1
|
Croft LV, Fisher M, Barbhuiya TK, El-Kamand S, Beard S, Rajapakse A, Gamsjaeger R, Cubeddu L, Bolderson E, O'Byrne K, Richard D, Gandhi NS. Sequence- and Structure-Dependent Cytotoxicity of Phosphorothioate and 2'- O-Methyl Modified Single-Stranded Oligonucleotides. Nucleic Acid Ther 2024. [PMID: 38648015 DOI: 10.1089/nat.2023.0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Single-stranded oligonucleotides (SSOs) are a rapidly expanding class of therapeutics that comprises antisense oligonucleotides, microRNAs, and aptamers, with ten clinically approved molecules. Chemical modifications such as the phosphorothioate backbone and the 2'-O-methyl ribose can improve the stability and pharmacokinetic properties of therapeutic SSOs, but they can also lead to toxicity in vitro and in vivo through nonspecific interactions with cellular proteins, gene expression changes, disturbed RNA processing, and changes in nuclear structures and protein distribution. In this study, we screened a mini library of 277 phosphorothioate and 2'-O-methyl-modified SSOs, with or without mRNA complementarity, for cytotoxic properties in two cancer cell lines. Using circular dichroism, nucleic magnetic resonance, and molecular dynamics simulations, we show that phosphorothioate- and 2'-O-methyl-modified SSOs that form stable hairpin structures through Watson-Crick base pairing are more likely to be cytotoxic than those that exist in an extended conformation. In addition, moderate and highly cytotoxic SSOs in our dataset have a higher mean purine composition than pyrimidine. Overall, our study demonstrates a structure-cytotoxicity relationship and indicates that the formation of stable hairpins should be a consideration when designing SSOs toward optimal therapeutic profiles.
Collapse
Affiliation(s)
- Laura V Croft
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Mark Fisher
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Tabassum Khair Barbhuiya
- School of Chemistry and Physics, Centre for Genomics and Personalised Health, Faculty of Science, Queensland University of Technology, Brisbane, Australia
| | - Serene El-Kamand
- School of Science, Western Sydney University, Penrith, Australia
| | - Samuel Beard
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Aleksandra Rajapakse
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | | | - Liza Cubeddu
- School of Science, Western Sydney University, Penrith, Australia
| | - Emma Bolderson
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Ken O'Byrne
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- Princess Alexandra Hospital, Woolloongabba, Australia
| | - Derek Richard
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Neha S Gandhi
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program at Translational Research Institute, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- School of Chemistry and Physics, Centre for Genomics and Personalised Health, Faculty of Science, Queensland University of Technology, Brisbane, Australia
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Karnataka, India
| |
Collapse
|
2
|
Dighe K, Moitra P, Gunaseelan N, Alafeef M, Jensen T, Rafferty C, Pan D. Highly-Specific Single-Stranded Oligonucleotides and Functional Nanoprobes for Clinical Determination of Chlamydia Trachomatis and Neisseria Gonorrhoeae Infections. Adv Sci (Weinh) 2023; 10:e2304009. [PMID: 37870167 PMCID: PMC10754082 DOI: 10.1002/advs.202304009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/18/2023] [Indexed: 10/24/2023]
Abstract
Early detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) is the key to controlling the spread of these bacterial infections. An important step in developing biosensors involves identifying reliable sensing probes against specific genetic targets for CT and NG. Here, the authors have designed single-stranded oligonucleotides (ssDNAs) targeting mutually conserved genetic regions of cryptic plasmid and chromosomal DNA of both CT and NG. The 5'- and 3'- ends of these ssDNAs are differentially functionalized with thiol groups and coupled with gold nanoparticles (AuNP) to develop absorbance-based assay. The AuNPs agglomerate selectively in the presence of its target DNA sequence and demonstrate a change in their surface plasmon resonance. The optimized assay is then used to detect both CT and NG DNA extracted from 60 anonymized clinical samples with a clinical sensitivity of ∼100%. The limit of detection of the assays are found to be 7 and 5 copies/µL for CT and NG respectively. Furthermore, it can successfully detect the DNA levels of these two bacteria without the need for DNA extraction and via a lateral flow-based platform. These assays thus hold the potential to be employed in clinics for rapid and efficient monitoring of sexually transmitted infections.
