Activation Mechanism of Oncogenic Deletion Mutations in BRAF, EGFR, and HER2

Abstract

Activating mutations in protein kinases drive many cancers. While how recurring point mutations affect kinase activity has been described, the effect of in-frame deletions is not well understood. We show that oncogenic deletions within the β3-αC loop of HER2 and BRAF are analogous to the recurrent EGFR exon 19 deletions. We identify pancreatic carcinomas with BRAF deletions mutually exclusive with KRAS mutations. Crystal structures of BRAF deletions reveal the truncated loop restrains αC in an active "in" conformation, imparting resistance to inhibitors like vemurafenib that bind the αC "out" conformation. Characterization of loop length explains the prevalence of five amino acid deletions in BRAF, EGFR, and HER2 and highlights the importance of this region for kinase activity and inhibitor efficacy.

Real-time genomic profiling of histiocytoses identifies early-kinase domain BRAF alterations while improving treatment outcomes

“…Akin to previous publications describing retrospective whole-exome sequencing (7, 9, 10, 24), we found mutations in MAP2K1 and the BRAF V600E point mutation. Additionally, we identified a recurrent novel deletion in BRAF, recently characterized biochemically (Supplemental Figure 2) (21,25). This deletion activates downstream ERK, similarly to BRAF V600E, but is resistant to BRAF V600E inhibitors (21).…”

KRAS: The Critical Driver and Therapeutic Target for Pancreatic Cancer

“…Although found infrequently in PDAC (<2%), BRAF -activating V600E mutations were mutually exclusive with KRAS mutations in PDAC (Witkiewicz et al 2015). The widely studied BxPC-3 PDAC cell line, commonly used as a KRAS WT control in comparison with KRAS -mutant cell lines, harbors an in-frame genomic DNA deletion in BRAF that encodes a constitutively activated and transforming BRAF protein with a five-amino-acid deletion (Chen et al 2016; Foster et al 2016). Database analyses found that similar BRAF deletions were found in 4%–5% of KRAS WT PDAC and were mutually exclusive of BRAF missense mutations.…”

New perspectives for targeting RAF kinase in human cancer

“…BRAF in-frame deletions do not overlap with KRAS or other BRAF mutations 80 , suggesting that they are sufficient to drive ERK signalling hyperactivation in these tumours. The deletions are mapped within the conserved β3/αC-helix loop of the kinase domain of BRAF, and they are predicted to activate the kinase by shortening the β3/αC-helix loop in a fashion analogous to that of in-frame deletions in epidermal growth factor receptor (EGFR) and HER2 (also known as ERBB2), also found in tumours 12 . This shortening of the β3/αC-helix loop results in a unique conformation that locks the αC-helix in the IN position through the formation of an intact K483-to-E501 salt bridge.…”

“…This shortening of the β3/αC-helix loop results in a unique conformation that locks the αC-helix in the IN position through the formation of an intact K483-to-E501 salt bridge. Two recent studies focused on the mechanism of activation of in-frame BRAF deletions and their response to RAF inhibitors 12,80 . Chen et al .…”

“…Point mutations are not the only alterations found in BRAF . Fusion proteins resulting from translocations containing the catalytic domain of BRAF, as well as in-frame deletions are also found in certain tumour types, resulting in constitutive activation of BRAF and downstream ERK signalling 12,13 .…”