1
|
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.
Collapse
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
| |
Collapse
|
2
|
Menon AP, Villanueva H, Meraviglia-Crivelli D, van Santen HM, Hellmeier J, Zheleva A, Nonateli F, Peters T, Wachsmann TL, Hernandez-Rueda M, Huppa JB, Schütz GJ, Sevcsik E, Moreno B, Pastor F. CD3 aptamers promote expansion and persistence of tumor-reactive T cells for adoptive T cell therapy in cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102198. [PMID: 38745854 PMCID: PMC11091522 DOI: 10.1016/j.omtn.2024.102198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/21/2024] [Indexed: 05/16/2024]
Abstract
The CD3/T cell receptor (TCR) complex is responsible for antigen-specific pathogen recognition by T cells, and initiates the signaling cascade necessary for activation of effector functions. CD3 agonistic antibodies are commonly used to expand T lymphocytes in a wide range of clinical applications, including in adoptive T cell therapy for cancer patients. A major drawback of expanding T cell populations ex vivo using CD3 agonistic antibodies is that they expand and activate T cells independent of their TCR antigen specificity. Therapeutic agents that facilitate expansion of T cells in an antigen-specific manner and reduce their threshold of T cell activation are therefore of great interest for adoptive T cell therapy protocols. To identify CD3-specific T cell agonists, several RNA aptamers were selected against CD3 using Systematic Evolution of Ligands by EXponential enrichment combined with high-throughput sequencing. The extent and specificity of aptamer binding to target CD3 were assessed through surface plasma resonance, P32 double-filter assays, and flow cytometry. Aptamer-mediated modulation of the threshold of T cell activation was observed in vitro and in preclinical transgenic TCR mouse models. The aptamers improved efficacy and persistence of adoptive T cell therapy by low-affinity TCR-reactive T lymphocytes in melanoma-bearing mice. Thus, CD3-specific aptamers can be applied as therapeutic agents which facilitate the expansion of tumor-reactive T lymphocytes while conserving their tumor specificity. Furthermore, selected CD3 aptamers also exhibit cross-reactivity to human CD3, expanding their potential for clinical translation and application in the future.
Collapse
Affiliation(s)
- Ashwathi Puravankara Menon
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Helena Villanueva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Daniel Meraviglia-Crivelli
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Hisse M. van Santen
- Immune System Development and Function Unit, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), 28049 Madrid, Spain
| | - Joschka Hellmeier
- Institute of Applied Physics, TU Wien, Lehargasse 6, 1060 Vienna, Austria
| | - Angelina Zheleva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Francesca Nonateli
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Timo Peters
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology, Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Mercedes Hernandez-Rueda
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Johannes B. Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology, Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gerhard J. Schütz
- Institute of Applied Physics, TU Wien, Lehargasse 6, 1060 Vienna, Austria
| | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Lehargasse 6, 1060 Vienna, Austria
| | - Beatriz Moreno
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Fernando Pastor
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Spanish Center for Biomedical Research Network in Oncology (CIBERONC), 28029 Madrid, Spain
| |
Collapse
|
3
|
Rogers J, Bajur AT, Salaita K, Spillane KM. Mechanical control of antigen detection and discrimination by T and B cell receptors. Biophys J 2024:S0006-3495(24)00347-3. [PMID: 38794795 DOI: 10.1016/j.bpj.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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.
Collapse
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.
| |
Collapse
|
4
|
Abendstein L, Noteborn WEM, Veenman LS, Dijkstra DJ, van de Bovenkamp FS, Trouw LA, Sharp TH. DNA Nanostructure-Templated Antibody Complexes Provide Insights into the Geometric Requirements of Human Complement Cascade Activation. J Am Chem Soc 2024; 146:13455-13466. [PMID: 38703132 PMCID: PMC11099972 DOI: 10.1021/jacs.4c02772] [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: 05/06/2024]
Abstract
The classical complement pathway is activated by antigen-bound IgG antibodies. Monomeric IgG must oligomerize to activate complement via the hexameric C1q complex, and hexamerizing mutants of IgG appear as promising therapeutic candidates. However, structural data have shown that it is not necessary to bind all six C1q arms to initiate complement, revealing a symmetry mismatch between C1 and the hexameric IgG complex that has not been adequately explained. Here, we use DNA nanotechnology to produce specific nanostructures to template antigens and thereby spatially control IgG valency. These DNA-nanotemplated IgG complexes can activate complement on cell-mimetic lipid membranes, which enabled us to determine the effect of IgG valency on complement activation without the requirement to mutate antibodies. We investigated this using biophysical assays together with 3D cryo-electron tomography. Our data revealed the importance of interantigen distance on antibody-mediated complement activation, and that the cleavage of complement component C4 by the C1 complex is proportional to the number of ideally spaced antigens. Increased IgG valency also translated to better terminal pathway activation and membrane attack complex formation. Together, these data provide insights into how nanopatterning antigen-antibody complexes influence the activation of the C1 complex and suggest routes to modulate complement activation by antibody engineering. Furthermore, to our knowledge, this is the first time DNA nanotechnology has been used to study the activation of the complement system.
Collapse
Affiliation(s)
- Leoni Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Willem E M Noteborn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Luc S Veenman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Douwe J Dijkstra
- Department of Immunology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | | | - Leendert A Trouw
- Department of Immunology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
| |
Collapse
|
5
|
Wilhelm KB, Vissa A, Groves JT. Differential Roles of Kinetic On- and Off-Rates in T-Cell Receptor Signal Integration Revealed with a Modified Fab'-DNA Ligand. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587588. [PMID: 38617215 PMCID: PMC11014569 DOI: 10.1101/2024.04.01.587588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly-binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide-MHC (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab'-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rate of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells (LAT), which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from synthetic ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.
