Abstract 6527: Fusion genes as novel putative biomarkers for head and neck squamous cell carcinomas

Abstract Head and neck squamous cell carcinomas (HNSCC) are highly aggressive types of cancers with a complex molecular etiology of disease and consequently result in delayed clinical detection, poor prognosis, and limited treatment strategies. Fusion genes, a hallmark of cancer, may be targeted for early identification and treatment of HNSCC; however, studies characterizing fusion genes in HNSCC remain limited. Oral Human Papillomavirus (HPV) infection is a major cause of HNSCC and can also promote the acquisition of fusion genes due to the genomic instability induced by its integration. Here, we retrieved RNA-sequencing data from 36 HNSCC tumors (18 HPV+ and 18 HPV-, GEO Accession: GSE74956) to identify fusion genes using the STAR fusion algorithm in each sample. Statistical analyses were performed in R statistical software. A total of 10 fusion genes were identified in at least 4 of the samples regardless of HPV status. We identified 3 fusion genes that were present in at least 4 of the HPV+ tumors: PMS2P9-CCDC146, MACC1-AC005062.1, AC096711.2-RPL7AP28, and one solely present in HPV- tumors: CTSC-RAB38. The remaining 6 fusion genes were present in both HPV+ and HPV- tumors: TVP23C-CDRT4, AC009271.1-LINC01905, MIR205HG-AOPEP, SEPTIN7P2-PSPH, KRT5-KRT84, KANSL1-ARL17A. While 4 of the identified fusion genes had been previously associated with cancer, there were 6 novel identified fusion genes, in which one or both partner genes have been associated with different cancers. Additionally, the identified fusion genes may be a product of transcription read-through of neighbor genes. The fusion genes associated with HPV infection might explain biological disparities in HPV+ versus HPV- HNSCC and may be targets for the prevention and diagnosis of HNSCC. Future studies need to determine the functional impact of the identified fusion genes in HPV+ tumors. Citation Format: Yabdiel A. Ramos Valerio, Hannah C. Van Wyk, Esther Peterson Peguero, Josué Pérez Santiago. Fusion genes as novel putative biomarkers for head and neck squamous cell carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6527.