Novel Ways of Analyzing RNA for Genetic Psychiatry

Studies suggest a critical overlap between the genes implicated in schizophrenia etiology and the cellular mechanisms of action of clinically effective antipsychotics in medium spiny neurons (MSNs). Our first objective was to use 10x Genomics single-cell RNA-seq to assess differentially expressed genes (DEGs) in specific striatal cell types in C57BL/6 mice that were chronically exposed to a typical antipsychotic (haloperidol), an atypical antipsychotic (olanzapine), or a placebo. We hypothesized that there would be a significant overlap of MSN DEGs for both typical and atypical antipsychotics with schizophrenia GWAS genes. To accomplish this goal we classify cell types and extract cell type specific expression levels to implement DEG analysis. Most genes can generate multiple isoforms which often have drastically different and even opposing functions. It is plausible that SNPs in GWAS implicated loci can change the distribution of isoform expression but not the overall expression level. These genes would not be differentially expressed in a typical DEG study. Hence, in the second study, we aim to generate a comprehensive isoform survey of human DLPFC and to identify isoform level differences in schizophrenia cases and controls. We combine the strength of PacBio SMRT long-read RNA-seq in conducting isoform census with the capacity of short-read RNA-seq for isoform quantification. We then implement a case vs control differential isoform usage analysis (DIU). Delay discounting is an important concept in psychiatric theory of addiction and attention deficit hyperactivity disorder. In the final study aged and young rats were exposed to reward delay choice trials. Tissue was harvested from the nucleus accumbens and the dorsolateral amygdala and sequenced with bulk RNA-seq technology. Network analysis of the expression is used to further examine genes implicated in aging and intertemporal choice.