Collapse
Affiliation(s)
- Ketan Dighe
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Biomedical EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Parikshit Moitra
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Nivetha Gunaseelan
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Biomedical EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Maha Alafeef
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Tor Jensen
- Cancer Center at IllinoisUniversity of Illinois Urbana‐Champaign405 N. Mathews Ave.UrbanaIL61801‐2325USA
| | - Carla Rafferty
- Department of Family MedicineCarle Health1818 E Windsor Rd.UrbanaIL61802USA
| | - Dipanjan Pan
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Biomedical EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Department of Materials Science and EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Huck Institutes of the Life Sciences101 Huck Life Sciences BuildingUniversity ParkPA16802USA
| |
Collapse
|
3
|
Goh KW, Stephen A, Wu YS, Sim MS, Batumalaie K, Gopinath SC, Guad RM, Kumar A, Sekar M, Subramaniyan V, Fuloria NK, Fuloria S, Velaga A, Sarker MMR. Molecular Targets of Aptamers in Gastrointestinal Cancers: Cancer Detection, Therapeutic Applications, and Associated Mechanisms. J Cancer 2023; 14:2491-2516. [PMID: 37670975 PMCID: PMC10475355 DOI: 10.7150/jca.85260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/03/2023] [Indexed: 09/07/2023] Open
Abstract
Gastrointestinal (GI) cancers are among the most common cancers that impact the global population, with high mortality and low survival rates after breast and lung cancers. Identifying useful molecular targets in GI cancers are crucial for improving diagnosis, prognosis, and treatment outcomes, however, limited by poor targeting and drug delivery system. Aptamers are often utilized in the field of biomarkers identification, targeting, and as a drug/inhibitor delivery cargo. Their natural and chemically modifiable binding capability, high affinity, and specificity are favored over antibodies and potential early diagnostic imaging and drug delivery applications. Studies have demonstrated the use of different aptamers as drug delivery agents and early molecular diagnostic and detection probes for treating cancers. This review aims to first describe aptamers' generation, characteristics, and classifications, also providing insights into their recent applications in the diagnosis and medical imaging, prognosis, and anticancer drug delivery system of GI cancers. Besides, it mainly discussed the relevant molecular targets and associated molecular mechanisms involved, as well as their applications for potential treatments for GI cancers. In addition, the current applications of aptamers in a clinical setting to treat GI cancers are deciphered. In conclusion, aptamers are multifunctional molecules that could be effectively used as an anticancer agent or drug delivery system for treating GI cancers and deserve further investigations for clinical applications.
Collapse
Affiliation(s)
- Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, 71800 Nilai, Malaysia
| | - Annatasha Stephen
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yuan Seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Selangor 47500, Malaysia
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor 47500, Malaysia
| | - Maw Shin Sim
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kalaivani Batumalaie
- Department of Biomedical Sciences, Faculty of Health Sciences, Asia Metropolitan University, 81750 Johor Bahru, Malaysia
| | - Subash C.B. Gopinath
- Faculty of Chemical Engineering & Technology, Arau 02600, Institute of Nano Electronic Engineering, Kangar 01000, Micro System Technology, Centre of Excellence, Arau 02600, Pauh Campus, Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600 Arau, Perlis, Malaysia
- Department of Computer Science and Engineering, Faculty of Science and Information Technology, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh
| | - Rhanye Mac Guad
- Department of Biomedical Science and Therapeutics, Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Ashok Kumar
- Department of Internal Medicine, University of Kansas Medical Centre, Kansas City, Kansas 66103, United States
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Vetriselvan Subramaniyan
- Department of Pharmacology, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Malaysia
- Department of Pharmacology, School of Medicine, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Selangor 42610, Malaysia
| | - Neeraj Kumar Fuloria
- Centre of Excellence for Biomaterials Engineering & Faculty of Pharmacy, AIMST University, Bedong 08100, Malaysia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospitals, Saveetha University, Chennai 600077, India
| | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Semeling, Bedong 08100, Malaysia
| | - Appalaraju Velaga
- Department of Medicinal Chemistry, Faculty of Pharmacy, MAHSA University, Selangor 42610, Malaysia
| | - Md. Moklesur Rahman Sarker
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh
- Health Med Science Research Network, 3/1, Block F, Lalmatia, Dhaka 1207, Bangladesh
| |
Collapse
|
4
|
Kowalczyk JE, Saha S, Mäkelä MR. Application of CRISPR/Cas9 Tools for Genome Editing in the White-Rot Fungus Dichomitus squalens. Biomolecules 2021; 11:1526. [PMID: 34680159 PMCID: PMC8533725 DOI: 10.3390/biom11101526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022] Open
Abstract
Dichomitus squalens is an emerging reference species that can be used to investigate white-rot fungal plant biomass degradation, as it has flexible physiology to utilize different types of biomass as sources of carbon and energy. Recent comparative (post-) genomic studies on D. squalens resulted in an increasingly detailed knowledge of the genes and enzymes involved in the lignocellulose breakdown in this fungus and showed a complex transcriptional response in the presence of lignocellulose-derived compounds. To fully utilize this increasing amount of data, efficient and reliable genetic manipulation tools are needed, e.g., to characterize the function of certain proteins in vivo and facilitate the construction of strains with enhanced lignocellulolytic capabilities. However, precise genome alterations are often very difficult in wild-type basidiomycetes partially due to extremely low frequencies of homology directed recombination (HDR) and limited availability of selectable markers. To overcome these obstacles, we assessed various Cas9-single guide RNA (sgRNA) ribonucleoprotein (RNP) -based strategies for selectable homology and non-homologous end joining (NHEJ) -based gene editing in D. squalens. We also showed an induction of HDR-based genetic modifications by using single-stranded oligodeoxynucleotides (ssODNs) in a basidiomycete fungus for the first time. This paper provides directions for the application of targeted CRISPR/Cas9-based genome editing in D. squalens and other wild-type (basidiomycete) fungi.
