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Frye C, Cunningham CL, Mihailescu MR. Characterization of the SARS-CoV-2 Genome 3'-Untranslated Region Interactions with Host MicroRNAs. ACS OMEGA 2024; 9:36148-36164. [PMID: 39220490 PMCID: PMC11360049 DOI: 10.1021/acsomega.4c01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/23/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The 2019 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. SARS-CoV-2 has exhibited increased disease severity and immune evasion across its variants, and the molecular mechanisms behind these phenomena remain largely unknown. Conserved elements of the viral genome, such as secondary structures within the 3'-untranslated region (UTR), could prove crucial in furthering our understanding of the host-virus interface. Analysis of the SARS-CoV-2 viral genome 3'-UTR revealed the potential for host microRNA (miR) binding sites, allowing for sequence-specific interactions. In this study, we demonstrate that the SARS-CoV-2 genome 3'-UTR binds the host cellular miRs miR-34a-5p, miR-34b-5p, and miR-760-3p in vitro. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to biophysically characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3'-UTR. Additionally, we investigated 2'-fluoro-d-arabinonucleic acid (FANA) analogs as competitive binding inhibitors for these interactions. These miRs modulate the translation of granulin (GRN), interleukin-6 (IL-6), and the IL-6 receptor (IL-6R), all of which are key modulators and activators of JAK/STAT3 signaling and are implicated in regulation of the immune response. Thus, we propose that hijacking of these miRs by SARS-CoV-2 could identify a mechanism of host immune modulation by the virus. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2, through direct targeting of the virus-host interface.
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Affiliation(s)
- Caleb
J. Frye
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caylee L. Cunningham
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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2
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Akimova T, Wang L, Bartosh Z, Christensen LM, Eruslanov E, Singhal S, Aishwarya V, Hancock WW. Antisense targeting of FOXP3+ Tregs to boost anti-tumor immunity. Front Immunol 2024; 15:1426657. [PMID: 39234236 PMCID: PMC11371716 DOI: 10.3389/fimmu.2024.1426657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/29/2024] [Indexed: 09/06/2024] Open
Abstract
Our goal is to improve the outcomes of cancer immunotherapy by targeting FOXP3+ T-regulatory (Treg) cells with a next generation of antisense oligonucleotides (ASO), termed FOXP3 AUMsilence ASO. We performed in vitro experiments with human healthy donor PBMC and clinical samples from patients with lung cancer, mesothelioma and melanoma, and tested our approach in vivo using ASO FOXP3 in syngeneic murine cancer models and in humanized mice. ASO FOXP3 had no effects on cell viability or cell division, did not affect expression of other FOXP members, but decreased expression of FOXP3 mRNA in PBMC by 54.9% and in cancer samples by 64.7%, with corresponding 41.0% (PBMC) and 60.0% (cancer) decreases of Treg numbers (all p<0.0001). Hence, intratumoral Treg were more sensitive to the effects of ASO FOXP3 than peripheral blood Tregs. Isolated human Treg, incubated with ASO FOXP3 for 3.5 hours, had significantly impaired suppressive function (66.4%) versus Scramble control. In murine studies, we observed a significant inhibition of tumor growth, while 13.6% (MC38) to 22% (TC1) of tumors were completely resorbed, in conjunction with ~50% decrease of Foxp3 mRNA by qPCR and decreased numbers of intratumoral Tregs. In addition, there were no changes in FOXP3 mRNA expression or in the numbers of Tregs in draining lymph nodes and in spleens of tumor bearing mice, confirming that intratumoral Treg had enhanced sensitivity to ASO FOXP3 in vivo compared to other Treg populations. ASO FOXP3 Treg targeting in vivo and in vitro was accompanied by significant downregulation of multiple exhaustion markers, and by increased expression of perforin and granzyme-B by intratumoral T cells. To conclude, we report that targeting the key Treg transcription factor FOXP3, with ASO FOXP3, has a powerful anti-tumoral effect and enhances T cell response in vitro and in vivo.
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Affiliation(s)
- Tatiana Akimova
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- AUM Biotech, LLC., Philadelphia, PA, United States
| | - Liqing Wang
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Zhanna Bartosh
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- AUM Biotech, LLC., Philadelphia, PA, United States
| | - Lanette M Christensen
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Evgeniy Eruslanov
- Division of Thoracic Surgery, Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Sunil Singhal
- Division of Thoracic Surgery, Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | | | - Wayne W Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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Bian T, Pei Y, Gao S, Zhou S, Sun X, Dong M, Song J. Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application. Adv Healthc Mater 2024:e2401207. [PMID: 39036821 DOI: 10.1002/adhm.202401207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.
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Affiliation(s)
- Tianyuan Bian
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shitao Gao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- College of Materials Science and Engineering, Zhejiang University of Technology, ChaoWang Road 18, HangZhou, 310014, China
| | - Songtao Zhou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinyu Sun
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Aarhus, DK-8000, Denmark
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
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4
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Kola NS, Patel D, Thakur A. RNA-Based Vaccines and Therapeutics Against Intracellular Pathogens. Methods Mol Biol 2024; 2813:321-370. [PMID: 38888787 DOI: 10.1007/978-1-0716-3890-3_21] [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: 06/20/2024]
Abstract
RNA-based vaccines have sparked a paradigm shift in the treatment and prevention of diseases by nucleic acid medicines. There has been a notable surge in the development of nucleic acid therapeutics and vaccines following the global approval of the two messenger RNA-based COVID-19 vaccines. This growth is fueled by the exploration of numerous RNA products in preclinical stages, offering several advantages over conventional methods, i.e., safety, efficacy, scalability, and cost-effectiveness. In this chapter, we provide an overview of various types of RNA and their mechanisms of action for stimulating immune responses and inducing therapeutic effects. Furthermore, this chapter delves into the varying delivery systems, particularly emphasizing the use of nanoparticles to deliver RNA. The choice of delivery system is an intricate process involved in developing nucleic acid medicines that significantly enhances their stability, biocompatibility, and site-specificity. Additionally, this chapter sheds light on the current landscape of clinical trials of RNA therapeutics and vaccines against intracellular pathogens.
