Duplication of 7q34 in Pediatric Low‐Grade Astrocytomas Detected by High‐Density Single‐Nucleotide Polymorphism‐Based Genotype Arrays Results in a Novel BRAF Fusion Gene

Abstract

In the present study, DNA from 28 pediatric low-grade astrocytomas was analyzed using Illumina HumanHap550K single-nucleotide polymorphism oligonucleotide arrays. A novel duplication in chromosome band 7q34 was identified in 17 of 22 juvenile pilocytic astrocytomas and three of six fibrillary astrocytomas. The 7q34 duplication spans 2.6 Mb of genomic sequence and contains approximately 20 genes, including two candidate tumor genes, HIPK2 and BRAF. There were no abnormalities in HIPK2, and analysis of two mutation hot-spots in BRAF revealed a V600E mutation in only one tumor without the duplication. Fluorescence in situ hybridization confirmed the 7q34 copy number change and was suggestive of a tandem duplication. Reverse transcription polymerase chain reaction-based sequencing revealed a fusion product between KIAA1549 and BRAF. The predicted fusion product includes the BRAF kinase domain and lacks the auto-inhibitory N-terminus. Western blot analysis revealed phosphorylated mitogen-activated protein kinase (MAPK) protein in tumors with the duplication, consistent with BRAF-induced activation of the pathway. Further studies are required to determine the role of this fusion gene in downstream MAPK signaling and its role in development of pediatric low-grade astrocytomas.

Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumours

“…We identify additional genetic regions in JPA without 7q34 duplication ( Table 3) and show that most genes within these regions are modulators of the immune system. Specificity of 7q34 duplication to JPA and its prevalence in infratentorial tumours contrast with previous reports alluding that 7q34 duplication may be present in non-JPA LGA (Deshmukh et al, 2008;Pfister et al, 2008;Sievert et al, 2008) and is more frequent in non-cerebellar LGA (Pfister et al, 2008;Sievert et al, 2008). Deshmukh et al showed 7q34 duplication in 8 of 10 cerebellar JPA and further used increased HIPK2 expression on tissue microarray as a surrogate for marker for this genetic event.…”

“…They also show that one sample was classified as a grade II astocytoma; however, the child had prolonged disease-free survival more in keeping with a diagnosis of JPA. This misclassification might also account for the findings of 7q34 duplication in some non-JPA LGA in the study by the other groups (Deshmukh et al, 2008;Pfister et al, 2008;Sievert et al, 2008). The central review of samples by senior paediatric neuropathologists we performed has been shown to increase reproducibility of neuropathologic classification of tumours (Pollack et al, 2003) and may account for increased accuracy in our dataset.…”

“…Recently several consecutive papers described duplication of 7q34 in LGA including JPA (Bar et al, 2008;Deshmukh et al, 2008;Jones et al, 2008;Pfister et al, 2008;Sievert et al, 2008). However, the data reported are conflicting regarding the subgroup of LGA affected by this genetic event, the size of the duplication and its anatomical localisation within the brain.…”

“…Recent reports have indicated a central role for the mitogenactivated protein kinase (MAPK) pathway in the tumorigenesis of pilocytic astrocytomas and showed that duplication at 7q34 leads to a fusion between KIAA1549 and BRAF resulting in constitutive activation of the BRAF kinase (Jones et al, 2008;Sievert et al, 2008). In particular, Jones et al (2008) focused on JPA and describe a tandem duplication at 7q34 producing a transforming BRAF fusion gene in 29 of 44 tumours (66%), and V600E point mutation of BRAF in two further cases.…”

Pilocytic astrocytomas of the optic nerve and their relation to pilocytic astrocytomas elsewhere in the central nervous system

“…[8][9][10][11][12][13] The biologic significance of BRAF duplication lies in the activation of the MAPK pathway, which can drive tumor proliferation. 9 In addition to KIAA1549:BRAF fusion product, other molecular alterations have been reported in pilocytic astrocytoma, including other BRAF fusion products, 14,15 rare BRAF V600E mutations, 16 BRAF insertions, 17 and KRAS mutations.…”