Antisense Oligonucleotide (ASO) Development for Rare and Neglected Diseases

National Center For Advancing Translational Sciences

Investigators

Linked publications, trials & patents

Abstract

In collaboration with NIH and external academic researchers and companies, we have developed assays that predict antisense oligonucleotide toxicity that can be applied across multiple projects. To date, we have engaged in productive partnerships across various therapeutic areas related to ASO therapies. ASO Toxicity Assay Development: We have developed high-content screening assays using cell-based platforms that will act as a substitute for low-throughput animal toxicity experiments. These screening platforms rely on organoids to predict the toxic side-effects of ASOs and improve the safety pharmacology of this drug class. In parallel, we are developing algorithms that predict toxicity, allowing bad ASOs to be eliminated early in the design phase. In this way, we will speed up the process of ASO development and make it cheaper and faster to produce disease-modifying therapies for rare diseases. Over time, we hope to affect the process required for regulatory approval positively. We collaborate with pharmaceutical companies and academic researchers to achieve these ambitious targets. For example, we are working with Ionis Pharmaceuticals and Roche, two of the leaders in the ASO field, on our in vitro and in vivo screening platform development. Our approach will make the domain knowledge accessible to all stakeholders. We are collaborating on developing and validating 2D and 3D human cell-based ASO toxicity assays using in vitro and nonclinical in vivo toxicity and safety data that our collaborators have previously generated. We incorporated iPSC-derived human neuronal cells into the development of these assays. The approach will support using a patient's cells in future IND-directed safety and toxicity studies for N=1 or a few diseases. Development of a Predictive Model of Safety and Toxicity of Candidate ASO Therapies: In collaboration with Charles River laboratories and our pharmaceutical partners, we are developing a platform to evaluate the safety and acute toxicity of ASOs in mice. These animal data will be compared to the results of cell-based screening assays to determine and validate the ability of the in vitro assays to predict the toxicity properties of ASOs in animals and to rely on the in vitro cell-based studies for future safety readouts. The project's initial focus is on acute and chronic dose-limiting toxicities encountered following intrathecal administration of ASOs targeting CNS neurological disorders. Our screening assay will reduce the need for future animal experimental testing and will help better predict the safety of prospective candidate ASOs intended for clinical use. The long-term aim of this project is to provide sufficient and confirmatory in vivo data to the point that the FDA accepts the cell-based in vitro data in place of conventional animal toxicology studies that are currently required for advancing new ASOs to clinical trials. N=1 Gene Identification in Neurodegenerative and Systemic Rare Diseases: Individualized N=1 therapies inherently target a minimal number of people, even as few as one. We work with the N=1 Collaborative, academia, foundations, and biotech companies to bring customizable treatments targeting the underlying genetic defect as safely and quickly as possible in rare diseases. In some instances, these efforts will apply to a specific mutation. We are initially focused on using antisense oligonucleotides (ASOs), as they are rapidly customizable, cost-efficient to manufacture, straightforward to administer and have a growing safety and efficacy record. Through these efforts, we intend to establish a standardized framework for individualized medicine that will extend to other customizable platform technologies such as siRNAs, RNA therapeutics, and CRISPR. To test our drug development pipeline, we have selected two genes, KIF5A and CHCHD10, that cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) as demonstration projects. ALS is a rare neurodegenerative disease characterized by progressive loss of motor neurons leading to respiratory failure and death. Approximately 7,000 Americans die of ALS yearly, which will increase dramatically in the future because of population aging. In collaboration with Dr. Derek Narendra (NINDS) and Dr. Justin Kwan, the director of the NINDS ALS clinic at the NIH Clinical Center, we work on developing ASOs and screening assays to identify lead ASOs for both genes and perform the IND-enabling studies with the aim of clinical trials. ASO Delivery Development: Most rare diseases affect the central nervous system, meaning gene therapies such as ASOs must be delivered intrathecally. While manageable, this route of administration adds to the complexity when scaling up treatments within the general rare disease population. We explore advanced delivery approaches, such as lipid nanoparticles, chemical structure, and conjugation with targeting moieties. Each system shows promise, but the goal of oral delivery of gene therapy agents will require considerable effort. The resources at NCATS bring key competencies to speed up research on delivery approaches. For example, we collaborate with Optimeos Life Sciences to apply their tunable lipid nanoparticle technology to deliver ASOs. We are working on in vitro and in vivo experiments to explore additional aspects of this innovative delivery system to neurons and other tissues. Together, we are exploring this payload delivery method to decrease the dose and mitigate the toxicity of ASOs. If successful, this novel modality will empower the ASO field in its search for a safe way to distribute this new class of therapeutics to target tissues. ASO Development for Infectious Diseases: In addition to treating rare diseases, we are also deploying ASO technologies to treat emerging viruses. In particular, we are using ASOs to knock down the viral replication of SARS-CoV-2. This project is in collaboration with colleagues in the Early Translation Branch (ETB) at NCATS and Dr. Avindra Nath at NINDS. This effort will map out regions of the viral genome that are amenable to RNA-directed therapies. The underlying notion is that this approach can be more broadly applied to emerging pathogens once their genomic sequence has been isolated. In collaboration with biotech companies, we also work on ASO liver and systemic toxicity discovery and assay development to test the candidate ASOs for infectious diseases.