A new NFIA:RAF1 fusion activating the MAPK pathway in pilocytic astrocytoma

Abstract

Pilocytic astrocytoma (PA) is one of the most common brain cancers among children and activation of the Mitogen-Activated Protein Kinase (MAPK) pathway is considered the hallmark. In the majority of cases, oncogenic BRAF fusions or BRAF V600E mutations are observed, while RAF1 or NF1 alterations are more rarely found. However, in some cases, no apparent cancer driver events can be identified. Here, we describe a novel fusion between the transcription factor nuclear factor 1A (NFIA) and Raf-1 proto-oncogene (RAF1) in a 5-year old boy with PA. The novel fusion was identified as part of a comprehensive genomic tumor profiling. We show that the NFIA:RAF1 fusion results in constitutive Raf1 kinase activity, leading to activation of downstream MEK1/2 cascade and increased proliferation of cancer cells. The NFIA:RAF1 fusion displayed distinct subcellular localization towards the plasma membrane indicative of Raf-1 activation, in contrast to both wild type NFIA and Raf-1, which were localized in the nucleus and cytoplasm, respectively. In conclusion, our data support the existence of rare oncogenic RAF1 fusions with constitutive Raf-1 activity. This highlights the need for broad genetic testing in order to refine diagnostics of PA and to unravel potential treatment options, e.g. with MEK inhibitors.

Nuclear factor one transcription factors as epigenetic regulators in cancer

“…Consistently, NFIs as fusion proteins appear to increase the activity of their respective fusion partners' downstream signalling pathways, but do not appear to effect NFI regulatory target gene expression . Fusion proteins have been reported with transcription factors (NFIB‐MYB), chromatin modifying complexes (NFIA‐CBFA2T3) and kinases (NFIA‐RAF1) and usually contain only a partial form of NFI . Studies discussed previously in this review highlight NFIs role in forming chromatin domain barrier/boundaries that block the propagation of silencing signals emanating from heterochromatic silent regions within the telomere .…”

The novel RAF1 mutation p.(Gly361Ala) located outside the kinase domain of the CR3 region in two patients with Noonan syndrome, including one with a rare brain tumor

“…RAF1 mutations have mostly been found in large bowel and skin cancer, but only once in glioma (COSMIC database). However, it is well established that rearrangements of RAF1 with for example SRGAP3 , NFIA , ATG7 , or QKI most likely lead to hyperactivation of RAF1 and, therefore, play a role as somatic events in pilocytic and low grade astrocytomas, or low grade gliomas (Jones et al, ; Phillips et al, ; Yde et al, ; Zhang et al, ). Development of two independent childhood tumors in patient 1 is very unusual for NS, but as a single observation it is still insufficient to support the hypothesis that the c.1082G>C/p.…”

Targeting Alterations in the RAF–MEK Pathway

“…RAF1 fusions are observed in some cancers, typically resulting (much like BRAF fusions) in an aberrant gene product fusing the C-terminal CRAF kinase domain to an N-terminal fusion partner with a dimerization domain that leads to RAS-independent dimerization and activation of CRAF kinase activity. These fusions are found in low-grade pediatric gliomas, prostate cancer, melanoma, and pancreatic cancer (26,(31)(32)(33).…”