Evaluation of Antisense Oligonucleotide-Associated Neuronal Lysosomal Changes

Antisense oligonucleotides (ASOs) are a rapidly growing therapeutic modality that directly modulate splicing or expression of disease-causing genes. ASOs are internalized through various endocytic mechanisms that converge on the endolysosomal pathway. Our work here aims to evaluate changes to the endolysosomal system following repeated ASO exposure. Histological examinations of nonhuman primates following repeated intrathecal administration of ASOs reveal dose-related neuronal microvesicular vacuolation in the hippocampus, cortex, and spinal cord. These changes are not associated with any neuronal degenerative changes or glial activation. Examination by electron microscopy reveals lysosomes containing stacked membranous material. We established an induced pluripotent stem cell–derived motor neuron (iPSC-MN) model that recapitulates these lysosome changes. ASO exposure did not cause any changes in iPSC-MN viability. To characterize lysosomal changes, we isolated lysosomes from iPSC-MNs after ASO treatment and quantified their protein and lipid contents by liquid chromatography–mass spectrometry. Our lipidomics studies documented increases in bis(monoacylglycerol)phosphate and lactosylceramide following ASO administration; proteomic analysis showed changes in several proteins, including decreases in four lysosomal hydrolases (Carboxypeptidase Q, ß-galactosidase, Cathepsin A, and α-