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Affiliation(s)
- Naga Suresh Kola
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dhruv Patel
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Aneesh Thakur
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
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Razi N, Li W, Ignacio MA, Loube JM, Agostino EL, Zhu X, Scull MA, DeStefano JJ. Inhibition of SARS-CoV-2 infection in human airway epithelium with a xeno-nucleic acid aptamer. Respir Res 2023; 24:272. [PMID: 37932762 PMCID: PMC10629106 DOI: 10.1186/s12931-023-02590-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND SARS-CoV-2, the agent responsible for the COVID-19 pandemic, enters cells through viral spike glycoprotein binding to the cellular receptor, angiotensin-converting enzyme 2 (ACE2). Given the lack of effective antivirals targeting SARS-CoV-2, we previously utilized systematic evolution of ligands by exponential enrichment (SELEX) and selected fluoro-arabino nucleic acid (FANA) aptamer R8-9 that was able to block the interaction between the viral receptor-binding domain and ACE2. METHODS Here, we further assessed FANA-R8-9 as an entry inhibitor in contexts that recapitulate infection in vivo. RESULTS We demonstrate that FANA-R8-9 inhibits spike-bearing pseudovirus particle uptake in cell lines. Then, using an in-vitro model of human airway epithelium (HAE) and SARS-CoV-2 virus, we show that FANA-R8-9 significantly reduces viral infection when added either at the time of inoculation, or several hours later. These results were specific to the R8-9 sequence, not the xeno-nucleic acid utilized to make the aptamer. Importantly, we also show that FANA-R8-9 is stable in HAE culture secretions and has no overt cytotoxic effects. CONCLUSIONS Together, these results suggest that FANA-R8-9 effectively prevents infection by specific SARS-CoV-2 variants and indicate that aptamer technology could be utilized to target other clinically-relevant viruses in the respiratory mucosa.
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Affiliation(s)
- Niayesh Razi
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742, USA
| | - Weizhong Li
- Division of Immunology, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Maxinne A Ignacio
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742, USA
| | - Jeffrey M Loube
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742, USA
| | - Eva L Agostino
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742, USA
| | - Xiaoping Zhu
- Division of Immunology, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Margaret A Scull
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742, USA.
| | - Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742, USA.
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6
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Razi N, Li W, Ignacio MA, Loube JM, Agostino EL, Zhu X, Scull MA, DeStefano JJ. Inhibition of SARS-CoV-2 Infection in Human Airway Epithelium with a Xeno-Nucleic Acid Aptamer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559799. [PMID: 37808754 PMCID: PMC10557761 DOI: 10.1101/2023.09.27.559799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Background SARS-CoV-2, the agent responsible for the COVID-19 pandemic, enters cells through viral spike glycoprotein binding to the cellular receptor, angiotensin-converting enzyme 2 (ACE2). Given the lack of effective antivirals targeting SARS-CoV-2, we previously utilized systematic evolution of ligands by exponential enrichment (SELEX) and selected fluoro-arabino nucleic acid (FANA) aptamer R8-9 that was able to block the interaction between the viral receptor-binding domain and ACE2. Methods Here, we further assessed FANA-R8-9 as an entry inhibitor in contexts that recapitulate infection in vivo. Results We demonstrate that FANA-R8-9 inhibits spike-bearing pseudovirus particle uptake in cell lines. Then, using an in-vitro model of human airway epithelium (HAE) and SARS-CoV-2 virus, we show that FANA-R8-9 significantly reduces viral infection when added either at the time of inoculation, or several hours later. These results were specific to the R8-9 sequence, not the xeno-nucleic acid utilized to make the aptamer. Importantly, we also show that FANA-R8-9 is stable in HAE culture secretions and has no overt cytotoxic effects. Conclusions Together, these results suggest that FANA-R8-9 effectively prevents infection by specific SARS-CoV-2 variants and indicate that aptamer technology could be utilized to target other clinically-relevant viruses in the respiratory mucosa.
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Affiliation(s)
- Niayesh Razi
- Department of Cell Biology and Molecular Genetics, and Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742
| | - Weizhong Li
- Division of Immunology, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, 20742
| | - Maxinne A. Ignacio
- Department of Cell Biology and Molecular Genetics, and Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742
| | - Jeffrey M. Loube
- Department of Cell Biology and Molecular Genetics, and Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742
| | - Eva L. Agostino
- Department of Cell Biology and Molecular Genetics, and Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742
| | - Xiaoping Zhu
- Division of Immunology, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, 20742
| | - Margaret A. Scull
- Department of Cell Biology and Molecular Genetics, and Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, and Maryland Pathogen Research Institute (MPRI), University of Maryland, College Park, MD, 20742
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7
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Pontarelli A, Wilds CJ. C5-Propynyl modified 2'-fluoroarabinonucleic acids form stable duplexes with RNA that are RNase H competent. Org Biomol Chem 2023; 21:7437-7446. [PMID: 37667655 DOI: 10.1039/d3ob01297b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The clinical success of the antisense approach for the treatment of genetic disorders is indisputably the result of chemical modifications along the oligonucleotide (ON) scaffold, which impart desirable properties including high RNA affinity, nuclease stability and improved drug delivery. While effective, many modifications are not capable of eliciting an RNase H response limiting their application in antisense systems. To contribute to the structural design and inventory of nucleoside analogues with favorable antisense properties, herein we describe the synthesis of C5-propynyl-2'-fluoroarabinonucleic acids (FANAP). Incorporation of individual and multiple uridine (FaraUP) and cytidine (FaraCP) inserts into ONs revealed, both stabilized duplexes formed with RNA. In contrast, these modifications demonstrated a negligible (FaraUP) or reduced (FaraCP) effect on DNA binding. Moreover, modified ONs containing these analogues supported E. coli RNase H cleavage of RNA with an altered cleavage pattern observed relative to controls. Moreover, a 2'-O-methoxyethyl (2'-O-MOE) gapmer with a FANAP core was able to elicit RNA cleavage at an increased rate compared to C5-propynyl-arabinonucleic acids (ANAP). Enzymatic hydrolysis of these gapmers was assessed with nuclease S1 digestion and revealed greater stability of ANAP compared to FANAP. These results suggest C5-propynyl ANA/FANA modifications demonstrate promising potential for the design of therapeutic ONs.
