1
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Tong AJ, Leylek R, Herzner AM, Rigas D, Wichner S, Blanchette C, Tahtinen S, Kemball CC, Mellman I, Haley B, Freund EC, Delamarre L. Nucleotide modifications enable rational design of TLR7-selective ligands by blocking RNase cleavage. J Exp Med 2024; 221:e20230341. [PMID: 38095631 PMCID: PMC10720541 DOI: 10.1084/jem.20230341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/10/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Toll-like receptors 7 (TLR7) and 8 (TLR8) each sense single-stranded RNA (ssRNA), but their activation results in different immune activation profiles. Attempts to selectively target either TLR7 or TLR8 have been hindered by their high degree of homology. However, recent studies revealed that TLR7 and TLR8 bind different ligands resulting from the processing of ssRNA by endolysosomal RNases. We demonstrate that by introducing precise 2' sugar-modified bases into oligoribonucleotides (ORNs) containing known TLR7 and TLR8 binding motifs, we could prevent RNase-mediated degradation into the monomeric uridine required for TLR8 activation while preserving TLR7 activation. Furthermore, a novel, optimized protocol for CRISPR-Cas9 knockout in primary human plasmacytoid dendritic cells showed that TLR7 activation is dependent on RNase processing of ORNs and revealed a previously undescribed role for RNase 6 in degrading ORNs into TLR ligands. Finally, 2' sugar-modified ORNs demonstrated robust innate immune activation in mice. Altogether, we identified a strategy for creating tunable TLR7-selective agonists.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ira Mellman
- Genentech, Inc., South San Francisco, CA, USA
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2
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Pollak AJ, Zhao L, Crooke ST. Characterization of cooperative PS-oligo activation of human TLR9. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:832-844. [PMID: 37675184 PMCID: PMC10477407 DOI: 10.1016/j.omtn.2023.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
Single-stranded phosphorothioate oligonucleotides (PS-oligos) can activate TLR9, leading to an innate immune response. This can occur with PS-oligos containing unmethylated CpG sites, the canonical motif, or PS-oligos that do not contain those motifs (non-CpG). Structural evidence shows that TLR9 contains two PS-oligo binding sites, and recent data suggest that synergistic cooperative activation of TLR9 can be achieved by adding two separate PS-oligos to cells, each engaging with a separate site on TLR9 to enhance TLR9 activation as a pair. Here, we demonstrate and characterize this cooperativity phenomenon using PS-oligos in human cell lines, and we introduce several novel PS-oligo pairs (CpG and non-CpG pairs) that show cooperative activation. Indeed, we find that cooperative PS-oligos likely bind at different sites on TLR9. Interestingly, we find that PS-oligos that generate little TLR9 activation on their own can prime TLR9 to be activated by other PS-oligos. Finally, we determine that previous models of TLR9 activation cannot be used to fully explain data from systems using human TLR9 and PS-oligos. Overall, we reveal new details of TLR9 activation, but we also find that more work needs to be done to determine where certain PS-oligos are binding to TLR9.
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Affiliation(s)
| | - Luyi Zhao
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
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3
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Yu CH, Sczepanski JT. The influence of chirality on the behavior of oligonucleotides inside cells: revealing the potent cytotoxicity of G-rich l-RNA. Chem Sci 2023; 14:1145-1154. [PMID: 36756313 PMCID: PMC9891384 DOI: 10.1039/d2sc05511b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/30/2022] [Indexed: 12/31/2022] Open
Abstract
Due to their intrinsic nuclease resistance, mirror image l-oligonucleotides are being increasingly employed in the development of biomedical research tools and therapeutics. Yet, the influence of chirality on the behavior of oligonucleotides in living systems, and specifically, the extent to which l-oligonucleotides interact with endogenous biomacromolecules and the resulting consequences remain unknown. In this study, we characterized the intracellular behavior of l-oligonucleotides for the first time, revealing important chirality-dependent effects on oligonucleotide cytotoxicity. We show that exogenously delivered l-oligonucleotides have the potential to be highly cytotoxic, which is dependent on backbone chemistry, sequence, and structure. Notably, for the sequences tested, we found that single-stranded G-rich l-RNAs are more cytotoxic than their d-DNA/RNA counterparts, exhibiting low nanomolar EC50 values. Importantly, RNA-seq analysis of differentially expressed genes suggests that G-rich l-RNAs stimulate an innate immune response and pro-inflammatory cytokine production. These data not only challenge the general perception that mirror image l-oligonucleotides are nontoxic and nonimmunogenic, but also reveal previously unrecognized therapeutic opportunities. Moreover, by establishing sequence/structure toxicity relationships, this work will guide how future l-oligonucleotide-based biotechnologies are designed and applied.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
