反义寡核苷酸选择性转录组范围评估工作流程。

IF 4.7 2区 医学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Sagar S Damle, Andy Watt, Steven Kuntz, Amanda Crutchfield, Emma Carlborg, Judy Webb, Clare Quirk, Dorde Relic, Scott Donovan, Christopher E Hart, Frank Rigo
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引用次数: 0

摘要

旨在招募RNase H1的反义寡核苷酸(ASOs)已成功用于下调治疗靶点的表达。可以鉴定出有选择性地减少含有完全互补的预期ASO靶位点的转录本的表达,而不影响非预期转录本的表达(选择性ASO)。然而,也可以鉴定出ASOs,这些ASOs减少了与ASO不完全互补的靶位点的意外转录本的表达(非选择性ASOs)。目前,对预测脱靶的计算机规则的理解是次优的。为了确定缺口分子ASOs的选择性,我们开发了一种称为浓度响应数字基因表达(CR-DGE)的实验工作流程。在CR-DGE中,以增加浓度的ASO处理,并使用3'Tag-Seq测量对转录组的影响。然后分析表达数据以鉴定具有浓度响应性敲低的基因。我们证明,CR-DGE鉴定缺口分子ASO浓度响应基因具有高重复性和比常规单浓度测定更高的灵敏度。将CR-DGE应用于一组间隙聚合物ASOs,可识别具有一定选择性的ASOs。这些结果表明,CR-DGE可以有效地用于评估间隙分子ASOs的选择性,为研究和治疗开发提供了有价值的工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A Workflow for Transcriptome-Wide Assessment of Antisense Oligonucleotide Selectivity.

Antisense oligonucleotides (ASOs) designed to recruit RNase H1 (gapmer ASOs) have been used successfully to downregulate the expression of therapeutic targets. Gapmer ASOs can be identified that selectively reduce the expression of transcripts containing the perfectly complementary intended ASO target site without affecting the expression of unintended transcripts (selective ASOs). However, ASOs can also be identified that reduce the expression of unintended transcripts with target sites that are not perfectly complementary to the ASO (nonselective ASOs). Currently, the understanding of in silico rules for predicting off-targets is suboptimal. In order to determine the selectivity of gapmer ASOs, we therefore developed an experimental workflow called concentration-response digital gene expression (CR-DGE). In CR-DGE, ASO treatment is performed at increasing concentrations, and the effect on the transcriptome is measured using 3'Tag-Seq. Expression data are then analyzed to identify genes with concentration-responsive knockdown. We demonstrate that CR-DGE identifies gapmer ASO concentration-responsive genes with high reproducibility and greater sensitivity than conventional single-concentration assays. Applying CR-DGE to a panel of gapmer ASOs identifies ASOs with a range of selectivity. These results demonstrate that CR-DGE can be used effectively to assess the selectivity of gapmer ASOs, offering a valuable tool for research and therapeutic development.

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来源期刊
Nucleic acid therapeutics
Nucleic acid therapeutics BIOCHEMISTRY & MOLECULAR BIOLOGY-CHEMISTRY, MEDICINAL
CiteScore
7.60
自引率
7.50%
发文量
47
审稿时长
>12 weeks
期刊介绍: Nucleic Acid Therapeutics is the leading journal in its field focusing on cutting-edge basic research, therapeutic applications, and drug development using nucleic acids or related compounds to alter gene expression. The Journal examines many new approaches for using nucleic acids as therapeutic agents or in modifying nucleic acids for therapeutic purposes including: oligonucleotides, gene modification, aptamers, RNA nanoparticles, and ribozymes.
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