Benjamin E. Deverman, Ph.D. - US grants

PROJECT SUMMARY In this proposal we aim to identify gene regulatory elements that permit the targeting and manipulation of brain circuit models of human brain function. Gaining genetic access to specific neuron populations in nontransgenic animals and humans would enable targeted circuit modulation for hypothesis testing and provide a means to evaluate the safety and efficacy of circuit modulation for the treatment of epilepsy and psychiatric disorders. Our approach capitalizes on our combined expertise in the development and maturation of brain cell-types and circuits (Gord Fishell), identification of CIS-regulatory elements that function across species (Jordane Dimidschstein) and AAV engineering combined with large-scale screening methods (Ben Deverman). Our efforts will benefit from an ongoing collaboration with John Reynolds at the Salk Institute on observation and manipulation of cortical circuits during complex visual perception tasks. This project will build upon success that we and others have had in identifying gene regulatory elements that enable cell type-restricted gene expression when used within recombinant adeno-associated virus (AAV) vectors. Identifying additional enhancer sequences that function in the context of the limited carrying capacity of AAV has been slow due to the limited success rate and low throughput nature of these efforts. Here we aim to apply a novel high-throughput screening approach for the rapid identification of a suite of enhancers that enable the study and manipulation of genetically defined cell types and circuits across species. Our preliminary data demonstrates that our enhancer identification strategy can yield novel and highly specific enhancers that restrict expression to target populations. In addition, we have demonstrated that it is possible to use the engineered AAV-PHP.eB capsid to screen enhancers across the brain with a single noninvasive injection. These successes have highlighted the need for more rapid and comprehensive assessment of putative enhancers. In the UH3 portion of this proposal we will examine the tolerance to neuronal activity manipulation within the target neuronal populations in several species. We will also apply the AAV-enhancer viruses for querying disease-related circuits using Rabies tracing in conjunction with optogenetics. This proposal will be transformative in devising methods to target and manipulate the brain activity of specific neuronal cell populations across species, including human cell-derived organoids.

Project Summary: Many genetic diseases that affect the central nervous system (CNS) remain untreatable due to a lack effective small molecule drugs or biologics. Targeting the genetic underpinnings of these diseases with somatic cell gene editing would therefore be particularly impactful, but its successful implementation will require methods to safely and efficiently deliver genes and gene editing machinery throughout the CNS. AAVs are the state-of-the-art vehicles for in vivo gene transfer because they can provide safe and long lasting in vivo gene expression. AAVs are the only gene therapy vectors that have been approved for direct administration to humans by regulatory agencies in both the US and Europe. Moreover, in 2017, AAVs became the first vehicle used as part of an early phase clinical trial to evaluate the safety of in vivo gene editing. Despite their impressive preclinical and clinical safety record, naturally occurring AAVs tested to date lack the efficiency required for gene delivery across most organ systems, including the CNS. To address the need for better vehicles for CNS gene delivery, we recently used directed evolution and a new cell type-specific in vivo selection method to engineer several novel AAVs, most notably AAV-PHP.B and AAV-PHP.eB, that have, for the first time, made it possible to noninvasively transfer genes to the majority of neurons and astrocytes throughout the adult mouse CNS. Here, we aim to build upon the success of this selection approach by engineering AAVs that enable efficient gene transfer throughout the CNS of multiple species, including nonhuman primates. The AAVs we develop will be evaluated in several species for their ability to provide CNS-wide transgene expression and targeted genome editing in neurons, and improved AAV variants will be shared with the scientific community. Successful completion of this project, which involves pairing the new AAVs with next-generation gene editing technologies, will provide support for evaluating the safety of CNS gene editing in human trials.