1
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Knappe GA, Gorman J, Bigley AN, Harvey SP, Bathe M. Heterovalent Click Reactions on DNA Origami. Bioconjug Chem 2025; 36:476-485. [PMID: 40042652 DOI: 10.1021/acs.bioconjchem.4c00552] [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: 03/20/2025]
Abstract
Nucleic acid nanoparticles (NANPs) fabricated by using the DNA origami method have broad utility in materials science and bioengineering. Their site-specific, heterovalent functionalization with secondary molecules such as proteins or fluorophores is a unique feature of this technology that drives its utility. Currently, however, there are few chemistries that enable fast, efficient covalent functionalization of NANPs with a broad conjugate scope and heterovalency. To address this need, we introduce synthetic methods to access inverse electron-demand Diels-Alder chemistry on NANPs. We demonstrate a broad conjugate scope, characterize application-relevant kinetics, and integrate this new chemistry with strain-promoted azide-alkyne cycloaddition chemistry to enable heterovalent click reactions on NANPs. We applied these chemistries to formulate a prototypical chemical countermeasure against chemical nerve agents. We envision this additional chemistry finding broad utility in the synthetic toolkit accessible to the nucleic acid nanotechnology community.
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Affiliation(s)
- Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrew N Bigley
- Department of Chemistry and Physics, Southwestern Oklahoma State University, Weatherford, Oklahoma 73096, United States
| | - Steven P Harvey
- U.S. Army Edgewood Chemical Biological Center, RDCB-DRC-C, Aberdeen Providing Ground, Maryland 21010, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
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2
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Meshry N, Carneiro KMM. DNA as a Promising Biomaterial for Bone Regeneration and Potential Mechanisms of Action. Acta Biomater 2025:S1742-7061(25)00198-9. [PMID: 40090507 DOI: 10.1016/j.actbio.2025.03.024] [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: 11/29/2024] [Revised: 02/25/2025] [Accepted: 03/13/2025] [Indexed: 03/18/2025]
Abstract
DNA nanotechnology has created new possibilities for the use of DNA in tissue regeneration - an important advance for DNA use beyond its paradigmatic role as the hereditary biomacromolecule. Biomaterials containing synthetic or natural DNA have been proposed for several applications including drug and gene delivery, and more recently, as osteoconductive biomaterials. This review provides an in-depth discussion of studies that have used DNA-based materials for biomineralization and/or bone repair, with expansion on the topic of DNA hydrogels specifically, and the advantages they offer for advancing the field of bone regeneration. Four mechanisms of action for the osteoconductive capabilities of DNA-based materials are discussed, and a proposed model for degradation of these materials and its link to their osteoconductive properties is later presented. Finally, the review considers current limitations of DNA-based materials and summarizes important aspects that need to be addressed for future application of DNA nanotechnology in tissue repair. STATEMENT OF SIGNIFICANCE: Herein we summarize the developing field of DNA-based materials for biomineralization and bone repair, with a focus on DNA hydrogels. We first provide a comprehensive review of different forms of DNA-based materials described thus far which have been shown to enhance bone repair and mineralization (namely DNA coatings, DNA-containing pastes, DNA nanostructures and DNA hydrogels). Next, we describe four different mechanisms by which DNA-based materials could be exerting their osteogenic effect. Then, we propose a novel model that links DNA degradation and osteoconductivity. Lastly, we suggest future research directions to enhance DNA-based materials for future clinical application. The suggested mechanisms and the proposed model can guide future research to better understand how DNA functions as a mineral- and bone-promoting molecule.
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Affiliation(s)
- Nadeen Meshry
- Faculty of Dentistry, University of Toronto, Toronto, Canada, 124 Edward Street, Toronto, ON, M5G 1G6, Canada
| | - Karina M M Carneiro
- Faculty of Dentistry, University of Toronto, Toronto, Canada, 124 Edward Street, Toronto, ON, M5G 1G6, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, Canada, 164 College St, Toronto, ON, M5S 3G9, Canada.
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3
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Karna D, Watanabe S, Sharma G, Sharma A, Zheng Y, Kawamata I, Suzuki Y, Mao H. Logic-Gated Modulation of Cell Migration via Mesoscale Mechanical Uncaging Effects. ACS NANO 2025; 19:8058-8069. [PMID: 39980204 DOI: 10.1021/acsnano.4c16194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2025]
Abstract
Mesoscopic objects ranging from molecular machinery to cells are prevalent in nature. Unlike atomic and nanoscopic objects that do not have pronounced mechanical properties due to their small sizes, mesoscale substances demonstrate their unique mechanical features that can interfere with cell functions, particularly those with a mechanical nature such as cell migrations. Here, we demonstrate mechanical caging/uncaging effects in a DNA origami nanospring system that precisely controls cancer cell migrations. By leveraging DNA as a programming language, our work demonstrates the creation of logic gates (Boolean AND and OR gates) responsive to various miRNA inputs, resulting in mechanical and structural changes in DNA origami nanosprings serving as processors, which uncage the arginyl-glycyl-aspartate (RGD) ligands to interact with integrins on the cell membrane surface. The mechanical uncaging effect inhibits the migration of cancer cells. The strategy can be readily harnessed for targeted drug delivery with minimal off-target effects. Our proof-of-concept mesoscale DNA origami self-assembly highlights the potential for exquisite multimodal control of mechanical functions of cells with future applications in synthetic biology and precision medicine.
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Affiliation(s)
- Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Shin Watanabe
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu 514-8507, Japan
| | - Grinsun Sharma
- School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Arpit Sharma
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Yaorong Zheng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Ibuki Kawamata
- Division of Physics and Astronomy, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuki Suzuki
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu 514-8507, Japan
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
- School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, Ohio 44242, United States
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4
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Romanov A, Knappe GA, Ronsard L, Suh H, Omer M, Chapman AP, Lewis VR, Spivakovsky K, Canales J, Reizis B, Tingle RD, Cottrell CA, Schiffner T, Lingwood D, Bathe M, Irvine DJ. DNA origami vaccines program antigen-focused germinal centers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.21.639354. [PMID: 40060683 PMCID: PMC11888200 DOI: 10.1101/2025.02.21.639354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/18/2025]
Abstract
Recruitment and expansion of rare precursor B cells in germinal centers (GCs) is a central goal of vaccination to generate broadly neutralizing antibodies (bnAbs) against challenging pathogens such as HIV. Multivalent immunogen display is a well-established method to enhance vaccine-induced B cell responses, typically accomplished by using natural or engineered protein scaffolds. However, these scaffolds themselves are targets of antibody responses, with the potential to generate competitor scaffold-specific B cells that could theoretically limit expansion and maturation of "on-target" B cells in the GC response. Here, we rationally designed T-independent, DNA-origami based virus-like particles (VLPs) with optimal antigenic display of the germline targeting HIV Env immunogen, eOD-GT8, and appropriate T cell help to achieve a potent GC response. In preclinical mouse models, these DNA-VLPs expanded significantly higher frequencies of epitope-specific GC B cells compared with a state-of-the-art clinical protein nanoparticle. Optimized DNA-VLPs primed germinal centers focused on the target antigen and rapidly expanded subdominant broadly neutralizing antibody precursor B cells for HIV with a single immunization. Thus, avoiding scaffold-specific responses augments priming of bnAb precursor B cells, and DNA-VLPs are a promising platform for promoting B cell responses towards challenging subdominant epitopes.
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Affiliation(s)
- Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Larance Ronsard
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Heikyung Suh
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Marjan Omer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Asheley P Chapman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Vanessa R Lewis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Katie Spivakovsky
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Josue Canales
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Ryan D Tingle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, United States
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, United States
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, United States
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Daniel Lingwood
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02139 United States
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, United States
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
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5
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Li C, Ke F, Mao S, Montemayor Z, Traore MDM, Balsa AD, Djibo M, Karekar N, Hu H, Wen H, Gao W, Sun D. SARS-CoV-2 B Epitope-Guided Neoantigen NanoVaccines Enhance Tumor-Specific CD4/CD8 T Cell Immunity through B Cell Antigen Presentation. ACS NANO 2025; 19:7038-7054. [PMID: 39943808 DOI: 10.1021/acsnano.4c15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2025]
Abstract
Current neoantigen cancer vaccines activate T cell immunity through dendritic cell/macrophage-mediated antigen presentation. It is unclear whether incorporating B cell-mediated antigen presentation into current neoantigen vaccines could enhance CD4/CD8 T cell immunity to improve their anticancer efficacy. We developed SARS-CoV-2 B cell epitope-guided neoantigen peptide/mRNA cancer nanovaccines (BSARSTNeoAgVax) to improve anticancer efficacy by enhancing tumor-specific CD4/CD8 T cell antitumor immunity through B cell-mediated antigen presentation. BSARSTNeoAgVax cross-linked with B cell receptor, promoted SARS-CoV-2 B cell-mediated antigen presentation to tumor-specific CD4 T cells, increased tumor-specific follicular/nonfollicular CD4 T cells, and enhanced B cell-dependent tumor-specific CD8 T cell immunity. BSARSTNeoAgVax achieved superior efficacy in melanoma, pancreatic, and breast cancer models compared with the current neoantigen vaccines. Our study provides a universal platform, SARS-CoV-2 B epitope-guided neoantigen nanovaccines, to improve anticancer efficacy against various cancer types by enhancing CD4/CD8 T cell antitumor immunity through viral-specific B cell-mediated antigen presentation.
