Specific Considerations for Preclinical Development of Inhaled Oligonucleotides

Ferrari, Nicoletta

doi:10.1002/9781119070153.ch12

Cited by 2 publications

(2 citation statements)

References 30 publications

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“…By employing the right chemical composition, these synthetic oligonucleotides are able to recruit an enzymatic complex (for example, RNase H1) that initiates the knockdown of gene expression through an enzymatic cleavage reaction. This capability not only highlights their potential as powerful tools for precise gene-expression modulation but also underscores their significance in therapeutic applications [4]. ASOs and siRNAs are two important clinically-proven therapeutic modalities in the broader class of Oligonucleotide-Based Medicines (OBMs) [4].…”

Section: Introductionmentioning

confidence: 99%

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A Dose-Response Model for Accurate Detection and Quantification of Transcriptome-Wide Gene Knockdown for Oligonucleotide-Based Medicines

Pekker,

Kuntz,

McArthur

et al. 2024

Preprint

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Synthetic antisense oligonucleotides and siRNAs are a class of Oligonucleotide-Based Medicines (OBMs) that can hybridize with pre-mRNA and mRNA, recruit a mechanism-of-action specific enzymatic complex, and knockdown target gene expression. This class of molecules provides an excellent substrate for designing precision gene-modulatory therapeutics; however, quantifying on- and off-target dose response as measured by next-generation sequencing for this class of therapeutics has remained under-powered and ambiguous. Often in silico predictions of off-targets (ranked by edit tolerance) are used as putative off-target analysis in ASO and siRNA drug design. We construct a simple, effective theory of transcriptional dynamics and enzymatic activity in order to describe the transcriptome-wide response to these oligonucleotides. We establish rigorous quantification methods of off-target analysis in oligonucleotide drug design. We also extend the DESeq work of Negative Binomial noise in gene expression measurements to describe noise, including outliers, in OBM-dose response NGS experiments. We demonstrate the performance of our model on both synthetic and experimental Digital Gene Expression (DGE) data of dose response in ASO-treated cells. We present our analysis package, DoReSeq, as a freely available resource for the community. We hope this will elevate the standards of off-target analysis for such an important class of precision therapeutics.

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Section: Introductionmentioning

confidence: 99%

“…This capability not only highlights their potential as powerful tools for precise gene-expression modulation but also underscores their significance in therapeutic applications [4]. ASOs and siRNAs are two important clinically-proven therapeutic modalities in the broader class of Oligonucleotide-Based Medicines (OBMs) [4].…”

Section: Introductionmentioning

confidence: 99%

A Dose-Response Model for Accurate Detection and Quantification of Transcriptome-Wide Gene Knockdown for Oligonucleotide-Based Medicines

Pekker,

Kuntz,

McArthur

et al. 2024

Preprint

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Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts

Shin

Chan

Cao

et al. 2022

Nucleic Acids Research

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The lung is a complex organ with various cell types having distinct roles. Antisense oligonucleotides (ASOs) have been studied in the lung, but it has been challenging to determine their effectiveness in each cell type due to the lack of appropriate analytical methods. We employed three distinct approaches to study silencing efficacy within different cell types. First, we used lineage markers to identify cell types in flow cytometry, and simultaneously measured ASO-induced silencing of cell-surface proteins CD47 or CD98. Second, we applied single-cell RNA sequencing (scRNA-seq) to measure silencing efficacy in distinct cell types; to the best of our knowledge, this is the first time scRNA-seq has been applied to measure the efficacy of oligonucleotide therapeutics. In both approaches, fibroblasts were the most susceptible to locally delivered ASOs, with significant silencing also in endothelial cells. Third, we confirmed that the robust silencing in fibroblasts is broadly applicable by silencing two targets expressed mainly in fibroblasts, Mfap4 and Adam33. Across independent approaches, we demonstrate that intratracheally administered LNA gapmer ASOs robustly induce gene silencing in lung fibroblasts. ASO-induced gene silencing in fibroblasts was durable, lasting 4–8 weeks after a single dose. Thus, lung fibroblasts are well aligned with ASOs as therapeutics.

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Specific Considerations for Preclinical Development of Inhaled Oligonucleotides

Cited by 2 publications

References 30 publications

A Dose-Response Model for Accurate Detection and Quantification of Transcriptome-Wide Gene Knockdown for Oligonucleotide-Based Medicines

A Dose-Response Model for Accurate Detection and Quantification of Transcriptome-Wide Gene Knockdown for Oligonucleotide-Based Medicines

Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts

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