Molecular Landscape of BRAF-Mutant NSCLC Reveals an Association Between Clonality and Driver Mutations and Identifies Targetable Non-V600 Driver Mutations

Abstract

Introduction: Approximately 4% of NSCLC harbor BRAF mutations, and approximately 50% of these are non-V600 mutations. Treatment of tumors harboring non-V600 mutations is challenging because of functional heterogeneity and lack of knowledge regarding their clinical significance and response to targeted agents. Methods: We conducted an integrative analysis of BRAF non-V600 mutations using genomic profiles of BRAF-mutant NSCLC from the Guardant360 database. BRAF mutations were categorized by clonality and class (1 and 2: RAS-independent; 3: RASdependent). Cell viability assays were performed in Ba/F3 models. Drug screens were performed in NSCLC cell lines. Results: A total of 305 unique BRAF mutations were identified. Missense mutations were most common (276, 90%), and 45% were variants of unknown significance. F468S and N581Y were identified as novel activating mutations. Class 1 to 3 mutations had higher clonality than mutations of unknown class (p < 0.01). Three patients were treated with MEK with or without BRAF inhibitors. Patients harboring G469V and D594G mutations did not respond, whereas a patient with the L597R mutation had a durable response. Trametinib with or without dabrafenib, LXH254, and lifirafenib had more potent inhibition of BRAF non-V600mutant NSCLC cell lines than other MEK, BRAF, and ERK inhibitors, comparable with the inhibition of BRAF V600E cell line. Conclusions: In BRAF-mutant NSCLC, clonality is higher in known functional mutations and may allow identification of variants of unknown significance that are more likely to be oncogenic drivers. Our data indicate that certain non-V600 mutations are responsive to MEK and BRAF inhibitors. This integration of genomic profiling and drug sensitivity may guide the treatment for BRAF-mutant NSCLC.

A Rare p.T599dup BRAF Mutant NSCLC in a Non-Smoker

“…Treatment of cancers harboring non-V600 mutations is challenging due to functional heterogeneity, lack of knowledge of their clinical significance, or response to target therapies [ 14 ]. There has been one case reported, where a double non-V600 BRAF NSCLC responded well to RAF/MEK inhibition that usually targets V600 mutations [ 15 ].…”

“…Another case by Dagogo-Jack presented a durable response to dabrafenib combined with trametinib in a non-V600 (specifically G469A) mutated NSCLC [ 16 ]. Negrao et al observed that trametinib with or without dabrafenib or lifirafenib had a more potent inhibition of BRAF non-V600 mutant NSCLC cell lines than other MEK, RAF, and ERK inhibitors when compared to the inhibition of V600 mutants [ 14 ]. Negrao et al also suggested that, while there are many unknown variants of the non-V600 BRAF mutant cancers, assessing for high clonality in addition to the class of the mutation will allow for identification of variants that are more likely to be oncogenic drivers and thus be more responsive to RAF/MEK therapy [ 14 ].…”

“…Negrao et al observed that trametinib with or without dabrafenib or lifirafenib had a more potent inhibition of BRAF non-V600 mutant NSCLC cell lines than other MEK, RAF, and ERK inhibitors when compared to the inhibition of V600 mutants [ 14 ]. Negrao et al also suggested that, while there are many unknown variants of the non-V600 BRAF mutant cancers, assessing for high clonality in addition to the class of the mutation will allow for identification of variants that are more likely to be oncogenic drivers and thus be more responsive to RAF/MEK therapy [ 14 ]. Our case of an extremely rare variant of a non-V600 BRAF mutant NSCLC also represented positive response to RAF/MEK inhibitors, but more research needs to be done to better assess RAF/MEK inhibitor’s activity in treatment of non-V600 mutations.…”

Durable Response to Dabrafenib Combined With Trametinib in a Patient With NSCLC Harboring a BRAF G469A Mutation

“…For example, a few case series revealed that a subset of class II mutations (K601E, L597S, and L597R) might respond to BRAF and MEK inhibitors. 6,7 In addition, preclinical models suggest that inhibiting the regulatory phosphatase SHP2 or blocking the upstream receptor tyrosine kinases can suppress the proliferation of tumors with class III BRAF mutations. 4,8 In their study, Negrao et al 7 reported that the BRAF G469-mutant H1755 cell line is sensitive to treatment with trametinib plus or minus dabrafenib.…”

MEK inhibitors in non-V600 BRAF mutations and fusions

“…What are the next steps? First, our study does not change available data suggesting that MEK inhibition may be still considered for melanoma patients whose tumors harbor class 2 BRAF mutations [ 22 , 23 ], or perhaps non-small cell lung cancer patients [ 24 ]. More recent studies have even suggested that combining BRAF and MEK inhibitors is the most active strategy in these patients [ 14 , 25 ].…”