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Affiliation(s)
- Chengyi Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fang Ke
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuai Mao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zera Montemayor
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mohamed Dit Mady Traore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alejandra Duran Balsa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mahamadou Djibo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Neha Karekar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hongxiang Hu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hanning Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Gao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology and Pharmaceutical Science, College of Pharmacy, The University of Houston, Houston, Texas 77204, United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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Do HN, Zhao M, Alam SM, Gnanakaran S. Dynamics and activation of membrane-bound B cell receptor assembly. Commun Biol 2025; 8:226. [PMID: 39948415 PMCID: PMC11825855 DOI: 10.1038/s42003-025-07478-1] [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: 08/19/2024] [Accepted: 01/07/2025] [Indexed: 02/16/2025] Open
Abstract
B-cell receptor (BCR) complexes are expressed on the surface of a B-cell and are critical in antigen recognition and modulating the adaptive immune response. Even though the relevance of antibodies has been known for almost a hundred years, the antigen-dependent activation mechanism of B-cells has remained elusive. Several models have been proposed for BCR activation, including cross-linking, conformation-induced oligomerization, and dissociation activation models. Recently, the first cryo-EM structures of the human B-cell antigen receptor of the IgM and IgG isotypes have been published that validates the asymmetric organization of the BCR complex. Here, we carry out extensive molecular dynamics simulations to probe the conformational changes upon antigen binding and the influence of the membrane lipids. We identify two critical dynamical events that could be associated with antigen-dependent activation of BCR. First, antigen binding causes increased flexibility in regions distal to the antigen binding site. Second, antigen binding alters the rearrangement of IgM transmembrane helices, including the relative interaction of Igα/Igβ that mediates intracellular signaling. Furthermore, these transmembrane rearrangements lead to changes in localized lipid composition. Our work indirectly supports the conformational-change induced models of BCR activation and contributes to the understanding of the antigen-dependent activation mechanism of BCRs.
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Affiliation(s)
- Hung N Do
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Mingfei Zhao
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, AL, 35487, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke School of Medicine, Durham, NC, 27710, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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7
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Rodríguez-Franco HJ, Hendrickx PBM, Bastings MMC. Tailoring DNA Origami Protection: A Study of Oligolysine-PEG Coatings for Improved Colloidal, Structural, and Functional Integrity. ACS POLYMERS AU 2025; 5:35-44. [PMID: 39958528 PMCID: PMC11826485 DOI: 10.1021/acspolymersau.4c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 11/28/2024] [Accepted: 12/10/2024] [Indexed: 02/18/2025]
Abstract
Application of protective polymer coatings to enhance the biostability of DNA-based nanomaterials (DONs) has become common practice in in vitro and in vivo experiments. While the functional effect of these coatings is obvious, a detailed molecular picture of what is protected and for how long remains unclear. Additionally, the use of the oligolysine-1kPEG protective polymer has been limited due to aggregation issues. In this study, we evaluated the colloidal stability, structural integrity, and functional preservation of DONs coated with oligolysine (K)-1k/5kPEG block copolymers. Dynamic light scattering and transmission electron microscopy were employed to assess colloidal stability before and after degradation. A FRET-based assay was developed to monitor the directionality of degradation, while quantitative PCR measured the protection of functional DNA handles, crucial for the design of ligand-functionalized DONs. Our results show that K10-1kPEG, while prone to aggregation, can offer similar protection against nucleases as K10-5kPEG, provided buffer conditions are carefully chosen. Maintaining the colloidal, structural, and functional stability before and after nuclease exposure supports DON applications, particularly at the biointerface. These insights provide valuable guidelines for selecting the most effective protection strategy and enhancing DON functionality across diverse biological environments.
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Affiliation(s)
- Hugo J. Rodríguez-Franco
- Programmable
Biomaterials Laboratory, Institute of Materials, Interfaculty Bioengineering
Institute, School of Engineering, Ecole
Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Pauline B. M. Hendrickx
- Programmable
Biomaterials Laboratory, Institute of Materials, Interfaculty Bioengineering
Institute, School of Engineering, Ecole
Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
- Louvain
Drug Research Institute, Advanced Drug Delivery and Biomaterials, Université Catholique de Louvain, UCLouvain, Brussels 1200, Belgium
| | - Maartje M. C. Bastings
- Programmable
Biomaterials Laboratory, Institute of Materials, Interfaculty Bioengineering
Institute, School of Engineering, Ecole
Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
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8
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Weck JM, Heuer-Jungemann A. Fully addressable designer superstructures assembled from one single modular DNA origami. Nat Commun 2025; 16:1556. [PMID: 39934172 PMCID: PMC11814417 DOI: 10.1038/s41467-025-56846-2] [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: 01/08/2025] [Accepted: 02/04/2025] [Indexed: 02/13/2025] Open
Abstract
DNA nanotechnology and especially the DNA origami method are primal tools to create precise nanoscale objects. For DNA origami, a long ssDNA scaffold strand is folded by a multitude of smaller staple strands into base-pair accurate shapes, allowing for precise modification and incorporation of guest molecules. However, DNA origami are limited in size, and thus is the area that can be controlled with nanoscale precision. Prior methods of creating larger assemblies were either costly or lacked structural control. Here, we incorporate two methods of modularity into one exemplary modular DNA origami (moDON). The modularity allows for the creation of over 50,000 diverse monomers and subsequently the assembly of a plethora of fully addressable designer superstructures while keeping the construction cost very low. The here-introduced methods for modularity in DNA origami design offer an efficient, cost-effective solution for constructing precisely organized, and fully addressable structures on a variety of scales.
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Affiliation(s)
- Johann M Weck
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany and Center for Nanoscience, Ludwig-Maximilians University, Munich, Germany.
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany and Center for Nanoscience, Ludwig-Maximilians University, Munich, Germany.
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9
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Xia Q, Zhou M, Jiao K, Li B, Guo L, Wang L, Li J. Recent Advances in DNA-Templated Protein Patterning. SMALL METHODS 2025:e2401835. [PMID: 39895184 DOI: 10.1002/smtd.202401835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/13/2025] [Indexed: 02/04/2025]
Abstract
In recent decades, the advancement of DNA nanotechnology enables precise nanoscale organization of diverse functional materials with DNA templates. Particularly, a variety of DNA-templated protein patterns are constructed as powerful tools for programming biomimetic protein complexes. In this review, recent progress in DNA-templated protein patterning, including cutting-edge methods for arranging proteins with DNA templates, and protein patterns across varying dimensions are briefly summarized. Representative applications in biological analysis and biomedicine are discussed. DNA-protein patterns with programmable dynamics, which hold promise in precision diagnosis and therapeutics are highlighted. Finally, current challenges and opportunities in the fabrication and application of DNA-templated protein pattering are discussed.
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Affiliation(s)
- Qinglin Xia
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mo Zhou
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhangjiang Laboratory, 100 Haike Road, Shanghai, 201210, China
| | - Kai Jiao
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
| | - Bin Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linjie Guo
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
| | - Lihua Wang
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
| | - Jiang Li
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, 200444, China
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10
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Tisza MJ, Lloyd RE, Hoffman K, Smith DP, Rewers M, Javornik Cregeen SJ, Petrosino JF. Longitudinal phage-bacteria dynamics in the early life gut microbiome. Nat Microbiol 2025; 10:420-430. [PMID: 39856391 PMCID: PMC11790489 DOI: 10.1038/s41564-024-01906-4] [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: 08/09/2024] [Accepted: 12/04/2024] [Indexed: 01/27/2025]
Abstract
Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.
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Affiliation(s)
- Michael J Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard E Lloyd
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristi Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel P Smith
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Sara J Javornik Cregeen
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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11
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Degn SE, Tolar P. Towards a unifying model for B-cell receptor triggering. Nat Rev Immunol 2025; 25:77-91. [PMID: 39256626 DOI: 10.1038/s41577-024-01073-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 09/12/2024]
Abstract
Antibodies are exceptionally versatile molecules with remarkable flexibility in their binding properties. Their natural targets range from small-molecule toxins, across viruses of different sizes, to bacteria and large multicellular parasites. The molecular determinants bound by antibodies include proteins, peptides, carbohydrates, nucleic acids, lipids and even synthetic molecules that have never existed in nature. Membrane-anchored antibodies also serve as receptors on the surface of the B cells that produce them. Despite recent structural insights, there is still no unifying molecular mechanism to explain how antibody targets (antigens) trigger the activation of these B-cell receptors (BCRs). After cognate antigen encounter, somatic hypermutation and class-switch recombination allow BCR affinity maturation and immunoglobulin class-specific responses, respectively. This raises the fundamental question of how one receptor activation mechanism can accommodate a plethora of variant receptors and ligands, and how it can ensure that individual B cells remain responsive to antigen after somatic hypermutation and class switching. There is still no definite answer. Here we give a brief historical account of the different models proposed to explain BCR triggering and discuss their merit in the context of the current knowledge of the structure of BCRs, their dynamic membrane distribution, and recent biochemical and cell biological insights.
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Affiliation(s)
- Søren E Degn
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark.
| | - Pavel Tolar
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
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12
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Lin B, Liu Y, Chen Q, Li M, Xu L, Chen Q, Tan Y, Liu Z. DNA Nanostructures-Based In Situ Cancer Vaccines: Mechanisms and Applications. SMALL METHODS 2025:e2401501. [PMID: 39840607 DOI: 10.1002/smtd.202401501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 11/29/2024] [Indexed: 01/23/2025]
Abstract
Current tumor vaccines suffer from inadequate immune responsive due to the insufficient release of tumor antigens, low tumor infiltration, and immunosuppressive microenvironment. DNA nanostructures with their ability to precisely engineer, controlled release, biocompatibility, and the capability to augment the immunogenicity of tumor microenvironment, have gained significant attention for their potential to revolutionize vaccine designing. This review summarizes various applications of DNA nanostructures in the construction of in situ cancer vaccines, which can generate tumor-associated antigens directly from damaged tumors for cancer immune-stimulation. The mechanisms and components of cancer vaccines are listed, the specific strategies for constructing in situ vaccines using DNA nanostructures are explored and their underlying mechanisms of action are elucidated. The immunogenic cell death (ICD) induced by chemotherapeutic agents, photothermal therapy (PTT), photodynamic therapy (PDT), and radiation therapy (RT) and the related cancer vaccines building strategies are systematically summarized. The applications of different DNA nanostructures in various cancer immunotherapy are elaborated, which exerts precise, long-lasting, and robust immune responses. The current challenges and future prospectives are proposed. This review provides a holistic understanding of the evolving role of DNA nanostructures for in situ vaccine development.
