A bioinformatic approach to the genetics, human cell models and animal models of autism spectrum disorder

Abstract

Autism Spectrum Disorder (ASD) is a group of complex neurodevelopmental disorders with diverse clinical manifestations and symptoms. In the last 10 years, there have been significant advances in understanding the genetic basis for ASD, critically supported through the establishment of ASD bio-collections and application in research. Here in Chapter 3, we summarise a selection of major ASD bio-collections and their associated findings. Collectively, these include mapping ASD candidate genes, assessing the nature and frequency of gene mutations and their association with ASD clinical subgroups, insights into related molecular pathways such as the synapses, chromatin remodelling, transcription, and ASD-related brain regions. We also briefly review emerging studies on the use of induced pluripotent stem cells (iPSCs) to potentially model ASD in culture. We provide perspectives concerning the utilities of ASD bio-collections and limitations and highlight considerations in setting up a new bio-collection for ASD research. In Chapter 4, we also hypothesised that critical ASD candidates should appear widely across different scoring systems, and that comorbidity pathways should be constituted by genes expressed in the relevant tissues. We analysed the Simons Foundation for Autism Research Initiative (SFARI) database and four independently published scoring systems and identified 292 overlapping genes. We examined their mRNA expression using the Genotype-Tissue Expression (GTEx) database and cross-examined protein expression levels using the human protein atlas (HPA) dataset. This led to clustering of the overlapping ASD genes into 2 groups; one with 91 genes primarily expressed in the central nervous system (CNS geneset) and another with 201 genes expressed in both CNS and peripheral tissues (CNS+PT geneset). Bioinformatic analyses showed a high enrichment of CNS development and synaptic transmission in the CNS geneset, and an enrichment of synapse, chromatin remodelling, gene regulation and endocrine signalling in the CNS+PT geneset. Calcium signalling and the glutamatergic synapse were found to be highly interconnected among pathways in the combined geneset. Our analyses demonstrate that 2/3 of ASD genes are expressed beyond the brain, which may impact peripheral function and involve in ASD co-morbidities, and relevant pathways may be explored for the treatment of ASD co-morbidities. Finally in Chapter 5, we analysed the transcriptome of the Nrxn1α knockout mouse cortex from postnatal day 1 (P1) to day 30 (P30) with relevant controls. No significant change was found at the gene or isoform level between WT littermates and Nrxn1α knockout mice at the same timepoint. RNA sequencing data found expression of fusion transcripts of Nrxn1α in Knockouts at P1-P30 with the majority of the first exon removed. Significant changes in expression were however found across the two time points within each genotype. Upregulated genes at P30 were functionally enriched for synaptic transmission and downregulated for neurogenesis. Differentially spliced genes between P1 and P30 were also found to be enriched in synaptic transmission, oligogenesis as well as cytoskeletal and chromatin organisation, with genes showing a profile towards maturation and late exon switching. ASD genes were also found to be expressed during this developmental period.