Fine-mapping psychiatricdisease variants that affect post-transcriptional gene regulation

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PROJECT SUMMARY Neuropsychiatric disorders (NPD) such as schizophrenia (SZ), autism spectrum disorders (ASD) and bipolar disorders (BD) are remarkably common, with SZ alone affecting nearly three million Americans. Despite more than fifty years of research, no cures exist for these conditions and the standard of treatment remains unsatisfactory. Genome-wide association studies (GWAS) indicate that, in addition to highly penetrant rare mutations, NPD risk also reflects the impact of hundreds of common single nucleotide polymorphisms with small effect sizes. A major challenge in the field has been illuminating the pathways connecting these genetic variants (the vast majority of which fall in non-coding sequences) to target genes and causal cellular phenotypes. To understand how these myriad risk loci causally contribute to disease risk, it is essential to screen for putatively causal variant(s) and determine how they influence gene expression, which has been shown to be cell-type specific, as well as cellular function. Recent evidence has emerged indicating a substantial contribution of RNA splicing variation to heritability across many complex genetic diseases, including SZ. Based on our preliminary analyses and the work of others, we hypothesize that a substantial proportion of NPD GWAS loci exert their pathogenic effects on neuronal function by impacting RNA: its structure, modifications, protein interactions and splicing. To test this, we will apply novel tools and machine learning methods to predict and quantify RNA splicing in the largest SZ, ASD and BD GWAS, in order to predict splicing quantitative trait loci (sQTLs, Aim 1). To confirm true effects on exon inclusion independently in glutamatergic and GABAergic neurons (i.e., the major cell-types impacted in NPD), up to several thousand of the predicted splice variants will be tested by a massively parallel reporter assay, MaPSy (Aim 2). Finally, in order to evaluate the cell-type-specific impact of putative causal sQTLs identified in Aims 1 and 2 on neuronal maturation and synaptic function, we will use CRISPR gene editing to engineer these mutations within human induced pluripotent stem cell (hiPSC)-based models of both neural cell types (Aim 3). Our overarching goal is to map and functionally evaluate the NPD-GWAS loci that impact alternative splicing and neuronal function. Our work may impact the field by delivering new insights into the role of common variants in NPD pathophysiology, which could inform ways of improving diagnostics, predicting clinical trajectories, and developing novel therapeutic interventions.