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Affiliation(s)
- Alexander Pontarelli
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec H4B 1R6, Canada.
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec H4B 1R6, Canada.
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Buthelezi LA, Pillay S, Ntuli NN, Gcanga L, Guler R. Antisense Therapy for Infectious Diseases. Cells 2023; 12:2119. [PMID: 37626929 PMCID: PMC10453568 DOI: 10.3390/cells12162119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Infectious diseases, particularly Tuberculosis (TB) caused by Mycobacterium tuberculosis, pose a significant global health challenge, with 1.6 million reported deaths in 2021, making it the most fatal disease caused by a single infectious agent. The rise of drug-resistant infectious diseases adds to the urgency of finding effective and safe intervention therapies. Antisense therapy uses antisense oligonucleotides (ASOs) that are short, chemically modified, single-stranded deoxyribonucleotide molecules complementary to their mRNA target. Due to their designed target specificity and inhibition of a disease-causing gene at the mRNA level, antisense therapy has gained interest as a potential therapeutic approach. This type of therapy is currently utilized in numerous diseases, such as cancer and genetic disorders. Currently, there are limited but steadily increasing studies available that report on the use of ASOs as treatment for infectious diseases. This review explores the sustainability of FDA-approved and preclinically tested ASOs as a treatment for infectious diseases and the adaptability of ASOs for chemical modifications resulting in reduced side effects with improved drug delivery; thus, highlighting the potential therapeutic uses of ASOs for treating infectious diseases.
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Affiliation(s)
- Lwanda Abonga Buthelezi
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Shandre Pillay
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Noxolo Nokukhanya Ntuli
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lorna Gcanga
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Cape Town 7925, South Africa; (L.A.B.); (S.P.); (N.N.N.); (L.G.)
- Department of Pathology, Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Faculty of Health Sciences, Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
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Isenmann M, Stoddart MJ, Schmelzeisen R, Gross C, Della Bella E, Rothweiler RM. Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods. MICROMACHINES 2023; 14:1321. [PMID: 37512632 PMCID: PMC10383872 DOI: 10.3390/mi14071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.
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Affiliation(s)
- Marie Isenmann
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Martin James Stoddart
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Rainer Schmelzeisen
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Christian Gross
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Elena Della Bella
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - René Marcel Rothweiler
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
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10
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Pesce E, Cordiglieri C, Bombaci M, Eppenberger-Castori S, Oliveto S, Manara C, Crosti M, Ercan C, Coto M, Gobbini A, Campagnoli S, Donnarumma T, Martinelli M, Bevilacqua V, De Camilli E, Gruarin P, Sarnicola ML, Cassinotti E, Baldari L, Viale G, Biffo S, Abrignani S, Terracciano LM, Grifantini R. TMEM123 a key player in immune surveillance of colorectal cancer. Front Immunol 2023; 14:1194087. [PMID: 37426665 PMCID: PMC10327427 DOI: 10.3389/fimmu.2023.1194087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-associated death. In the tumor site, the interplay between effector immune cells and cancer cells determines the balance between tumor elimination or outgrowth. We discovered that the protein TMEM123 is over-expressed in tumour-infiltrating CD4 and CD8 T lymphocytes and it contributes to their effector phenotype. The presence of infiltrating TMEM123+ CD8+ T cells is associated with better overall and metastasis-free survival. TMEM123 localizes in the protrusions of infiltrating T cells, it contributes to lymphocyte migration and cytoskeleton organization. TMEM123 silencing modulates the underlying signaling pathways dependent on the cytoskeletal regulator WASP and the Arp2/3 actin nucleation complex, which are required for synaptic force exertion. Using tumoroid-lymphocyte co-culture assays, we found that lymphocytes form clusters through TMEM123, anchoring to cancer cells and contributing to their killing. We propose an active role for TMEM123 in the anti-cancer activity of T cells within tumour microenvironment.
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Affiliation(s)
- Elisa Pesce
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Cordiglieri
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Mauro Bombaci
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stefania Oliveto
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Manara
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Mariacristina Crosti
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Caner Ercan
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Mairene Coto
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Andrea Gobbini
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | | | - Valeria Bevilacqua
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa De Camilli
- Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria L. Sarnicola
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Cassinotti
- Department of Surgery, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Ludovica Baldari
- Department of Surgery, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giuseppe Viale
- Department of Pathology, European Institute of Oncology, Milan, Italy
- Department of Oncology and Hemato-oncology, Università degli Studi di Milano, Milan, Italy
| | - Stefano Biffo
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Luigi M. Terracciano
- IRCCS Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Renata Grifantini
- Istituto Nazionale Genetica Molecolare (INGM), Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
- CheckmAb Srl, Milan, Italy
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11
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Frye CJ, Cunningham CL, Mihailescu MR. Host microRNA interactions with the SARS-CoV-2 viral genome 3'-untranslated region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541401. [PMID: 37292986 PMCID: PMC10245713 DOI: 10.1101/2023.05.18.541401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. While the viral life cycle is well understood, most of the interactions at the virus-host interface remain elusive. Furthermore, the molecular mechanisms behind disease severity and immune evasion are still largely unknown. Conserved elements of the viral genome such as secondary structures within the 5'- and 3'-untranslated regions (UTRs) serve as attractive targets of interest and could prove crucial in furthering our understanding of virus-host interactions. It has been proposed that microRNA (miR) interactions with viral components could be used by both the virus and host for their own benefit. Analysis of the SARS-CoV-2 viral genome 3'-UTR has revealed the potential for host cellular miR binding sites, providing sites for specific interactions with the virus. In this study, we demonstrate that the SARS-CoV-2 genome 3'-UTR binds the host cellular miRNAs miR-760-3p, miR-34a-5p, and miR-34b-5p, which have been shown to influence translation of interleukin-6 (IL-6), the IL-6 receptor (IL-6R), as well as progranulin (PGRN), respectively, proteins that have roles in the host immune response and inflammatory pathways. Furthermore, recent work suggests the potential of miR-34a-5p and miR-34b-5p to target and inhibit translation of viral proteins. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3'-UTR. Additionally, we investigated 2'-fluoro-D-arabinonucleic acid (FANA) analogs of these miRNAs as competitive binding inhibitors for these miR binding interactions. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2 infection, and provide a potential molecular basis for cytokine release syndrome and immune evasion which could implicate the host-virus interface.
