Safe-OPTION: Optical Physiology To Interrogate Oligonucleotide Neurotoxicity

Project Summary: Safe-OPTION: Optical Physiology To Interrogate Oligonucleotide Neurotoxicity Antisense oligonucleotides (ASOs) are powerful tools for regulating gene expression and have emerged as a transformative approach for addressing nervous system disorders. Their clinical success in treating conditions like spinal muscular atrophy has paved the way for a diverse pipeline targeting severe neurological disorders such as Dravet syndrome, ALS, Huntington’s Disease and Angelman syndrome. Despite these advancements, there remains significant clinical need and commercial opportunity to efficiently design ASOs without toxic liabilities in the central nervous system (CNS). ASOs can induce acute and delayed neurobehavioral side effects in a dose-dependent manner when administered to the cerebrospinal fluid of pre-clinical species. While ASOs hold promise for treating neurological disorders, there are few publicly disclosed resources used to accurately predict CNS toxicity without resorting to costly and labor-intensive in vivo studies in animal models. As preclinical in vivo toxicity studies are expensive and generally limited to a small number of ASO candidates, the development of tools for identifying and filtering out ASOs with neurotoxic effects prior to conducting in vivo studies would be of significant scientific impact and commercial value. In this direct to Phase II proposal, we aim to establish an integrated platform by combining machine learning (ML)-based ASO design tools and a series of in vitro neuronal functional assays using our all-optical electrophysiology platform to improve predictivity of ASO in vivo CNS toxicity. This will address current challenges hindering toxicity prediction in the CNS, which is a major technical hurdle in developing optimized therapeutic candidates. First, we will perform data mining and then create an integrated platform to predict rodent ASO acute neurotoxicity through ML analysis of sequence features and in vitro neuronal assays. Subsequently, we will assess a set of approximately 200 ASOs using both in vitro and in vivo assays, aiming to establish a predictive model for rodent delayed in vivo CNS toxicity using electrophysiological measurements and sequence feature analysis. Finally, we will develop nonhuman primate (NHP) iPSC-derived neuronal toxicity models to qualify candidate ASOs prior to in vivo evaluation in preclinical models. These advancements in the platform will enhance our ability to identify neurotoxic ASOs early in the design and screening process, thereby accelerating the development of novel CNS therapeutics. Success in Phase II is anticipated to be a significant commercial milestone for QuellTx, facilitating new internal and partnered therapeutic programs and enabling the delivery of safer and more effective treatments for debilitating nervous system disorders.