Convergent Pathways in Idiopathic Autism Revealed by Time Course Transcriptomic Analysis of Patient-Derived Neurons

Abstract

Potentially pathogenic alterations have been identified in individuals with autism spectrum disorders (ASDs) within a variety of key neurodevelopment genes. While this hints at a common ASD molecular etiology, gaps persist in our understanding of the neurodevelopmental mechanisms impacted by genetic variants enriched in ASD patients. Induced pluripotent stem cells (iPSCs) can model neurodevelopment in vitro, permitting the characterization of pathogenic mechanisms that manifest during corticogenesis. Taking this approach, we examined the transcriptional differences between iPSC-derived cortical neurons from patients with idiopathic ASD and unaffected controls over a 135-day course of neuronal differentiation. Our data show ASD-specific misregulation of genes involved in neuronal differentiation, axon guidance, cell migration, DNA and RNA metabolism, and neural region patterning. Furthermore, functional analysis revealed defects in neuronal migration and electrophysiological activity, providing compelling support for the transcriptome analysis data. This study reveals important and functionally validated insights into common processes altered in early neuronal development and corticogenesis and may contribute to ASD pathogenesis.

Human in vitro models for understanding mechanisms of autism spectrum disorder

“…Dysregulation in neuronal differentiation and synaptic and dendritic deficits may underlie the decreased spontaneous activity and decreased excitability found in many studies. These are often observed in neurons derived from individuals with idiopathic forms of ASD [112,116,167], as well as from individuals with genetically defined forms of ASD such as SHANK3 [127,130], 16p11.2 deletion and duplication [125], Angelman syndrome [121], Dup15q syndrome [122], NRXN1 mutations [133,135,137], and PTCHD1-AS [140]. Decreases in spontaneous neuronal activity were also found in five out of ten genes associated with ASD when mutations were introduced into neurons derived from typically developing individuals (ATRX, AFF2, KCNQ2, SCN2A, and ASTN2; see Table 1 for the full list of genes tested) [147].…”

“…Two kinds of genetic modeling have been performed using cells either from individuals whose genetic contributions are unknown or undefined, so called idiopathic [59,60,[112][113][114][115][116][117][118][119][120], or from individuals harboring major effect mutations that are presumed causal or which have been engineered to carry these mutations. These mutations include ASD-associated CNVs such as 15q11q13 deletion (Angelman syndrome) [121] and duplication (Dup15q syndrome) [122], 22q11.2 deletion (DiGeorge syndrome) [123,124], 16p11.2 deletion and duplication [125], and 15q13.3 deletion [126], as well as single-gene mutations including SHANK3 [127][128][129][130], CHD8 [131,132], NRXN1 [133][134][135][136][137], NLGN4 [138], EHMT1 (Kleefstra syndrome) [139], PTCHD1-AS [140], UBE3A (Angelman's syndrome) [141], and CACNA1C (Timothy syndrome) [142] (summarized in Table 1).…”

Assessment of Spontaneous Neuronal ActivityIn VitroUsing Multi-Well Multi-Electrode Arrays: Implications for Assay Development

“…From the published literature, studies performing MEA experiments using primary cultures of rodent cortical neurons have a range of reported age of cultures: DIV post plating from dissected brain, and the time of analysis ranges from DIV7 to DIV35, although DIV14 -DIV28 is most common (Table 2). Conversely, studies that instead used neuronal cultures derived from stem cells have a range of culture ages differing to a greater degree, over 30 d (DeRosa et al, 2018;Russo et al, 2018), including up to DIV70 (García-León et al, 2018). This broad range is expected given the variety of differentiation protocols used and increased interval until these cells become electrically active.…”

Probing disrupted neurodevelopment in autism using human stem cell‐derived neurons and organoids: An outlook into future diagnostics and drug development

“…183 A transcriptomic profiling study of iPSC-derived neurons from individuals with idiopathic ASD shows enriched differentially expressed genes in functional pathways related to axon guidance, neuronal migration, and synaptic function. 184 Interestingly, POU3F2 has been identified as a candidate risk gene located within rs238834 through a recent ASD GWAS meta-analysis. 13 POU3F2 encodes for member of the POU-III class of neural transcription factor that plays a role in cortical neuron migration and layering.…”