Genetic architecture of treatment-resistant schizophrenia across East Asian and European cohorts: insights from GWAS, TWAS, and synaptic pathway analyses

In about a quarter of people with schizophrenia-spectrum disorder (SSD), the illness is unresponsive to standard antipsychotic treatment, yet the biological mechanisms underlying this remain poorly understood. Although such treatment-resistant schizophrenia (TRS) shares a substantial genetic liability with treatment-responsive schizophrenia, the limited efficacy of dopamine antagonists in TRS indicates that mechanisms beyond dopamine signalling likely contribute to treatment-resistance, requiring the identification of alternative biological pathways. This is the first cross-ancestry genetic study to investigate the genetic architecture of TRS, by directly comparing patients with treatment-resistant and treatment-responsive schizophrenia in two independent Hong Kong (N=798) and STRATA-G consortium (N=1243) cohorts. Using an integrated multi-level analytic framework, we conducted a genome-wide association study (GWAS) with gene-based and gene set-based analyses, pathway polygenic-risk-scores, and transcriptome-wide association study (TWAS). We further conducted gene-set enrichment analysis focusing on expert-curated synaptic pathways and brain tissues. Genetic signals at the gene, pathway, and genetically predicted expression levels were identified within each ancestry. Whereas limited power constrained individual loci discovery and cross-ancestry concordance, enrichment analyses indicated heterogeneous signals across cohorts, including differences in effect direction, but highlighted cohort-specific, synapse-related biology, particularly pathways involved in presynaptic vesicle dynamics, neurotransmission, and synaptic organization. Collectively, these findings highlight synaptic biology as one potential pathway-level signal from common-variant genetic effects associated with treatment resistance in SSD, despite minimal SNP-level discovery. Our work suggests there is promise in pathway-level and multi-omics approaches to elucidate biologically meaningful heterogeneity within SSD and provides support for synaptic mechanisms as potential targets for understanding and stratifying treatment-resistance.