Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion

Abstract

BackgroundIndividuals with 22q11.2 Deletion Syndrome (22q11.2 DS) are a specific high-risk group for developing schizophrenia (SZ), schizoaffective disorder (SAD) and autism spectrum disorders (ASD). Several genes in the deleted region have been implicated in the development of SZ, e.g., PRODH and DGCR8. However, the mechanistic connection between these genes and the neuropsychiatric phenotype remains unclear. To elucidate the molecular consequences of 22q11.2 deletion in early neural development, we carried out RNA-seq analysis to investigate gene expression in early differentiating human neurons derived from induced pluripotent stem cells (iPSCs) of 22q11.2 DS SZ and SAD patients.MethodsEight cases (ten iPSC-neuron samples in total including duplicate clones) and seven controls (nine in total including duplicate clones) were subjected to RNA sequencing. Using a systems level analysis, differentially expressed genes/gene-modules and pathway of interests were identified. Lastly, we related our findings from in vitro neuronal cultures to brain development by mapping differentially expressed genes to BrainSpan transcriptomes.ResultsWe observed ~2-fold reduction in expression of almost all genes in the 22q11.2 region in SZ (37 genes reached p-value < 0.05, 36 of which reached a false discovery rate < 0.05). Outside of the deleted region, 745 genes showed significant differences in expression between SZ and control neurons (p < 0.05). Function enrichment and network analysis of the differentially expressed genes uncovered converging evidence on abnormal expression in key functional pathways, such as apoptosis, cell cycle and survival, and MAPK signaling in the SZ and SAD samples. By leveraging transcriptome profiles of normal human brain tissues across human development into adulthood, we showed that the differentially expressed genes converge on a sub-network mediated by CDC45 and the cell cycle, which would be disrupted by the 22q11.2 deletion during embryonic brain development, and another sub-network modulated by PRODH, which could contribute to disruption of brain function during adolescence.ConclusionsThis study has provided evidence for disruption of potential molecular events in SZ patient with 22q11.2 deletion and related our findings from in vitro neuronal cultures to functional perturbations that can occur during brain development in SZ.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0366-0) contains supplementary material, which is available to authorized users.

Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress

“…Quantitative real-time PCR (qPCR) was carried out as previously described using the 2 −∆∆Ct method to calculate relative expression levels, with β2-microglobulin ( β2M ) and G6PD as reference genes [39, 40]. Briefly, cDNA was generated using iScript cDNA Synthesis Kit (Bio-Rad).…”

Genetic and clinical features of social cognition in 22q11.2 deletion syndrome

“…Liu et al () identified specific genetic alterations such as pseudogene‐like variants in the PRODH/DGCR6 locus on chromosome 22, assuming it could interfere with the production of the enzyme. PRODH is also involved in the apoptosis of neural cells, which can imply a function in central nervous system development (Hu et al, ; Lin et al, ). Furthermore, PRODH mutations have proven to be more frequent in patients with schizophrenia, providing a stronger evidence for a role in this disease pathogenesis (Clelland et al, ; Maynard et al, ).…”

Modeling schizophrenia pathogenesis using patient-derived induced pluripotent stem cells (iPSCs)

“…In addition, genes involved in cell cycle, apoptosis and MAPK pathway were affected [38]. Consistent with this finding, another group also observed disruption of the MAPK pathway in 22q11.2 deletion syndrome in mixed neuronal populations [39], though there was differences in miRNA findings between these two studies [39,40].…”

“…Subject selection criteria vary in these studies, spanning from specific genetic abnormalities like CNVs such as 22q11.2 deletion [38–40], 15q11.2 deletion [41] or CNTNAP2 deletion [42] and mutations such as DISC1 mutation [43,44] to SCZ patients with no identified genetic risk factor drawn from clinical populations [45–48]. Childhood onset SCZ (COS) [49], has also been studied since COS exhibits more severe psychopathology as compared to adult onset SCZ and thus would likely have a more robust cellular phenotype.…”

“…In these studies, the neural populations generated, range from neural progenitor cells (NPC) [41–43,45,46,48,49,52] to mixed neural populations [38–40,47,53] and to more specific neural subtypes such as highly enriched glutamatergic neurons [44]. These iPSC-derived neural populations recapitulate the normal developmental time frame and more closely resemble fetal neural progenitors and neuronal populations, suitable for analysis of developmental abnormalities.…”