Abstract 3254: Multiomics detect potential mechanisms of resistance to BRAF targeted therapy in patients with BRAFV600E mutated solid tumors
Authors: Eriksen Martina , Nielsen Annelaura Bach , Mundt Filip , Duel Josephine Kerzel , Mann Matthias , Lassen Ulrik , Yde Christina Westmose , Qvortrup Camilla , Højgaard Martin , Spanggaard Iben , Rohrberg Kristoffer Staal 
Published: June 2022

Abstract
Purpose: The purpose of this study was to identify mechanisms of resistance to BRAF targeted therapy using proteomics together with genomics and transcriptomics in patients with BRAFV600E mutated solid tumors.
Experimental procedures: A total of nine patients with BRAFV600E mutated advanced solid tumors (5 with colorectal cancer, 2 with neuroendocrine carcinoma, 1 with cholangiocarcinoma and 1 with breast cancer) treated with BRAF targeted therapy (BRAF inhibitor in combination with either MEK inhibitor and/or EGRF antibody) as part of the Copenhagen Prospective Personalized Oncology study, were included in this study. Tumor biopsies at baseline and at disease progression were analyzed with whole exome/genome sequencing (WES/WGS), transcriptomics (RNA sequencing) and proteomics. Genomic variants were analyzed together with changes in protein expression. Three filtering steps were used to identify potential resistance mechanisms from the proteomics measurements. Proteins were filtered for 1) proteins with a high shift in abundance between baseline and progression 2) proteins with known associations to the patient’s primary cancer based on text-mining and 3) proteins in pathways where BRAF is also involved.
Results: Alterations conferring resistance were identified in 2 out of 9 patients when comparing data from WES/WGS and RNA sequencing at baseline and at disease progression (one patient with PTBP2-BRAF fusion and one with NRAS mutation). Genomic or transcriptomic alterations conferring resistance were not detected in the remaining 7 patients. Notably, there was not a single protein shared between all 9 patients after our filtering, but when comparing overlap on pathway level, six pathways related to RAF and MAPK signaling were affected in all 9 patients. Particularly, paradoxical activation of RAF signaling seems to be an interesting candidate to explain resistance, where formation of RAF dimer structures happens as a response to treatment with BRAF inhibitors, selectively inhibiting BRAF monomer structures (i.e. BRAFV600E).
Conclusion: With a multiomic approach using proteomics together with genomics and transcriptomics, potential mechanisms of resistance were detected in all patients at disease progression, where resistance to BRAF targeted therapies had occurred. Six mechanisms of resistance were shared independently of diagnosis and BRAF inhibitor combination regimes. The potential of integrating proteomics with genomics and transcriptomics is promising and may potentially guide therapy for future patients with treatment resistant BRAFV600E mutated solid tumors.
Citation Format: Martina Eriksen, Annelaura Bach Nielsen, Filip Mundt, Josephine Kerzel Duel, Matthias Mann, Ulrik Lassen, Christina Westmose Yde, Camilla Qvortrup, Martin Højgaard, Iben Spanggaard, Kristoffer Staal Rohrberg. Multiomics detect potential mechanisms of resistance to BRAF targeted therapy in patients with BRAFV600E mutated solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3254.