Unveiling sequence-agnostic mixed-chemical modification patterns for splice-switching oligonucleotides using the NATURA platform

Unveiling sequence-agnostic mixed-chemical modification patterns for splice-switching oligonucleotides using the NATURA platform

Molecular Therapy Nucleic Acids

10.1016/j.omtn.2024.102422

https://doi.org/10.1016/j.omtn.2024.102422

Tommaso Tabaglio, Taniya Agarwal, Wei Yuan Cher, Jin Rong Ow, Ah Keng Chew, Priscila Yun Qian Sun, Raja Sekhar Reddy Gurrampati, Hongfang Lu, Praveena Naidu, Hong Kai Ng, Xavier Le Guezennec, Shi Yan Ng, Manikandan Lakshmanan, Ernesto Guccione, Keng Boon Wee

antisense oligonucleotide, exon-skipping antisense oligonucleotides, reporter system, nucleic acid therapeutics, nucleic acid chemical modifications, Splice modulation, mixmers, gapmers, splice-switching oligonucleotides

07 January 2025

Tabaglio, T., Agarwal, T., Cher, W. Y., Ow, J. R., Chew, A. K., Sun, P. Y. Q., Reddy Gurrampati, R. S., Lu, H., Naidu, P., Ng, H. K., Le Guezennec, X., Ng, S. Y., Lakshmanan, M., Guccione, E., & Wee, K. B. (2025). Unveiling sequence-agnostic mixed-chemical modification patterns for splice-switching oligonucleotides using the NATURA platform. Molecular Therapy Nucleic Acids, 36(1), 102422. https://doi.org/10.1016/j.omtn.2024.102422

Chemical optimization of ribose has significantly advanced nucleic acid therapeutics (NATs) by improving the stability, specificity, and safety of therapies like small interfering RNAs, CRISPR-Cas9 guide RNAs, and GAPmers. Recent research has extended this approach to splice-switching oligonucleotides (SSOs), which target splicing events. Our study identifies a set of mixed-modification patterns—combining 2′-O-Methyl, 2′-MethOxyEthyl, 2′-Locked Nucleic Acid, and 2′-Constrained Ethyl ribose moieties (2′OMe, 2′MOE, LNA, and cET)—that enhance SSO potency. We term this strategy lateral mixed positional configuration, which improves SSO efficacy across various sequences and could reduce the trial-and-error process in SSO development. This advancement is supported by NAT Unlabeled Reporter Assay (NATURA), a novel platform for high-throughput quantification of NATs' functional delivery and potency. NATURA uses a reporter gene system and a comprehensive sequence library to test modifications and delivery methods, validated in a transgenic mouse model. This approach aims to accelerate NAT development and address challenges in delivering these therapies to patients.

Attribution 4.0 International (CC BY 4.0)

This research / project is supported by the Agency for Science, Technology and Research - Industry Alignment Fund - Pre-positioning Program
Grant Reference no. : H20C6a0034

This research / project is supported by the Agency for Science, Technology and Research - Cell and Gene Therapy GAP Fund
Grant Reference no. : ACCL/19-GAP009-R20H

This research / project is supported by the Agency for Science, Technology and Research - A∗STAR Career Development Fund
Grant Reference no. : C210812001

© 2025 The Authors. Published by Elsevier Inc. on behalf of The American Society of Gene and Cell Therapy. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

https://oar.a-star.edu.sg/communities-collections/articles/21741

2162-2531

Institute of Molecular and Cell Biology