Transcriptomic and functional studies of fusion oncogene-driven salivary gland tumors

Abstract

Fusion genes are potent oncogenic drivers resulting from exchange of regulatory/coding sequences between two genes. They were originally identified in leukemias but are now recognized as key oncogenic events also in many solid tumors, including salivary gland tumors (SGTs). Adenoid cystic carcinoma (ACC) is a highly malignant SGT with no effective treatment for patients with recurrent and/or metastatic disease. The MYB-NFIB fusion is the main genomic hallmark of ACC and a potential therapeutic target. Here, oncogenic signaling pathways as well as the molecular consequences and regulation of MYB-NFIB were assessed in cultured ACC cells and in ACC surgical samples. A combination of molecular and functional assays was used including RNAi, qPCR, western blot, phospho-receptor tyrosine kinase (RTK) arrays, proliferation/apoptosis/sphere assays, and gene expression microarrays. ACC patient-derived xenografts (PDX) were used to study the effects of RTK-inhibition on tumor growth. MYBNFIB was shown to promote proliferation and spherogenesis of ACC cells. The fusion regulated expression of genes involved in DNA replication/repair, cell cycle, and RNA processing, and induced an MYC-like transcriptional program. MYB-NFIB was shown to be regulated by IGF1R through IGF2-activated AKTsignaling and pharmacological inhibition of IGF1R partially reversed the transcriptional program induced by MYB-NFIB. Moreover, IGF1R, EGFR, and MET were co-activated in ACC cells. Combined inhibition of these receptors in ACC cells and PDX-models induced differentiation and synergistic growth inhibition. The results provide new insights about the function and regulation of MYB-NFIB and are the first to show that a druggable cell surface receptor can regulate a fusion oncogene encoding a transcription factor. Importantly, the results also highlight novel potential treatment strategies for ACC patients. Pleomorphic adenoma (PA) is the most common SGT. Although it is a benign tumor, treatment may be complicated by recurrence and/or malignant transformation. Previous studies of PA have revealed recurrent chromosomal rearrangements that activate the key oncogenes PLAG1 and HMGA2 by gene fusion events. Here, detailed studies of previously uncharacterized subsets of PAs with 8;9- or 9;12-rearrangements revealed breakpoints within or in the proximity of either PLAG1 or HMGA2, and NFIB. Further analyses using RNA-seq, RT-PCR, qPCR, and arrayCGH revealed a novel NFIB-PLAG1 fusion in a PA with an ins(9;8) and HMGA2-NFIB fusions in cases with t(9;12). These findings highlight the role of NFIB as a fusion partner gene in both benign and malignant SGTs and indicate that NFIB can activate both PLAG1 and HMGA2 by gene fusion/enhancer hijacking events in PA. Furthermore, RNA-seq based transcriptomic analysis of PAs revealed a high frequency of PLAG1 and HMGA2 fusions (≈80% of the cases) and multiple novel fusion partner genes. The findings indicate that gene fusions are more common in PA than previously documented. Global gene expression and pathway analyses revealed several activated oncogenic signaling pathways and showed that the expression profile reflects certain morphological features typical of PA. Finally, the results showed that PLAG1 and HMGA2 drive tumorigenesis via shared signaling pathways.