Molecular Landscape of Acquired Resistance to Targeted Therapy Combinations in BRAF-Mutant Colorectal Cancer

Abstract

Summary Although recent clinical trials of BRAF inhibitor combinations have demonstrated improved efficacy in BRAF mutant colorectal cancer, emergence of acquired resistance limits clinical benefit. Here, we undertook a comprehensive effort to define mechanisms underlying drug resistance with the goal of guiding development of therapeutic strategies to overcome this limitation. We generated a broad panel of BRAF mutant resistant cell line models across seven different clinically-relevant drug combinations. Combinatorial drug treatments were able to abrogate ERK1/2 phosphorylation in parental sensitive cells, but not in their resistant counterparts, indicating that resistant cells escaped drug treatments through one or more mechanisms leading to biochemical reactivation of the MAPK signaling pathway. Genotyping of resistant cells identified gene amplification of EGFR, KRAS and mutant BRAF, as well as acquired mutations in KRAS, EGFR, and MAP2K1. These mechanisms were clinically relevant, as we identified emergence of a KRAS G12C mutation and increase of mutant BRAF V600E allele frequency in the circulating tumor DNA of a patient at relapse from combined treatment with BRAF and MEK inhibitors. In order to identify therapeutic combinations capable of overcoming drug resistance, we performed a systematic assessment of candidate therapies across the panel of resistant cell lines. Independent of the molecular alteration acquired upon drug pressure, most resistant cells retained sensitivity to vertical MAPK pathway suppression when combinations of ERK, BRAF, and EGFR inhibitors were applied. These therapeutic combinations represent promising strategies for future clinical trials in BRAF mutant colorectal cancer.

Acquired RAS or EGFR mutations and duration of response to EGFR blockade in colorectal cancer

“…These results are aligned with previous reports that CRC cell lines may contain pre-existing but low levels of RAS mutations, but they can also acquire mutations de novo 20. This would apply to the acquisition of mutations in the EGFR ECD during anti-EGFR therapy as there have been no reports of these mutations pre-existing in cell lines or patients before anti-EGFR therapy1011122136.…”

Targeting BRAF-Mutant Colorectal Cancer: Progress in Combination Strategies

“…The detection of acquired mutations or amplification of KRAS in disease progression tumor biopsies in 4 of 6 responders is an important finding, and is consistent with drug resistance being driven through MAPK pathway reactivation in BRAF mutant CRC (1,7,9). Preliminary data from the SWOG S1406 randomized phase 2 trial of irinotecan and cetuximab, with or without vemurafenib, in BRAF mutant metastatic CRC reported an improvement in progression-free survival with the triplet combination, with toxicity rates similar to doublet regimens of irinotecan and cetuximab.…”

MicroRNA-Based Combinatorial Cancer Therapy: Effects of MicroRNAs on the Efficacy of Anti-Cancer Therapies

“…However, the occurrence of therapeutic resistance continues to be a significant cause of the failure of current combination therapy. It has been demonstrated that the acquisition of resistance can occur following combination treatment and that the use of a third agent can address the emergence of resistance by inhibiting a factor involved in the resistance [10,11,189]. This implies that the multiple targeting of resistance-mediating factors is better than the current approach to increase the cellular response to cancer therapy and that the development of new combination strategies is still required to improve treatment outcomes.…”