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American Society of Clinical Oncology, Journal of Clinical Oncology, 16_suppl(40), p. e17005-e17005, 2022

DOI: 10.1200/jco.2022.40.16_suppl.e17005

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Pan-cancer analysis of BRAF alterations and tumor-specific mechanisms of activation.

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Data provided by SHERPA/RoMEO

Abstract

e17005 Background: BRAF is a proto-oncogene that is altered in various cancers and is a druggable target. Particularly, the selective BRAF kinase inhibitors Dabrafenib and Vemurafenib are FDA approved for melanoma and thyroid cancer that harbor the activating BRAF V600 hotspot mutations. In pre-clinical studies, activated BRAF promotes tumor cell function across many additional cancer types in which therapeutics have not been considered. We propose that identifying BRAF-activated cancers will guide future pre-clinical investigations and potentially expand the usage of existing BRAF-targeting therapeutics. Methods: We utilized bioinformatics to investigate the molecular profiles of pan-cancer cohorts from two platforms based on distinct sequencing technology. This included a custom curated dataset (whole exome, 6 studies, 39 cancer types, n = 12,019) and GENIE9.1 (targeted gene panel, 62 cancer types, n = 78,619). Studies were included based on genomic modalities (copy number alterations, mutations, gene fusions). We cataloged the frequency and all types of BRAF genomic alterations pan-cancer. We also examined other genomic features, including tumor mutational burden (TMB) and fraction of the genome altered (FGA), and their association with types of BRAF alterations across cancer types. Results: In both platforms, we found that BRAF alterations were observed across over 80% of cancer types. Melanoma, thyroid, and colorectal tumors exhibited the greatest rates of mutations. Regarding gene body rearrangements, we noted endocrine-driven cancers including ovarian and metastatic prostate tumors (mPC) exhibited relative robust rates of amplification. In addition, thyroid carcinoma and mPC harbored recurrent BRAF gene fusion events. In mPC, we found that the BRAF gene fusions often included an N-terminus gene fragment from known androgen-target genes (TMPRSS2 and SND1). These fusion events represented a dysregulated hormone-driven mechanism of BRAF activation. We also found that hotspot missense mutations were cancer-type specific, including K601 hotspots in mPC, G469 hotspots in non-small cell lung cancers, and G466 hotspots in ovarian cancers. Lastly, BRAF-amplified endocrine tumors harbored a 1.5-fold increase in FGA medians, whereas BRAF-mutated lung and colorectal tumors exhibited a 1.6-fold increase in TMB medians. Conclusions: Our molecular analysis revealed that cancers accrued activated BRAF through cancer-type-specific and divergent genomic mechanisms. These molecular features provide genomic evidence to expand the application of BRAF-targeted therapies in additional cancer lineages, including mPC. BRAF mutations were also associated with genomic biomarkers, such as TMB, which may predict response to immune therapies. This suggests that BRAF alterations can be considered as an additional feature to aid therapy selection.