Integrative analyses of N6-methyladenosine-associated single-nucleotide polymorphisms (m6A-SNPs) identify tumor suppressor gene AK9 in lung cancer

N6-methyladenosine (m6A) modification has been identified as one of the most important epigenetic regulation mechanisms in the development of human cancers. However, the association between m(6)A-associated single-nucleotide polymorphisms (m(6)A-SNPs) and lung cancer risk remains largely unknown. Here, we identified m6A-SNPs and examined the association of these m(6)A-SNPs with lung cancer risk in 13,793 lung cancer cases and 14,027 controls. In silico functional annotation was used to identify causal m(6)A-SNPs and target genes. Furthermore, methylated RNA immunoprecipitation and quantitative real-time polymerase chain reaction (MeRIP-qPCR) assay was performed to assess the m6A modification level of different genotypes of the causal SNP. In vitro assays were performed to validate the potential role of the target gene in lung cancer. A total of 8794 m(6)A-SNPs were detected, among which 397 SNPs in nine susceptibility loci were associated with lung cancer risk, including six novel loci. Bioinformatics analyses indicated that rs1321328 in 6q21 was located around the m6A modification site of AK9 and significantly reduced AK9 expression (beta = -0.15, p = 2.78 x 10(-8)). Moreover, AK9 was significantly downregulated in lung cancer tissues than that in adjacent normal tissues of samples from the Cancer Genome Atlas and Nanjing Lung Cancer Cohort. MeRIP-qPCR assay suggested that C allele of rs1321328 could significantly decrease the m(6)Amodification level of AK9 compared with G allele. In vitro assays verified the tumor-suppressing role of AK9 in lung cancer. These findings shed light on the pathogenic mechanism of lung cancer susceptibility loci linked with m6A modification.

Automated summary

N6-methyladenosine (m6A) modification is identified as an important epigenetic mechanism in human cancer development. This study investigates the association between m(6)A-associated single-nucleotide polymorphisms (m(6)A-SNPs) and lung cancer risk. The findings reveal several novel susceptibility loci linked to lung cancer, which may affect cancer development through gene expression and m6A modification levels.