Transcriptomics analysis of iPSC-derived neurons and modeling of neurogenesis and neuropsychiatric disorders

Abstract

Induced pluripotent stem cell (iPSC)-derived neurons and neural progenitors are excellent resources for studying neural development and differentiation and their disruptions in disease conditions, and hold the promise of future cell therapy. In particular, it is an ideal model system for gene expression profiling to explore the genetic programs regulating neurodevelopment and study effects of patient-specific genetic background in terms of disease penetrance and severity under different environmental conditions in human neurons, a previously inaccessible cell type. In a series of pilot experiments using iPSCs from healthy subjects, I characterized iPSC model in terms of progression of in vitro-differentiation, potential variation and appropriateness for brain disorder, and demonstrated the power of RNA-seq analysis, especially in understanding the cell composition and differentiation stage of iPSC-derived neuronal cultures, as well as discovering biological importance beyond differential expression analysis. To provide novel insight into molecular impacts of specific genes (e.g. ZNF804A and CHD8) and environmental factors (e.g. fever in maternal immune activation) implicated in schizophrenia, I disrupted these risk factors in iPSC models and then performed transcriptomic analyses to study outcomes. These results provided supports for common pathways underlying schizophrenia and demonstrated the importance of studying single variant in iPSC models for addressing the complexity of psychiatric disorders. Last, to elucidate molecular defect and disease predisposition in schizophrenia, and explore genetic contribution of 22q11.2 deletion syndrome (the strongest known risk factor for schizophrenia) to developmental pathogenesis underlying schizophrenia, I conducted an integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22g11.2 deletion. The result highlighted disruption in pathways such as apoptosis, cell cycle/proliferation, catabolic process /synaptic transmission, and inflammation/immune response. After integration with spatiotemporal transcriptomic profiles of normal human brain development, my study showed that the differentially expressed genes converge on a sub-network mediated by CDC45 and the cell cycle during embryonic brain development, and another sub-network modulated by PRODH and mitochondria function during adolescence. In sum, gene expression analysis using patient-specific iPSC-derived neurons or control iPSC lines with perturbed expression of candidate genes provides an excellent opportunity for tackling the complexity of psychiatric disorders.