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Affiliation(s)
- Caleb J Frye
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
| | - Caylee L Cunningham
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
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12
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Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023; 52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
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Affiliation(s)
- Karola Gerecht
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Wei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Yang Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Maximilian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
- Current address: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
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13
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Page JJ, Almanza JR, Xiong S, Aishwarya V, Kroner A. Self-delivering mRNA inhibitors of MK2 improve outcomes after spinal cord injury. J Neuroimmunol 2023; 379:578103. [PMID: 37172370 DOI: 10.1016/j.jneuroim.2023.578103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/03/2023] [Accepted: 05/05/2023] [Indexed: 05/14/2023]
Abstract
Functional recovery and tissue damage after spinal cord injury (SCI) are influenced by secondary damage mechanisms, including inflammation. The inflammatory response after SCI relies on a variety of cell types with both protective and cytotoxic functions. The macrophage derived MAPK-activated protein kinase 2 has been described as a critical regulator of inflammation with detrimental function after SCI. Targeted modification of inflammatory effector molecules after SCI faces challenges of optimal timing, dosage and location of administration. Modified RNA inhibitors, FANA antisense oligonucleotides, are promising inhibitors due to their stability, local penetration of cells and high efficacy in targeted suppression. Here, we describe the use of anti- MAPK-activated protein kinase 2 FANA antisense oligonucleotides in a mouse model of contusional SCI. The most efficient inhibitor was selected with in vitro and in vivo techniques and then applied via intrathecal injections after SCI. This treatment resulted in improved gait applying DigiGait assessments and tissue preservation, indicating the usefulness of the target and inhibition approach.
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Affiliation(s)
- Justin J Page
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA; Clement J. Zablocki Veterans Affairs Medical Center, Milwaukee, WI, USA
| | - Jose Rosas Almanza
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA; Clement J. Zablocki Veterans Affairs Medical Center, Milwaukee, WI, USA
| | - Shuana Xiong
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA; Clement J. Zablocki Veterans Affairs Medical Center, Milwaukee, WI, USA
| | - Veenu Aishwarya
- AUM LifeTech, Inc., 3675 Market Street, Suite 200, Philadelphia, PA 19104, USA
| | - Antje Kroner
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA; Clement J. Zablocki Veterans Affairs Medical Center, Milwaukee, WI, USA.
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14
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Lachance‐Brais C, Rammal M, Asohan J, Katolik A, Luo X, Saliba D, Jonderian A, Damha MJ, Harrington MJ, Sleiman HF. Small Molecule-Templated DNA Hydrogel with Record Stiffness Integrates and Releases DNA Nanostructures and Gene Silencing Nucleic Acids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205713. [PMID: 36752390 PMCID: PMC10131789 DOI: 10.1002/advs.202205713] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/18/2022] [Indexed: 05/31/2023]
Abstract
Deoxyribonucleic acid (DNA) hydrogels are a unique class of programmable, biocompatible materials able to respond to complex stimuli, making them valuable in drug delivery, analyte detection, cell growth, and shape-memory materials. However, unmodified DNA hydrogels in the literature are very soft, rarely reaching a storage modulus of 103 Pa, and they lack functionality, limiting their applications. Here, a DNA/small-molecule motif to create stiff hydrogels from unmodified DNA, reaching 105 Pa in storage modulus is used. The motif consists of an interaction between polyadenine and cyanuric acid-which has 3-thymine like faces-into multimicrometer supramolecular fibers. The mechanical properties of these hydrogels are readily tuned, they are self-healing and thixotropic. They integrate a high density of small, nontoxic molecules, and are functionalized simply by varying the molecule sidechain. They respond to three independent stimuli, including a small molecule stimulus. These stimuli are used to integrate and release DNA wireframe and DNA origami nanostructures within the hydrogel. The hydrogel is applied as an injectable delivery vector, releasing an antisense oligonucleotide in cells, and increasing its gene silencing efficacy. This work provides tunable, stimuli-responsive, exceptionally stiff all-DNA hydrogels from simple sequences, extending these materials' capabilities.
