Using RNA-seq to Assess Off-Target Effects of Antisense Oligonucleotides in Human Cell Lines
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ORIGINAL RESEARCH ARTICLE
Using RNA‑seq to Assess Off‑Target Effects of Antisense Oligonucleotides in Human Cell Lines Sven Michel1 · Ksenija Schirduan1 · Yimin Shen2 · Richard Klar1 · Jörg Tost2 · Frank Jaschinski1 Accepted: 20 November 2020 © Springer Nature Switzerland AG 2020
Abstract Background The field of antisense oligonucleotide therapeutics is rapidly growing and in addition to small molecules and therapeutic antibodies, oligonucleotide-based gene expression modifiers have been developed as fully accepted therapeutics. Antisense oligonucleotides are designed to modify gene expression of their specific target genes. However, as their effect relies on Watson–Crick base pairing, they could also bind to other unintended complementary RNAs showing sufficient sequence homology, which in turn could lead to off-target effects. It is assumed that these off-target effects depend on the degree of complementarity between the antisense oligonucleotides and off-target sequences. Objective Aim of this study was the investigation of the effects of antisense oligonucleotides on the expression of potential off-targets having a defined number of mismatches to the oligonucleotide sequence. Methods We extend recent studies by investigating the off-target profile of two 17-mer antisense oligonucleotides in two distinct human cell lines by a whole-transcriptome study using RNA sequencing. Results The relatively high percentage of significantly downregulated off-target genes for which one mismatch is present corroborates the requirement for intense bioinformatic screens and stringent specificity criteria to design antisense oligonucleotides with only minimal sequence complementarity to any non-target sequence. Conclusions Avoiding suppression of off-target genes by a thorough bioinformatics screen should strongly reduce the risk for toxicities caused by antisense oligonucleotide-mediated off-target RNA suppression and finally result in safer antisense oligonucleotide-based therapeutics.
1 Introduction The field of antisense oligonucleotide (ASO) therapeutics is rapidly growing and in addition to small molecules and therapeutic antibodies, oligonucleotide-based gene expression modifiers have developed as fully accepted therapeutics. By the end of 2019, seven treatments based on antisense Supplementary information The online version of this article (https://doi.org/10.1007/s40291-020-00504-4) contains supplementary material, which is available to authorized users. * Sven Michel [email protected] * Frank Jaschinski [email protected] 1
Secarna Pharmaceuticals, GmbH & Co. KG, Am Klopferspitz 19, 82152 Planegg/Martinsried, Germany
Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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Key Points RNA sequencing provides a useful tool to assess antisense oligonucleotide-mediated off-target effects. Applying RNA sequencing during the drug candidate selection process can result in the selection of s
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