Association of class II and III BRAF mutations with EGFR blockade therapy response and representation of molecularly distinct subgroups of BRAF mutations in MMR proficient CRC.
Authors: Sahin Ibrahim Halil , Xiu Joanne , Khushman Moh'd M. , Palumbo Emily , Weinberg Benjamin Adam , Akce Mehmet , Singhi Aatur D. , Bell Phoenix D. , Kasi Anup , Shields Anthony F. , Oberley Matthew James , Sledge George W. , Shen John Paul Y.C. , Saeed Anwaar , Tejani Mohamedtaki Abdulaziz 
Published: January 2024

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Background: BRAF mutations (mts) represent a highly heterogeneous group of molecular alterations seen in colorectal cancer (CRC). Class I BRAF mts (V600) render aggressive biology to CRC and poor response to anti EGFR inhibitors. Currently there are limited data on clinical and molecular features of class II and III BRAF mts. In this study, we investigated the clinical and molecular characteristics of BRAF mutation classes and their impact on clinical outcomes in a large cohort of patients (pts) with mismatch proficient (pMMR) CRC. Methods: A total of 18575 pMMR CRC specimens were profiled by next-generation sequencing (592-gene, NextSeq; WES, WTS NovaSeq) (Caris Life Sciences, Phoenix, AZ). BRAF mutations were detected by NGS and classified using published literature (Sahin et al. JCO OP 2021). Interferon gamma signature and MAPK pathway activity score (MPAS) were calculated using RNA expression data (TPM). Real-world overall survival information was obtained from insurance claims and calculated from tissue collection to last contact, while post-treatment survival from first of treatment to last contact. KM estimates were calculated for molecularly defined cohorts. Significance was determined as p values of <0.05. Results: A total of 930,105, and 262 pts with class I, II, and III BRAF mts were identified. Pts with class III BRAF mts were significantly more common among younger pts (age<45) compared to class I and class II (8.8% vs. 4.8% vs. 1.0 % respectively; P<0.05). Class I BRAF mts were significantly enriched with consensus molecular subtype 1 (CMS1) (Class I, II and III: 44% vs. 17% vs. 18%) while class II and III BRAF mts were more often CMS2 subtype (canonical) compared to class I (2%, 30% and 35%, p<0.05). Class I BRAF and KRAS/ NRAS mts were mutually exclusive, while KRAS mts incidences were 15% and 22% for class II and class III, and NRAS mts incidence were 8% and 12%, respectively. MPAS score was significantly lower for class III (-0.32, arbitrary unit) compared to Class I (p<0.05), but similar MPAS scores were seen in class I and II (1.3 versus 1.38). No difference in interferon gamma signature was noted between classes. Pts with class II and III mts had significantly better overall survival compared to patients with class I mts (HR=0.69 CI: 0.597-0.804 p<0.0001) and slightly worse overall survival compared to wild-type BRAF pts. (HR; 0.85 CI: 0.74-0.96 P=0.011). Among pts treated with anti-EGFR, pts with class II and III BRAF mts had significantly better post-anti-EGFR survival compared to class I BRAF mts (HR 0.498 CI 0.32-0.766 P=0.001 and similar survival compared to those with BRAF wild-type (P=0.21). Conclusions: Class II and III BRAF mts are associated with improved outcomes with EGFR blockade and represent a distinct biological subgroup of pMMR CRC. Class III BRAF mts have lower MAPK activation, consistent with the pattern of kinase-dead mutations.