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Affiliation(s)
- Bingyu Lin
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, P. R. China
| | - Qiwen Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, P. R. China
| | - Mingfeng Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Lishang Xu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Qianqian Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, P. R. China
| | - Yifu Tan
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410013, P. R. China
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13
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Douglas TR, Alexander S, Chou LYT. Patterned Antigens on DNA Origami Controls the Structure and Cellular Uptake of Immune Complexes. ACS NANO 2025; 19:621-637. [PMID: 39757925 DOI: 10.1021/acsnano.4c11183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2025]
Abstract
Immune complexes (ICs), formed via antibody (Ab)-antigen (Ag) binding, trigger diverse immune responses, which are critical for natural immunity and have uses for vaccines and immunotherapies. While IC-elicited immune responses depend on its structure, existing methods for IC synthesis produce heterogeneous assemblies, which limits control over their cellular interactions and pharmacokinetics. In this study, we demonstrate the use of DNA origami to create synthetic ICs with defined shape, size, and solubility by displaying Ags in prescribed spatial patterns. We find that Ag arrangement relative to the spatial tolerance of IgG Fab arms (∼13-18 nm) determines IC formation into "monomeric" versus "multimeric" regimes. When Ag spacing matches Fab arm tolerance, ICs are exclusively monomeric, while spacing mismatches favor the formation of multimeric ICs. Within each IC regime, parameters such as the number of Ags and Ab-Ag ratios, as well as DNA origami shape, further fine-tune IC size, shape, and Fc valency. These parameters influenced IC interactions with FcγR-expressing immune cells, with uptake by macrophages showing greater sensitivity to IC cross-linking while dendritic cells were more responsive to Ab valency. Our findings thus provide design principles for controlling the structure and cellular interactions of synthetic ICs and highlight DNA origami-scaffolded ICs as a programmable platform for investigating IC immunology and developing FcγR-targeted therapeutics and vaccines.
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Affiliation(s)
- Travis R Douglas
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 2E3, Canada
| | - Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 2E3, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 2E3, Canada
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14
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Yang C, Fan J, Zhu H, Wang H, He Y, Liu J, Ding B. Genetically Encoded Nucleic Acid Nanostructures for Biological Applications. Chembiochem 2025:e202400991. [PMID: 39809714 DOI: 10.1002/cbic.202400991] [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: 12/04/2024] [Revised: 01/14/2025] [Accepted: 01/14/2025] [Indexed: 01/16/2025]
Abstract
Nucleic acid, as a carrier of genetic information, has been widely employed as a building block for the construction of versatile nanostructures with pre-designed sizes and shapes through complementary base pairing. With excellent programmability, addressability, and biocompatibility, nucleic acid nanostructures are extensively applied in biomedical researches, such as bio-imaging, bio-sensing, and drug delivery. Notably, the original gene-encoding capability of the nucleic acids themselves has been utilized in these structurally well-defined nanostructures. In this review, we will summarize the recent progress in the design of double-stranded DNA and mRNA-encoded nanostructures for various biological applications, such as gene regulation, gene expression, and mRNA transcription. Furthermore, the challenges and future opportunities of genetically encoded nucleic acid nanostructures in biomedical applications will be discussed.
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Affiliation(s)
- Changping Yang
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jing Fan
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Hanyin Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuling He
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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15
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Jia F, Luo T, Zhuang JY, Guo P, Fang N, Jiang YB, Jiang T. Noncovalently Bridging Cell-Surface Proteins Using Synthetic Peptides to Modulate Cell Apoptosis. NANO LETTERS 2025; 25:268-275. [PMID: 39680928 DOI: 10.1021/acs.nanolett.4c04959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
Abstract
Controlled high-order clustering of cell-surface proteins is an essential but unmatched regulatory mechanism in living systems for the modulation of cell behavior. Here, we present a strategy for generating extended and tunable one-dimensional clusters of death receptors on live cell surfaces by employing synthetic peptides to noncovalently bridging the proteins. The on-cell assembly process is validated through super-resolution fluorescence imaging and fluorescence lifetime imaging analyses. By adjusting the number of spacing peptides between the receptors before and even after the cluster formation, receptor separation can be precisely varied at nanoscale to drive cells into apoptotic or antiapoptotic states. Remarkably, this approach results in higher levels of cell apoptosis compared to the conventional practice of using preformed ligand-appended peptide coassemblies. These results demonstrate that in situ fabrication of cell-interfacing materials with compositional control permits robust and effective manipulation of high-order clustering of cell-surface proteins, advancing our ability to regulate cell behavior.
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Affiliation(s)
- Fan Jia
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Tian Luo
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Jin-Yan Zhuang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Pan Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
| | - Ning Fang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Tao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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16
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Wang H, Yang C, Wu T, Fan J, Zhu H, Liu J, Ding B. A Highly Tumor-Permeating DNA Nanoplatform for Efficient Remodeling of Immunosuppressive Tumor Microenvironments. Angew Chem Int Ed Engl 2025; 64:e202412804. [PMID: 39225768 DOI: 10.1002/anie.202412804] [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: 07/08/2024] [Revised: 08/27/2024] [Accepted: 09/03/2024] [Indexed: 09/04/2024]
Abstract
The immunosuppressive tumor microenvironment and limited intratumoral permeation have largely constrained the outcome of tumor therapy. Herein, we report a tailored DNA structure-based nanoplatform with striking tumor-penetrating capability for targeted remodeling of the immunosuppressive tumor microenvironment in vivo. In our design, chemo-immunomodulator (gemcitabine) can be precisely grafted on DNA sequences through a reactive oxygen species (ROS)-sensitive linker. After self-assembly, the gemcitabine-grafted DNA structure can site-specifically organize legumain-activatable melittin pro-peptide (promelittin) on each vertex for intratumoral delivery and further function as the template to load photosensitizers (methylene blue) for ROS production. The tailored DNA nanoplatform can achieve targeted accumulation, highly improved intratumoral permeation, and efficient immunogenic cell death of tumor cells by laser irradiation. Finally, the immunosuppressive tumor microenvironment can be successfully remodeled by reducing multi-type immunosuppressive cells and enhancing the infiltration of cytotoxic lymphocytes in the tumor. This rationally developed multifunctional DNA nanoplatform provides a new avenue for the development of tumor therapy.
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Affiliation(s)
- Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Changping Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Tiantian Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Pharmaceutical Sciences, Hainan Medical University, Haikou, 570228, China
| | - Jing Fan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Hanyin Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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17
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Liang J, Yao L, Liu Z, Chen Y, Lin Y, Tian T. Nanoparticles in Subunit Vaccines: Immunological Foundations, Categories, and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025; 21:e2407649. [PMID: 39501996 DOI: 10.1002/smll.202407649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 10/12/2024] [Indexed: 01/11/2025]
Abstract
Subunit vaccines, significant in next-generation vaccine development, offer precise targeting of immune responses by focusing on specific antigens. However, this precision often comes at the cost of eliciting strong and durable immunity, posing a great challenge to vaccine design. To address this limitation, recent advancements in nanoparticles (NPs) are utilized to enhance antigen delivery efficiency and boost vaccine efficacy. This review examines how the physicochemical properties of NPs influence various stages of the immune response during vaccine delivery and analyzes how different NP types contribute to immune activation and enhance vaccine performance. It then explores the unique characteristics and immune activation mechanisms of these NPs, along with their recent advancements, and highlights their application in subunit vaccines targeting infectious diseases and cancer. Finally, it discusses the challenges in NP-based vaccine development and proposes future directions for innovation in this promising field.
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Affiliation(s)
- Jiale Liang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West ChinaHospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lan Yao
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West ChinaHospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zhiqiang Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West ChinaHospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ye Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West ChinaHospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West ChinaHospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Taoran Tian
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, 610041, China
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18
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Tanwar S, Date S, Goel L, Wu L, Chatterjee A, Barman I. Raman Imaging of Targeted Drug Delivery with DNA-Based Nano-Optical Devices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2402631. [PMID: 39707677 DOI: 10.1002/smll.202402631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 10/15/2024] [Indexed: 12/23/2024]
Abstract
Raman spectroscopy (RS) has emerged as a novel optical imaging modality by identifying molecular species through their bond vibrations, offering high specificity and sensitivity in molecule detection. However, its application in intracellular molecular probing has been limited due to challenges in combining vibrational tags with functional probes. DNA nanostructures, known for their high programmability, have been instrumental in fields like biomedicine and nanofabrication. So far, their ability to customize Raman signals remains largely untapped. In this study, a new class of Raman active DNA origami-based hybrid nanodevice (ND) for targeted cancer cell drug delivery and imaging is engineered. The ND is specifically engineered for metastatic prostate cancer treatment, featuring a legumain enzyme-responsive sequence for the controlled release of the chemotherapeutic agent doxorubicin. Integrating RS with precise targeting, the ND enables imaging of aggressive cancer cells and efficient drug delivery with minimal off-target effects. The developed device offers stimuli-responsive behavior, enhanced stability, exceptional tunability, and potent targeting abilities, positioning it as a highly promising strategy for advancing precision cancer imaging and therapy.
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Affiliation(s)
- Swati Tanwar
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Siddhi Date
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Linika Goel
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Arnab Chatterjee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA
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19
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Neyra K, Desai S, Mathur D. Plugging synthetic DNA nanoparticles into the central dogma of life. Chem Commun (Camb) 2024; 61:220-231. [PMID: 39611736 PMCID: PMC11606385 DOI: 10.1039/d4cc04648j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 11/11/2024] [Indexed: 11/30/2024]
Abstract
Synthetic DNA nanotechnology has emerged as a powerful tool for creating precise nanoscale structures with diverse applications in biotechnology and materials science. Recently, it has evolved to include gene-encoded DNA nanoparticles, which have potentially unique advantages compared to alternative gene delivery platforms. In exciting new developments, we and others have shown how the long single strand within DNA origami nanoparticles, the scaffold strand, can be customized to encode protein-expressing genes and engineer nanoparticles that interface with the transcription-translation machinery for protein production. Remarkably, therefore, DNA nanoparticles - despite their complex three-dimensional shapes - can function as canonical genes. Characteristics such as potentially unlimited gene packing size and low immunogenicity make DNA-based platforms promising for a variety of gene therapy applications. In this review, we first outline various techniques for the isolation of the gene-encoded scaffold strand, a crucial precursor for building protein-expressing DNA nanoparticles. Next, we highlight how features such as sequence design, staple strand optimization, and overall architecture of gene-encoded DNA nanoparticles play a key role in the enhancement of protein expression. Finally, we discuss potential applications of these DNA origami structures to provide a comprehensive overview of the current state of gene-encoded DNA nanoparticles and motivate future directions.
