Shared genetic architecture between schizophrenia and subcortical brain susceptibility phenotypes

Schizophrenia (SCZ) is a highly heritable and complex neuropsychiatric disorder. Emerging evidence implicates dysregulated brain iron, particularly in subcortical regions, in SCZ pathophysiology. Here, we systematically dissected the shared genetic architecture between SCZ and subcortical brain susceptibility phenotypes by integrating large-scale genome-wide association study (GWAS) data with quantitative susceptibility mapping (QSM) phenotypes across 16 subcortical regions. Using the MiXeR framework, we quantified the extent and pattern of shared genetic overlap between SCZ and each QSM phenotype, revealing the strongest overlap in the left and right nucleus accumbens. Conditional and conjunction false discovery rate analyses identified 666 unique shared SNPs. Functional annotation highlighted enrichment in pathways related to synaptic function and neuronal development, with pronounced expression in neurons. Additionally, we characterized their spatio-temporal expression patterns of shared genes and identified 89 significant expression-trait associations linked to SCZ-related phenotypes. Furthermore, the virtual drug screen identified 691 potential protein-drug pairs that may contribute to both iron regulation and SCZ. Our findings provide new insights into the complex interaction between subcortical brain susceptibility phenotypes and SCZ, highlighting pathways that may offer novel therapeutic strategies for SCZ and related brain susceptibility-associated conditions.