Collapse
Affiliation(s)
| | | | - Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland; (J.E.K.); (S.S.)
| |
Collapse
|
5
|
Kocher T, Bischof J, Haas SA, March OP, Liemberger B, Hainzl S, Illmer J, Hoog A, Muigg K, Binder HM, Klausegger A, Strunk D, Bauer JW, Cathomen T, Koller U. A non-viral and selection-free COL7A1 HDR approach with improved safety profile for dystrophic epidermolysis bullosa. Mol Ther Nucleic Acids 2021; 25:237-250. [PMID: 34458008 PMCID: PMC8368800 DOI: 10.1016/j.omtn.2021.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/25/2021] [Indexed: 12/26/2022]
Abstract
Gene editing via homology-directed repair (HDR) currently comprises the best strategy to obtain perfect corrections for pathogenic mutations of monogenic diseases, such as the severe recessive dystrophic form of the blistering skin disease epidermolysis bullosa (RDEB). Limitations of this strategy, in particular low efficiencies and off-target effects, hinder progress toward clinical applications. However, the severity of RDEB necessitates the development of efficient and safe gene-editing therapies based on perfect repair. To this end, we sought to assess the corrective efficiencies following optimal Cas9 nuclease and nickase-based COL7A1-targeting strategies in combination with single- or double-stranded donor templates for HDR at the COL7A1 mutation site. We achieved HDR-mediated correction efficiencies of up to 21% and 10% in primary RDEB keratinocytes and fibroblasts, respectively, as analyzed by next-generation sequencing, leading to full-length type VII collagen restoration and accurate deposition within engineered three-dimensional (3D) skin equivalents (SEs). Extensive on- and off-target analyses confirmed that the combined treatment of paired nicking and single-stranded oligonucleotides constituted a highly efficient COL7A1-editing strategy, associated with a significantly improved safety profile. Our findings, therefore, represent a further advancement in the field of traceless genome editing for genodermatoses.
Collapse
Affiliation(s)
- Thomas Kocher
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Simone Alexandra Haas
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, 79106 Freiburg, Germany
| | - Oliver Patrick March
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Bernadette Liemberger
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Stefan Hainzl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Julia Illmer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Anna Hoog
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Katharina Muigg
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Heide-Marie Binder
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Alfred Klausegger
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Dirk Strunk
- Cell Therapy Institute, SCI-TReCS, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Johann Wolfgang Bauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
- Corresponding author Ulrich Koller, EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Strubergasse 22, 5020 Salzburg, Austria.