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Affiliation(s)
- Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Sara Desai
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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20
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Zhao C, Jiang X, Wang M, Gui S, Yan X, Dong Y, Liu D. Constructing protein-functionalized DNA origami nanodevices for biological applications. NANOSCALE 2024; 17:142-157. [PMID: 39564893 DOI: 10.1039/d4nr03599b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2024]
Abstract
In living systems, proteins participate in various physiological processes and the clustering of multiple proteins is essential for efficient signaling. Therefore, understanding the effects of the number, distance and orientation of proteins is of great significance. With programmability and addressability, DNA origami technology has enabled fabrication of sophisticated nanostructures with precise arrangement and orientation control of proteins to investigate the effects of these parameters on protein-involved cellular processes. Herein, we highlight the construction and applications of protein-functionalized DNA origami nanodevices. After the introduction of the structural design principles of DNA origami and the strategies of protein-DNA conjugation, the emerging applications of protein-functionalized DNA origami nanodevices with controlled key parameters are mainly discussed, including the regulation of enzyme cascade reactions, modulation of cellular behaviours, drug delivery therapy and protein structural analysis. Finally, the current challenges and potential directions of protein-functionalized DNA origami nanodevices are also presented, advancing their applications in biomedicine, cell biology and structural biology.
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Affiliation(s)
- Chuangyuan Zhao
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xinran Jiang
- School of Life Sciences Fudan University, Shanghai, 200433, China
| | - Miao Wang
- Chemistry and chemical biology, Cornell university, 122 Baker Laboratory, Ithaca, NY 14853, USA
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100071, Beijing, China.
| | - Xin Yan
- Department of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing, 100191, China.
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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21
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Young OJ, Dembele H, Rajwar A, Kwon IC, Ryu JH, Shih WM, Zeng YC. Cargo Quantification of Functionalized DNA Origami for Therapeutic Application. SMALL METHODS 2024:e2401376. [PMID: 39651835 DOI: 10.1002/smtd.202401376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/25/2024] [Indexed: 12/18/2024]
Abstract
In recent years, notable advances in nanotechnology-based drug delivery have emerged. A particularly promising platform in this field is DNA origami-based nanoparticles, which offer highly programmable surfaces, providing precise control over the nanoscale spacing and stoichiometry of various cargo. These versatile particles are finding diverse applications ranging from basic molecular biology to diagnostics and therapeutics. This growing interest creates the need for effective methods to quantify cargo on DNA origami nanoparticles. The study consolidates several previously validated methods focusing on gel-based and fluorescence-based techniques, including multiplexed quantification of protein, peptide, and nucleic acid cargo on these nanoparticles. In this work, how gel band intensity and nanodrop fluorescence readings can be used to quantify protein, peptide, and RNA cargo on a DNA origami nanoparticle is demonstrated. This work may serve as a valuable resource for groups of researchers keen on utilizing DNA origami-based nanoparticles in therapeutic applications.
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Affiliation(s)
- Olivia J Young
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hawa Dembele
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anjali Rajwar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ick Chan Kwon
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Ju Hee Ryu
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - William M Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Yang C Zeng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
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Li D, Dong J, Zhou Y, Wang Q. Toward Precise Fabrication of Finite-Sized DNA Origami Superstructures. SMALL METHODS 2024:e2401629. [PMID: 39632670 DOI: 10.1002/smtd.202401629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 11/22/2024] [Indexed: 12/07/2024]
Abstract
DNA origami enables the precise construction of 2D and 3D nanostructures with customizable shapes and the high-resolution organization of functional materials. However, the size of a single DNA origami is constrained by the length of the scaffold strand, and since its inception, scaling up the size and complexity has been a persistent pursuit. Hierarchical self-assembly of DNA origami units offers a feasible approach to overcome the limitation. Unlike periodic arrays, finite-sized DNA origami superstructures feature well-defined structural boundaries and uniform dimensions. In recent years, increasing attention has been directed toward precise control over the hierarchical self-assembly of DNA origami structures and their applications in fields such as nanophotonics, biophysics, and material science. This review summarizes the strategies for fabricating finite-sized DNA origami superstructures, including heterogeneous self-assembly, self-limited self-assembly, and templated self-assembly, along with a comparative analysis of the advantages and limitations of each approach. Subsequently, recent advancements in the application of these structures are discussed from a structure design perspective. Finally, an outlook on the current challenges and potential future directions is provided, highlighting opportunities for further research and development in this rapidly evolving field.
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Affiliation(s)
- Dongsheng Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qiangbin Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China
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23
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Chen Q, Liu Y, Chen Q, Li M, Xu L, Lin B, Tan Y, Liu Z. DNA Nanostructures: Advancing Cancer Immunotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2405231. [PMID: 39308253 DOI: 10.1002/smll.202405231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/28/2024] [Indexed: 12/06/2024]
Abstract
Cancer immunotherapy is a groundbreaking medical revolution and a paradigm shift from traditional cancer treatments, harnessing the power of the immune system to target and destroy cancer cells. In recent years, DNA nanostructures have emerged as prominent players in cancer immunotherapy, exhibiting immense potential due to their controllable structure, surface addressability, and biocompatibility. This review provides an overview of the various applications of DNA nanostructures, including scaffolded DNA, DNA hydrogels, tetrahedral DNA nanostructures, DNA origami, spherical nucleic acids, and other DNA-based nanostructures in cancer immunotherapy. These applications explore their roles in vaccine development, immune checkpoint blockade therapies, adoptive cellular therapies, and immune-combination therapies. Through rational design and optimization, DNA nanostructures significantly bolster the immunogenicity of the tumor microenvironment by facilitating antigen presentation, T-cell activation, tumor infiltration, and precise immune-mediated tumor killing. The integration of DNA nanostructures with cancer therapies ushers in a new era of cancer immunotherapy, offering renewed hope and strength in the battle against this formidable foe of human health.
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Affiliation(s)
- Qianqian Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China
| | - Qiwen Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China
| | - Mingfeng Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan Province, 410013, P. R. China
| | - Lishang Xu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan Province, 410013, P. R. China
| | - Bingyu Lin
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China
| | - Yifu Tan
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan Province, 410013, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan Province, 410013, P. R. China
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24
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Gupta A, Rudra A, Reed K, Langer R, Anderson DG. Advanced technologies for the development of infectious disease vaccines. Nat Rev Drug Discov 2024; 23:914-938. [PMID: 39433939 DOI: 10.1038/s41573-024-01041-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2024] [Indexed: 10/23/2024]
Abstract
Vaccines play a critical role in the prevention of life-threatening infectious disease. However, the development of effective vaccines against many immune-evading pathogens such as HIV has proven challenging, and existing vaccines against some diseases such as tuberculosis and malaria have limited efficacy. The historically slow rate of vaccine development and limited pan-variant immune responses also limit existing vaccine utility against rapidly emerging and mutating pathogens such as influenza and SARS-CoV-2. Additionally, reactogenic effects can contribute to vaccine hesitancy, further undermining the ability of vaccination campaigns to generate herd immunity. These limitations are fuelling the development of novel vaccine technologies to more effectively combat infectious diseases. Towards this end, advances in vaccine delivery systems, adjuvants, antigens and other technologies are paving the way for the next generation of vaccines. This Review focuses on recent advances in synthetic vaccine systems and their associated challenges, highlighting innovation in the field of nano- and nucleic acid-based vaccines.
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Affiliation(s)
- Akash Gupta
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arnab Rudra
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Kaelan Reed
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Langer
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel G Anderson
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA.
- Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
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25
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Aksel T, J. Navarro E, Fong N, Douglas SM. Design principles for accurate folding of DNA origami. Proc Natl Acad Sci U S A 2024; 121:e2406769121. [PMID: 39570311 PMCID: PMC11621765 DOI: 10.1073/pnas.2406769121] [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: 04/03/2024] [Accepted: 10/24/2024] [Indexed: 11/22/2024] Open
Abstract
We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate design rules, we reduced the problem of DNA strand routing to the known problem of shortest-path finding in a weighted graph. To score candidate DNA strand routes we used a thermodynamic model that accounts for enthalpic and entropic contributions of initial binding, hybridization, and DNA loop closure. We encoded and analyzed new and previously reported design heuristics. Using design principles emerging from this analysis, we redesigned and fabricated multiple shapes and compared their folding accuracy using electrophoretic mobility analysis and electron microscopy imaging. Redesigned shapes showed 6- to 30-fold improvements in yield compared to original designs. We demonstrate accurate folding can be achieved by optimizing staple routes using our model and provide a computational framework for applying our methodology to any design.
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Affiliation(s)
- Tural Aksel
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco, CA94143
| | - Erik J. Navarro
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco, CA94143
| | - Nicholas Fong
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco, CA94143
| | - Shawn M. Douglas
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco, CA94143
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26
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Thakur B, Alam J, Cronin K, Patel P, Anasti K, Kane AP, Hossain A, Do H, Mansouri K, Spence TN, Edwards RJ, Janowska K, Lella M, Cook A, Saunders K, Gnanakaran S, Haynes BF, Acharya P, Alam SM. Anti-HIV-1 B cell antigen receptor signaling and structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.15.623645. [PMID: 39605516 PMCID: PMC11601489 DOI: 10.1101/2024.11.15.623645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
The B cell antigen receptor (BCR) complex, comprised of antigen recognition and signaling components, functions in initiating B cell activation. While structural studies have described BCR domain organization, gaps remain in our understanding of its antigen binding domain (Fab, fragment antigen-binding) disposition, and how antigen binding is sensed to initiate signaling. Here, we report antigen affinity and signaling of the immunoglobulin (Ig) class IgM and IgG BCRs and define conformational states of full-length BCRs of two human broadly neutralizing antibodies, the glycan-specific, heavy chain domain-swapped, I-shaped 2G12, and a canonical Y-shaped antibody, CH31, that recognizes the CD4-binding site on the HIV-1 Envelope protein (Env). The BCRs adopted the shapes (I or Y) of their respective soluble antibodies, and both Ig class of BCRs of the same specificity bound Env trimers with similar affinities. We observed antigen-valenc y dependent differential signaling by the 2G12 IgM and IgG BCRs with trimeric Envs. Cryo-electron microscopy of the 2G12 IgG and CH31 IgM BCRs revealed varied Fab orientations. Structural comparisons revealed hinge points and regions of flexibility in the BCRs suggesting a highly dynamic structure of the BCR complex. Taken together, our results provide an integrated understanding of BCR structure, conformation, antigen recognition and signaling, and provide the basis for understanding antigen induced BCR signal transmission. One Sentence Summary Cryo-electron microscopy structures of full-length B cell antigen receptor complex provide a novel dynamic BCR model and a basis for understanding antigen binding induced signal transmission.
