Deciphering the impact of antisense oligonucleotide activity on RNA and protein level

Most classes of oligonucleotide drugs (ONDs) target RNA with the aim to modify expression on the protein level. The majority of studies evaluating on- and unintended off-target (OffT) activity of ONDs focus on transcriptomic assessment, especially for global changes. The lack of global proteomics studies for antisense oligonucleotides (ASOs) can be attributed to previous bottlenecks, such as high cost, insufficient depth, sensitivity, throughput and variable protein half-life. Here, we leveraged recent breakthroughs in proteomics technology to overcome these bottlenecks and systematically dissect global activity on RNA and protein level upon ASO transfection in HepG2 cells. First, we discovered that safe and liver toxic ASOs showed distinct expression patterns in both RNA sequencing and proteomics datasets. Interestingly, we observed similar ASO on- and OffT activity time courses for RNA and protein, despite longer reported protein half-life. Finally, we distinguished higher numbers of in silico predicted OffTs affected on RNA compared to protein level, which correlated with most predicted OffTs showing a larger reduction on RNA level. We believe that these results demonstrate the importance of studying OND activity on both RNA and protein level and anticipate that our study will stimulate similar work to expand our current understanding of ONDs.