Frequent Gains at Chromosome 7q34 Involving BRAF in Pilocytic Astrocytoma

Abstract

Relatively little is known about the molecular changes that promote the formation or growth of pilocytic astrocytomas. We investigated genomic alterations in 25 pilocytic astrocytomas, including 5 supratentorial and 20 posterior fossa tumors, using oligonucleotide array comparative genomic hybridization. Large changes were identified in 7 tumors and included gains of chromosomes 5, 6, and 7 and losses of chromosomes 16, 17, 19, and 22. The most common alteration was a 1.9-MB region of low-level gain at chromosome 7q34 identified in 17 of 20 posterior fossa tumors. In most tumors, the region of gain ended within the BRAF locus and encompassed only exons that encode the BRAF kinase domain. We confirmed copy number increase at the 7q34 locus using quantitative polymerase chain reaction with primers adjacent to the HIPK2, RAB19B, and BRAF genes. Western blot analysis revealed that 3 of 6 pilocytic astrocytomas with 7q34 gain contained high levels of phosphorylated extracellular signal-related kinase (ERK) and nitrogen-activated protein kinase/ERK kinase (MEK), while 1 tumor lacking 7q34 gain and 2 normal brain specimens did not. Immunohistochemical stains of a tissue microarray containing 43 pilocytic astrocytoma identified ERK phosphorylation in 35 (81%). These data indicate that focal gains at chromosome 7q34 and increased BRAF-MEK-ERK signaling are common findings in sporadic pilocytic astrocytomas.

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

“…8,9,18,20 Our molecular analysis of BRAF in pilocytic astrocytoma of the optic nerve showed KIAA1549:BRAF fusion and BRAF V600E point mutation, which further supports the presence of BRAF alterations in pilocytic astrocytoma. However, the rate of BRAF fusion in pilocytic astrocytoma of the optic nerve was significantly lower than for posterior fossa pilocytic astrocytoma (optic nerve, 38%; posterior fossa, 84%; P ¼ 0.011, Fischer's exact test).…”

“…[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. 18 This list further highlights the critical importance of the MAPK pathway in these tumors.…”

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

“…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.…”

Intratumoral patterns of clonal evolution in gliomas

“…Such profiles were consistent with tetraploidy and less frequently, with chromosome 7 gains in the absence of losses of chromosomes 9p21 and 10q23, immediately followed by tetraploidization in subsequent tumor cell clones. Based on these observations, it could be hypothesized that early occurrence of tetraploidization in association with duplication of the BRAF gene in pylocytic astrocytomas [43,44] could prevent histopathological grade I/II astrocytomas from evolving into an invasive phenotype and a highly progressive clinical behavior tied to aggressive histopathological features; this could be due to the fact that p16/p14 ARF and chromosome 10q losses that occur after tetraploidization would have a more limited impact in the aggressiveness of the tumor because at least one copy of each allele of these genes would still be retained. In line with this, a tetraploidy checkpoint has been associated with prevention of tumor progression among gliomas [45,46] and these cytogenetic profiles were also much less frequently observed among high-grade gliomas, where acquisition of multiple cytogenetic abnormalities leading to relatively complex cytogenetic profiles, typically preceded tetraploidization.…”