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27
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Feng Q, Cheng K, Zhang L, Wang D, Gao X, Liang J, Liu G, Ma N, Xu C, Tang M, Chen L, Wang X, Ma X, Zou J, Shi Q, Du P, Wang Q, Wang H, Nie G, Zhao X. Rationally designed multimeric nanovaccines using icosahedral DNA origami for display of SARS-CoV-2 receptor binding domain. Nat Commun 2024; 15:9581. [PMID: 39505890 PMCID: PMC11542012 DOI: 10.1038/s41467-024-53937-4] [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: 10/25/2023] [Accepted: 10/28/2024] [Indexed: 11/08/2024] Open
Abstract
Multivalent antigen display on nanoparticles can enhance the immunogenicity of nanovaccines targeting viral moieties, such as the receptor binding domain (RBD) of SARS-CoV-2. However, particle morphology and size of current nanovaccines are significantly different from those of SARS-CoV-2. Additionally, surface antigen patterns are not controllable to enable the optimization of B cell activation. Herein, we employ an icosahedral DNA origami (ICO) as a display particle for RBD nanovaccines, achieving morphology and diameter like the virus (91 ± 11 nm). The surface addressability of DNA origami permits facile modification of the ICO surface with numerous RBD antigen clusters (ICO-RBD) to form various antigen patterns. Using an in vitro screening system, we demonstrate that the antigen spacing, antigen copies within clusters and cluster number parameters of the surface antigen pattern all impact the ability of the nanovaccines to activate B cells. Importantly, the optimized ICO-RBD nanovaccines evoke stronger and more enduring humoral and T cell immune responses in female mouse models compared to soluble RBD antigens, and the multivalent display broaden the protection range of B cell responses to more mutant strains. Our vaccines activate similar humoral immunity, observable stronger cellular immunity and more memory immune cells compared to trimeric mRNA vaccines.
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Affiliation(s)
- Qingqing Feng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Keman Cheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lizhuo Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongshu Wang
- State Key Laboratory of Pathogens and Biosecurity, Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Xiaoyu Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangna Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Nana Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chen Xu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Tang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liting Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinwei Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuehui Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Jiajia Zou
- Beijing Intell Nanomedicine, No. 9, Chengwan Street, Haidian District, Beijing, 100000, China
| | - Quanwei Shi
- Beijing Intell Nanomedicine, No. 9, Chengwan Street, Haidian District, Beijing, 100000, China
| | - Pei Du
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Hengliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing, 100071, China.
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Göpfrich K, Platten M, Frischknecht F, Fackler OT. Bottom-up synthetic immunology. NATURE NANOTECHNOLOGY 2024; 19:1587-1596. [PMID: 39187581 DOI: 10.1038/s41565-024-01744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 07/02/2024] [Indexed: 08/28/2024]
Abstract
Infectious diseases and cancer evade immune surveillance using similar mechanisms. Targeting immune mechanisms using common strategies thus represents a promising avenue to improve prevention and treatment. Synthetic immunology can provide such strategies by applying engineering principles from synthetic biology to immunology. Synthetic biologists engineer cells by top-down genetic manipulation or bottom-up assembly from nanoscale building blocks. Recent successes in treating advanced tumours and diseases using genetically engineered immune cells highlight the power of the top-down synthetic immunology approach. However, genetic immune engineering is mostly limited to ex vivo applications and is subject to complex counter-regulation inherent to immune functions. Bottom-up synthetic biology can harness the rich nanotechnology toolbox to engineer molecular and cellular systems from scratch and equip them with desired functions. These are beginning to be tailored to perform targeted immune functions and should hence allow intervention strategies by rational design. In this Perspective we conceptualize bottom-up synthetic immunology as a new frontier field that uses nanotechnology for crucial innovations in therapy and the prevention of infectious diseases and cancer.
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Affiliation(s)
- Kerstin Göpfrich
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany.
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany.
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience (MCTN), Heidelberg University, Mannheim, Germany
- DKFZ Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
| | - Friedrich Frischknecht
- Parasitology, Department of Infectious Diseases, Department of Infectious Diseases, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, DZIF, Partner Site Heidelberg, Heidelberg, Germany
| | - Oliver T Fackler
- German Center for Infection Research, DZIF, Partner Site Heidelberg, Heidelberg, Germany.
- Integrative Virology, Center of Integrative Infectious Disease Research, Department of Infectious Diseases, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
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29
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Matthews MM, Kim TG, Kim KY, Meshcheryakov V, Iha HA, Tamai M, Sasaki D, Laurino P, Toledo-Patiño S, Collins M, Hsieh TY, Shibata S, Shibata N, Obata F, Fujii J, Ito T, Ito H, Ishikawa H, Wolf M. Engineered protein subunit COVID19 vaccine is as immunogenic as nanoparticles in mouse and hamster models. Sci Rep 2024; 14:25528. [PMID: 39462119 PMCID: PMC11512993 DOI: 10.1038/s41598-024-76377-y] [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: 03/31/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
Initial studies on the immunogenicity of SARS-CoV-2 (CoV-2) S glycoprotein ("spike") as a protein subunit vaccine suggested sub-optimal efficacy in mammals. Although protein engineering efforts have produced CoV-2 spike protein sequences with greatly improved immunogenicity, additional strategies for improving the immunogenicity of CoV-2 protein subunit vaccines are scaffolding and the use of adjuvants. Comparisons of the effectiveness of engineered protein-only and engineered protein-nanoparticles vaccines have been rare. To explore this knowledge gap, we inoculated mice with two doses of either sequence-optimized trimeric spike protein or one of several sequence-optimized spike nanoparticles. We measured their immune response up to two months after the first dose. We also measured the immune response and protection against live virus in hamsters inoculated with either sequence-optimized trimeric spike protein or a liposome-based sequence-optimized spike nanoparticle. We found that in the presence of adjuvant, the antibody and neutralization titers elicited by spike-nanoparticles were not significantly greater than those elicited by spike-only in mice, even at doses as low as 0.1 µg/animal. Hamsters vaccinated with spike-only or spike-nanoparticles were equally protected from live virus one month after their first inoculation. These results suggest that sequence-optimized protein subunit vaccines in the form of individual prefusion-stabilized trimers can be as effective in improving immunogenicity as scaffolded forms.
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Affiliation(s)
- Melissa M Matthews
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Tae Gyun Kim
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Keon Young Kim
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Vladimir Meshcheryakov
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Higor Alves Iha
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Miho Tamai
- Immune Signal Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Daiki Sasaki
- Immune Signal Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Saacnicteh Toledo-Patiño
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Mary Collins
- Office of the Provost, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Tzung-Yang Hsieh
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Noriko Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Fumiko Obata
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Jun Fujii
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Toshihiro Ito
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Tottori, Japan
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Tottori, Japan
| | - Hiroshi Ito
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori, Tottori, Japan
- Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Tottori, Japan
| | - Hiroki Ishikawa
- Immune Signal Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Okinawa, Japan.
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan.
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30
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Mezgec K, Snoj J, Ulčakar L, Ljubetič A, Tušek Žnidarič M, Škarabot M, Jerala R. Coupling of Spectrin Repeat Modules for the Assembly of Nanorods and Presentation of Protein Domains. ACS NANO 2024; 18:28748-28763. [PMID: 39392430 PMCID: PMC11503911 DOI: 10.1021/acsnano.4c07701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 09/25/2024] [Accepted: 10/01/2024] [Indexed: 10/12/2024]
Abstract
Modular protein engineering is a powerful approach for fabricating high-molecular-weight assemblies and biomaterials with nanoscale precision. Herein, we address the challenge of designing an extended nanoscale filamentous architecture inspired by the central rod domain of human dystrophin, which protects sarcolemma during muscle contraction and consists of spectrin repeats composed of three-helical bundles. A module of three tandem spectrin repeats was used as a rigid building block self-assembling via coiled-coil (CC) dimer-forming peptides. CC peptides were precisely integrated to maintain the spectrin α-helix continuity in an appropriate frame to form extended nanorods. An orthogonal set of customizable CC heterodimers was harnessed for modular rigid domain association, which could be additionally regulated by metal ions and chelators. We achieved a robust assembly of rigid rods several micrometers in length, determined by atomic force microscopy and negative stain transmission electron microscopy. Furthermore, these rigid rods can serve as a scaffold for the decoration of diverse proteins or biologically active peptides along their length with adjustable spacing up to tens of nanometers, as confirmed by the DNA-PAINT super-resolution microscopy. This demonstrates the potential of modular bottom-up protein engineering and tunable CCs for the fabrication of functionalized protein biomaterials.
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Affiliation(s)
- Klemen Mezgec
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate
School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jaka Snoj
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate
School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Liza Ulčakar
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate
School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department
of Biotechnology and Systems Biology, National
Institute of Biology, SI-1000 Ljubljana, Slovenia
| | - Miha Škarabot
- Condensed
Matter Department, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- CTGCT, Centre
of Technology of Gene and Cell Therapy, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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31
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García-Chamé M, Mayer I, Schneider L, Niemeyer CM, M. Domínguez C. Fluidic Interface for Surface-based DNA Origami Studies. ACS APPLIED MATERIALS & INTERFACES 2024; 16:53489-53498. [PMID: 39348886 PMCID: PMC11472258 DOI: 10.1021/acsami.4c10874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 10/02/2024]
Abstract
Traditionally, the use of DNA origami nanostructures (DONs) to study early cell signaling processes has been conducted using standard laboratory equipment with DONs typically utilized in solution. Surface-based technologies simplify the microscopic analysis of cells treated with DON agents by anchoring them to solid substrates, thus avoiding the complications of receptor-mediated endocytosis. A robust microfluidic platform for real-time monitoring and precise functionalization of surfaces with DONs was developed here. The combination of controlled flow conditions with an upright total internal reflection fluorescence microscope enabled the kinetic analysis of the immobilization of DONs on DNA-functionalized surfaces. The results revealed that DON morphology and binding tags influence the binding kinetics and that DON hybridization on surfaces is more effective in microfluidic devices with larger-than-standard dimensions, addressing the low diffusivity challenge of DONs. The platform enabled the decoration of DONs with protein-binding ligands and in situ investigation of ligand occupancy on DONs to produce high-quality bioactive surfaces. These surfaces were used to recruit and activate the epidermal growth factor receptor (EGFR) through clustering in the membranes of living cancer cells (MCF-7) using an antagonistic antibody (Panitumumab). The activation was quantified depending on the interligand distances of the EGFR-targeting antibody.
