Identification of a Recurrent <i>LMO7–BRAF</i> Fusion in Papillary Thyroid Carcinoma

Abstract

Background: The BRAFV600E mutation is the most common driver in papillary thyroid carcinoma (PTC) tumors. In recent years, gene fusions have also been recognized as important drivers of cancer in PTC. Previous studies have suggested that thyroid tumors with fusion genes frequently display an aggressive course. These observations prompted further exploration of gene fusions in PTC tumors. The aim was to search for previously unrecognized gene fusions using thyroid tissue samples from PTC patients. Methods: Gene fusions were analyzed in RNA sequencing data obtained from 12 PTC tumors and paired unaffected thyroid tissue samples. Candidate fusions were further filtered and validated using reverse transcriptase polymerase chain reaction, Sanger sequencing, and fluorescence in situ hybridization. An Ohio cohort of 148 PTC tumor samples was screened for a LMO7–BRAF fusion and the BRAFV600E mutation. Functional assays were performed to assess the LMO7–BRAF fusion. Results: Two coding fusions (CCDC6–RET and LMO7–BRAF) were found in one tumor sample each. The novel LMO7–BRAF fusion was validated by reverse transcriptase polymerase chain reaction and fluorescence in situ hybridization. The LMO7–BRAF fusion was a recurrent somatic alteration with a frequency of 2.0% (3/148) in PTC tumors, while the BRAFV600E point mutation was found in 63.5% (94/148) of tumors. Enforced expression of LMO7–BRAF fusion protein stimulated endogenous ERK1/2 phosphorylation and promoted anchorage independent cell growth to an extent similar to BRAFV600E. Conclusions: A novel fusion gene, LMO7-BRAF, was identified in PTC tumors. The results indicate that the LMO7–BRAF fusion behaves as an oncogenic alteration. This observation expands the spectrum of fusion genes involving kinases in thyroid cancer.