BRAF activating mutations involving the β3-αC loop in V600E-negative anaplastic pleomorphic xanthoastrocytoma
© The Author(s). 2018
Received: 22 February 2018
Accepted: 25 February 2018
Published: 15 March 2018
Genomic alterations in BRAF V600E-negative anaplastic pleomorphic xanthoastrocytoma
Number of cases
Alteration (s) (cases/total tested)
Clinical outcome (s)
Mistry et al., 2015
CDKN2A HD (1/3) TP53 mutation (1/2)
No individual case data available
Phillips et al., 2016
Case 1: NRF1-BRAF (1/2)
Case 2: ATG7-RAF1 (1/2)
CDKN2A HD (2/2)
Case 1: GTR with recurrence, f/u 48 months, deceased
Case 2: GTR with recurrence, f/u 15 months, alive
Alexandrescu et al., 2016
FISH, methylation analysis (450 k)
Gains: + 5, 7, 9q, 12p, 14q, 16q, 22q
Losses: −1, 6, 13q, 14q, 21q
GTR, no recurrence, f/u 10 months, alive
Hsiao et al., 2017
Resection, PFS 6 months, field radiation, contralateral recurrence, STR, progression, chemo with TMZ, stable and alive
Vaubel et al., 2017
Chromosomal microarray (OncoScan)
Gains: + 7 (3/6), + 5 (2/6)
Losses: −22 (4/6), −14 (4/6), − 13 (3/6), − 10 (3/6), −1p (chromothripsis)
CDKN2A HD (5/6)
No individual case data available
Korshunov et al., 2017
Methylation analysis (450 k), targeted sequencing
TERT c.-124C > T (5/20); CDKN2A HD (8/20)
No individual case data available
WES, WGS, transcriptome
Case 1: BRAF p.L485_P490delinsF; FOXO1 p.A38T; HTR2A p.D48N; CDKN2A HD
Case 2: BRAF p.V504_R506dup; KAT6A p.T1210 fs (subclonal)
Gains (case 2): + 5, 6, 7, 10, 12, 15
Losses (case 1): −9, 22
Case 1: near-GTR, A9952 (carboplatin, vincristine), f/u 6 months, alive
Case 2: subtotal resection, chemoradiation with TMZ, alive at last f/u 4 months post-dx
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 . 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]) .
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 . During this process, the αC-helix undergoes an “out” to “in” shift that facilitates interaction with the β3 strand and initiates catalysis  (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 . 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 . Mutations in the R-spine have been shown to stabilize the active state and result in constitutive kinase activation . 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 .
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.
The Venneti lab is supported by grants from NCI K08 CA181475, Mathew Larson, Sidney Kimmel, St Baldrick’s, Claire McKenna, Chad Tough, Doris Duke and Sontag Foundations and the University of Michigan Pediatric Brain Tumor Initiative.
Ethics approval and consent to participate
Sequencing studies were performed at the University of Michigan after approval by our Institutional Review Board.
All authors declare that they have no competing interests.
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