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Affiliation(s)
- Miguel García-Chamé
- Institute for Biological Interfaces
(IBG-1), Karlsruhe Institute of Technology
(KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ivy Mayer
- Institute for Biological Interfaces
(IBG-1), Karlsruhe Institute of Technology
(KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Leonie Schneider
- Institute for Biological Interfaces
(IBG-1), Karlsruhe Institute of Technology
(KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces
(IBG-1), Karlsruhe Institute of Technology
(KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Carmen M. Domínguez
- Institute for Biological Interfaces
(IBG-1), Karlsruhe Institute of Technology
(KIT), 76344 Eggenstein-Leopoldshafen, Germany
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32
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Dvorscek AR, McKenzie CI, Stäheli VC, Ding Z, White J, Fabb SA, Lim L, O'Donnell K, Pitt C, Christ D, Hill DL, Pouton CW, Burnett DL, Brink R, Robinson MJ, Tarlinton DM, Quast I. Conversion of vaccines from low to high immunogenicity by antibodies with epitope complementarity. Immunity 2024; 57:2433-2452.e7. [PMID: 39305904 DOI: 10.1016/j.immuni.2024.08.017] [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] [Received: 11/10/2023] [Revised: 05/06/2024] [Accepted: 08/27/2024] [Indexed: 10/11/2024]
Abstract
Existing antibodies (Abs) have varied effects on humoral immunity during subsequent infections. Here, we leveraged in vivo systems that allow precise control of antigen-specific Abs and B cells to examine the impact of Ab dose, affinity, and specificity in directing B cell activation and differentiation. Abs competing with the B cell receptor (BCR) epitope showed affinity-dependent suppression. By contrast, Abs targeting a complementary epitope, not overlapping with the BCR, shifted B cell differentiation toward Ab-secreting cells. Such Abs allowed for potent germinal center (GC) responses to otherwise poorly immunogenic sites by promoting antigen capture and presentation by low-affinity B cells. These mechanisms jointly diversified the B cell repertoire by facilitating the recruitment of high- and low-affinity B cells into Ab-secreting cell, GC, and memory B cell fates. Incorporation of small amounts of monoclonal Abs into protein- or mRNA-based vaccines enhanced immunogenicity and facilitated sustained immune responses, with implications for vaccine design and our understanding of protective immunity.
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Affiliation(s)
- Alexandra R Dvorscek
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Craig I McKenzie
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Vera C Stäheli
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Zhoujie Ding
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Jacqueline White
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Stewart A Fabb
- Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Leonard Lim
- Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Kristy O'Donnell
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Catherine Pitt
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Danika L Hill
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Deborah L Burnett
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2010, Australia
| | - Robert Brink
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Marcus J Robinson
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - David M Tarlinton
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Isaak Quast
- Department of Immunology, Monash University, 89 Commercial Rd, Melbourne, VIC 3004, Australia.
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33
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Georgiou E, Cabello-Garcia J, Xing Y, Howorka S. DNA Origami - Lipid Membrane Interactions Controlled by Nanoscale Sterics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2404720. [PMID: 39162223 DOI: 10.1002/smll.202404720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/04/2024] [Indexed: 08/21/2024]
Abstract
DNA nanostructures designed to interact with bilayer membranes are of fundamental interest as they mimic biological cytoskeletons and other membrane-associated proteins for applications in synthetic biology, biosensing, and biological research. Yet, there is limited insight into how the binary interactions are influenced by steric effects produced by 3D geometries of DNA structures and membranes. This work uses a 3D DNA nanostructure with membrane anchors in four different steric environments to elucidate the interaction with membrane vesicles of varying sizes and different local bilayer morphology. It is found that interactions are significantly affected by the steric environments of the anchors -often against predicted accessibility- as well as local nanoscale morphology of bilayers rather than on the usually considered global vesicle size. Furthermore, anchor-mediated bilayer interactions are co-controlled by weak contacts with non-lipidated DNA regions, as showcased by pioneering size discrimination between 50 and 200 nm vesicles. This study extends DNA nanotechnology to controlled bilayer interactions and can facilitate the design of nanodevices for vesicle-based diagnostics, biosensing, and protocells.
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Affiliation(s)
- Elena Georgiou
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Javier Cabello-Garcia
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Yongzheng Xing
- National Engineering Research Center for Colloidal Materials, Shandong University, Jinan, Shandong, 250100, China
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, UK
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34
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Huang Z, Zhu Z, Liu L, Song W, Chen X. Preparation of viromimetic rod-like nanoparticle vaccines (RLNVax) and study of their humoral immune activation efficacy. Biomater Sci 2024; 12:5115-5122. [PMID: 39225616 DOI: 10.1039/d4bm00827h] [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: 09/04/2024]
Abstract
Virus-like nanoparticle vaccines can efficiently activate the humoral immune response by cross-linking B cell receptors with their surface multivalent antigen arrays. This structurally dependent mechanism makes it crucial to regulate and optimize structural parameters to enhance the efficacy of nanoparticle vaccines. In this study, we prepared nanoparticle vaccines with different aspect ratios by chemically modifying antigen proteins onto the surfaces of poly(amino acid) nanoparticles of various shapes (spherical, ellipsoidal, and rod-like). This allowed us to investigate the impact of structural anisotropy on the humoral immune activation efficacy of nanoparticle vaccines. Furthermore, the end-group molecules of poly(amino acid) materials possess aggregation-induced emission (AIE) properties, which facilitate monitoring the dynamics of nano-assemblies within the body. Results showed that rod-like nanoparticle vaccines (RLNVax) with a higher aspect ratio (AR = 5) exhibited greater lymph node draining efficiency and could elicit more effective B cell activation compared to conventional isotropic spherical nanoparticle vaccines. In a murine subcutaneous immunization model using ovalbumin (OVA) as a model antigen, RLNVax elicited antigen-specific antibody titers that were about 64 times and 4.6 times higher than those induced by free antigen proteins and spherical nanoparticle vaccines, respectively. Additionally, when combined with an aluminum adjuvant, antibody titers elicited by RLNVax were further enhanced by 4-fold. These findings indicate that the anisotropic rod-like structure is advantageous for improving the humoral immune activation efficacy of nanoparticle vaccines, providing significant insights for the design and optimization of next-generation nanoparticle vaccines.
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Affiliation(s)
- Zichao Huang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhenyi Zhu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Liping Liu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wantong Song
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
- Jilin Biomedical Polymers Engineering Laboratory, Changchun, 130022, China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
- Jilin Biomedical Polymers Engineering Laboratory, Changchun, 130022, China
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35
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Yu S, Shi T, Li C, Xie C, Wang F, Liu X. Programming DNA Nanoassemblies into Polyvalent Lysosomal Degraders for Potent Degradation of Pathogenic Membrane Proteins. NANO LETTERS 2024; 24:11573-11580. [PMID: 39225423 DOI: 10.1021/acs.nanolett.4c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Lysosome-targeting chimera (LYTAC) shows great promise for protein-based therapeutics by targeted degradation of disease-associated membrane or extracellular proteins, yet its efficiency is constrained by the limited binding affinity between LYTAC reagents and designated proteins. Here, we established a programmable and multivalent LYTAC system by tandem assembly of DNA into a high-affinity protein degrader, a heterodimer aptamer nanostructure targeting both pathogenic membrane protein and lysosome-targeting receptor (insulin-like growth factor 2 receptor, IGF2R) with adjustable spatial distribution or organization pattern. The DNA-based multivalent LYTACs showed enhanced efficacy in removing immune-checkpoint protein programmable death-ligand 1 (PD-L1) and vascular endothelial growth factor receptor 2 (VEGFR2) in tumor cell membrane that respectively motivated a significant increase in T cell activity and a potent effect on cancer cell growth inhibition. With high programmability and versatility, this multivalent LYTAC system holds considerable promise for realizing protein therapeutics with enhanced activity.
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Affiliation(s)
- Shuyi Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Tianhui Shi
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chenbiao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chongyu Xie
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Beijing Life Science Academy, Beijing 102209, China
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36
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Li G, Chen C, Li Y, Wang B, Wen J, Guo M, Chen M, Zhang XB, Ke G. DNA-Origami-Based Precise Molecule Assembly and Their Biological Applications. NANO LETTERS 2024; 24:11335-11348. [PMID: 39213537 DOI: 10.1021/acs.nanolett.4c03297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Inspired by efficient natural biomolecule assembly with precise control on key parameters such as distance, number, orientation, and pattern, the constructions and applications of artificial precise molecule assembly are highly important in many research areas including chemistry, biology, and medicine. DNA origami, a sophisticated DNA nanotechnology with rational design, can offer a predictable, programmable, and addressable nanoscale scaffold for the precise assembly of various kinds of molecules. Herein, we summarize recent progress, particularly in the last three years, in DNA-origami-based precise molecule assembly and their emerging biological applications. We first introduce DNA origami and the progress on DNA-origami-based precise molecule assembly, including assembly of various kinds of molecules (e.g., nucleic acids, proteins, organic molecules, nanoparticles), and precise control of important parameters (e.g., distance, number, orientation, pattern). Their biological applications in sensing, imaging, therapy, bionics, biophysics, and chemical biology are then summarized, and current challenges and opportunities are finally discussed.
