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Flynn LL, Li R, Pitout IL, Aung-Htut MT, Larcher LM, Cooper JAL, Greer KL, Hubbard A, Griffiths L, Bond CS, Wilton SD, Fox AH, Fletcher S. Single Stranded Fully Modified-Phosphorothioate Oligonucleotides can Induce Structured Nuclear Inclusions, Alter Nuclear Protein Localization and Disturb the Transcriptome In Vitro. Front Genet 2022; 13:791416. [PMID: 35464859 PMCID: PMC9019733 DOI: 10.3389/fgene.2022.791416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/02/2022] [Indexed: 01/12/2023] Open
Abstract
Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2′ O- fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects.
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Affiliation(s)
- Loren L Flynn
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,Black Swan Pharmaceuticals, Wake Forest, NC, United States
| | - Ruohan Li
- Cell and Tissue Therapies WA, Royal Perth Hospital, Perth, WA, Australia.,School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Ianthe L Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Leon M Larcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Jack A L Cooper
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Kane L Greer
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Alysia Hubbard
- Centre for Microscopy, Characterization and Analysis, The University of Western Australia, Nedlands, WA, Australia
| | - Lisa Griffiths
- Anatomical Pathology, Department of Health, Nedlands, WA, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
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Culbertson MC, Temburnikar KW, Sau SP, Liao JY, Bala S, Chaput JC. Evaluating TNA stability under simulated physiological conditions. Bioorg Med Chem Lett 2016; 26:2418-2421. [PMID: 27080186 DOI: 10.1016/j.bmcl.2016.03.118] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 12/11/2022]
Abstract
Chemically modified oligonucleotides are routinely used as diagnostic and therapeutic agents due to their enhanced biological stability relative to natural DNA and RNA. Here, we examine the biological stability of α-l-threofuranosyl nucleic acid (TNA), an artificial genetic polymer composed of repeating units of α-l-threofuranosyl sugars linked by 2',3'-phosphodiester bonds. We show that TNA remains undigested after 7days of incubation in the presence of either 50% human serum or human liver microsomes and is stable against snake venom phosphordiesterase (a highly active 3' exonuclease). We further show that TNA will protect internal DNA residues from nuclease digestion and shield complementary RNA strands from RNA degrading enzymes. Together, these results demonstrate that TNA is an RNA analogue with high biological stability.
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Affiliation(s)
| | | | - Sujay P Sau
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Jen-Yu Liao
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Saikat Bala
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - John C Chaput
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA; Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5301, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA.
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