Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders

A meta-genome-wide association study across eight psychiatric disorders has shed light on the genetic architecture of pleiotropy in major psychiatric disorders. However, the mechanisms underlying pleiotropic effects of the associated variants remain to be investigated. We conducted a massively parallel reporter assay to decipher the regulatory logic of variants with disorder-specific and pleiotropic effects. We found that pleiotropic variants differ from disorder-specific variants by manifesting chromatin accessibility that extends across diverse cell types in the neuronal lineage, as well as by altering motifs for transcription factors with higher connectivity in protein-protein interaction networks. Next, we mapped pleiotropic and disorder-specific variants to putative target genes using functional genomics approaches. CRISPR-mediated validation confirmed the functional impact of selected variants on predicted target genes. Furthermore, in vivo CRISPR perturbation of a pleiotropic and a disease-specific gene suggests that pleiotropy is mediated by the regulation of genes expressed in a broader range of neuronal types and with higher network connectivity. Overall design: To functionally validate emVar-gene relationships, we used CRISPR droplet sequencing (CROP-seq) in human induced pluripotent stem cell (hiPSC)-derived neurons that constitutively express dCas9-KRAB and an inducible NGN2 cassette. Cells containing the CROP-seq construct were isolated by using Fluorescence-activated cell sorting (FACS) for RFP signal and analyzed via scRNA-seq.