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

ABSTRACT: Most classes of oligonucleotide drugs (OND) 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 transcriptomics assessment, especially for global changes. The lack of global proteomics studies for 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 than 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 this study will stimulate similar work to expand our current understanding of ONDs.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Anthony Iannetta

LAB HEAD: Anthony Iannetta

PROVIDER: PXD065583 | Pride | 2026-03-18

REPOSITORIES: Pride

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			Action	DRS
	Human_TIMScore_library.tsv.speclib	Tabular
	PE211_2023_ASO_OTS_Pilot.pg_matrix.tsv	Tabular
	RawFiles.zip	Other
	library.tsv.speclib	Tabular
	uniprot_canonical_Homo_sapiens_02-22-2021.fasta	Fasta

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