Benjamin Blencowe aims to systematically elucidate the molecular and genetic mechanisms associated with the (mis)regulation and function of a neuronal microexon network frequently disrupted in autism. The methods and datasets generated by the project are expected to provide a framework for future investigations of RNA regulatory networks disrupted in autism as well as in other nervous system disorders and diseases.

Mutations in the SLC6A1 gene result in a form of pediatric epileptic encephalopathy, intellectual disability and autism spectrum disorder. Allison Bradbury and colleagues are evaluating AAV9-mediated gene replacement as a treatment for SLC6A-related disorders using delivery directly to the cerebrospinal fluid and targeting cell types of interest, neurons and astrocytes. They will perform a dose response study on a candidate vector and determine efficacy with additional clinically relevant readouts of seizure monitoring and electrophysiology.

Many individuals with ASD have mutations in chromatin modifiers and transcription factors. Neville Sanjana’s team aims to understand how mutations in these genes and in nearby noncoding regions alter chromatin structure and transcriptional regulation, generating a large-scale integrated dataset. Such data is expected to help pinpoint which ASD risk genes will yield the biggest benefit when targeted with gene augmentation therapeutics.

The role of dysregulated chromatin biology in ASD has become increasingly apparent as genome sequencing has implicated numerous epigenetic regulatory genes in ASD etiology. As genome sequencing results in significant rates (approximately 28 percent) of variants of uncertain significance, Rosanna Weksberg and colleagues propose to derive DNA methylation signatures for 23 SPARK genes with known or potential functions in chromatin biology that can be developed into predictive tools to enhance accurate diagnostic classification of such variants.

In the current project, Nael Nadif Kasri aims to establish an all-human iPSC-based neuronal network platform to rigorously and multiparametrically assess the consequences of specific mutations in ASD risk genes on neuronal network function. The platform will be used to assess selected ASD gene variants of unknown significance and as a first-tier in vitro selection platform for testing genetic strategies for the amelioration of neuropathological phenotypes associated with genetically defined ASDs.

Rett syndrome (RTT) is a currently incurable neurodevelopmental disorder in urgent need of novel therapies capable of correcting its underlying genetic causes. To accomplish this critical objective, Pablo Perez-Pinera and Thomas Gaj plan to develop a gene therapy for reverting RTT mutations in vivo using CRISPR base editing technology. They anticipate that this work will provide key preclinical data for advancing a cure for this condition.

In the current project, Amy Ramsey and colleagues aim to develop gene therapy for a group of syndromic autism conditions called GRIN disorders. They plan to use a gene replacement strategy where GRIN1 or GRIN2B genes are delivered by adeno-associated viruses. They plan to test different virus capsids, promoters and routes of administration in three mouse models of patient variants. Studies are designed to measure liver and brain toxicity, vector and cargo distribution, and molecular, cellular and behavioral aspects of efficacy.

In the current project, Arpiar Saunders and his lab plan to determine how variants in the ASD risk genes GRIN2B and SYNGAP1 alter molecular and synaptic properties of mouse somatosensory cortical circuits. To achieve this goal, they will use next-generation viral tools and high-throughput single-cell RNA sequencing that enable highly parallelized connectivity and molecular phenotyping of mouse cells expressing human alleles in the intact brain.

Chaolin Zhang and colleagues aim to develop antisense oligonucleotides for dominant haploinsufficiencies associated with autism and related neurodevelopmental conditions. In the current project, the researchers will focus on chromatin regulators that are high-confidence ASD risk genes as a proof-of-concept for such a therapeutic approach.