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Affiliation(s)
| | - Mostafa Rammal
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Jathavan Asohan
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Adam Katolik
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Xin Luo
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Antranik Jonderian
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Masad J. Damha
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | | | - Hanadi F. Sleiman
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
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15
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Gerber PP, Donde MJ, Matheson NJ, Taylor AI. XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nat Commun 2022; 13:6716. [PMID: 36385143 PMCID: PMC9668987 DOI: 10.1038/s41467-022-34339-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The unprecedented emergence and spread of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, underscores the need for diagnostic and therapeutic technologies that can be rapidly tailored to novel threats. Here, we show that site-specific RNA endonuclease XNAzymes - artificial catalysts composed of single-stranded synthetic xeno-nucleic acid oligonucleotides (in this case 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid) - may be designed, synthesised and screened within days, enabling the discovery of a range of enzymes targeting SARS-CoV-2 ORF1ab, ORF7b, spike- and nucleocapsid-encoding RNA. Three of these are further engineered to self-assemble into a catalytic nanostructure with enhanced biostability. This XNA nanostructure is capable of cleaving genomic SARS-CoV-2 RNA under physiological conditions, and when transfected into cells inhibits infection with authentic SARS-CoV-2 virus by RNA knockdown. These results demonstrate the potential of XNAzymes to provide a platform for the rapid generation of antiviral reagents.
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Affiliation(s)
- Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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16
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Amanat M, Nemeth CL, Fine AS, Leung DG, Fatemi A. Antisense Oligonucleotide Therapy for the Nervous System: From Bench to Bedside with Emphasis on Pediatric Neurology. Pharmaceutics 2022; 14:2389. [PMID: 36365206 PMCID: PMC9695718 DOI: 10.3390/pharmaceutics14112389] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 09/05/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are disease-modifying agents affecting protein-coding and noncoding ribonucleic acids. Depending on the chemical modification and the location of hybridization, ASOs are able to reduce the level of toxic proteins, increase the level of functional protein, or modify the structure of impaired protein to improve function. There are multiple challenges in delivering ASOs to their site of action. Chemical modifications in the phosphodiester bond, nucleotide sugar, and nucleobase can increase structural thermodynamic stability and prevent ASO degradation. Furthermore, different particles, including viral vectors, conjugated peptides, conjugated antibodies, and nanocarriers, may improve ASO delivery. To date, six ASOs have been approved by the US Food and Drug Administration (FDA) in three neurological disorders: spinal muscular atrophy, Duchenne muscular dystrophy, and polyneuropathy caused by hereditary transthyretin amyloidosis. Ongoing preclinical and clinical studies are assessing the safety and efficacy of ASOs in multiple genetic and acquired neurological conditions. The current review provides an update on underlying mechanisms, design, chemical modifications, and delivery of ASOs. The administration of FDA-approved ASOs in neurological disorders is described, and current evidence on the safety and efficacy of ASOs in other neurological conditions, including pediatric neurological disorders, is reviewed.
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Affiliation(s)
- Man Amanat
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christina L. Nemeth
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amena Smith Fine
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Doris G. Leung
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ali Fatemi
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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17
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Taylor AI, Wan CJK, Donde MJ, Peak-Chew SY, Holliger P. A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Nat Chem 2022; 14:1295-1305. [PMID: 36064973 PMCID: PMC7613789 DOI: 10.1038/s41557-022-01021-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/08/2022] [Indexed: 11/07/2022]
Abstract
Nucleic-acid catalysts (ribozymes, DNA- and XNAzymes) cleave target (m)RNAs with high specificity but have shown limited efficacy in clinical applications. Here we report on the in vitro evolution and engineering of a highly specific modular RNA endonuclease XNAzyme, FR6_1, composed of 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid (FANA). FR6_1 overcomes the activity limitations of previous DNA- and XNAzymes and can be retargeted to cleave highly structured full-length (>5 kb) BRAF and KRAS mRNAs at physiological Mg2+ concentrations with allelic selectivity for tumour-associated (BRAF V600E and KRAS G12D) mutations. Phosphorothioate-FANA modification enhances FR6_1 biostability and enables rapid KRAS mRNA knockdown in cultured human adenocarcinoma cells with a G12D-allele-specific component provided by in vivo XNAzyme cleavage activity. These results provide a starting point for the development of improved gene-silencing agents based on FANA or other XNA chemistries.
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Affiliation(s)
- Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK.
| | | | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
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18
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Donde MJ, Rochussen AM, Kapoor S, Taylor AI. Targeting non-coding RNA family members with artificial endonuclease XNAzymes. Commun Biol 2022; 5:1010. [PMID: 36153384 PMCID: PMC9509326 DOI: 10.1038/s42003-022-03987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Non-coding RNAs (ncRNAs) offer a wealth of therapeutic targets for a range of diseases. However, secondary structures and high similarity within sequence families make specific knockdown challenging. Here, we engineer a series of artificial oligonucleotide enzymes (XNAzymes) composed of 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid (FANA) that specifically or preferentially cleave individual ncRNA family members under quasi-physiological conditions, including members of the classic microRNA cluster miR-17~92 (oncomiR-1) and the Y RNA hY5. We demonstrate self-assembly of three anti-miR XNAzymes into a biostable catalytic XNA nanostructure, which targets the cancer-associated microRNAs miR-17, miR-20a and miR-21. Our results provide a starting point for the development of XNAzymes as a platform technology for precision knockdown of specific non-coding RNAs, with the potential to reduce off-target effects compared with other nucleic acid technologies.
