The somatic and germline mutational landscape of HPV-negative oral cancer patients with a history of chewing tobacco and betel nut use

Head and neck cancer (HNC) is highly prevalent in South-Asia, driven by additional region-specific exposures such as chewing tobacco and betel nut. Despite therapeutic advances, five-year survival rate remains around 50-60%, underscoring urgent need to identify novel therapeutic targets and improve disease-free survival. This study was designed to identify both somatic and germline drivers contributing to HNC pathogenesis. Through whole-exome sequencing of 103 patients, we detected mutations in known HNC drivers (TP53, CDKN2A, NOTCH1) as well as novel hotspots in several genes, including TRIM48, MAP3K19, and CDC20. A recurrent hotspot mutation (p.A187T) in POLQ gene was identified in patients with high tumor mutation burden and was absent in both TCGA and ICGC cohorts. Among known hotspots, the MYC p.T73A mutation was highly prevalent, occurring in over 50% of patients. As MYC is considered an "undruggable" target, alternative strategies targeting upstream regulators such as BRD4 with specific inhibitors may hold promise for South-Asian HNSCC patients harboring the p.T73A mutation. Copy-number variation analysis further revealed EGFR amplification and TP73 deletion in the majority of patients, highlighting additional layers of genomic dysregulation. Comparative genomic analyses showed no recurrent mutations in epigenetic regulators (ARID2, EP300, KMT2B/MLL2, KMT2D/MLL4, NSD1, and TET1). We report p.S456L germline variant in SDHA consistently among South-Asian cohorts. Patients with p.S456L mutation were younger than those without it, reflecting typical epidemiological signature of a genetic variant that increases susceptibility. Systematic molecular characterization of recurrent mutations is required to elucidate mechanism of action of these variants and to find actionable therapeutic targets.