Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells

Antisense oligonucleotide (ASO) has the potential to induce off-target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. In this study, we evaluated off-target effects of gapmer ASOs, which cleave the target RNA in an RNase H-dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off-target effects depending on the degree of complementarity between the ASO and off-target candidate genes. Based on our results, we also propose a scheme for assessment of off-target effects of gapmer ASOs. The Huh-7 cells were seeded in 12-well plates (n = 4/group) and transfected with the LNA-gapmer ASOs using Lipofectamine® 2000 according to the manufacturer’s protocol.Cells treated with transfection reagent in the absence of ASO were used as a control. After a further 24 h, total RNA was isolated.