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4
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Sapkota S, Gantier MP. Selecting Therapeutic Antisense Oligonucleotides with Gene Targeting and TLR8 Potentiating Bifunctionality. Methods Mol Biol 2023; 2691:225-234. [PMID: 37355549 DOI: 10.1007/978-1-0716-3331-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Abstract
A growing body of preclinical evidence has led to the hypothesis that human Toll-like receptor 8 (hTLR8) activation in the tumor microenvironment (TME) could have potent anticancer effects through its action on monocytes, myeloid dendritic cells (mDCs), and natural killer (NK) cells. This has motivated the initiation of several clinical trials for chemical hTLR8 agonists in a variety of cancers. Concurrently, a growing number of synthetic antisense oligonucleotides (ASOs) are being developed as cancer therapeutics. We have recently reported that 2'-O-methyl (2'OMe)-modified ASOs can potentiate sensing of hTLR8 chemical agonists in a sequence-dependent manner. This suggests that select gene-targeting ASOs with anticancer activity may synergize with low-dose hTLR8 agonists in the TME. Here, we provide a detailed protocol to rapidly screen and identify such synthetic bifunctional oligonucleotides with synergistic activity on hTLR8 sensing.
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Affiliation(s)
- Sunil Sapkota
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
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5
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Zhang C, Wang H, Wang H, Shi S, Zhao P, Su Y, Wang H, Yang M, Fang M. A microsatellite DNA-derived oligodeoxynucleotide attenuates lipopolysaccharide-induced acute lung injury in mice by inhibiting the HMGB1-TLR4-NF-κB signaling pathway. Front Microbiol 2022; 13:964112. [PMID: 35992691 PMCID: PMC9386506 DOI: 10.3389/fmicb.2022.964112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022] Open
Abstract
Acute lung injury (ALI) with uncontrolled inflammatory response has high morbidity and mortality rates in critically ill patients. Pathogen-associated molecular patterns (PAMPs) are involved in the development of uncontrolled inflammatory response injury and associated lethality. In this study, we investigated the inhibit effect of MS19, a microsatellite DNA-derived oligodeoxynucleotide (ODN) with AAAG repeats, on the inflammatory response induced by various PAMPs in vitro and in vivo. In parallel, a microsatellite DNA with AAAC repeats, named as MS19-C, was used as controls. We found that MS19 extensively inhibited the expression of inflammatory cytokines interleukin (IL)-6 and tumor necrosis factor (TNF)-α induced by various PAMPs stimulation, including DNA viruses, RNA viruses, bacterial components lipopolysaccharide (LPS), and curdlan, as well as the dsDNA and dsRNA mimics, in primed bone marrow-derived macrophage (BMDM). Other than various PAMPs, MS19 also demonstrated obvious effects on blocking the high mobility group box1 (HMGB1), a representative damage-associated-molecular pattern (DAMP), nuclear translocation and secretion. With the base substitution from G to C, MS19-C has been proved that it has lost the inhibitory effect. The inhibition is associated with nuclear factor kappa B (NF-κB) signaling but not the mitogen-activated protein kinase (MAPK) transduction. Moreover, MS19 capable of inhibiting the IL-6 and TNF-α production and blocking the HMGB1 nuclear translocation and secretion in LPS-stimulated cells was used to treat mice ALI induced by LPS in vivo. In the ALI mice model, MS19 significantly inhibited the weight loss and displayed the dramatic effect on lessening the ALI by reducing consolidation, hemorrhage, intra-alveolar edema in lungs of the mice. Meanwhile, MS19 could increase the survival rate of ALI by downregulating the inflammation cytokines HMGB1, TNF-a, and IL-6 production in the bronchoalveolar lavage fluid (BALF). The data suggest that MS19 might display its therapeutic role on ALI by inhibiting the HMGB1-TLR4-NF-κB signaling pathway.
