The efficacy of therapeutic targeting oncogenically activated kinases in BRAF-mutant cancers depends on structural variations in the kinase domain. For example, the BRAF V600E mutation is often sensitive to kinase inhibitors such as vemurafenib, while β3-αC deletions and non-canonical BRAF mutations are often resistant to this small molecular inhibitor [2]. Therefore, from a therapeutic aspect, it is imperative to define the spectrum of BRAF alterations in these aggressive tumors. Here, we report two newly identified A-PXAs with activating mutations in the β3-αC loop of the BRAF kinase domain discovered through whole-exome, whole-genome, and transcriptome sequencing (Michigan Oncology Sequencing Project [MI-ONCOSEQ]) [8].

The first case is a 5-year-old male presenting with a large (11.7 × 7.3 cm) temporoparietal mass with subfalcine and uncal herniation (Fig. 1a). Molecular profiling revealed an oncogenic BRAF in-frame deletion (p.L485_P490delinsF) located adjacent to the β3-αC loop that results in a helix-constraining conformational change in the kinase domain. The second case is a 23-year-old male with a parietal ring-enhancing cystic mass. Sequencing revealed a novel 9 bp tandem duplication (p.V504_R506dup) in the β3-αC loop that results in a three codon in-frame insertion in the open reading frame (ORF) of BRAF [see Fig. 1a-d and Online Resource for details and representative images from both cases (Additional file 1)]. Consistently, both cases demonstrated MAPK activation with strong expression of phospho-ERK1/2 in tumor cells (Fig. 1g).

Both of the mutations reported here affect the β3-αC loop in the kinase domain. To function properly, protein kinases must maintain a level of structural flexibility in order to switch between inactive and active states. This conformational change involves two regulatory regions in the catalytic domain: the activation segment and the αC-helix [2]. During this process, the αC-helix undergoes an “out” to “in” shift that facilitates interaction with the β3 strand and initiates catalysis [2] (Fig. 1e). Case #1 demonstrated a deletion mutation in the BRAF β3-αC loop that results in a shortened αC-helix that constrains the loop conformation to a constitutively kinase active “in” state. Similar “in” state activating alterations have been reported in other major signaling pathway kinases including HER2 and EGFR [2]. β3-αC deletion mutations render tumors resistant to small molecule inhibitors, such as vemurafenib, that bind to and inhibit kinases with an “out” conformation, but are ineffective against the “in” state [1, 2] (Fig. 1e, f). Case #2 contained a mutation in a structural element (R-spine) of the αC-helix [9]. Mutations in the R-spine have been shown to stabilize the active state and result in constitutive kinase activation [3]. However, the effect of this mutation on the conformational state of the kinase domain remains to be determined. Because RAF dimers are often formed in tumors with β3-αC kinase loop alterations, RAF dimer inhibition has been proposed as an alternative therapy for these genetic alterations [10].

Recent reports of clinical responses in V600E-mutated A-PXAs with BRAF “out” inhibitors [5, 7] have been encouraging. However, selection of effective targeted therapies requires a mechanistic understanding of oncogenic kinase activation in tumors. We present two A-PXAs that contain BRAF β3-αC loop alterations that may not be sensitive to traditional BRAF inhibitors. Therefore, treatment approaches for A-PXAs with or without V600E mutations may differ depending on the specific type of BRAF genetic alteration.