Activity-Dependent Changes in Gene Expression in Schizophrenia Human-Induced Pluripotent Stem Cell Neurons

Abstract

IMPORTANCE Schizophrenia candidate genes participate in common molecular pathways that are regulated by activity-dependent changes in neurons. One important next step is to further our understanding on the role of activity-dependent changes of genes expression in the etiopathogenesis of schizophrenia. OBJECTIVE To examine whether neuronal activity-dependent changes of gene expression is dysregulated in schizophrenia. DESIGN, SETTING, AND PARTICIPANTS Neurons differentiated from human induced pluripotent stem cells (hiPSCs) derived from 4 cases with schizophrenia and 4 unaffected controls were depolarized using potassium chloride. RNA was extracted followed by genome-wide profiling of the transcriptome. MAIN OUTCOMES AND MEASURES We performed differential expression analysis and gene co-expression analysis to identify activity-dependent or disease-specific changes of the transcriptome. Gene expression differences were assessed with linear models. Further, we used gene set analyses to identify co-expressed modules that are enriched for schizophrenia risk genes. RESULTS We identified 1,669 genes that are significantly different in schizophrenia-associated vs. control hiPSC-derived neurons and 1,199 genes that are altered in these cells in response to depolarization (linear models at false discovery rate ≤ 0.05). We show that the effect of activity-dependent changes of gene expression in schizophrenia-associated neurons (59 significant genes at false discovery rate ≤ 0.05) is attenuated compared to controls (594 significant genes at false discovery rate ≤ 0.05). Using gene co-expression analysis, we identified 2 modules (turquoise and brown) that are associated with diagnosis status and 2 modules (yellow and green) that are associated with depolarization at false discovery rate ≤ 0.05. For 3 out of the 4 modules we found enrichment with schizophrenia-associated variants: brown (Fisher’s P = 0.002), turquoise (Fisher’s P = 0.044) and yellow (Fisher’s P = 0.018). CONCLUSIONS AND RELEVANCE Our results show that schizophrenia candidate genes cluster within gene networks that are associated with a blunted effect of activity-dependent changes of gene expression in schizophrenia-associated neurons. Overall, these findings link schizophrenia candidate genes with specific molecular functions in neurons, which could be utilized to examine underlying mechanisms and therapeutic interventions related to schizophrenia.

Common developmental genome deprogramming in schizophrenia — Role of Integrative Nuclear FGFR1 Signaling (INFS)

“…596 genes were differentially expressed in neurons derived from schizophrenic patients versus controls, reflecting the phenotypic differences between the differentiated neuronal populations (Brennand et al, 2011). Previous work has shown that schizophrenia hiPSC-derived NPCs have aberrant migration (Brennand et al, 2014b) and cellular polarity (Yoon et al, 2014), perturbed WNT signaling (Srikanth et al, 2015; Topol et al, 2015b), increased oxidative stress (Brennand et al, 2014b; Paulsen et al, 2011; Robicsek et al, 2013) and altered responses to environmental stressors (Hashimoto-Torii et al, 2014); while schizophrenia hiPSC-derived neurons exhibit decreased neurite number (Brennand et al, 2011), reduced synaptic maturation (Brennand et al, 2011; Robicsek et al, 2013; Wen et al, 2014; Yu et al, 2014) and synaptic activity (Wen et al, 2014; Yu et al, 2014), and blunted activity-dependent response (Roussos et al, 2016). Extensive immunocytochemical validation of the NPC lines used in the present study showed they are positive for diverse NPC markers including nestin, Sox2, vimentin, Pax6 and TBR2(Brennand et al, 2015).…”

Tracing Early Neurodevelopment in Schizophrenia with Induced Pluripotent Stem Cells

“…In light of the retained spontaneous activity in SCZ iPSC-neurons, Roussos et al [ 76 ] moved on to investigate differences in activity dependent gene expression. Potassium chloride treatment was used for neuronal depolarization of iPSC-derived case/control forebrain neurons.…”

Prefrontal co-expression of schizophrenia risk genes is associated with treatment response in patients

“…WGCNA ( 13 , 64 ) uses gene-gene Pearson’s correlation indices as a continuous, i.e., weighted, measure of gene-gene relationships. We computed unsigned networks, i.e., negatively correlated genes are considered connected rather than non-connected ( 65 ). The correlation matrix was transformed into an adjacency matrix by raising Pearson’s coefficients to a positive exponent, β, which is chosen to meet the “scale-free” power law connectivity distribution.…”