Authors :
Presenting Author: James Fink, PhD – Quiver Bioscience
Karthiayani Harikrishnan, BS – Quiver Bioscience
Aishwarya Dhandapani, BS – Quiver Bioscience
Mahdi Torkashvand, PhD – Quiver Bioscience
Caitlin Lewarch, PhD – Quiver Bioscience
Fabricio Simao, PhD – Quiver Bioscience
Steven Ryan, PhD – Quiver Bioscience
David Gerber, PhD – Quiver Bioscience
Luis Williams, PhD – Quiver Bioscience
Graham Dempsey, PhD – Quiver Bioscience
Rationale:
Dup15q syndrome is a neurodevelopmental disorder characterized by hypotonia, language impairments, intellectual disability, and seizures, and associated with an increased risk of sudden unexpected death in epilepsy (SUDEP).Dup15q results from duplications of the maternal chromosome 15q11-q13 region, leading to overexpression of >20 genes, including the imprinted gene UBE3A. UBE3A encodes an E3 ubiquitin ligase and is a critical pathogenic factor in Dup15q. Antisense oligonucleotides (ASOs) have emerged as a powerful therapeutic modality for genetic diseases, in particular for neurogenetic disorders where these molecules can be directly targeted to central nervous system (CNS) tissue via intrathecal (IT) administration. We are developing ASOs to target the knockdown of excess UBE3A as a disease modifying therapeutic approach for Dup15q. The overall objective of this program is to bring a much-needed, genetically targeted precision therapeutic to Dup15q patients.
Methods:
We combined traditional molecular biology techniques for measuring transcript and protein (qPCR and immunoblotting, respectively) and Dup15q patient induced pluripotent stem cell (iPSC) models with our novel data layer of all-optical single cell electrophysiology to select and rank antisense oligonucleotide lead molecules for better in vitro efficacy and reduced in vivo toxicity. Mouse intracerebroventricular (ICV) and rat IT studies were used to assess CNS tolerability to high ASO doses. Dup15q in vitro phenotypes based on all-optical electrophysiology of human iPSC-derived neurons were used to further assess therapeutic window and dose-response effects on phenotypic rescue. We are now using AI/ML to build a classifier of toxicity for gapmer ASOs trained on external data and our in vitro neuronal functional assays using our proprietary optical physiology technologies to dramatically improve predictivity of ASO in vivo CNS toxicity.
Results:
UBE3A-targeting ASOs passed stringent in silico filters to avoid binding to off-target transcripts, undesired thermodynamic properties, and sequence motif liabilities. Using our in vitro assays, we identified ASOs achieving >70% UBE3A transcript and protein knockdown that are de-risked to avoid perturbations of neuronal physiology. Based on this characterization, we 11 selected optimal UBE3A ASO leads for assessment in vivo, and demonstrated desirable tolerability in both mouse ICV and rat IT studies, with Ube3a knockdown in different CNS tissues.
Conclusions:
Our UBE3A ASOs show desirable efficacy, rescuing Dup15q-associated phenotypes in vitro, and have been de-risked for in vivo CNS tolerability. Lead ASOs will now proceed to tolerability and dose-range finding evaluations in non-human primates to then select a development candidate for IND-enabling studies.
Funding: NA