation in pilocytic astrocytomas results more commonly from gene duplication than from point mutations.[28–30] Duplications lead to a fusion between the KIAA1549 and BRAF genes. Fusions have been identified in 60–80% of cerebellar pilocytic astrocytomas.[31–33] Genomic sequencing has revealed a few breakpoint variants (KIAA1549 exon 16–BRAF exon 9, KIAA1549 exon 15–BRAF exon 9, KIAA1549 exon 16–BRAF exon 11 and the recently discovered exon 19–BRAF exon 9, and KIAA1549 exon 18–BRAF exon fusions) (Figure 1B).[31,33] The common effect of these breakpoint variants is the formation of an oncogenic BRAF–KIAA1549 fusion incorporating the BRAF kinase domain but lacking the N-terminal autoinhibitory domain.[31,32,34] This truncated BRAF is constitutively active. BRAF duplication or fusion events also occur frequently in pilomyxoid astrocytomas, suggesting that pilocytic and pilomyxoid astrocytomas may be part of a single disease spectrum.[33,35,36] In addition, other types of tandem duplication with inframe oncogenic fusions of BRAF or other serine/threonine kinase proteins (e.g., FAM131B–BRAF and SRGAP3–RAF1) have also been rarely described in pilocytic astrocytomas.[37,38] Tandem duplications and BRAF point mutations are mutually exclusive and do not occur in the same frequency in pilocytic astrocytomas at all sites in the CNS. Cerebellar pilocytic astrocytomas harbor frequent BRAF–KIAA1549 fusion (ranging from 60 to 90% according to various reports) in comparison with BRAF mutations more frequently observed in tumors outside the posterior fossa.[24,35,39,40] Furthermore, BRAF fusions seem to be less frequent among pilocytic astrocytomas affecting older patients and adults.[41]

Although several studies have confirmed a strong association between pilocytic astrocytoma histology and BRAF fusions, some exceptions exist.[3,33,36,42,43] The reports of rare cases with fusions in diffuse astrocytomas[29,35,36] and other nonpilocytic lesions suggest that such molecular changes involving BRAF are very common in pilocytic astrocytomas, but are not absolutely specific for these tumors. BRAF fusions have also been recently identified in only few diffusely infiltrating gliomas of adulthood with the concomitant presence of IDH-1 mutations.[44,45] Taken together, the evidence of a BRAF–KIAA1549 fusion in a glioma of uncertain or doubtful histology strongly points toward the diagnosis of a pilocytic astrocytoma, but it does not prove the diagnosis of pilocytic astrocytoma. The identification of BRAF–KIAA1549 fusion can be very helpful, in particular, in the case of a supratentorial tumor, in order to distinguish pilocytic astrocytoma from other diffuse infiltrating gliomas; unfortunately, adult and supratentorial cases show a significantly lower frequency of BRAF–KIAA1549 fusions than cerebellar pilocytic astrocytomas. The BRAF fusion status is to be discussed further in light of neuroradiology and, when available, of the status of molecular markers for pediatric high-grade glioma (e.g., H3.3 K27M mutation).[43,46]

Given the high frequency of BRAF mutation in several different CNS tumor entities, BRAFV600E testing may also add limited additional information to the differential diagnosis of primary brain tumors.[16,43,47] In pediatric gliomas, the presence of BRAFV600E mutation is not quite as helpful as BRAF fusion in differentiating noninfiltrative from infiltrative gliomas, particularly if the differential diagnosis is between a ganglioglioma and a diffuse glioma.[4]BRAF mutational analysis can be of clinical value in tissue samples of melanoma brain metastases from patients with unknown mutation status in order to identify cases suitable for treatment with specific inhibitors (see below).[47] The BRAF status has been shown to not vary between different tumor manifestations of the same patient.[47]

The prognostic significance of the presence of BRAF–KIAA1549 fusion in patients with pilocytic astrocytomas is still unclear, although a few studies have found no differences in survival between tumors with and without BRAF duplication/fusion.[24,33,34,48,49] The prognostic significance of BRAF mutations in patients with high-grade gliomas, with anaplastic gangliogliomas or PXA with anaplastic features, is indeed yet to be determined in larger case series.[20,21]