Shared genetic architecture of schizophrenia and Alzheimer's disease and related dementias implicates 16p11.2 and lifespan brain vulnerability.

Epidemiological and clinical observations linking schizophrenia (SCZ) to increased dementia risk, together with the occurrence of psychosis in Alzheimer's disease and related dementias (ADRD), suggest that shared genetic liabilities may contribute to their co-occurrence. Leveraging large-scale genome-wide association study summary statistics for SCZ (53,386 cases and 77,258 controls) and ADRD (111,326 cases and 677,663 controls), we systematically investigated their shared genetic architecture and potential biological mechanisms. We identified three significant local genetic correlations (P < 2.0 × 10⁻⁵) and cross-trait polygenic enrichment between SCZ and ADRD, with 39 genomic loci jointly associated at conjunctional false discovery rate (conjFDR) < 0.05. Fifteen high-confidence genes (CNIH4, CD302, PCGF3, TFR2, EPHX2, SNX32, EFEMP2, CTSW, ASPHD1, TAOK2, INO80E, DOC2A, MAPK3, KANSL1, and XPNPEP3) were consistently prioritized across positional, expression quantitative trait locus, and chromatin-interaction mapping. Tissue- and cell-type enrichment analyses highlighted cerebellar tissues and ependymal-cell-related signals, while pathway analyses implicated synaptic signaling, axonal growth, and presynaptic structural organization. At the locus level, colocalization and transcriptome-wide association analyses converged on 16p11.2, prioritizing INO80E, YPEL3, SLX1B, and TMEM219. Developmental trajectory modeling further revealed region- and stage-specific expression divergence of prioritized 16p11.2 genes, with prominent differences spanning childhood and adulthood. Brain-wide association analysis linked the 16p11.2 lead variant rs9932702 to cortical gray-white contrast (β = -0.062, P = 7.5 × 10⁻¹⁵), a neuroimaging phenotype related to gray-white boundary microstructure and myelination. Finally, bidirectional Mendelian randomization supported a modest directional association between genetic liability to SCZ and increased ADRD risk, but not the reverse direction. Collectively, these findings provide convergent genetic, regulatory, transcriptomic, developmental, and imaging evidence for partial shared liability between SCZ and ADRD, highlighting 16p11.2 and biological processes related to neurodevelopment, synaptic and axonal organization, myelination-related microstructure, and later-life brain vulnerability.