Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development

Abstract

The development of the human cerebral cortex is a complex and dynamic process, in which neural stem cell proliferation, neuronal migration, and post-migratory neuronal organization need to occur in a well-organized fashion. Alterations at any of these crucial stages can result in malformations of cortical development (MCDs), a group of genetically heterogeneous neurodevelopmental disorders that present with developmental delay, intellectual disability and epilepsy. Recent progress in genetic technologies, such as next generation sequencing, most often focusing on all protein-coding exons (e.g., whole exome sequencing), allowed the discovery of more than a 100 genes associated with various types of MCDs. Although this has considerably increased the diagnostic yield, most MCD cases remain unexplained. As Whole Exome Sequencing investigates only a minor part of the human genome (1–2%), it is likely that patients, in which no disease-causing mutation has been identified, could harbor mutations in genomic regions beyond the exome. Even though functional annotation of non-coding regions is still lagging behind that of protein-coding genes, tremendous progress has been made in the field of gene regulation. One group of non-coding regulatory regions are enhancers, which can be distantly located upstream or downstream of genes and which can mediate temporal and tissue-specific transcriptional control via long-distance interactions with promoter regions. Although some examples exist in literature that link alterations of enhancers to genetic disorders, a widespread appreciation of the putative roles of these sequences in MCDs is still lacking. Here, we summarize the current state of knowledge on cis -regulatory regions and discuss novel technologies such as massively-parallel reporter assay systems, CRISPR-Cas9-based screens and computational approaches that help to further elucidate the emerging role of the non-coding genome in disease. Moreover, we discuss existing literature on mutations or copy number alterations of regulatory regions involved in brain development. We foresee that the future implementation of the knowledge obtained through ongoing gene regulation studies will benefit patients and will provide an explanation to part of the missing heritability of MCDs and other genetic disorders.

The Spectrum of PAX6 Mutations and Genotype-Phenotype Correlations in the Eye

“…An increasing number of reports point to the implication of mutations in non-coding regions in neurodevelopmental and eye disorders [94][95][96]. In the PAX6 Mutations Database, approximately 15% of all variants are located in the intronic regions and they are generally associated with classical aniridia phenotypes.…”

Interpreting the impact of noncoding structural variation in neurodevelopmental disorders

“…Moreover, de novo variants identified in patients with NDDs were also found to be enriched in regulatory elements, including promoter regions 50 and brain-specific enhancer elements 51 (Vas et al, unpublished data). For a more detailed discussion on enhancer function in brain development and disease we refer to other reviews [52][53][54] .…”

Recent advances in epilepsy genomics and genetic testing

“…Despite state-of-the-art genetic testing, more than 50% of patients with DEE remain without a genetic diagnosis. Whole GS is increasingly being used to uncover the role of non-coding genetic material in the human genome 48,49 . Undoubtedly, massively parallel sequencing has greatly accelerated disease gene (and variant) discovery, but most studies and nearly all clinical testing employ gene panels or ES, limiting the genomic search space and the types of variants that can potentially be identified.…”