Effects of combinations of gapmer antisense oligonucleotides on the target reduction

BACKGROUND: The co-administration of several therapeutic oligonucleotides targeting the same transcript is a beneficial approach. It broadens the target sites for diseases associated with various mutations or splice variants. However, little is known how a combination of antisense oligonucleotides (ASOs), which is one of the major modalities of therapeutic oligonucleotides, affects the potency. In this study, we aimed to elucidate the combination-effects of ASOs and the relationship between the target sites and potency of different combinations. METHOD AND RESULTS: We designed 113 ASOs targeting human superoxide dismutase 1 pre-mRNA and found 13 ASOs that had comparable silencing activity in vitro. An analysis of combination-effects on the silencing potency of 37 pairs of two ASOs on HeLa cells revealed that 29 pairs had comparable potency to that of two ASOs; on the other hand, eight pairs had reduced potency, indicating a negative impact on the activity. A reduced potency was seen in pairs targeting the same intron, exon-intron combination, or two different introns. The sequence distance of target sites was not the major determinant factor of combination-effects. In addition, a combination of three ASOs preserving the potency could be designed by avoiding two-ASO pairs, which had a reduced potency. CONCLUSIONS: This study revealed that more than half of the combinations retain their potency by paring two ASOs; in contrast, some pairs had a reduced potency. This could not be predicted only by the distance between the target sites. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11033-022-08224-0.