| |
Collapse
|
6
|
Pålsson SA, Dondalska A, Bergenstråhle J, Rolfes C, Björk A, Sedano L, Power UF, Rameix-Welti MA, Lundeberg J, Wahren-Herlenius M, Mastrangelo P, Eleouet JF, Le Goffic R, Galloux M, Spetz AL. Single-Stranded Oligonucleotide-Mediated Inhibition of Respiratory Syncytial Virus Infection. Front Immunol 2020; 11:580547. [PMID: 33363532 PMCID: PMC7752805 DOI: 10.3389/fimmu.2020.580547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/09/2020] [Indexed: 01/01/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections in young children. Currently, there is no RSV vaccine or universally accessible antiviral treatment available. Addressing the urgent need for new antiviral agents, we have investigated the capacity of a non-coding single-stranded oligonucleotide (ssON) to inhibit RSV infection. By utilizing a GFP-expressing RSV, we demonstrate that the ssON significantly reduced the proportion of RSV infected A549 cells (lung epithelial cells). Furthermore, we show that ssON's antiviral activity was length dependent and that both RNA and DNA of this class of oligonucleotides have antiviral activity. We reveal that ssON inhibited RSV infection by competing with the virus for binding to the cellular receptor nucleolin in vitro. Additionally, using a recombinant RSV that expresses luciferase we show that ssON effectively blocked RSV infection in mice. Treatment with ssON in vivo resulted in the upregulation of RSV-induced interferon stimulated genes (ISGs) such as Stat1, Stat2, Cxcl10, and Ccl2. This study highlights the possibility of using oligonucleotides as therapeutic agents against RSV infection. We demonstrate that the mechanism of action of ssON is the inhibition of viral entry in vitro, likely through the binding of the receptor, nucleolin and that ssON treatment against RSV infection in vivo additionally results in the upregulation of ISGs.
Collapse
Affiliation(s)
- Sandra Axberg Pålsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Aleksandra Dondalska
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Joseph Bergenstråhle
- Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - Caroline Rolfes
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Albin Björk
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura Sedano
- UR0892 Unité VIM, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ultan F. Power
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - Marie-Anne Rameix-Welti
- UMR INSERM U1173 I2, UFR des Sciences de la Santé Simone Veil—UVSQ, Montigny-Le-Bretonneux, France
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Mastrangelo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | - Ronan Le Goffic
- UR0892 Unité VIM, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marie Galloux
- UR0892 Unité VIM, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Anna-Lena Spetz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| |
Collapse
|
7
|
Dondalska A, Rönnberg E, Ma H, Pålsson SA, Magnusdottir E, Gao T, Adam L, Lerner EA, Nilsson G, Lagerström M, Spetz AL. Amelioration of Compound 48/80-Mediated Itch and LL-37-Induced Inflammation by a Single-Stranded Oligonucleotide. Front Immunol 2020; 11:559589. [PMID: 33101278 PMCID: PMC7554336 DOI: 10.3389/fimmu.2020.559589] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
Numerous inflammatory skin disorders display a high prevalence of itch. The Mas-related G protein coupled receptor X2 (MRGPRX2) has been shown to modulate itch by inducing non-IgE-mediated mast cell degranulation and the release of endogenous inducers of pruritus. Various substances collectively known as basic secretagogues, which include inflammatory peptides and certain drugs, can trigger MRGPRX2 and thereby induce pseudo-allergic reactions characterized by histamine and protease release as well as inflammation. Here, we investigated the capacity of an immunomodulatory single-stranded oligonucleotide (ssON) to modulate IgE-independent mast cell degranulation and, more specifically, its ability to inhibit the basic secretagogues compound 48/80 (C48/80)-and LL-37 in vitro and in vivo. We examined the effect of ssON on MRGPRX2 activation in vitro by measuring degranulation in a human mast cell line (LAD2) and calcium influx in MRGPRX2-transfected HEK293 cells. To determine the effect of ssON on itch, we performed behavioral studies in established mouse models and collected skin biopsies for histological analysis. Additionally, with the use of a rosacea mouse model and RT-qPCR, we investigated the effect on ssON on LL-37-induced inflammation. We reveal that both mast cell degranulation and calcium influx in MRGPRX2 transfected HEK293 cells, induced by the antimicrobial peptide LL-37 and the basic secretagogue C48/80, are effectively inhibited by ssON in a dose-dependent manner. Further, ssON demonstrates a capability to inhibit LL-37 and C48/80 activation in vivo in two mouse models. We show that intradermal injection of ssON in mice is able to block itch induced via C48/80 in a dose-dependent manner. Histological staining revealed that ssON inhibits acute mast cell degranulation in murine skin treated with C48/80. Lastly, we show that ssON treatment ameliorates LL-37-induced inflammation in a rosacea mouse model. Since there is a need for new therapeutics targeting non-IgE-mediated activation of mast cells, ssON could be used as a prospective drug candidate to resolve itch and inflammation in certain dermatoses.
