There are hundreds of neurodevelopmental disorder (NDD) syndromes that cause autism because of the insufficient production of protein due to de novo mutations of specific genes. In most such syndromes, one copy of the key gene remains intact, but one copy alone does not produce enough protein to allow normal brain function. Thus, haploinsufficiency leads to disease. While each individual syndrome is rare, collectively such diseases cause to 10 to 20 percent of autism cases. Critically, while numerous pipelines exist to identify drugs that block the activity of gene products, there are no readily scalable solutions to identifying therapeutics that can be used to promote gene expression and thus restore function to treat the molecular cause of these syndromes.

Joseph Dougherty and colleagues propose to pilot a platform dedicated to adapting a flexible, modular class of therapeutics traditionally used to decrease gene expression – antisense oligonucleotides (ASOs) – to instead promote expression by designing ASOs that block negative regulatory elements in non-coding sequences downstream of disease genes, in the 3’ untranslated region (UTR). To do so, they will implement a new approach ISOMPRA (inferred stability optimized massively parallel reporter assay) to systematically identify such negative regulatory elements, thus developing a platform to discover novel ASOs – promoting expression (ASOPEs) therapeutics. Notably, this proposal focuses on a drug class which have been successfully developed for neurodevelopmental syndromes, including the strikingly efficacious ASO treatment (Nusinersen) for spinal muscular atrophy, typically a lethal neurodevelopmental degenerative condition. The Nusinersen example demonstrates that ASOs can be applied for childhood neurological disorders. The key bottleneck addressed here is figuring out how to scalably design ASOs to upregulate gene expression, applying the approach here for numerous autism syndromes caused by haploinsufficiency.

This project grows out of the Dougherty team’s expertise in studying the function of untranslated regions (UTRs) of transcripts. In preliminary data, they have tested the ISOMPRA approach by tiling the flanking regulatory sequence (the 3’ UTR) of a key NDD gene (WAC), identifying high-priority ASOs leads for inducing gene upregulation. The team will pursue these specific leads, and in parallel, pilot ISOMPRAs ability to identify additional targetable negative regulatory elements, by pursuing the following aims: Aim 1: Identify ASOPEs that can elevate and restore expression of WAC in human neurons. Aim 2: Implement cell-type-specific ISOMPRA to define targetable negative regulatory elements for 12 NDD haploinsufficiency syndromes.