Large-Scale Whole-Exome Sequencing Association Study Implicates Genetic Effects on Viral Oncogenesis and Tumor Microenvironment in Nasopharyngeal Carcinoma

Abstract

Nasopharyngeal carcinoma (NPC) poses a substantial clinical challenge with limited understanding of its genetic underpinnings. Here we conduct the largest-scale whole-exome sequencing association study of NPC to date, involving 6,969 NPC cases and 7,100 controls and revealing three novel germline genetic variants linked to NPC susceptibility: a common variant rs2276868 in RPL14, a rare variant rs5361 in SELE, and a common variant rs1050462 in HLA-B. Through a multiomics approach, which integrates both bulk (n=206) and single-cell RNA-sequencing (n=56) data along with experimental validations, we demonstrate that the RPL14 variant modulates Epstein-Barr virus (EBV) life cycle and NPC pathogenesis. Additionally, we show that the SELE variant plays a role in modifying endothelial cell function, thus promoting NPC progression. Our study also underscores the critical impact of rare genetic variants on NPC heritability. We introduce a refined composite polygenic risk score (rcPRS) that outperforms existing models in predicting NPC risk. Notably, our findings reveal that the polygenic risk for NPC is mediated by EBV infection status. Overall, our study provides crucial insights into the intricate genetic architecture of NPC. It highlights the critical interplay between genetic variations and essential elements of the tumor microenvironment, such as EBV and endothelial cells, in predisposing to NPC. This work opens new avenues for personalized risk assessments, early diagnosis, and targeted therapeutic strategies for NPC.