Abstract 4374: Activation mechanism of oncogenic C-helix shifting mutations in BRAF, EGFR, and HER2
Authors: Foster Scott , Whalen Dan , Ozen Aysegul , Wongchenko Matt , Yin JianPing , Yen Ivana , Schaefer Gabriele , Mayfield John , Chmielecki Juliann , Stephens Phil , Albacker Lee , Yan Yibing , Song Kyung , Hatzivassiliou Georgia , Eigenbrot Charles , Yu Christine , Shaw Andrey , Manning Gerard , Skelton Nicholas , Hymowitz Sarah , Malek Shiva 
Published: July 2016

Abstract
Kinase domain mutations are frequent drivers of many different types of cancer. While the effect of hotspot point mutations (such as BRAF V600E or EGFR L858R) is well described, the mechanism of deletion mutations, such as the recurrent EGFR exon 19 deletions is not fully understood. In this work, we have discovered and characterized analogous deletions in BRAF mutant patient samples of varying tumor types, with the highest frequency (15 patients) in pancreatic cancer representing ∼5% of KRAS wildtype patients in this data set. In addition, we have identified additional patients (3) with similar deletions in HER2 that have been previously reported at low frequency in breast cancer. The crystal structure of the most frequent BRAF deletion, molecular modeling of lower frequency BRAF deletions, and extensive molecular modeling in conjunction with molecular dynamic simulations of the most frequent EGFR deletion highlight the commonality of the mechanism of activation of this class of oncogenic alterations. These deletions truncate the loop between the β3 strand and αC-helix (β3-αC loop) of the kinase domain, forcing αC into the active (“in”) conformation, and constitutively activating these kinases. Similar to BRAF V600E mutations, constitutive activity of these BRAF β3-αC deletions is CRAF-independent and dimer-independent. Because these deletions genetically restrict the flexibility of this region of the kinase domain, they render these kinases resistant to inhibitors such as vemurafenib (for BRAF) or lapatinib (for EGFR and HER2) that bind in the αC “out” conformation. Functional characterization of the full spectrum of deletion lengths explains the high prevalence of 5 amino acid deletions in BRAF, EGFR, and HER2 in various cancers, with deletions of this length resulting in the strongest activation of kinase activity likely due to the optimal positioning of αC. This work exploits the selective power of oncogenic mutations to highlight a conserved mechanism of kinase activation and underscores the importance of conformation-specific kinase inhibitors to target mutationally activated kinases in cancer.
Citation Format: Scott Foster, Dan Whalen, Aysegul Ozen, Matt Wongchenko, JianPing Yin, Ivana Yen, Gabriele Schaefer, John Mayfield, Juliann Chmielecki, Phil Stephens, Lee Albacker, Yibing Yan, Kyung Song, Georgia Hatzivassiliou, Charles Eigenbrot, Christine Yu, Andrey Shaw, Gerard Manning, Nicholas Skelton, Sarah Hymowitz, Shiva Malek. Activation mechanism of oncogenic C-helix shifting mutations in BRAF, EGFR, and HER2. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4374.