Yoshida Tokuyuki, Naito Yuki, Sasaki Kiyomi, Uchida Eriko, Sato Yoji, Naito Mikihiko, Kawanishi Toru, Obika Satoshi, Inoue Takao
Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
Genes Cells. 2018 Jun;23(6):448-455. doi: 10.1111/gtc.12587. Epub 2018 Apr 18.
Antisense oligonucleotide (ASO) therapeutics are single-stranded oligonucleotides which bind to RNA through sequence-specific Watson-Crick base pairings. A unique mechanism of toxicity for ASOs is hybridization-dependent off-target effects that can potentially occur due to the binding of ASOs to complementary regions of unintended RNAs. To reduce the off-target effects of ASOs, it would be useful to know the approximate number of complementary regions of ASOs, or off-target candidate sites of ASOs, of a given oligonucleotide length and complementarity with their target RNAs. However, the theoretical number of complementary regions with mismatches has not been reported to date. In this study, we estimated the general number of complementary regions of ASOs with mismatches in human mRNA sequences by mathematical calculation and in silico analysis using several thousand hypothetical ASOs. By comparing the theoretical number of complementary regions estimated by mathematical calculation to the actual number obtained by in silico analysis, we found that the number of complementary regions of ASOs could be broadly estimated by the theoretical number calculated mathematically. Our analysis showed that the number of complementary regions increases dramatically as the number of tolerated mismatches increases, highlighting the need for expression analysis of such genes to assess the safety of ASOs.
反义寡核苷酸（ASO）疗法是通过序列特异性的沃森-克里克碱基配对与RNA结合的单链寡核苷酸。ASO的一种独特毒性机制是杂交依赖性脱靶效应，这种效应可能由于ASO与非预期RNA的互补区域结合而发生。为了减少ASO的脱靶效应，了解给定寡核苷酸长度及其与靶RNA互补性的ASO互补区域的大致数量，即ASO的脱靶候选位点，将是很有用的。然而，有错配的互补区域的理论数量迄今尚未见报道。在本研究中，我们通过数学计算和使用数千个假设ASO的计算机分析，估计了人类mRNA序列中有错配的ASO互补区域的一般数量。通过将数学计算估计的互补区域理论数量与计算机分析获得的实际数量进行比较，我们发现ASO的互补区域数量可以通过数学计算的理论数量大致估计。我们的分析表明，随着可容忍错配数量的增加，互补区域的数量急剧增加，这突出了对这类基因进行表达分析以评估ASO安全性的必要性。
