Comprehensive genomic and immune profiling of non-V600 BRAF-mutated melanomas: Implications for therapeutic strategies beyond BRAF/MEK inhibitors.
Authors: Maria-Fernanda Senosain, Sarabjot Pabla, R.J. Seager, Erik Van Roey, Shuang Gao, Hardik Parikh, Yamuna Pulivendula, Kyle C. Strickland, Rebecca A. Previs, Mary K. Nesline, Stephanie B. Hastings, Taylor J. Jensen, Eric A. Severson, Marcia Eisenberg, Brian Caveney, Kamal Veer Saini, Pratheesh Sathyan, Shakti H Ramkissoon, Heidi Chwan Ko
Journal: Journal of Clinical Oncology (2024)

e21544 Background: The development of targeted therapies ( BRAF plus MEK inhibitors) and immune checkpoint inhibitors (ICIs) has significantly improved the outcomes of patients with advanced melanoma, particularly those harboring BRAF V600 mutations (Class 1). However, melanomas with non-V600 BRAF mutations (classes 2 and 3) remain a subset where effective therapeutic options beyond ICIs are lacking. In this study, we investigated the distinct genomic and immune profile of non-V600 BRAF melanomas to further understand the mechanism of resistance to BRAF/MEK inhibitors and explore other pathways of potential therapeutic targets. Methods: A retrospective cohort of 175 melanoma samples was evaluated by comprehensive genomic and immune profiling, including tumor mutational burden (TMB) and the expression of 395 immune genes. Tumor specimens were classified as BRAF Class1 , BRAF Class2 , and BRAF Class3 . TMB (high ≥10 Mut/Mb) was obtained by DNA sequencing. Gene expression signatures of tumor inflammation and cell proliferation were determined by targeted RNA-sequencing. We used chi-square and Wilcoxon rank-sum tests to determine the association of BRAF mutational status to genomic and immune correlates. Results: The median age of diagnosis was 69 years, with 57% of patients being male. A total of 152 (86.9%), 13 (7.4%), and 10 (5.7%) patients had BRAF Class1 , BRAF Class2 , and BRAF Class3 alterations, respectively. Genomic alterations in TP53, NF1, MET and ROS1 were more prevalent in BRAF Class2 and BRAF Class3 as opposed to BRAF Class1 . BRAF Class2 and BRAF Class3 tumors combined had significantly higher tumor inflammation (median = 55.38; p &lt; 0.05) compared to BRAF Class1 (median = 41.79) as well as higher TMB (median = 54.8; p &lt; 0.001) compared to BRAF Class1 (median = 9.75). BRAF Class3 tumors showed significantly higher cellular proliferation (median = 47.5; p &lt; 0.05) compared to BRAF Class1 (median = 33.5) and BRAF Class2 (median = 31.8) tumors, as well as higher TMB (median = 71.5; p &lt; 0.01) compared to BRAF Class1 (median = 10.9). When looking at differentially expressed genes, CDK1 was upregulated in BRAF Class3 compared to BRAF Class1 and BRAF Class2 , and IL12B was upregulated in BRAF Class2 compared to BRAF Class1 . Conclusions: Our study showed that the non-Class 1 BRAF (V600E or K) mutated tumors have higher immune response suggesting a favorable response to ICIs. Additionally, we found that BRAF Class2 and BRAF Class3 tumors more commonly harbor alterations in NF1 and TP53, supporting the prior understanding that BRAF non-V600 tumors have a more aggressive clinical course. Comprehensive molecular analysis offers insight into the immunogenicity and distinct oncogenic drivers associated with unfavorable clinical outcomes, which could guide therapeutic development beyond BRAF and MEK inhibitors in BRAF non-V600 melanomas.