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Affiliation(s)
- Chenghua Zhang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
- Department of Endoscopy, Jilin Provincial Cancer Hospital, Changchun, China
| | - Hui Wang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Hongrui Wang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Shuyou Shi
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Peiyan Zhao
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yingying Su
- Department of Anatomy, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Hua Wang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Ming Yang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
- Ming Yang,
| | - Mingli Fang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
- *Correspondence: Mingli Fang,
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6
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Oligonucleotide correction of an intronic TIMMDC1 variant in cells of patients with severe neurodegenerative disorder. NPJ Genom Med 2022; 7:9. [PMID: 35091571 PMCID: PMC8799713 DOI: 10.1038/s41525-021-00277-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 12/09/2021] [Indexed: 11/08/2022] Open
Abstract
TIMMDC1 encodes the Translocase of Inner Mitochondrial Membrane Domain-Containing protein 1 (TIMMDC1) subunit of complex I of the electron transport chain responsible for ATP production. We studied a consanguineous family with two affected children, now deceased, who presented with failure to thrive in the early postnatal period, poor feeding, hypotonia, peripheral neuropathy and drug-resistant epilepsy. Genome sequencing data revealed a known, deep intronic pathogenic variant TIMMDC1 c.597-1340A>G, also present in gnomAD (~1/5000 frequency), that enhances aberrant splicing. Using RNA and protein analysis we show almost complete loss of TIMMDC1 protein and compromised mitochondrial complex I function. We have designed and applied two different splice-switching antisense oligonucleotides (SSO) to restore normal TIMMDC1 mRNA processing and protein levels in patients' cells. Quantitative proteomics and real-time metabolic analysis of mitochondrial function on patient fibroblasts treated with SSOs showed restoration of complex I subunit abundance and function. SSO-mediated therapy of this inevitably fatal TIMMDC1 neurologic disorder is an attractive possibility.
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7
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Ma Y, Wang X, Luo W, Xiao J, Song X, Wang Y, Shuai H, Ren Z, Wang Y. Roles of Emerging RNA-Binding Activity of cGAS in Innate Antiviral Response. Front Immunol 2021; 12:741599. [PMID: 34899698 PMCID: PMC8660693 DOI: 10.3389/fimmu.2021.741599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
cGAS, a DNA sensor in mammalian cells, catalyzes the generation of 2'-3'-cyclic AMP-GMP (cGAMP) once activated by the binding of free DNA. cGAMP can bind to STING, activating downstream TBK1-IRF-3 signaling to initiate the expression of type I interferons. Although cGAS has been considered a traditional DNA-binding protein, several lines of evidence suggest that cGAS is a potential RNA-binding protein (RBP), which is mainly supported by its interactions with RNAs, RBP partners, RNA/cGAS-phase-separations as well as its structural similarity with the dsRNA recognition receptor 2'-5' oligoadenylate synthase. Moreover, two influential studies reported that the cGAS-like receptors (cGLRs) of fly Drosophila melanogaster sense RNA and control 3'-2'-cGAMP signaling. In this review, we summarize and discuss in depth recent studies that identified or implied cGAS as an RBP. We also comprehensively summarized current experimental methods and computational tools that can identify or predict RNAs that bind to cGAS. Based on these discussions, we appeal that the RNA-binding activity of cGAS cannot be ignored in the cGAS-mediated innate antiviral response. It will be important to identify RNAs that can bind and regulate the activity of cGAS in cells with or without virus infection. Our review provides novel insight into the regulation of cGAS by its RNA-binding activity and extends beyond its DNA-binding activity. Our review would be significant for understanding the precise modulation of cGAS activity, providing the foundation for the future development of drugs against cGAS-triggering autoimmune diseases such as Aicardi-Gourtières syndrome.
