The genetic basis of malformation of cortical development syndromes: primary focus on Aicardi Syndrome

Aicardi Syndrome is a rare neurodevelopmental disorder recognized by a classical triad of chorioretinal lacunae, infantile spasms and agenesis of the corpus callosum. The revised diagnostic criteria of Aicardi Syndrome have been broadened to include additional phenotypes outside of the classical triad that are frequently observed. Early investigations into the genetics of Aicardi Syndrome were predominantly focused on chromosome X for two reasons. Firstly, the first chromosomal aberration reported in a suspected Aicardi female was an X/3 translocation. Secondly, an X-linked male-lethal cause would best explain the predominance of the disease in females, which are represented in more than 99% of cases reported in literature. Despite 70 years of genetic and genomic investigations, an X-linked cause has yet to be established. We performed whole exome and genome sequencing on a cohort of 13 individuals diagnosed with or suspected of Aicardi Syndrome. The phenotypes displayed by of our cohort were clinically heterogeneous, which enabled us to query whether there are: (1) different genetic causes underlying different clinical subsets of Aicardi Syndrome or (2) mutations in a recurring gene that is pleiotropic and with variable penetrance or expressivity. We also investigated the molecular consequences of candidate genes using protein-specific in vitro assays and/or the phenotypic consequences of morpholino-mediated knockdown in zebrafish embryos. We utilised a list-based approach to enrich for variants in genes associated with eye and brain development. To test the efficiency of this list-based approach in finding a genetic diagnosis, we performed whole exome sequencing in a family with autosomal dominant disorder comprising of porencephaly, focal epilepsy and lens opacities. From the affected individuals in this multi-generation family, who were negative for mutations in COL4A1, we found a rare variant in COL4A2. Mutations in COL4A1 are well described and result in brain abnormalities manifesting with severe neurological deficits. Our findings expanded the phenotypic spectrum associated with COL4A2 and highlight the increasing overlap with phenotypes associated with COL4A1. We applied the same list-based approach to our Aicardi Syndrome cohort study. In five unrelated individuals, we identified de novo variants in HCN1, KMT2B, SLF1, SZT2 and WNT8B respectively. Next, we assessed the likely pathogenicity of the autosomal variants we identified using a combination of: pre-existing in vitro assays (HCN1 and WNT8B), published expression and phenotype studies in human or mice and morpholino knockdown in zebrafish (Danio rerio) embryos. Our findings show that causes underlying AIC are genetically heterogeneous but converge on molecular pathways central to cortical development. We highlighted the importance of utilising genetic studies to guide differential diagnosis of syndromes like Aicardi Syndrome that involve multiple complex traits. This will lead to better understanding of how these brain disorders arise, accurate genetic diagnosis and potentially gene-tailored treatments.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 201