27P - Extending a classification system for atypical BRAF mutations to improve targeted therapies in colorectal cancer cells

Background

Unlike other types of cancer that are sensitive to single-target agents, such as lung cancer and chronic myeloid leukemia, colorectal cancer (CRC) involves a complex network of interactions between activating oncogenes and is thus more likely to respond to multi-target therapy. Approximately 10% of CRC mutations are within the BRAF gene, the most frequent being BRAFV600E. While this mutation can be targeted with relatively high efficacy by single-target therapies, there exists a cohort of atypical BRAF mutations that confer higher resistance to currently available treatments. Furthermore, a large proportion of these atypical BRAF mutations are poorly understood.

Methods

We used principal component analysis and semi-supervised clustering learning methods to classify mutants unassigned by the previous BRAF classification system. By leveraging previously established protein-protein networks, we overlaid them with gene essentiality data to successfully classify 84 new BRAF mutations. We then evaluated the oncogenic potential of the newly classified atypical class-2 or -3 BRAF mutations compared to wild-type and class-1 BRAF mutations to validate that our extended system was consistent with the previously established BRAF classes. We also performed a network analysis to determine which genes were co-mutated for each BRAF class.

Results

Cell viability analysis of the BRAF-mutant Ba/F3 cells yielded no significant differences in the median AUC values between the new and old classification systems. Several key genes (including PIK3CA, EGFR, and MEK) were identified as potential drug targets (IC 50: 0.1 μM) for cell lines with class-2 and -3 atypical BRAF mutations. We found that atypical BRAF mutations have significantly more positive CERES scores than class-1 mutations and thus need to partner with other oncogenes to drive oncogenesis due to their lower oncogenic potential.

Conclusions

In conclusion, we extended the previous Yao classification system to establish a more comprehensive BRAF-mutant classification system, Yao Classification System Plus, that encompasses more atypical BRAF mutations. This allows for greater therapeutic options to target cells carrying these previously uncharacterized mutations.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

University of Texas MD Anderson Cancer Center.

Funding

National Cancer Institute , the Cancer Center Support Grant, and the Cancer Prevention & Research Institute of Texas.

Disclosure

All authors have declared no conflicts of interest.