Genetic risk and brain structure both predict teen cannabis use, but operate independently

Adolescent substance use initiation is shaped by multiple genetic and neurobiological factors. Externalizing liability, a transdiagnostic genetic dimension capturing shared predisposition to impulsivity, disinhibition, and related traits, is among the strongest polygenic predictors of early substance initiation. Yet how this genetic risk relates to brain structure and function, and whether baseline brain phenotypes statistically account for or instead act in parallel with genetic liability, remains unresolved. Using the ABCD Study, we analyzed an analytic cohort of 10,608 participants with genotype data, baseline multimodal neuroimaging-derived phenotypes (IDPs), and longitudinal substance initiation assessments. Outcome-specific models included up to 10,599 participants after complete-case filtering for survival variables and covariates. We implemented a multistage framework linking an externalizing polygenic risk score (extPRS) to baseline IDPs and longitudinal substance initiation outcomes, including alcohol, nicotine, cannabis, and any substance. Stage 1 screened extPRS-IDP associations using covariate-adjusted linear models with false discovery rate (FDR) control. Stage 2 estimated extPRS effects on time-to-initiation using Cox proportional hazards models. Stage 3 fit joint extPRS + IDP Cox models to identify IDPs that predicted initiation beyond extPRS. Stage 4 conducted bootstrap-based mediation analyses to quantify average causal mediation effects (ACME), average direct effects (ADE), and the proportion of the extPRS-initiation association statistically accounted for by individual IDPs. Higher extPRS was robustly associated with earlier initiation across all substances: alcohol, hazard ratio (HR) = 1.13; nicotine, HR = 1.63; cannabis, HR = 1.67; and any substance, HR = 1.15. Thousands of extPRS-associated IDPs were identified at baseline, with highly concordant effect profiles across robustness specifications. In joint models, numerous IDPs independently predicted initiation timing above and beyond extPRS: 31 for alcohol, 32 for any substance, 137 for cannabis, and 459 for nicotine, with a replicated core set across specifications. Cannabis and nicotine initiation were jointly predicted by superficial white matter (SWM) microstructural integrity in sensorimotor cortex as a protective factor, and by irregular activity in a right-hemisphere region as a risk factor. Alcohol initiation was predicted by a largely distinct, strongly left-lateralized frontolimbic SWM intensity axis. Nicotine initiation additionally and uniquely involved restricted gray matter diffusion in the anterior cingulate cortex and subcallosal cortex. Despite these robust independent IDP associations, mediation analyses showed that indirect effects through individual baseline IDPs were very small in magnitude, approximately 10^-4 for ACME, accounting for less than 2% of the total extPRS effect, with FDR-significant mediation surviving only for alcohol and any-substance initiation. Within the scope of externalizing polygenic risk and baseline neuroimaging, the predominant pattern is one of largely parallel, additive contributions to adolescent substance initiation rather than a dominant genetic -> brain -> behavior pathway. Baseline brain features, particularly prefrontal functional variability and frontolimbic and sensorimotor white matter integrity, predict initiation risk beyond extPRS, indicating neurobiological vulnerabilities not captured by this genetic dimension. However, these baseline IDPs explain only a small fraction of the extPRS-initiation association, suggesting that externalizing genetic liability may operate through pathways not fully represented by cross-sectional baseline imaging. Whether other genetic risk dimensions, such as substance-specific PRS, or dynamic longitudinal brain measures show stronger mediation patterns remains an important open question.