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Affiliation(s)
- Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Adam M Rochussen
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Saksham Kapoor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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19
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Della Valle F, Reddy P, Yamamoto M, Liu P, Saera-Vila A, Bensaddek D, Zhang H, Prieto Martinez J, Abassi L, Celii M, Ocampo A, Nuñez Delicado E, Mangiavacchi A, Aiese Cigliano R, Rodriguez Esteban C, Horvath S, Izpisua Belmonte JC, Orlando V. LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes. Sci Transl Med 2022; 14:eabl6057. [PMID: 35947677 DOI: 10.1126/scitranslmed.abl6057] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Constitutive heterochromatin is responsible for genome repression of DNA enriched in repetitive sequences, telomeres, and centromeres. During physiological and pathological premature aging, heterochromatin homeostasis is profoundly compromised. Here, we showed that LINE-1 (Long Interspersed Nuclear Element-1; L1) RNA accumulation was an early event in both typical and atypical human progeroid syndromes. L1 RNA negatively regulated the enzymatic activity of the histone-lysine N-methyltransferase SUV39H1 (suppression of variegation 3-9 homolog 1), resulting in heterochromatin loss and onset of senescent phenotypes in vitro. Depletion of L1 RNA in dermal fibroblast cells from patients with different progeroid syndromes using specific antisense oligonucleotides (ASOs) restored heterochromatin histone 3 lysine 9 and histone 3 lysine 27 trimethylation marks, reversed DNA methylation age, and counteracted the expression of senescence-associated secretory phenotype genes such as p16, p21, activating transcription factor 3 (ATF3), matrix metallopeptidase 13 (MMP13), interleukin 1a (IL1a), BTG anti-proliferation factor 2 (BTG2), and growth arrest and DNA damage inducible beta (GADD45b). Moreover, systemic delivery of ASOs rescued the histophysiology of tissues and increased the life span of a Hutchinson-Gilford progeria syndrome mouse model. Transcriptional profiling of human and mouse samples after L1 RNA depletion demonstrated that pathways associated with nuclear chromatin organization, cell proliferation, and transcription regulation were enriched. Similarly, pathways associated with aging, inflammatory response, innate immune response, and DNA damage were down-regulated. Our results highlight the role of L1 RNA in heterochromatin homeostasis in progeroid syndromes and identify a possible therapeutic approach to treat premature aging and related syndromes.
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Affiliation(s)
- Francesco Della Valle
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | - Pradeep Reddy
- Salk Institute for Biological Studies, La Jolla, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Mako Yamamoto
- Salk Institute for Biological Studies, La Jolla, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Peng Liu
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | - Dalila Bensaddek
- King Abdullah University of Science and Technology (KAUST), Bioscience Core Lab
| | - Huoming Zhang
- King Abdullah University of Science and Technology (KAUST), Bioscience Core Lab
| | | | - Leila Abassi
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | - Mirko Celii
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | | | - Arianna Mangiavacchi
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | | | | | | | - Valerio Orlando
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
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20
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Spitale RC, Chaput JC. Reply to: On gene silencing by the X10-23 DNAzyme. Nat Chem 2022; 14:859-861. [DOI: 10.1038/s41557-022-00983-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
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21
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On gene silencing by the X10-23 DNAzyme. Nat Chem 2022; 14:855-858. [DOI: 10.1038/s41557-022-00990-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/21/2022] [Indexed: 11/08/2022]
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22
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Pontarelli A, Wilds CJ. Arabinonucleic acids containing C5-propynyl modifications form stable hybrid duplexes with RNA that are efficiently degraded by E. coli RNase H. Bioorg Med Chem Lett 2022; 67:128744. [PMID: 35452799 DOI: 10.1016/j.bmcl.2022.128744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/07/2022] [Accepted: 04/13/2022] [Indexed: 11/02/2022]
Abstract
The promise of the antisense approach to treat a variety of diseases with oligonucleotides and solutions to challenges that have been encountered in their development is attributable to chemical modification of the nucleic acid scaffold. Herein, we describe preliminary data regarding the synthesis of a novel C5-propynyl-β-d-arabinouridine (araUP) phosphoramidite and its incorporation into oligonucleotides. Substitution of araUP in dT18 results in minor stabilization of duplexes formed with RNA when modifications are placed consecutively and a uniformly modified araUP 18-mer increases stability by 34 °C relative to DNA. The modified oligomer exhibits improved nuclease and serum stability when compared to DNA and duplexes formed between RNA and araUP oligonucleotides are substrates for E. coli RNase H. These preliminary results merit further investigation into C5-propynyl modified arabino nucleic acids for potential therapeutic gene silencing applications.
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Affiliation(s)
- Alexander Pontarelli
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada.
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23
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Kupryushkin MS, Filatov AV, Mironova NL, Patutina OA, Chernikov IV, Chernolovskaya EL, Zenkova MA, Pyshnyi DV, Stetsenko DA, Altman S, Vlassov VV. Antisense oligonucleotide gapmers containing phosphoryl guanidine groups reverse MDR1-mediated multiple drug resistance of tumor cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:211-226. [PMID: 34976439 PMCID: PMC8693280 DOI: 10.1016/j.omtn.2021.11.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/28/2021] [Indexed: 10/26/2022]
Abstract
Antisense gapmer oligonucleotides containing phosphoryl guanidine (PG) groups, e.g., 1,3-dimethylimidazolidin-2-imine, at three to five internucleotidic positions adjacent to the 3' and 5' ends were prepared via the Staudinger chemistry, which is compatible with conditions of standard automated solid-phase phosphoramidite synthesis for phosphodiester and, notably, phosphorothioate linkages, and allows one to design a variety of gapmeric structures with alternating linkages, and deoxyribose or 2'-O-methylribose backbone. PG modifications increased nuclease resistance in serum-containing medium for more than 21 days. Replacing two internucleotidic phosphates by PG groups in phosphorothioate-modified oligonucleotides did not decrease their cellular uptake in the absence of lipid carriers. Increasing the number of PG groups from two to seven per oligonucleotide reduced their ability to enter the cells in the carrier-free mode. Cationic liposomes provided similar delivery efficiency of both partially PG-modified and unmodified oligonucleotides. PG-gapmers were designed containing three to four PG groups at both wings and a central "window" of seven deoxynucleotides with either phosphodiester or phosphorothioate linkages targeted to MDR1 mRNA providing multiple drug resistance of tumor cells. Gapmers efficiently silenced MDR1 mRNA and restored the sensitivity of tumor cells to chemotherapeutics. Thus, PG-gapmers can be considered as novel, promising types of antisense oligonucleotides for targeting biologically relevant RNAs.
