Normal development and healthy life are the result of the coordinated function of gene networks that appropriately adjust their equilibrium as needed. Functional genetic variation can shift network equilibrium and under unfavorable circumstances make networks fail, leading to disease. Most common functional genetic variants have small effects at the organism level, however our and others' data suggest that they may have much larger effects on isolated cells, in the absence of the organism's buffering defense mechanisms. In cells changes can be more striking, the most immediate change being in the cell's transcriptional output. The transcriptional signature of a functional variant reflects the specific networks it disrupts and when studied across many variants can help identify intervention targets. We propose to study 10 SZ associated loci and identify their common networks and candidate pharmacological interventions through the following specific aims: 1) We will choose loci where one or few experiments can confidently achieve targeting the functional variant. We will edit the genome of one male and one female induced pluripotent stem cell (iPSc) line to generate homozygotes for the risk and non-risk allele. These will be a resource for the next aims and for sharing with others. 2) We will differentiate the iPSc to cortical neurons and to astrocytes and compare the transcriptomes of the two homozygotes that are otherwise isogenic. We will perform 20 locus specific transcriptome analyses per cell type (10 in male and 10 in female cells) and compare results. 3) We will analyze all loci together to identify gene clusters that similarly change their expression in response to many modified loci. We will perform exploratory analyses that may offer insights in the involvement of these clusters in disease risk, the best candidate cluster for follow up and the specific relationship of each cluster to clinical presentation. We will then do a first screen for complementary drug signatures utilizing public resources, follow up select compounds to verify complementarity in neurons and astrocytes, test for rescue of the SZ variant induced changes and identify possible male-female differences. At the end of the project we will have created the first resource of modified iPS cells carrying functionally confirmed SZ-risk alleles. We will have identified gene clusters reflecting signatures of network disruptions shared by many SZ loci. We will have determined the specificity each cluster contributes to the disease phenotype and identified candidate pharmacological interventions for further testing.
Recent studies have uncovered over 100 genetic variants that increase the risk for schizophrenia, yet the genes they affect and the consequences that they have on cell function in most cases remain unknown. Our laboratory has data showing that using cutting edge genome editing tools and working with single cells under controlled conditions can uncover the consequences of functional genetic variants, point to their common denominators and use this information to identify potential drugs to reverse them. In this project we will edit the genome of human cells to introduce multiple schizophrenia-associated genetic variants, differentiate them into brain cells, determine each variant's molecular consequences and perform an exploratory screen for common drugs that may reverse them.
