Understanding Convergent Pathobiology in Idiopathic Autism Using Human iPSCs
Objective: Patient-specific induced pluripotent stem cells (iPSCs) present a unique opportunity to examine the hypothesis that heterogeneous ASD loci converge on specific molecular pathways during early neural development.
Methods: iPSC lines were derived from individuals with idiopathic autism and differentiated into cortical neurons. We examined the transcriptional differences between iPSC-derived cortical neurons from individuals with ASD and cognitively normal control individuals over a 135 day neuronal differentiation approach using RNAseq analysis. Bioinformatic analysis was performed by weighted gene coexpression network analysis (WGCNA) and Ingenuity Pathway Analysis (IPA). This RNA-seq analysis was complemented by functional studies of these developing neurons using electrophysiological, morphological, and biochemical analyses.
Results: Transcriptional analyses of ASD and control neurons at culture days 35 and 135 of their in vitro development showed ASD-specific transcriptional signatures, including differences in coding genes, alternative splicing, and non-coding RNAs. These changes in transcription mainly affecting pathways/networks involved in neuronal differentiation, the cytoskeletal matrix structure formation (i.e. axon guidance and cell migration), regionalization, patterning, and DNA and RNA metabolism. Additionally, developing networks of neurons were analyzed using multi-electrode array (MEA) recordings, measurements of calcium transients, and cell migration assays. Neurons from ASD individuals demonstrated significantly decreased network spiking activity and decreased numbers of calcium transients. Additionally, ASD lines showed significant differences in neurite morphology and decreased cell migration at early neuronal differentiation times.
Conclusions: The results of this study suggest that iPSC-derived neurons from individuals with ASD may have early deficits in network activity and morphology based on a combination of cell based assays, including spontaneous action potentials, calcium transients, and neurite outgrowth complementing the transcriptomic analyses. Taken together, these data suggest that, although there is significant genetic diversity in ASD, there is a convergence of pathophysiological processes that effect neuronal functionality.