Activating mutations in BRAF characterize a spectrum of pediatric low-grade gliomas

Abstract

In the present study, DNA from 27 grade I and grade II pediatric gliomas, including ganglioglioma, desmoplastic infantile ganglioglioma, dysembryoplastic neuroepithelial tumor, and pleomorphic xanthoastrocytoma was analyzed using the Illumina 610K Beadchip SNP-based oligonucleotide array. Several consistent abnormalities, including gain of chromosome 7 and loss of 9p21 were observed. Based on our previous studies, in which we demonstrated BRAF mutations in 3 gangliogliomas, 31 tumors were screened for activating mutations in exons 11 and 15 of the BRAF oncogene or a KIAA1549-BRAF fusion product. There were no cases with a KIAA1549-BRAF fusion. A BRAF V600E mutation was detected in 14 of 31 tumors, which was not correlated with any consistent pattern of aberrations detected by the SNP array analysis. Tumors were also screened for mutations in codon 132 in exon 4 of IDH1, exons 2 and 3 of KRAS, and exons 2-9 of TP53. No mutations in KRAS or TP53 were identified in any of the samples, and there was only 1 IDH1 R132H mutation detected among the sample set. BRAF mutations constitute a major genetic alteration in this histologic group of pediatric brain tumors and may serve as a molecular target for biologically based inhibitors.

Fig. 1.

Illumina BeadStudio results for case 04-234. (A) Chromosome 1 shows a split in the B allele frequency and increase in the log R ratio at 1q44 consistent with a duplication. (B) Chromosome 9 shows a number of abnormalities. At 9p21.3-pter there is a normal log R ratio with a split in the B allele frequency consistent with a CN LOH. There is also a significant decrease in the log R ratio consistent with a homozygous deletion at 9p21.3. At 9p21.3-21.2, the log R ratio is decreased and the B allele frequency is split, consistent with a heterozygous deletion. (C) Chromosome 12 shows a split in the B allele frequency and an increase in the log R ratio at 12q21.1-21.2. A small deletion in 12q21.33 is a normal population variant.

Fig. 2.

Summary of chromosomal abnormalities in 20 tumors detected by SNP array analysis. Results for case 95-56 have been shown separately due to the large number of abnormalities detected.

Fig. 3.

Immunohistochemical expression of p-ERK in tumors with and without a BRAF mutation. GG case 05-253 (A) has a BRAF mutation, however p-ERK (B) is expressed only in the cytoplasm of rare neoplastic cells. In contrast, GG/DNT case 00-358 (C) without a BRAF mutation, demonstrates diffuse cytoplasmic expression of p-ERK only in the glial component (D) while the “free floating” neurons are negative (inset). Similarly, DIG case 06-223 (E) without a BRAF mutation, is strongly and diffusely reactive for p-ERK (F). A, B, E, and F magnification x200, C and D magnification x400, insets magnification x600.