Yoon-Ming Chin, Taisei Mushiroda, Atsushi Takahashi, Michiaki Kubo, Gopala Krishnan, Lee-Fah Yap, Soo-Hwang Teo, Paul Vey-Hong Lim, Yoke-Yeow Yap, Kin-Choo Pua, Naoyuki Kamatani, Yusuke Nakamura, Choon-Kook Sam, Alan Soo-Beng Khoo, The Malaysian NPC Study Group and Ching-Ching Ng (2015). HLA-A SNPs and amino acid variants are associated with nasopharyngeal carcinoma in Malaysian Chinese. International Journal of Cancer 136(3): 678-687
Nasopharyngeal carcinoma (NPC) arises from the mucosal epithelium of the nasopharynx and is constantly associated with Epstein–Barr virus type 1 (EBV-1) infection. We carried out a genome-wide association study (GWAS) of 575,247 autosomal SNPs in 184 NPC patients and 236 healthy controls of Malaysian Chinese ethnicity. Potential association signals were replicated in a separate cohort of 260 NPC patients and 245 healthy controls. We confirmed the association of HLA-A to NPC with the strongest signal detected in rs3869062 (p = 1.73 × 10−9). HLA-A fine mapping revealed associations in the amino acid variants as well as its corresponding SNPs in the antigen peptide binding groove (pHLA-A-aa-site-99 = 3.79 × 10−8, prs1136697 = 3.79 × 10−8) and T-cell receptor binding site (pHLA-A-aa-site-145 = 1.41 × 10−4,prs1059520 = 1.41 × 10−4) of the HLA-A. We also detected strong association signals in the 5′-UTR region with predicted active promoter states (prs41545520 = 7.91 × 10−8). SNP rs41545520 is a potential binding site for repressor ATF3, with increased binding affinity for rs41545520-G correlated with reduced HLA-A expression. Multivariate logistic regression diminished the effects of HLA-A amino acid variants and SNPs, indicating a correlation with the effects of HLA-A*11:01, and to a lesser extent HLA-A*02:07. We report the strong genetic influence of HLA-A on NPC susceptibility in the Malaysian Chinese.