Analysis of 14q12 microdeletions reveals novel regulatory loci for the neurodevelopmental disorder-related gene, FOXG1

Structural variants (SVs) are genetic variants that can vary widely in size, but are generally greater than 50bp. While there are many different types of SVs, deletions are perhaps the easiest to interpret given the loss of genetic material. As such up to 17% of neurodevelopmental disorders (NDDs) can be explained by SVs that disrupt coding regions causing gene dosage defects. Conversely, the contribution of non-coding SVs to the etiology of NDDs is unknown., From a few NDDs, and other mendelian disorders we know that non-coding SVs can perturb cis-regulatory elements (CREs) and disrupt downstream gene expression. In this study, we identified multiple deletions in the 14q12 region downstream of NDD-related gene FOXG1 in individuals with epilepsy, microcephaly, intellectual disability (ID) and/or developmental delays. This gene encodes a transcription factor essential for cerebral corticogenesis, and FOXG1 haploinsufficiency is associated with epilepsy and other NDDs. To test whether the 14q12 deletions alter FOXG1 expression, we chose the minimum region overlapping these deletions (MRO), and modeled this deletion in HAP1s, a haploid line expressing FOXG1. Deletion of the MRO reduced FOXG1 mRNA and protein levels, while altering FOXG1s native genomic interactions. We identified at least two novel putative FOXG1 CREs in the MRO and propose multiple CREs coregulate FOXG1. Moreover, changes in the transcriptomic profiles seen with MRO loss overlap in part with FOXG1 loss, indicating converging molecular pathways of FOXG1 haploinsufficiency. These findings expand the scope of FOXG1s complex regulatory mechanisms, and more broadly, of regulatory SVs in NDD susceptibility. A comprehensive understanding of regulatory SVs will enable the identification of regulatory elements that are potential targets for gene-targeting therapies, including in FOXG1-related NDDs.