Lithium partially rescues gene expression and enhancer activity from heterozygous knockout of AKAP11 while inducing novel differential changes [RNA-Seq]

Bipolar disorder (BD) is a complex psychiatric condition usually requiring long-term treatment. Lithium (Li) remains the most effective mood stabilizer for BD, yet it benefits only a subset of patients, and its precise mechanism of action remains elusive. Exome sequencing has identified AKAP11 (A-kinase anchoring protein 11) as a shared risk gene for BD and schizophrenia (SCZ). Given that both the AKAP11-Protein Kinase A (PKA) complex and Li target and inhibit Glycogen Synthase Kinase-3 beta (GSK3ß), we hypothesize that Li may partially normalize the transcriptomic and/or epigenomic alterations observed in heterozygous AKAP11-knockout (Het-AKAP11-KO) iPSC-derived neurons. In this study, we employed genome-wide approaches to assess the effects of Li on the transcriptome and epigenome of human iPSC-derived Het-AKAP11-KO neuronal culture. We show that chronic Li treatment in this cellular model upregulates key pathways that were initially downregulated by Het-AKAP11-KO, several of which have also been reported as downregulated in synapses of BD and SCZ post-mortem brain tissues. Moreover, we demonstrated that Li treatment partially rescues certain transcriptomic alterations resulting from Het-AKAP11-KO, bringing them closer to the WT state. We suggest two possible mechanisms underlying these transcriptomic effects: (1) Li modulates histone H3K27ac levels at intergenic and intronic enhancers, influencing enhancer activity and transcription factor binding, and (2) Li enhances GSK3ß serine 9 phosphorylation, impacting WNT/ß-catenin signaling and downstream transcription. These findings underscore Li's potential as a therapeutic agent for BD and SCZ patients carrying AKAP11 loss-of-function variants or exhibiting similar pathway alterations to those observed in Het-AKAP11-KO models. Overall design: We utilized our previously generated heterozygous AKAP11-knockout (Het-AKAP11-KO) isogenic clones (three clones, neuronal-glial cultures) and their WT counterparts (three replicates, neuronal-glial cultures) and treated them chronically with lithium (1.5 mM for 11 days). We then performed gene expression profiling on the three AKAP11-KO clones and the three WT replicates, both untreated and lithium-treated, to analyze differential gene expression. Specifically, we aimed to (1) identify differentially expressed genes in AKAP11-KO-Li compared to AKAP11-KO-UNT, (2) detect genes that were differentially expressed in AKAP11-KO-UNT vs. WT-UNT but lost their differential expression in AKAP11-KO-Li vs. WT-UNT, and (3) identify genes that were not differentially expressed in AKAP11-KO-UNT vs. WT-UNT but became differentially expressed in AKAP11-KO-Li vs. WT-UNT.