Nicotine dependence partially mediates the association between IP6K3 genetic variation and risk of lung squamous cell carcinoma among smokers

INTRODUCTION : Nicotine dependence is a heritable trait that may mediate genetic susceptibility to lung cancer. Building on a prior integrative genomic study that identified significant SNPs and their annotated genes located within tracts of homozygosity (TOH) overlapping differentially methylated regions (DMRs) in lung tissue, we investigated whether these SNPs and haplotypes within these methylation-driven genes were associated with Non-Small Cell Lung Cancer (NSCLC) risk through pathways involving nicotine dependence among smokers. METHODS : The study included individuals with lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and population-based controls from a genome-wide association study (GWAS). Genes exhibiting differential expression with an absolute log₂ fold-change ≥2 between tumor and adjacent normal tissues were retained as candidate loci for SNP- and haplotype-based mediation models. Within candidate genes, linkage disequilibrium blocks were defined to construct haplotypes. Multivariable logistic regression models adjusted for age and sex were used to estimate SNP- and haplotype-level associations with NSCLC risk by subtypes. Individuals carrying a significant haplotype were coded as exposed. Causal mediation analyses were used to estimate the proportion of each SNP or haplotype's effect on NSCLC risk that was mediated by nicotine dependence, measured by the Fagerström Test for Nicotine Dependence (FTND). Structural equation modeling (SEM) further quantified direct and indirect associations among age, sex, cancer status, smoking cessation status, smoking pack years, nicotine dependence (FTND), and carrier status for the significant haplotypes. RESULTS : The IP6K3 haplotype “GTGTG” (rs649775-rs2966-10947433-rs4713668-rs6457740) was inversely associated with LUSC risk, with approximately 39% of its protective association mediated by nicotine dependence (average causal mediation effect [ACME]=-0.023, 95% CI: -0.039, -0.010). Consistent with this pattern, IP6K3 rs2966 (TT vs CC; CT vs CC) and rs4713668 (TT vs CC; CT vs CC) exhibited significant indirect effects via nicotine dependence (ACME ranges from -0.023 to -0.027; p -values between 0.004 and 0.024), accounting for 33-38% of their total protective effects on LUSC risk. CONCLUSION : These findings identify IP6K3 as a potential candidate gene in nicotine-related lung carcinogenesis and highlight the relevance of neurobiological dependence pathways in personalized smoking cessation and lung cancer prevention strategies.