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Affiliation(s)
- Guize Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Chuangyi Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Yingying Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Bo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Jialin Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Mingye Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Mei Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Hunan University, Changsha 410082, China
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37
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Young OJ, Dembele H, Rajwar A, Kwon IC, Ryu JH, Shih WM, Zeng YC. Cargo quantification of functionalized DNA origami for therapeutic application. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609963. [PMID: 39253502 PMCID: PMC11383041 DOI: 10.1101/2024.08.27.609963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
In recent years, notable advances in nanotechnology-based drug delivery have emerged. A particularly promising platform in this field is DNA origami-based nanoparticles, which offer highly programmable surfaces, providing precise control over the nanoscale spacing and stoichiometry of various cargo. These versatile particles are finding diverse applications ranging from basic molecular biology to diagnostics and therapeutics. This growing interest creates the need for effective methods to quantify cargo on DNA origami nanoparticles. Our study consolidates several previously validated methods focusing on gel-based and fluorescence-based techniques, including multiplexed quantification of protein, peptide, and nucleic acid cargo on these nanoparticles. This work may serve as a valuable resource for groups researchers keen on utilizing DNA origami-based nanoparticles in therapeutic applications.
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Affiliation(s)
- Olivia J. Young
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Hawa Dembele
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anjali Rajwar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ick Chan Kwon
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Ju Hee Ryu
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - William M. Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yang C. Zeng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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38
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Cinti I, Vezyrgianni K, Denton AE. Unravelling the contribution of lymph node fibroblasts to vaccine responses. Adv Immunol 2024; 164:1-37. [PMID: 39523027 DOI: 10.1016/bs.ai.2024.07.001] [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: 11/16/2024]
Abstract
Vaccination is one of the most effective medical interventions, saving millions of lives and reducing the morbidity of infections across the lifespan, from infancy to older age. The generation of plasma cells and memory B cells that produce high affinity class switched antibodies is central to this protection, and these cells are the ultimate output of the germinal centre response. Optimal germinal centre responses require different immune cells to interact with one another in the right place and at the right time and this delicate cellular ballet is coordinated by a network of interconnected stromal cells. In this review we will discuss the various types of lymphoid stromal cells and how they coordinate immune cell homeostasis, the induction and maintenance of the germinal centre response, and how this is disorganised in older bodies.
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Affiliation(s)
- Isabella Cinti
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Kassandra Vezyrgianni
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Alice E Denton
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom.
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39
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Hong Y, Kwak K. Both sides now: evolutionary traits of antigens and B cells in tolerance and activation. Front Immunol 2024; 15:1456220. [PMID: 39185403 PMCID: PMC11341355 DOI: 10.3389/fimmu.2024.1456220] [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: 06/28/2024] [Accepted: 07/25/2024] [Indexed: 08/27/2024] Open
Abstract
B cells are the cornerstone of our body's defense system, producing precise antibodies and safeguarding immunological memory for future protection against pathogens. While we have a thorough understanding of how naïve B cells differentiate into plasma or memory B cells, the early B cell response to various antigens-whether self or foreign-remains a thrilling and evolving area of study. Advances in imaging have illuminated the molecular intricacies of B cell receptor (BCR) signaling, yet the dynamic nature of B cell activation continues to reveal new insights based on the nature of antigen exposure. This review explores the evolutionary journey of B cells as they adapt to the unique challenges presented by pathogens. We begin by examining the specific traits of antigens that influence their pathogenic potential, then shift our focus to the distinct characteristics of B cells that counteract these threats. From foundational discoveries to the latest cutting-edge research, we investigate how B cells are effectively activated and distinguish between self and non-self antigens, ensuring a balanced immune response that defends against pathogenic diseases but not self-antigens.
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Affiliation(s)
- Youngjae Hong
- Department of Microbiology and Immunology, College of Medicine, Yonsei University, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Kihyuck Kwak
- Department of Microbiology and Immunology, College of Medicine, Yonsei University, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul, Republic of Korea
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40
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Huang K, Yang Q, Bao M, Wang S, Zhao L, Shi Q, Yang Y. Modulated Cell Internalization Behavior of Icosahedral DNA Framework with Programmable Surface Modification. J Am Chem Soc 2024; 146:21442-21452. [PMID: 39038211 DOI: 10.1021/jacs.4c04106] [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: 07/24/2024]
Abstract
Surface modification could enhance the cell internalization efficiency of nanovehicles for targeted gene or drug delivery. However, the influence of surface modification parameters, including recognition manners, valences, and patterns, is often clouded, especially for the endocytosis of DNA nanostructures in customized shapes. Focusing on an icosahedral DNA framework, we systematically programmed three distinct types of ligands with diverse valence and spatial distribution on their outer surface to study the internalization efficiency, endocytic pathways, and postinternalization fate. The comparison in different aspects of parameters deepens our understanding of the intricate relationship between surface modification and cell entry behavior, offering insights crucial for designing and optimizing DNA framework nanostructures for potent cell-targeted purposes.
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Affiliation(s)
- Kui Huang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qiulan Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Bao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shengwen Wang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Luming Zhao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qian Shi
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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41
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Iliopoulou M, Bajur AT, McArthur HCW, Gabai M, Coyle C, Ajao F, Köchl R, Cope AP, Spillane KM. Extracellular matrix rigidity modulates physical properties of subcapsular sinus macrophage-B cell immune synapses. Biophys J 2024; 123:2282-2300. [PMID: 37840242 PMCID: PMC11331050 DOI: 10.1016/j.bpj.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/17/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023] Open
Abstract
Subcapsular sinus macrophages (SSMs) play a key role in immune defense by forming immunological barriers that control the transport of antigens from lymph into lymph node follicles. SSMs participate in antibody responses by presenting antigens directly to naive B cells and by supplying antigens to follicular dendritic cells to propagate germinal center reactions. Despite the prominent roles that SSMs play during immune responses, little is known about their cell biology because they are technically challenging to isolate and study in vitro. Here, we used multicolor fluorescence microscopy to identify lymph node-derived SSMs in culture. We focused on the role of SSMs as antigen-presenting cells, and found that their actin cytoskeleton regulates the spatial organization and mobility of multivalent antigens (immune complexes [ICs]) displayed on the cell surface. Moreover, we determined that SSMs are mechanosensitive cells that respond to changes in extracellular matrix rigidity by altering the architecture of the actin cytoskeleton, leading to changes in cell morphology, membrane topography, and IC mobility. Changes to extracellular matrix rigidity also modulate actin remodeling by both SSMs and B cells when they form an immune synapse. This alters synapse duration but not IC internalization nor NF-κB activation in the B cell. Taken together, our data reveal that the mechanical microenvironment may influence B cell responses by modulating physical characteristics of antigen presentation by SSMs.
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Affiliation(s)
- Maro Iliopoulou
- Department of Physics, King's College London, London, United Kingdom
| | - Anna T Bajur
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell & Molecular Biophysics, King's College London, London, United Kingdom
| | | | - Michael Gabai
- Department of Physics, King's College London, London, United Kingdom
| | - Carl Coyle
- Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom
| | - Favour Ajao
- Department of Physics, King's College London, London, United Kingdom
| | - Robert Köchl
- Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Andrew P Cope
- Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom
| | - Katelyn M Spillane
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell & Molecular Biophysics, King's College London, London, United Kingdom.
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42
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Hou Y, Treanor B. DNA origami: Interrogating the nano-landscape of immune receptor activation. Biophys J 2024; 123:2211-2223. [PMID: 37838832 PMCID: PMC11331043 DOI: 10.1016/j.bpj.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
The immune response is orchestrated by elaborate protein interaction networks that interweave ligand-mediated receptor reorganization with signaling cascades. While the biochemical processes have been extensively investigated, delineating the biophysical principles governing immune receptor activation has remained challenging due to design limitations of traditional ligand display platforms. These constraints have been overcome by advances in DNA origami nanotechnology, enabling unprecedented control over ligand geometry on configurable scaffolds. It is now possible to systematically dissect the independent roles of ligand stoichiometry, spatial distribution, and rigidity in immune receptor activation, signaling, and cooperativity. In this review, we highlight pioneering efforts in manipulating the ligand presentation landscape to understand immune receptor triggering and to engineer functional immune responses.
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Affiliation(s)
- Yuchen Hou
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario.
| | - Bebhinn Treanor
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario; Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario; Department of Immunology, University of Toronto, Toronto, Ontario.
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43
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Rogers J, Bajur AT, Salaita K, Spillane KM. Mechanical control of antigen detection and discrimination by T and B cell receptors. Biophys J 2024; 123:2234-2255. [PMID: 38794795 PMCID: PMC11331051 DOI: 10.1016/j.bpj.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Abstract
The adaptive immune response is orchestrated by just two cell types, T cells and B cells. Both cells possess the remarkable ability to recognize virtually any antigen through their respective antigen receptors-the T cell receptor (TCR) and B cell receptor (BCR). Despite extensive investigations into the biochemical signaling events triggered by antigen recognition in these cells, our ability to predict or control the outcome of T and B cell activation remains elusive. This challenge is compounded by the sensitivity of T and B cells to the biophysical properties of antigens and the cells presenting them-a phenomenon we are just beginning to understand. Recent insights underscore the central role of mechanical forces in this process, governing the conformation, signaling activity, and spatial organization of TCRs and BCRs within the cell membrane, ultimately eliciting distinct cellular responses. Traditionally, T cells and B cells have been studied independently, with researchers working in parallel to decipher the mechanisms of activation. While these investigations have unveiled many overlaps in how these cell types sense and respond to antigens, notable differences exist. To fully grasp their biology and harness it for therapeutic purposes, these distinctions must be considered. This review compares and contrasts the TCR and BCR, placing emphasis on the role of mechanical force in regulating the activity of both receptors to shape cellular and humoral adaptive immune responses.
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Affiliation(s)
- Jhordan Rogers
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Anna T Bajur
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
| | - Katelyn M Spillane
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom; Department of Life Sciences, Imperial College London, London, United Kingdom.
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44
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Zhang Y, Liu X, Hou S, Wu R, Yang J, Zhang C. Enzyme-Programmed Self-Assembly of Nanoparticles. Chembiochem 2024; 25:e202400384. [PMID: 38819745 DOI: 10.1002/cbic.202400384] [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: 04/27/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/01/2024]
Abstract
Nanoparticles are a hot topic in the field of nanomaterial research due to their excellent physical and chemical properties. In recent years, DNA-directed nanoparticle self-assembly technology has been widely applied to the development of numerous complex nanoparticle superstructures. Due to the inherent stability and surface electric repulsion of nanoparticles, it is difficult to make nanoparticle superstructures respond to molecular signals in the external environment. In fact, enzyme-programmed molecular systems are developed to allow diverse functions, including logical operations, signal amplification, and dynamic assembly control. Therefore, combining enzyme-controlled DNA systems may endow nanoparticle assembly systems with more flexibility in program design, allowing them to respond to a variety of external signals. In this review, we summarize the basic principles of enzyme-controlled DNA/nanoparticle self-assembly and introduce its applications in heavy metal detection, gene expression, proteins inside living cells, cancer cell therapy, and drug delivery. With the continuous development of new nanoparticle materials and the increasing functionality of enzyme DNA circuits, enzyme-directed DNA/nanoparticle self-assembled probe technology is expected to see significant future development.
