Long read sequencing identifies complex structural variant landscape and recurrent TERT rearrangements in mucoepidermoid carcinoma

• Published in: Oral oncology 2024-12, Vol.159, p.107108, Article 107108
• Main Authors: Gensterblum-Miller, Elizabeth, Bhangale, Apurva, Majid, Dana Al, Pienkowski, Victor Murcia, Rydzanicz, Malgorzata, Janiszewska, Joanna, Kostrzewska-Poczekaj, Magdalena, Chang, Clifford, Brummel, Collin, Michmerhuizen, Nicole L., Wang, Jiayu, Sandford, Erin, Tewari, Muneesh, Wierzbicka, Malgorzata, Birkeland, Andrew C., McHugh, Jonathan B., Spector, Matthew E., Giefing, Maciej, Jarmuz-Szymczak, Malgorzata, Heft Neal, Molly E., Brenner, J. Chad
• Format: Article
• Language: English
• Subjects: Carcinoma, Mucoepidermoid - genetics; Carcinoma, Mucoepidermoid - pathology; Cell Line, Tumor; CRTC1; DNA-Binding Proteins - genetics; Female; Gene Rearrangement; Humans; Male; MAML2; MEC; NOTCH2; Oncogene Proteins, Fusion - genetics; Proto-Oncogene Proteins; Salivary Gland Neoplasms - genetics; Salivary Gland Neoplasms - pathology; Structural variation; Telomerase - genetics; TERT; Trans-Activators - genetics; Transcription Factors - genetics; Translocation; Translocation, Genetic - genetics
• ISSN: 1368-8375; 1879-0593; 1879-0593
• DOI: 10.1016/j.oraloncology.2024.107108

•We sequence a chain of structural variations, leading to the CRTC1::MAML2 driver translocation in mucoepidermoid carcinoma.•We discovered recurrent TERT structural variation in mucoepidermoid carcinoma tumors and cell lines.•In a cell line with TERT promoter rearrangement, TERT (telomerase) expression is critical for cell survival. Mucoepidermoid Carcinoma (MEC) is a common salivary malignant neoplasm. Approximately 60 % of MECs harbor translocations between CRTC1 or CRTC3 and MAML2, which are thought to drive disease pathogenesis. However, the precise structural mechanism driving this rearrangement remains uncharacterized. Here, we performed multi-omic and long read genomic sequencing, discovering a chain of alterations that created the CRTC1::MAML2 fusion, but also an unexpected MAML2 to MYBL1 rearrangement, suggesting that MYBL1 may play a larger role in salivary gland cancers than previously recognized. Furthermore, we discovered and validated recurrent TERT rearrangements and amplifications in MEC models. 5/5 MEC cell lines and 36/39 (92 %) primary MEC tumors harbored a TERT rearrangement or copy number amplification. Custom sequencing of the TERT locus confirmed translocation breakpoints in 13/33 (39 %) MECs, while exome sequencing confirmed frequent TERT amplifications. Critically, TERT knockdown in NCI-H292, a cell line with TERT promoter rearrangement, reduced clonogenic cell survival, supporting a critical role of this gene in MEC tumorigenesis. Overall, our data suggest that complex chromothripsis rearrangement mechanisms drive the formation of structural variation in CRTC1::MAML2 fusion positive and negative tumors and reveal highly recurrent structural variation driving TERT rearrangement in MEC.