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Affiliation(s)
- Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Anton V Filatov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Olga A Patutina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Ivan V Chernikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Elena L Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
| | - Dmitry A Stetsenko
- Department of Physics, Novosibirsk State University, Pirogov Str. 2, Novosibirsk 630090, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 10, Novosibirsk 630090, Russia
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Life Sciences, Arizona State University, Tempe, AZ 85281, USA.,Montreal Clinical Research Institute, Montreal QC H2W 1R7, Canada
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave., 8, Novosibirsk 630090, Russia
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24
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Antisense Oligonucleotide-Based Therapy of Viral Infections. Pharmaceutics 2021; 13:pharmaceutics13122015. [PMID: 34959297 PMCID: PMC8707165 DOI: 10.3390/pharmaceutics13122015] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid-based therapeutics have demonstrated their efficacy in the treatment of various diseases and vaccine development. Antisense oligonucleotide (ASO) technology exploits a single-strand short oligonucleotide to either cause target RNA degradation or sterically block the binding of cellular factors or machineries to the target RNA. Chemical modification or bioconjugation of ASOs can enhance both its pharmacokinetic and pharmacodynamic performance, and it enables customization for a specific clinical purpose. ASO-based therapies have been used for treatment of genetic disorders, cancer and viral infections. In particular, ASOs can be rapidly developed for newly emerging virus and their reemerging variants. This review discusses ASO modifications and delivery options as well as the design of antiviral ASOs. A better understanding of the viral life cycle and virus-host interactions as well as advances in oligonucleotide technology will benefit the development of ASO-based antiviral therapies.
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25
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Barkau CL, O'Reilly D, Eddington SB, Damha MJ, Gagnon KT. Small nucleic acids and the path to the clinic for anti-CRISPR. Biochem Pharmacol 2021; 189:114492. [PMID: 33647260 PMCID: PMC8725204 DOI: 10.1016/j.bcp.2021.114492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-based therapeutics have entered clinical trials but no methods to inhibit Cas enzymes have been demonstrated in a clinical setting. The ability to inhibit CRISPR-based gene editing or gene targeting drugs should be considered a critical step in establishing safety standards for many CRISPR-Cas therapeutics. Inhibitors can act as a failsafe or as an adjuvant to reduce off-target effects in patients. In this review we discuss the need for clinical inhibition of CRISPR-Cas systems and three existing inhibitor technologies: anti-CRISPR (Acr) proteins, small molecule Cas inhibitors, and small nucleic acid-based CRISPR inhibitors, CRISPR SNuBs. Due to their unique properties and the recent successes of other nucleic acid-based therapeutics, CRISPR SNuBs appear poised for clinical application in the near-term.
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Affiliation(s)
- Christopher L Barkau
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Seth B Eddington
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA.
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26
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El-Khoury R, Damha MJ. 2'-Fluoro-arabinonucleic Acid (FANA): A Versatile Tool for Probing Biomolecular Interactions. Acc Chem Res 2021; 54:2287-2297. [PMID: 33861067 DOI: 10.1021/acs.accounts.1c00125] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Account highlights the structural features that render 2'-deoxy-2'-fluoro-arabinonucleic acid (FANA) an ideal tool for mimicking DNA secondary structures and probing biomolecular interactions relevant to chemical biology.The high binding affinity of FANA to DNA and RNA has had implications in therapeutics. FANA can hybridize to complementary RNA, resulting in a predominant A-form helix stabilized by a network of 2'F-H8(purine) pseudohydrogen bonding interactions. We have shown that FANA/RNA hybrids are substrates of RNase H and Ago2, both implicated in the mechanism of action of antisense oligonucleotides (ASOs) and siRNA, respectvely. This knowledge has helped us study the conformational preferences of ASOs and siRNA as well as crRNA in CRISPR-associated Cas9, thereby revealing structural features crucial to biochemical activity.Additionally, FANA is of particular use in stabilizing noncanonical DNA structures. For instance, we have taken advantage of the anti N-glycosidic bond conformation of FANA monomers to induce a parallel topology in telomeric G-quadruplexes. Subsequent single-molecule FRET studies elucidated the mechanism by which these parallel G-quadruplexes are recognized and extended by telomerase. Similarly, we have utilized FANA to stabilize elusive telomeric i-motifs in the presence of concomitant parallel G-quadruplexes and under physiological conditions, thereby reinforcing their potential relevance to telomere biology. In another study, we adapted microarray technology and used FANA substitutions to enhance the binding affinity of the G-quadruplex thrombin-binding aptamer to its thrombin target.Finally, we discovered that DNA polymerases can synthesize FANA strands from DNA templates. On the basis of this property, other groups demonstrated that FANA, like DNA, can store hereditary information. They did so by engineering polymerases to efficiently transfer genetic information from DNA to FANA and retrieve it back into DNA. Subsequent studies showed that FANA could be evolved to acquire ribozyme-like endonuclease or ligase activity and to form high-affinity aptamers.Overall, the implications of these studies are remarkable because they promise a deeper understanding of human biochemistry for innovative therapeutic avenues. This Account summarizes past achievements and provides an outlook for inspiring the increased use of FANA in biological applications and fostering interdisciplinary collaborations.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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27
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Use of a Self-Delivering Anti-CCL3 FANA Oligonucleotide as an Innovative Approach to Target Inflammation after Spinal Cord Injury. eNeuro 2021; 8:ENEURO.0338-20.2021. [PMID: 33632814 PMCID: PMC7986543 DOI: 10.1523/eneuro.0338-20.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/23/2020] [Accepted: 01/01/2021] [Indexed: 12/11/2022] Open
Abstract
Secondary damage after spinal cord injury (SCI) occurs because of a sequence of events after the initial injury, including exacerbated inflammation that contributes to increased lesion size and poor locomotor recovery. Thus, mitigating secondary damage is critical to preserve neural tissue and improve neurologic outcome. In this work, we examined the therapeutic potential of a novel antisense oligonucleotide (ASO) with special chemical modifications [2′-deoxy-2-fluoro-D-arabinonucleic acid (FANA) ASO] for specifically inhibiting an inflammatory molecule in the injured spinal cord. The chemokine CCL3 plays a complex role in the activation and attraction of immune cells and is upregulated in the injured tissue after SCI. We used specific FANA ASO to inhibit CCL3 in a contusive mouse model of murine SCI. Our results show that self-delivering FANA ASO molecules targeting the chemokine CCL3 penetrate the spinal cord lesion site and suppress the expression of CCL3 transcripts. Furthermore, they reduce other proinflammatory cytokines such as tumor necrosis factor (TNF) and interleukin (IL)-1β after SCI. In summary, we demonstrate for the first time the potential of FANA ASO molecules to penetrate the spinal cord lesion site to specifically inhibit CCL3, reducing proinflammatory cytokines and improve functional recovery after SCI. This novel approach may be used in new treatment strategies for SCI and other pathologic conditions of the CNS.