Collapse
Affiliation(s)
- Aleksandra Dondalska
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Elin Rönnberg
- Immunology and Allergy Division, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Haisha Ma
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Sandra Axberg Pålsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Tianle Gao
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Lucille Adam
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ethan A. Lerner
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital/Harvard Medical School, Boston, MA, United States
| | - Gunnar Nilsson
- Immunology and Allergy Division, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Anna-Lena Spetz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| |
Collapse
|
8
|
Poux C, Dondalska A, Bergenstråhle J, Pålsson S, Contreras V, Arasa C, Järver P, Albert J, Busse DC, LeGrand R, Lundeberg J, Tregoning JS, Spetz AL. A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection. Front Immunol 2019; 10:2161. [PMID: 31572376 PMCID: PMC6751283 DOI: 10.3389/fimmu.2019.02161] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022] Open
Abstract
The initiation of an immune response is dependent on the activation and maturation of dendritic cells after sensing pathogen associated molecular patterns by pattern recognition receptors. However, the response needs to be balanced as excessive pro-inflammatory cytokine production in response to viral or stress-induced pattern recognition receptor signaling has been associated with severe influenza A virus (IAV) infection. Here, we use an inhibitor of Toll-like receptor (TLR)3, a single-stranded oligonucleotide (ssON) with the capacity to inhibit certain endocytic routes, or a TLR3 agonist (synthetic double-stranded RNA PolyI:C), to evaluate modulation of innate responses during H1N1 IAV infection. Since IAV utilizes cellular endocytic machinery for viral entry, we also assessed ssON's capacity to affect IAV infection. We first show that IAV infected human monocyte-derived dendritic cells (MoDC) were unable to up-regulate the co-stimulatory molecules CD80 and CD86 required for T cell activation. Exogenous TLR3 stimulation did not overcome the IAV-mediated inhibition of co-stimulatory molecule expression in MoDC. However, TLR3 stimulation using PolyI:C led to an augmented pro-inflammatory cytokine response. We reveal that ssON effectively inhibited PolyI:C-mediated pro-inflammatory cytokine production in MoDC, notably, ssON treatment maintained an interferon response induced by IAV infection. Accordingly, RNAseq analyses revealed robust up-regulation of interferon-stimulated genes in IAV cultures treated with ssON. We next measured reduced IAV production in MoDC treated with ssON and found a length requirement for its anti-viral activity, which overlapped with its capacity to inhibit uptake of PolyI:C. Hence, in cases wherein an overreacting TLR3 activation contributes to IAV pathogenesis, ssON can reduce this signaling pathway. Furthermore, concomitant treatment with ssON and IAV infection in mice resulted in maintained weight and reduced viral load in the lungs. Therefore, extracellular ssON provides a mechanism for immune regulation of TLR3-mediated responses and suppression of IAV infection in vitro and in vivo in mice.
Collapse
Affiliation(s)
- Candice Poux
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Aleksandra Dondalska
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Joseph Bergenstråhle
- Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - Sandra Pålsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vanessa Contreras
- CEA, UMR1184, IDMIT Department, Institut de Biologie François Jacob, DRF, Fontenay-aux-Roses, France
| | - Claudia Arasa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Peter Järver
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - David C Busse
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Roger LeGrand
- CEA, UMR1184, IDMIT Department, Institut de Biologie François Jacob, DRF, Fontenay-aux-Roses, France
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - John S Tregoning
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Anna-Lena Spetz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| |
Collapse
|
9
|
Takahashi M, Contu VR, Kabuta C, Hase K, Fujiwara Y, Wada K, Kabuta T. SIDT2 mediates gymnosis, the uptake of naked single-stranded oligonucleotides into living cells. RNA Biol 2017; 14:1534-1543. [PMID: 28277980 PMCID: PMC5785214 DOI: 10.1080/15476286.2017.1302641] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Single-stranded oligonucleotides (ssOligos) are efficiently taken up by living cells without the use of transfection reagents. This phenomenon called ‘gymnosis’ enables the sequence-specific silencing of target genes in various types of cells. Several antisense ssOligos are used for the treatment of human diseases. However, the molecular mechanism underlying the uptake of naked ssOligos into cells remains to be elucidated. Here, we show that systemic RNA interference deficient-1 (SID-1) transmembrane family 2 (SIDT2), a mammalian ortholog of the Caenorhabditis elegans double-stranded RNA channel SID-1, mediates gymnosis. We show that the uptake of naked ssOligos into cells is significantly downregulated by knockdown of SIDT2. Furthermore, knockdown of SIDT2 inhibited the effect of antisense RNA mediated by gymnosis. Overexpression of SIDT2 enhanced the uptake of naked ssOligos into cells, while a single amino acid mutation in SIDT2 abolished this effect. Our findings highlight the mechanism of extra- and intracellular RNA transport and may contribute to the further development of nucleic acid-based therapies.
