Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer

Area of Science:

• Oncology
• Molecular Biology
• Genetics

Background:

• Oncogenic gene fusions are key drivers of human cancers.
• Efficient methods for functional evaluation of fusion genes are crucial for understanding cancer mechanisms and developing targeted therapies.

Purpose of the Study:

• To develop a versatile methodology for rapid construction and functional evaluation of oncogenic gene fusions.
• To identify novel fusion genes with oncogenic potential and validate their sensitivity to existing kinase inhibitors.
• To investigate the functional impact of specific domains within fusion genes, particularly BRAF fusions.

Main Methods:

• Engineered known fusion oncogenes (BCR-ABL1, EML4-ALK, ETV6-NTRK3) and 20 novel fusion genes from The Cancer Genome Atlas.
• Validated the oncogenic activity and transforming potential of engineered fusion genes.
• Conducted domain-function studies on BRAF fusion genes and screened for activating mutations in the N-terminal inhibitory domain.

Main Results:

• Successfully engineered known and novel fusion genes, confirming the oncogenic activity of known fusions.
• Identified five novel fusion genes involving MET, NTRK2, and BRAF kinases with potent transforming activity.
• Demonstrated that BRAF fusion transforming activity stems from loss of N-terminal inhibitory domains.
• Discovered a novel oncogenic BRAF mutation (F247L) activating the MAPK pathway and conferring sensitivity to BRAF/MEK inhibitors.

Conclusions:

• The developed fusion gene construction strategy facilitates rapid functional characterization of oncogenic fusions.
• The identified novel fusion genes and BRAF mutation represent potential therapeutic targets.
• This methodology supports the translation of fusion gene discoveries into personalized cancer treatment strategies.