Cell-type-specific genetic architecture reveals neuronal and immune contributions to neuropsychiatric disorders

Neuropsychiatric disorders exhibit complex polygenic architectures, yet the cell-type-specific mechanisms underlying most risk loci remain unclear. Here, we integrate single-cell expression quantitative trait locus (sc-eQTL) data from brain and blood tissues with genome-wide association studies (GWAS) of six neuropsychiatric disorders (schizophrenia (SCZ), Parkinson's disease (PD), bipolar disorder (BP), major depressive disorder (MDD), attention-deficit/hyperactivity disorder (ADHD), and autism spectrum disorder (ASD)) to systematically identify putative causal genes at cellular resolution. Employing summary-data-based Mendelian randomization (SMR) across diverse neuronal and immune cell types, we discovered 345 cell-type-specific risk genes for various diseases, including both replicated candidates (such as MAPT in astrocytes for SCZ and PD and FLOT1 in excitatory neurons and inhibitory neurons for SCZ, BP and MDD) and novel associations (such as APTX in microglia for SCZ). Cross-disorder analyses revealed shared pathways in synaptic function and immune regulation. In contrast, disease-specific and tissue-specific patterns were observed across different disorders. Strikingly, we found that brain-derived risk genes exhibited significantly higher cell-type specificity than those identified in blood, underscoring the more focused cellular context of genetic effects in the central nervous system. Our findings suggest that neuropsychiatric disorders arise from a combination of neuronal dysfunction and immune system dysregulation. The study demonstrates how cell-type-specific mapping uncovers etiological mechanisms obscured in bulk-tissue analyses, proving novel information for clarifying the biological mechanism of gene expression implicated in the development of the six neuropsychiatric disorders.