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Valentin R, Wong C, Alharbi AS, Pradeloux S, Morros MP, Lennox KA, Ellyard JI, Garcin AJ, Ullah TR, Kusuma GD, Pépin G, Li HM, Pearson JS, Ferrand J, Lim R, Veedu RN, Morand EF, Vinuesa CG, Behlke MA, Gantier MP. Sequence-dependent inhibition of cGAS and TLR9 DNA sensing by 2'-O-methyl gapmer oligonucleotides. Nucleic Acids Res 2021; 49:6082-6099. [PMID: 34057477 PMCID: PMC8216285 DOI: 10.1093/nar/gkab451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 12/26/2022] Open
Abstract
Oligonucleotide-based therapeutics have the capacity to engage with nucleic acid immune sensors to activate or block their response, but a detailed understanding of these immunomodulatory effects is currently lacking. We recently showed that 2′-O-methyl (2′OMe) gapmer antisense oligonucleotides (ASOs) exhibited sequence-dependent inhibition of sensing by the RNA sensor Toll-Like Receptor (TLR) 7. Here we discovered that 2′OMe ASOs can also display sequence-dependent inhibitory effects on two major sensors of DNA, namely cyclic GMP-AMP synthase (cGAS) and TLR9. Through a screen of 80 2′OMe ASOs and sequence mutants, we characterized key features within the 20-mer ASOs regulating cGAS and TLR9 inhibition, and identified a highly potent cGAS inhibitor. Importantly, we show that the features of ASOs inhibiting TLR9 differ from those inhibiting cGAS, with only a few sequences inhibiting both pathways. Together with our previous studies, our work reveals a complex pattern of immunomodulation where 95% of the ASOs tested inhibited at least one of TLR7, TLR9 or cGAS by ≥30%, which may confound interpretation of their in vivo functions. Our studies constitute the broadest analysis of the immunomodulatory effect of 2′OMe ASOs on nucleic acid sensing to date and will support refinement of their therapeutic development.
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Affiliation(s)
- Roxane Valentin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Christophe Wong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Arwaf S Alharbi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia.,The Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Turabah 29179, Saudi Arabia
| | - Solène Pradeloux
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Makala P Morros
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Kim A Lennox
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Julia I Ellyard
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.,Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Aurélie J Garcin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Tomalika R Ullah
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Gina D Kusuma
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria 3800, Australia
| | - Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Hong-Mei Li
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Jonathan Ferrand
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
| | - Rebecca Lim
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia.,Perron Institute for Neurological and Translational Science, Perth, Western Australia 6150, Australia
| | - Eric F Morand
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria 3168, Australia
| | - Carola G Vinuesa
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.,Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA 52241, USA
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3800, Australia
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