Collapse
Affiliation(s)
- Masayuki Takahashi
- a Department of Degenerative Neurological Diseases , National Institute of Neuroscience, National Center of Neurology and Psychiatry , Kodaira, Tokyo , Japan
| | - Viorica Raluca Contu
- a Department of Degenerative Neurological Diseases , National Institute of Neuroscience, National Center of Neurology and Psychiatry , Kodaira, Tokyo , Japan.,b Department of Neurology, Interdisciplinary Graduate School of Medicine and Engineering , University of Yamanashi , Yamanashi , Japan
| | - Chihana Kabuta
- a Department of Degenerative Neurological Diseases , National Institute of Neuroscience, National Center of Neurology and Psychiatry , Kodaira, Tokyo , Japan
| | - Katsunori Hase
- a Department of Degenerative Neurological Diseases , National Institute of Neuroscience, National Center of Neurology and Psychiatry , Kodaira, Tokyo , Japan
| | - Yuuki Fujiwara
- a Department of Degenerative Neurological Diseases , National Institute of Neuroscience, National Center of Neurology and Psychiatry , Kodaira, Tokyo , Japan
| | - Keiji Wada
- a Department of Degenerative Neurological Diseases , National Institute of Neuroscience, National Center of Neurology and Psychiatry , Kodaira, Tokyo , Japan
| | - Tomohiro Kabuta
- a Department of Degenerative Neurological Diseases , National Institute of Neuroscience, National Center of Neurology and Psychiatry , Kodaira, Tokyo , Japan
| |
Collapse
|
10
|
van Ravesteyn TW, Dekker M, Fish A, Sixma TK, Wolters A, Dekker RJ, Te Riele HP. LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells. Proc Natl Acad Sci U S A 2016; 113:4122-7. [PMID: 26951689 DOI: 10.1073/pnas.1513315113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Synthetic single-stranded DNA oligonucleotides (ssODNs) can be used to generate subtle genetic modifications in eukaryotic and prokaryotic cells without the requirement for prior generation of DNA double-stranded breaks. However, DNA mismatch repair (MMR) suppresses the efficiency of gene modification by >100-fold. Here we present a commercially available ssODN design that evades MMR and enables subtle gene modification in MMR-proficient cells. The presence of locked nucleic acids (LNAs) in the ssODNs at mismatching bases, or also at directly adjacent bases, allowed 1-, 2-, or 3-bp substitutions in MMR-proficient mouse embryonic stem cells as effectively as in MMR-deficient cells. Additionally, in MMR-proficient Escherichia coli, LNA modification of the ssODNs enabled effective single-base-pair substitution. In vitro, LNA modification of mismatches precluded binding of purified E. coli MMR protein MutS. These findings make ssODN-directed gene modification particularly well suited for applications that require the evaluation of a large number of sequence variants with an easy selectable phenotype.
Collapse
|
11
|
Rivera-Torres N, Kmiec EB. Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides. Plant Biotechnol J 2016; 14:463-470. [PMID: 26402400 DOI: 10.1111/pbi.12473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/07/2015] [Accepted: 08/12/2015] [Indexed: 06/05/2023]
Abstract
Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and utilize inherent metabolic functions to execute the genetic alteration within the context of a chromosome. The mechanism of action of gene editing is now being elucidated as well as an understanding of its regulatory circuitry, work that has been particularly important in establishing a foundation for designing effective gene editing strategies in plants. Double-strand DNA breakage and the activation of the DNA damage response pathway play key roles in determining the frequency with which gene editing activity takes place. Cellular regulators respond to such damage and their action impacts the success or failure of a particular nucleotide exchange reaction. A consequence of such activation is the natural slowing of replication fork progression, which naturally creates a more open chromatin configuration, thereby increasing access of the oligonucleotide to the DNA template. Herein, how critical reaction parameters influence the effectiveness of gene editing is discussed. Functional interrelationships between DNA damage, the activation of DNA response pathways and the stalling of replication forks are presented in detail as potential targets for increasing the frequency of gene editing by ssODNs in plants and plant cells.
Collapse
Affiliation(s)
- Natalia Rivera-Torres
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA
| | - Eric B Kmiec
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA
| |
Collapse
|