Summary

Genetics have nominated many schizophrenia risk genes and identified convergent signals between schizophrenia and neurodevelopmental disorders. However, functional interpretation of the nominated genes in the relevant brain cell types is often lacking. We executed interaction proteomics for six schizophrenia risk genes that have also been implicated in neurodevelopment in human induced cortical neurons. The resulting protein network is enriched for common variant risk of schizophrenia in Europeans and East Asians, is down-regulated in layer 5/6 cortical neurons of individuals affected by schizophrenia, and can complement fine-mapping and eQTL data to prioritize additional genes in GWAS loci. A sub-network centered on HCN1 is enriched for common variant risk and contains proteins (HCN4 and AKAP11) enriched for rare protein-truncating mutations in individuals with schizophrenia and bipolar disorder. Our findings showcase brain cell-type-specific interactomes as an organizing framework to facilitate interpretation of genetic and transcriptomic data in schizophrenia and its related disorders.

Introduction

Schizophrenia is a debilitating psychiatric disorder occurring in ∼۰٫۳% of the global population with severe repercussions for patients, families, and society.1,2 The last years have seen great advances in mapping the genetic architecture of schizophrenia, identifying hundreds of common and rare variants that confer risk for the disorder across diverse populations.3,4,5,6,7,8,9,10 These studies also revealed overlapping genetic signals between schizophrenia, autism spectrum disorders (ASD), and severe developmental disorders (DD), supporting the importance of neurodevelopmental processes in the pathophysiology of schizophrenia.9,10,11 However, although the identified schizophrenia risk genes provide a good entry point for systematic studies of the disorder and its related conditions, their molecular functions and interactions in the brain remain poorly understood, hindering the development of effective treatments and therapeutics.12,13

In parallel, analyses of postmortem brains from individuals with schizophrenia and integration of genetic and transcriptomic data from human and mouse brains have converged on cortical excitatory neurons as a key biological conduit of genetically encoded risk.14,15,16,17 This suggests that systematic mapping of schizophrenia risk genes onto protein-protein interaction (PPI) networks in this cell type could reveal mechanisms and pathways underlying schizophrenia.18,19 A seminal study showed that adding extrinsic neuronal patterning to pluripotent stem cells (PSCs) overexpressing NGN2 generates glutamatergic induced neurons (iNs) that behave like cortical excitatory neurons at the molecular, morphological, and functional levels.20,21 Here, we leveraged this protocol to perform interaction proteomics for six schizophrenia risk genes that have also been implicated in neurodevelopment in a neuronal cell model. By integrating the resulting PPI networks with orthogonal datasets, we showed that our approach creates a unique opportunity to investigate the roles of schizophrenia risk genes and their associated pathways in a brain cell-type-specific context.

Results

Prioritization of schizophrenia index genes with shared neurodevelopmental signals
To identify schizophrenia risk genes as the basis of our interactome experiments we designed and executed a three-step procedure (Figure 1A and Table S1). First, we identified 445 genes (Set 1) in previously reported genome-wide significant loci from the Psychiatric Genomics Consortium (PGC) genome-wide association study3 (GWAS; phase 2). Second, we filtered this set to 37 genes (Set 2) within single protein-coding gene loci, excluding other genes in loci with more ambiguous association signals. Third, we integrated data from orthogonal studies (e.g., high-density genotyping, exome sequencing, and earlier targeted studies of individual genes; STAR Methods and Table S1) to identify a subset of 10 genes (Set 3) supported by multiple independent lines of evidence. Importantly, we used orthogonal evidence from rare variant studies of ASD/DD to prioritize schizophrenia risk genes that have also been implicated in neurodevelopmental conditions. We additionally included SYNGAP1 in the major histocompatibility complex (MHC) region in all three sets because of strong orthogonal evidence for its involvement in schizophrenia and neurodevelopmental disorders.