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Affiliation(s)
- Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Xuan Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Siqi Hou
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
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45
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Hills RA, Tan TK, Cohen AA, Keeffe JR, Keeble AH, Gnanapragasam PNP, Storm KN, Rorick AV, West AP, Hill ML, Liu S, Gilbert-Jaramillo J, Afzal M, Napier A, Admans G, James WS, Bjorkman PJ, Townsend AR, Howarth MR. Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses. NATURE NANOTECHNOLOGY 2024; 19:1216-1223. [PMID: 38710880 PMCID: PMC11329374 DOI: 10.1038/s41565-024-01655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/15/2024] [Indexed: 05/08/2024]
Abstract
Defending against future pandemics requires vaccine platforms that protect across a range of related pathogens. Nanoscale patterning can be used to address this issue. Here, we produce quartets of linked receptor-binding domains (RBDs) from a panel of SARS-like betacoronaviruses, coupled to a computationally designed nanocage through SpyTag/SpyCatcher links. These Quartet Nanocages, possessing a branched morphology, induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented in the vaccine. Equivalent antibody responses are raised to RBDs close to the nanocage or at the tips of the nanoparticle's branches. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increase the strength and breadth of an otherwise narrow immune response. A Quartet Nanocage including the Omicron XBB.1.5 'Kraken' RBD induced antibodies with binding to a broad range of sarbecoviruses, as well as neutralizing activity against this variant of concern. Quartet nanocages are a nanomedicine approach with potential to confer heterotypic protection against emergent zoonotic pathogens and facilitate proactive pandemic protection.
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Affiliation(s)
- Rory A Hills
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | | | - Kaya N Storm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Annie V Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michelle L Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Javier Gilbert-Jaramillo
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Madeeha Afzal
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Amy Napier
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gabrielle Admans
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - William S James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Alain R Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
| | - Mark R Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Department of Pharmacology, University of Cambridge, Cambridge, UK.
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46
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Hendricks GG, Grigoryan L, Navarro MJ, Catanzaro NJ, Hubbard ML, Powers JM, Mattocks M, Treichel C, Walls AC, Lee J, Ellis D, Wang JY(J, Cheng S, Miranda MC, Valdez A, Chao CW, Chan S, Men C, Johnson MR, Hui H, Wu SY, Lujan V, Muramatsu H, Lin PJ, Sung MM, Tam YK, Leaf EM, Pardi N, Baric RS, Pulendran B, Veesler D, Schäfer A, King NP. Computationally designed mRNA-launched protein nanoparticle vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604655. [PMID: 39091730 PMCID: PMC11291046 DOI: 10.1101/2024.07.22.604655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Both protein nanoparticle and mRNA vaccines were clinically de-risked during the COVID-19 pandemic1-6. These vaccine modalities have complementary strengths: antigen display on protein nanoparticles can enhance the magnitude, quality, and durability of antibody responses7-10, while mRNA vaccines can be rapidly manufactured11 and elicit antigen-specific CD4 and CD8 T cells12,13. Here we leverage a computationally designed icosahedral protein nanoparticle that was redesigned for optimal secretion from eukaryotic cells14 to develop an mRNA-launched nanoparticle vaccine for SARS-CoV-2. The nanoparticle, which displays 60 copies of a stabilized variant of the Wuhan-Hu-1 Spike receptor binding domain (RBD)15, formed monodisperse, antigenically intact assemblies upon secretion from transfected cells. An mRNA vaccine encoding the secreted RBD nanoparticle elicited 5- to 28-fold higher levels of neutralizing antibodies than an mRNA vaccine encoding membrane-anchored Spike, induced higher levels of CD8 T cells than the same immunogen when delivered as an adjuvanted protein nanoparticle, and protected mice from vaccine-matched and -mismatched SARS-CoV-2 challenge. Our data establish that delivering protein nanoparticle immunogens via mRNA vaccines can combine the benefits of each modality and, more broadly, highlight the utility of computational protein design in genetic immunization strategies.
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Affiliation(s)
- Grace G. Hendricks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Lilit Grigoryan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nicholas J. Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miranda L. Hubbard
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John M. Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa Mattocks
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jing Yang (John) Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Suna Cheng
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Marcos C. Miranda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Adian Valdez
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cara W. Chao
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Christine Men
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Max R. Johnson
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Harold Hui
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Sheng-Yang Wu
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Victor Lujan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Elizabeth M. Leaf
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Lead contact
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47
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Wang W, Wang W, Chen Y, Lin M, Chen YR, Zeng R, He T, Shen Z, Wu ZS. Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity. ACS NANO 2024; 18:18257-18281. [PMID: 38973121 DOI: 10.1021/acsnano.3c13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.
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Affiliation(s)
- Weijun Wang
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- College of Chemistry and Food Science, Nanchang Normal University, Nanchang 330032, China
| | - Wenqing Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Yaxin Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Mengling Lin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Yan-Ru Chen
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ruijin Zeng
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Tenghang He
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zai-Sheng Wu
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
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48
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García-Chamé M, Wadhwani P, Pfeifer J, Schepers U, Niemeyer CM, Domínguez CM. A Versatile Microfluidic Platform for Extravasation Studies Based on DNA Origami-Cell Interactions. Angew Chem Int Ed Engl 2024; 63:e202318805. [PMID: 38687094 DOI: 10.1002/anie.202318805] [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: 12/07/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
The adhesion of circulating tumor cells (CTCs) to the endothelial lumen and their extravasation to surrounding tissues are crucial in the seeding of metastases and remain the most complex events of the metastatic cascade to study. Integrins expressed on CTCs are major regulators of the extravasation process. This knowledge is primarily derived from animal models and biomimetic systems based on artificial endothelial layers, but these methods have ethical or technical limitations. We present a versatile microfluidic device to study cancer cell extravasation that mimics the endothelial barrier by using a porous membrane functionalized with DNA origami nanostructures (DONs) that display nanoscale patterns of adhesion peptides to circulating cancer cells. The device simulates physiological flow conditions and allows direct visualization of cell transmigration through microchannel pores using 3D confocal imaging. Using this system, we studied integrin-specific adhesion in the absence of other adhesive events. Specifically, we show that the transmigration ability of the metastatic cancer cell line MDA-MB-231 is influenced by the type, distance, and density of adhesion peptides present on the DONs. Furthermore, studies with mixed ligand systems indicate that integrins binding to RGD (arginine-glycine-aspartic acid) and IDS (isoleucine-aspartic acid-serine) did not synergistically enhance the extravasation process of MDA-MB-231 cells.
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Affiliation(s)
- Miguel García-Chamé
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 2 (IBG 2), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Juliana Pfeifer
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
| | - Carmen M Domínguez
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz, 76344, Eggenstein-Leopoldshafen, Germany
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49
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Berreiros-Hortala H, Vilchez-Pinto G, Diaz-Perales A, Garrido-Arandia M, Tome-Amat J. Virus-like Particles as Vaccines for Allergen-Specific Therapy: An Overview of Current Developments. Int J Mol Sci 2024; 25:7429. [PMID: 39000536 PMCID: PMC11242184 DOI: 10.3390/ijms25137429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
Immune engineering and modulation are the basis of a novel but powerful tool to treat immune diseases using virus-like particles (VLPs). VLPs are formed by the viral capsid without genetic material making them non-infective. However, they offer a wide variety of possibilities as antigen-presenting platforms, resulting in high immunogenicity and high efficacy in immune modulation, with low allergenicity. Both animal and plant viruses are being studied for use in the treatment of food allergies. These formulations are combined with adjuvants, T-stimulatory epitopes, TLR ligands, and other immune modulators to modulate or enhance the immune response toward the presented allergen. Here, the authors present an overview of VLP production systems, their immune modulation capabilities, and the applicability of actual VLP-based formulations targeting allergic diseases.
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Affiliation(s)
- Helena Berreiros-Hortala
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain; (H.B.-H.); (G.V.-P.); (A.D.-P.); (M.G.-A.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040 Madrid, Spain
| | - Gonzalo Vilchez-Pinto
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain; (H.B.-H.); (G.V.-P.); (A.D.-P.); (M.G.-A.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040 Madrid, Spain
| | - Araceli Diaz-Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain; (H.B.-H.); (G.V.-P.); (A.D.-P.); (M.G.-A.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040 Madrid, Spain
| | - Maria Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain; (H.B.-H.); (G.V.-P.); (A.D.-P.); (M.G.-A.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040 Madrid, Spain
| | - Jaime Tome-Amat
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain; (H.B.-H.); (G.V.-P.); (A.D.-P.); (M.G.-A.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040 Madrid, Spain
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Yuan C, Zhou F, Xu Z, Wu D, Hou P, Yang D, Pan L, Wang P. Functionalized DNA Origami-Enabled Detection of Biomarkers. Chembiochem 2024; 25:e202400227. [PMID: 38700476 DOI: 10.1002/cbic.202400227] [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: 03/12/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/05/2024]
Abstract
Biomarkers are crucial physiological and pathological indicators in the host. Over the years, numerous detection methods have been developed for biomarkers, given their significant potential in various biological and biomedical applications. Among these, the detection system based on functionalized DNA origami has emerged as a promising approach due to its precise control over sensing modules, enabling sensitive, specific, and programmable biomarker detection. We summarize the advancements in biomarker detection using functionalized DNA origami, focusing on strategies for DNA origami functionalization, mechanisms of biomarker recognition, and applications in disease diagnosis and monitoring. These applications are organized into sections based on the type of biomarkers - nucleic acids, proteins, small molecules, and ions - and concludes with a discussion on the advantages and challenges associated with using functionalized DNA origami systems for biomarker detection.
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Affiliation(s)
- Caiqing Yuan
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Zhou
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zhihao Xu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Dunkai Wu
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Hou
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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