Identification of genetic susceptibility genes and characterization of somatic mutations in nasopharyngeal carcinoma

Abstract

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy arising from the nasopharynx. It has a remarkable ethnic and geographical distribution. Southern China is among the regions with the highest prevalence of NPC. It is well-accepted that host genetics, Epstein-Barr virus (EBV) infection, and environmental factors together contribute to NPC development. Much progress has been made in deciphering the genetic risk factors and critical somatic events in NPC development over the past decades. However, the overall picture of the genetic susceptibility and molecular changes underlying NPC tumourigenesis is still not completely elucidated. Thus, this study sought to apply the powerful next-generation sequencing approaches to investigate the genetic susceptibility genes in NPC, as well as somatic mutation landscape and important genes and pathways in tumourigenesis. In the somatic mutation profiling study, the biopsies from 124 primary tumours, the tissues from eight recurrent tumours and three lymph node metastatic tumours were subjected to whole-exome sequencing (WES) and targeted sequencing. The matching blood samples from the cases were also sequenced. The median somatic mutation prevalence of NPC is 0.9 per megabase in the exome coding regions. An APOBEC cytidine deaminase mutagenesis signature was revealed in the somatic mutations, which is likely due to the activity of APOBEC3A and APOBEC3B. TP53 is the most frequently mutated gene in NPC, occurring in 7-8% of primary tumours. Notably, multiple novel loss-of-function (LOF) mutations were identified in several NF-κB signalling negative regulators, NFKBIA, CYLD, and TNFAIP3, accounting for 6-7% of primary tumours. The LOF mutations may contribute to altered NF-κB activity, which is critical for NPC tumourigenesis. Functional studies confirmed that NFKBIA inhibition and the identified LOF mutations in NFKBIA had a significant impact on NF-κB activity and NPC cell growth. In addition, somatic mutations were found in several cancer-relevant processes including cell cycle phase transition, cell death, Epstein-Barr virus infection, viral carcinogenesis and epigenetic regulation. In the genetic susceptibility study, 67 family history-positive (FH+) cases, 39 early-age onset (EAO) cases (four overlapped with FH+), and 59 sporadic cases were subjected to WES. The data from 895 Southern Chinese were used as non-cancer controls. Three approaches were applied to analyse the dataset, including association test, systematic filtering, and a family-based approach. The top candidate from the gene-based association test and the systematic filtering approaches was macrophage stimulating 1 receptor (MST1R), with 11 rare deleterious variants in 13 independent cases; 53.8% of these are EAO cases, indicating MST1R variants are associated with disease early-age onset. MST1R plays important roles in host defence and immune response. Importantly, the top genes from the association test, including MST1R, were enriched in the chromosome 3p21, a critical region for tumourigenesis. In addition, the genes prioritized from systematic filtering are enriched in DNA repair, ABC transporters, and extracellular matrix organization pathways. These findings provide an enhanced road map for understanding the genetic and genomic basis underlying NPC and new perspectives for targetable signalling pathways for novel therapies in NPC.