Assessment of <i>RAS</i> Dependency for <i>BRAF</i> Alterations Using Cancer Genomic Databases
Authors: Yiqing Zhao, Hanzhong Yu, Cris M. Ida, Kevin C. Halling, Benjamin R. Kipp, Katherine Geiersbach, Kandelaria M. Rumilla, Sounak Gupta, Ming-Tseh Lin, Gang Zheng
Journal: JAMA Network Open (2021)

<h3>Importance</h3> Understanding<i>RAS</i>dependency and mechanisms of<i>RAS</i>activation in non-V600<i>BRAF</i>variant cancers has important clinical implications. This is the first study to date to systematically assess<i>RAS</i>dependency of<i>BRAF</i>alterations with real-world cancer genomic databases. <h3>Objective</h3> To evaluate<i>RAS</i>dependency of individual<i>BRAF</i>alterations through alteration coexistence analysis using cancer genomic databases. <h3>Design and Setting</h3> A cross-sectional data analysis of 119 538 nonredundant cancer samples using cancer genomics databases including GENIE (Genomics Evidence Neoplasia Information Exchange) and databases in cBioPortal including TCGA (The Cancer Genome Atlas) (accessed March 24, 2020), in addition to 2745 cancer samples from Mayo Clinic Genomics Laboratory (January 1, 2015, to July 1, 2020). Frequencies and odds ratios of coexisting alterations of<i>RAS</i>(<i>KRAS</i>,<i>NRAS</i>and<i>HRAS</i>) and<i>RAS</i>regulatory genes (<i>NF1</i>,<i>PTPN11</i>and<i>CBL</i>) were calculated for individual<i>BRAF</i>alterations, and compared according to the current<i>BRAF</i>alteration classification; cancer type specificity of coexisting alterations of<i>RAS</i>or<i>RAS</i>regulatory genes was also evaluated. <h3>Main Outcomes and Measures</h3> Primary outcome measurement is enrichment of<i>RAS</i>(<i>KRAS</i>,<i>NRAS</i>and<i>HRAS</i>) alterations in<i>BRAF</i>variant cancers. Secondary outcome measurement is enrichment of<i>RAS</i>regulatory gene (<i>NF1</i>,<i>PTPN11</i>, and<i>CBL</i>) in<i>BRAF</i>variant cancers. <h3>Results</h3> A total of 2745 cancer samples from 2708 patients (female/male ratio: 1.0) tested by Mayo Clinic Genomics Laboratory and 119 538 patients (female/male ratio: 1.1) from GENIE and cBioPortal database were included in the study. In 119 538 nonredundant cancer samples, class 1<i>BRAF</i>alterations and<i>BRAF</i>fusions were found to be mutually exclusive to alterations of<i>RAS</i>or<i>RAS</i>regulatory genes (odds ratio range 0.03-0.13 and 0.03-0.73 respectively), confirming their<i>RAS</i>independency. Both class 2 and class 3<i>BRAF</i>alterations show variable and overlapping levels of enriched<i>RAS</i>alterations (odds ratio range: 0.03-5.9 and 0.63-2.52 respectively), suggesting heterogeneity in<i>RAS</i>dependency and a need to revisit<i>BRAF</i>alteration classification. For<i>RAS</i>-dependent<i>BRAF</i>alterations, the coexisting alterations also involve<i>RAS</i>regulatory genes by enrichment analysis (for example, S467L shows an odds ratio of 8.26 for<i>NF1</i>, 9.87 for<i>PTPN11</i>, and 15.23 for<i>CBL</i>) and occur in a variety of cancer types with some coalterations showing cancer type specificity (for example,<i>HRAS</i>variations account for 46.7% of all coexisting RAS alterations in BRAF variant bladder cancers, but 0% in non–small cell lung cancers). Variant-level assessment shows that<i>BRAF</i>alterations involving the same codon may differ in RAS dependency. In addition,<i>RAS</i>dependency of previously unclassified<i>BRAF</i>alterations could be assessed. <h3>Conclusions and Relevance</h3> Current<i>BRAF</i>alteration classification based on in vitro assays does not accurately predict RAS dependency in vivo for non-V600<i>BRAF</i>alterations.<i>RAS</i>-dependent<i>BRAF</i>variant cancers with different mechanisms of<i>RAS</i>activation suggest the need for different treatment strategies.