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Affiliation(s)
- Yuying Ma
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Xiaohui Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Weisheng Luo
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Ji Xiao
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Xiaowei Song
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Yifei Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Hanlin Shuai
- Department of Obstetrics and Gynecology, The Fifth Affiliated Hospital of Jinan University, Heyuan, China
| | - Zhe Ren
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China
| | - Yiliang Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China.,Key Laboratory of Virology of Guangdong Province, Jinan University, Guangzhou, China.,Guangdong Province Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou, China.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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8
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Tetrasubstituted imidazoles as incognito Toll-like receptor 8 a(nta)gonists. Nat Commun 2021; 12:4351. [PMID: 34272380 PMCID: PMC8285539 DOI: 10.1038/s41467-021-24536-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 06/21/2021] [Indexed: 12/20/2022] Open
Abstract
Small-molecule modulators of TLR8 have drawn much interests as it plays pivotal roles in the innate immune response to single-stranded RNAs (ssRNAs) derived from viruses. However, their clinical uses are limited because they can invoke an uncontrolled, global inflammatory response. The efforts described herein culminate in the fortuitous discovery of a tetrasubstituted imidazole CU-CPD107 which inhibits R848-induced TLR8 signaling. In stark contrast, CU-CPD107 shows unexpected synergistic agonist activities in the presence of ssRNA, while CU-CPD107 alone is unable to influence TLR8 signaling. CU-CPD107’s unique, dichotomous behavior sheds light on a way to approach TLR agonists. CU-CPD107 offers the opportunity to avoid the undesired, global inflammation side effects that have rendered imidazoquinolines clinically irrelevant, providing an insight for the development of antiviral drugs. Toll-like receptor 8 (TLR8) plays essential roles in the innate immune response to viral single-stranded RNA (ssRNA), so small molecule modulators of TLR8 are of interest, however adverse effects limit their use. Here, the authors report a tetrasubstituted imidazole CU-CPD107 with dichotomous behaviour, which inhibits R848-induced TLR8 signaling, but shows synergistic activity in the presence of ssRNA, making it a potential antiviral agent.
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9
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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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10
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Yang CW, Chen MF. Low compositions of human toll-like receptor 7/8-stimulating RNA motifs in the MERS-CoV, SARS-CoV and SARS-CoV-2 genomes imply a substantial ability to evade human innate immunity. PeerJ 2021; 9:e11008. [PMID: 33665043 PMCID: PMC7912611 DOI: 10.7717/peerj.11008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
Background The innate immune system especially Toll-like receptor (TLR) 7/8 and the interferon pathway, constitutes an important first line of defense against single-stranded RNA viruses. However, large-scale, systematic comparisons of the TLR 7/8-stimulating potential of genomic RNAs of single-stranded RNA viruses are rare. In this study, a computational method to evaluate the human TLR 7/8-stimulating ability of single-stranded RNA virus genomes based on their human TLR 7/8-stimulating trimer compositions was used to analyze 1,002 human coronavirus genomes. Results The human TLR 7/8-stimulating potential of coronavirus genomic (positive strand) RNAs followed the order of NL63-CoV > HKU1-CoV >229E-CoV ≅ OC63-CoV > SARS-CoV-2 > MERS-CoV > SARS-CoV. These results suggest that among these coronaviruses, MERS-CoV, SARS-CoV and SARS-CoV-2 may have a higher ability to evade the human TLR 7/8-mediated innate immune response. Analysis with a logistic regression equation derived from human coronavirus data revealed that most of the 1,762 coronavirus genomic (positive strand) RNAs isolated from bats, camels, cats, civets, dogs and birds exhibited weak human TLR 7/8-stimulating potential equivalent to that of the MERS-CoV, SARS-CoV and SARS-CoV-2 genomic RNAs. Conclusions Prediction of the human TLR 7/8-stimulating potential of viral genomic RNAs may be useful for surveillance of emerging coronaviruses from nonhuman mammalian hosts.
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Affiliation(s)
- Chu-Wen Yang
- Department of Microbiology, Center for Applied Artificial Intelligence Research, Soochow University, Taipei, Taiwan
| | - Mei-Fang Chen
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
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11
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Spinal muscular atrophy: Broad disease spectrum and sex-specific phenotypes. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166063. [PMID: 33412266 DOI: 10.1016/j.bbadis.2020.166063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% of cases of SMA result from deletions of or mutations in the Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. The spectrum of SMA is broad, ranging from prenatal death to infant mortality to survival into adulthood. All tissues, including brain, spinal cord, bone, skeletal muscle, heart, lung, liver, pancreas, gastrointestinal tract, kidney, spleen, ovary and testis, are directly and/or indirectly affected in SMA. Accumulating evidence on impaired mitochondrial biogenesis and defects in X chromosome-linked modifying factors, coupled with the sexual dimorphic nature of many tissues, point to sex-specific vulnerabilities in SMA. Here we review the role of sex in the pathogenesis of SMA.
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