A single-cell map of antisense oligonucleotide activity in the brain

Abstract

Antisense oligonucleotides (ASOs) dosed into cerebrospinal fluid (CSF) distribute broadly throughout the brain and hold the promise of treating myriad brain diseases by modulating RNA. CNS tissue is not routinely biopsied in living individuals, leading to reliance on CSF biomarkers to inform on drug target engagement. Animal models can link CSF biomarkers to brain parenchyma, but our understanding of how individual cells contribute to bulk tissue signal is limited. Here we employed single nucleus transcriptomics on tissue from mice treated with RNase H1 ASOs against Prnp and Malat1 and macaques treated with an ASO against PRNP. Activity was observed in every cell type, though sometimes with substantial differences in magnitude. Single cell RNA count distributions implied target suppression in every single sequenced cell, rather than intense knockdown in only some cells. Duration of action up to 12 weeks post-dose differed across cell types, being shorter in microglia than in neurons. Suppression in neurons was generally similar to, or more robust than, the bulk tissue. In macaques, PrP in CSF was lowered 40% in conjunction with PRNP knockdown across all cell types including neurons, arguing that a CSF biomarker readout is likely to reflect disease-relevant cells in a neuronal disorder.

Global Huntingtin Knockout in Adult Mice Leads to Fatal Neurodegeneration that Spares the Pancreas

“…We find that near-complete loss of HTT is poorly tolerated in the brain, suggesting that a straightforward genome editing approach to complete elimination of both HTT alleles is likely not a desirable approach to HD therapeutics (34) and that the allele-selective genome editing approaches that have been proposed would be better tolerated (35)(36)(37). However, an important limitation of this study is that we used an experimental tool -tamoxifen-inducible Cre -that drives HTT cellular expression from normal levels to near-zero very quickly, which is distinct from pharmacological approaches such as ASOs which result in graded lowering of target genes across cell types (38). The ubiquitous and strong promoters used in this study also drive expression across every cell type of the body (and brain), and so deconvolving the impact of HTT loss on different cell types is not feasible with our approach.…”

Genome wide association study of clinical duration and age at onset of sporadic CJD

“…PRNP cis-eQTL SNPs are predominantly associated with localised tissue expression of PrP, typically in cerebellum or cerebellar hemispheres, and are relatively modest effects. Therapeutic strategies aim for more profound protein knock-down, which will be critical to achieve across a wide range of central nervous system tissues and cell types (36).…”

Treatability of the KMT2-Associated Neurodevelopmental Disorders Using Antisense Oligonucleotide-Based Treatments

“…Neurological disorders are, at this point, the most suitable type of disease for ASO development as the organs that are predominantly affected-the brain, spinal cord, and retina-can easily be reached through local administration, e.g., intrathecal and intraventricular injections. This permits high local exposure while allowing for a lower treatment frequency, lower dosage, and lower systemic effects [60,61]. For a disorder to be eligible for genetic treatments, clinical manifestations must be treatable and clear clinical outcome measures should be definable.…”