Davis Sarah M, Hildebrand Samuel, MacMillan Hannah J, Monopoli Kathryn R, Buchwald Julianna, Sousa Jacquelyn, Cooper David, Ly Socheata, Echeverria Dimas, McHugh Nicholas, Ferguson Chantal, Coles Andrew, Hariharan Vignesh N, O'Reilly Daniel, Tang Qi, Furgal Raymond, Yamada Ken, Alterman Julia F, Gilbert James W, Knox Emily, Pineda Yamilett, Weston Caitlyn N, Baer Christina E, Pai Athma A, Khvorova Anastasia
Morningside Graduate School of Biomedical Sciences, T.H. Chan School of Medicine, Interdisciplinary Graduate Program, RNA Therapeutics Institute, Program in Molecular Medicine, Systems Biology, Biochemistry and Molecular Biotechnology, Microbiology and Physiological Systems, MD/PhD Program, University of Massachusetts Chan Medical School, Worcester, MA 01655, United States.
Quantitative and Computational Biosciences and Bioengineering Program, University of Massachusetts Chan Medical School and Worcester Polytechnic Institute, Worcester, MA 01655, United States.
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf479.
Chemically modified small interfering RNAs (siRNAs) are a promising drug class that silences disease-causing genes via mRNA degradation. Both siRNA-specific features (e.g. sequence, modification pattern, and structure) and target mRNA-specific factors contribute to observed efficacy. Systematically defining the relative contributions of siRNA sequence, structure, and modification pattern versus the native context of the target mRNA is necessary to inform design considerations and facilitate the widespread application of this therapeutic platform. To address this, we synthesized a panel of ∼1260 differentially modified siRNAs and evaluated their silencing efficiency against therapeutically relevant mRNAs (APP, BACE1, MAPT, and SNCA) using both reporter-based and native expression assays. Our results demonstrate that the siRNA modification pattern (e.g. level of 2'-O-methyl content) significantly impacts efficacy, while structural features (e.g. symmetric versus asymmetric configurations) do not. Furthermore, we observed substantial differences in the number of effective siRNAs identified per target. These target-specific differences in hit rates are largely mitigated when efficacy is tested in the context of a reporter assay, confirming that native mRNA-specific features influence siRNA performance. Key target-specific factors, including exon usage, polyadenylation site selection, and ribosomal occupancy, partially explained efficacy variability. These insights led to a proposed framework of parameters for optimizing therapeutic siRNA design.
化学修饰的小干扰RNA（siRNA）是一类很有前景的药物，可通过mRNA降解使致病基因沉默。siRNA的特异性特征（如序列、修饰模式和结构）以及靶mRNA的特异性因素都会影响观察到的疗效。系统地确定siRNA序列、结构和修饰模式相对于靶mRNA天然环境的相对贡献，对于指导设计考量并促进这一治疗平台的广泛应用至关重要。为了解决这个问题，我们合成了一组约1260种差异修饰的siRNA，并使用基于报告基因的检测方法和天然表达检测方法评估了它们对治疗相关mRNA（APP、BACE1、MAPT和SNCA）的沉默效率。我们的结果表明，siRNA修饰模式（如2'-O-甲基含量水平）对疗效有显著影响，而结构特征（如对称与不对称构型）则没有。此外，我们观察到每个靶标鉴定出的有效siRNA数量存在很大差异。当在报告基因检测的背景下测试疗效时，这些命中率的靶标特异性差异在很大程度上得到缓解，这证实了天然mRNA的特异性特征会影响siRNA的性能。关键的靶标特异性因素，包括外显子使用、聚腺苷酸化位点选择和核糖体占用率，部分解释了疗效的变异性。这些见解导致了一个用于优化治疗性siRNA设计的参数框架的提出。