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28
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Hennessy EJ, FitzGerald GA. Battle for supremacy: nucleic acid interactions between viruses and cells. J Clin Invest 2021; 131:144227. [PMID: 33290272 PMCID: PMC7843224 DOI: 10.1172/jci144227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since the COVID-19 pandemic swept across the globe, researchers have been trying to understand its origin, life cycle, and pathogenesis. There is a striking variability in the phenotypic response to infection with SARS-CoV-2 that may reflect differences in host genetics and/or immune response. It is known that the human epigenome is influenced by ethnicity, age, lifestyle, and environmental factors, including previous viral infections. This Review examines the influence of viruses on the host epigenome. We describe general lessons and methodologies that can be used to understand how the virus evades the host immune response. We consider how variation in the epigenome may contribute to heterogeneity in the response to SARS-CoV-2 and may identify a precision medicine approach to treatment.
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29
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Fakih HH, Katolik A, Malek-Adamian E, Fakhoury JJ, Kaviani S, Damha MJ, Sleiman HF. Design and enhanced gene silencing activity of spherical 2'-fluoroarabinose nucleic acids (FANA-SNAs). Chem Sci 2021; 12:2993-3003. [PMID: 34164068 PMCID: PMC8179377 DOI: 10.1039/d0sc06645a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Drug delivery vectors for nucleic acid therapeutics (NATs) face significant barriers for translation into the clinic. Spherical nucleic acids (SNAs) – nanoparticles with an exterior shell made up of DNA strands and a hydrophobic interior – have recently shown great potential as vehicles to improve the biodistribution and efficacy of NATs. To date, SNA design has not taken advantage of the powerful chemical modifications available to NATs. Here, we modify SNAs with 2′-deoxy-2′-fluoro-d-arabinonucleic acid (FANA-SNA), and show increased stability, enhanced gene silencing potency and unaided uptake (gymnosis) as compared to free FANA. By varying the spacer region between the nucleic acid strand and the attached hydrophobic polymer, we show that a cleavable DNA based spacer is essential for maximum activity. This design feature will be important when implementing functionalized nucleic acids into nanostructures for gene silencing. The modularity of the FANA-SNA was demonstrated by silencing two different targets. Transfection-free delivery was superior for the modified SNA compared to the free FANA oligonucleotide. Optimizing FANA modified spherical nucleic acids (FANA-SNAs) for highly efficient delivery of nucleic acid therapeutics.![]()
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Affiliation(s)
- Hassan H Fakih
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Adam Katolik
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | | | - Johans J Fakhoury
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Sepideh Kaviani
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Masad J Damha
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
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30
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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31
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Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Snijder E, van Hemert MJ, Bujnicki JM, Incarnato D. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements. Nucleic Acids Res 2020; 48:12436-12452. [PMID: 33166999 PMCID: PMC7736786 DOI: 10.1093/nar/gkaa1053] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 01/25/2023] Open
Abstract
SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally-conserved coronavirus structural RNA elements have been identified to date. Here, we performed RNA structure probing to obtain single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Probing data recapitulate the previously described coronavirus RNA elements (5' UTR and s2m), and reveal new structures. Of these, ∼10.2% show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. Secondary structure-restrained 3D modeling of these segments further allowed for the identification of putative druggable pockets. In addition, we identify a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.
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Affiliation(s)
- Ilaria Manfredonia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz K Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tycho Marinus
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn J van Hemert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
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32
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KCTD15 is overexpressed in human childhood B-cell acute lymphoid leukemia. Sci Rep 2019; 9:20108. [PMID: 31882877 PMCID: PMC6934626 DOI: 10.1038/s41598-019-56701-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Leukemic cells originate from the malignant transformation of undifferentiated myeloid/lymphoid hematopoietic progenitors normally residing in bone marrow. As the precise molecular mechanisms underlying this heterogeneous disease are yet to be disclosed, the identification and the validation of novel actors in leukemia is of extreme importance. Here, we show that KCTD15, a member of the emerging class of KCTD ((K)potassium Channel Tetramerization Domain containing) proteins, is strongly upregulated in patients affected by B-cell type acute lymphoblastic leukemia (B-ALL) and in continuous cell lines (RS4;11, REH, TOM-1, SEM) derived from this form of childhood leukemia. Interestingly, KCTD15 downregulation induces apoptosis and cell death suggesting that it has a role in cellular homeostasis and proliferation. In addition, stimulation of normal lymphocytes with the pokeweed mitogen leads to increased KCTD15 levels in a fashion comparable to those observed in proliferating leukemic cells. In this way, the role of KCTD15 is likely not confined to the B-ALL pathological state and extends to activation and proliferation of normal lymphocytes. Collectively, data here presented indicate that KCTD15 is an important and hitherto unidentified player in childhood lymphoid leukemia, and its study could open a new scenario for the identification of altered and still unknown molecular pathways in leukemia.
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