Introduction: A BRAF^V600E mutation is an unfavorable prognostic biomarker for CRC and is associated with short-lived treatment response to BRAF and EGFR blockade. Anti-PD-1 therapies are ineffective in MSS CRC but demonstrate efficacy in combination with BRAF + EGFR inhibition for MSS BRAF^V600E CRC. A comprehensive characterization of MSS BRAF^V600E CRC as an immunologically distinct subpopulation of MSS CRC has not been performed. Here, we characterize the clinicopathological and transcriptomic features of MSS BRAF^V600E CRC patients, relative to BRAF^WT MSS CRC patients.

Methods: De-identified records of 12,009 MSS CRC patients were retrospectively analyzed from the Tempus clinicogenomic database. CMS subtypes were derived using the CMScaller algorithm. Survival was assessed using Kaplan-Meier survival analysis with risk set adjustment (RSA) method; log-rank test was used to compare survival. Categorical and continuous variables were compared using chi-squared test and Wilcoxon rank sum test, respectively.

Results: BRAF^V600E was found in 5% (n=630) of the patients. Demographics and clinicopathological features varied significantly between the BRAF^WT and BRAF^V600E cohorts (Table 1). Relative to the BRAF^WT cohort, BRAF^V600E tumors were enriched for the immune-activated CMS1 signature (53% vs 11%, p< .001), PD-L1 detection (9.5% vs 3%, p<0.001), and CD8+ T-cell infiltration (4.6% vs. 2.5%, p<0.001). CMS4 was linked to an unfavorable prognosis in the BRAF^WT cohort (HR=0.58 compared to CMS1, p=0.026), yet this was not observed in the BRAF^V600E cohort (HR=2.60 compared to CMS1, p=0.083).

Conclusions: BRAF^V600E MSS CRC exhibited immune activation characteristics that were not observed in the BRAF^WT group, including greater CMS1 status, PD-L1 expression, and CD8-T cell infiltration. Our findings support investigation of novel immune-based therapeutic strategies of MSS BRAF^V600E CRC as an immunologically distinct subpopulation of MSS CRC.

Cohort characteristics