Collapse
Affiliation(s)
- Kiera B Wilhelm
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
| | - Anand Vissa
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
| | - Jay T Groves
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
| |
Collapse
|
6
|
Long J, Wang Y, Jiang X, Ge J, Chen M, Zheng B, Wang R, Wang M, Xu M, Ke Q, Wang J. Nanomaterials Boost CAR-T Therapy for Solid Tumors. Adv Healthc Mater 2024:e2304615. [PMID: 38483400 DOI: 10.1002/adhm.202304615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/29/2024] [Indexed: 05/22/2024]
Abstract
T cell engineering, particularly via chimeric antigen receptor (CAR) modifications for enhancing tumor specificity, has shown efficacy in treating hematologic malignancies. The extension of CAR-T cell therapy to solid tumors, however, is impeded by several challenges: The absence of tumor-specific antigens, antigen heterogeneity, a complex immunosuppressive tumor microenvironment, and physical barriers to cell infiltration. Additionally, limitations in CAR-T cell manufacturing capacity and the high costs associated with these therapies restrict their widespread application. The integration of nanomaterials into CAR-T cell production and application offers a promising avenue to mitigate these challenges. Utilizing nanomaterials in the production of CAR-T cells can decrease product variability and lower production expenses, positively impacting the targeting and persistence of CAR-T cells in treatment and minimizing adverse effects. This review comprehensively evaluates the use of various nanomaterials in the production of CAR-T cells, genetic modification, and in vivo delivery. It discusses their underlying mechanisms and potential for clinical application, with a focus on improving specificity and safety in CAR-T cell therapy.
Collapse
Affiliation(s)
- Jun Long
- Shenzhen Geim Graphene Center, Tsinghua-Berkeley Shenzhen Institute & Tsinghua Shenzhen International Graduate School, Tsinghua University, 1001 Xueyuan Road, Shenzhen, 518055, China
| | - Yian Wang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Changsha, 410013, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Junshang Ge
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, 410078, China
| | - Mingfen Chen
- Department of Radiation Oncology, The Second Affiliated Hospital of Fujian Medical University, Fujian Medical University, Quanzhou, 362000, China
| | - Boshu Zheng
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, No.1 Xuefu North Road University Town, Fuzhou, 350122, China
| | - Rong Wang
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, No.1 Xuefu North Road University Town, Fuzhou, 350122, China
| | - Meifeng Wang
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, No.1 Xuefu North Road University Town, Fuzhou, 350122, China
| | - Meifang Xu
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, No.1 Xuefu North Road University Town, Fuzhou, 350122, China
| | - Qi Ke
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, No.1 Xuefu North Road University Town, Fuzhou, 350122, China
| | - Jie Wang
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, No.1 Xuefu North Road University Town, Fuzhou, 350122, China
| |
Collapse
|
7
|
Cui H, Zhang L, Shi Y. Biomaterials-mediated ligation of immune cell surface receptors for immunoengineering. IMMUNO-ONCOLOGY TECHNOLOGY 2024; 21:100695. [PMID: 38405432 PMCID: PMC10891334 DOI: 10.1016/j.iotech.2023.100695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A wide variety of cell surface receptors found on immune cells are essential to the body's immunological defense mechanisms. Cell surface receptors enable immune cells to sense extracellular stimuli and identify pathogens, transmitting activating or inhibitory signals that regulate the immune cell state and coordinate immunological responses. These receptors can dynamically aggregate or disperse due to the fluidity of the cell membrane, particularly during interactions between cells or between cells and pathogens. At the contact surface, cell surface receptors form microclusters, facilitating the recruitment and amplification of downstream signals. The strength of the immune signal is influenced by both the quantity and the specific types of participating receptors. Generally, receptor cross-linking, meaning multivalent ligation of receptors on one cell, leads to greater interface connectivity and more robust signaling. However, intercellular interactions are often spatially restricted by other cellular structures. Therefore, it is essential to comprehend these receptors' features for developing effective immunoengineering approaches. Biomaterials can stimulate and simulate interactions between immune cells and their targets. Biomaterials can activate immune cells to act against pathogenic organisms or cancer cells, thereby offering a valuable immunoengineering toolset for vaccination and immunotherapy. In this review, we systematically summarize biomaterial-based immunoengineering strategies that consider the biology of diverse immune cell surface receptors and the structural attributes of pathogens. By combining this knowledge, we aim to advance the development of rational and effective approaches for immune modulation and therapeutic interventions.
Collapse
Affiliation(s)
- H. Cui
- Department of Polymer Therapeutics, Institute for Experimental Molecular Imaging, Uniklinik RWTH Aachen and Helmholtz Institute for Biomedical Engineering, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - L. Zhang
- Department of Mechanical and Production Engineering, Aarhus University, Aarhus N, Denmark
| | - Y. Shi
- Department of Polymer Therapeutics, Institute for Experimental Molecular Imaging, Uniklinik RWTH Aachen and Helmholtz Institute for Biomedical Engineering, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
8
|
Sengupta K, Dillard P, Limozin L. Morphodynamics of T-lymphocytes: Scanning to spreading. Biophys J 2024:S0006-3495(24)00157-7. [PMID: 38425041 DOI: 10.1016/j.bpj.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Binding of the T cell receptor complex to its ligand, the subsequent molecular rearrangement, and the concomitant cell-scale shape changes represent the very first steps of adaptive immune recognition. The first minutes of the interaction of T cells and antigen presenting cells have been extensively scrutinized; yet, gaps remain in our understanding of how the biophysical properties of the environment may impact the sequence of events. In particular, many pioneering experiments were done on immobilized ligands and gave major insights into the process of T cell activation, whereas later experiments have indicated that ligand mobility was of paramount importance, especially to enable the formation of T cell receptor clusters. Systematic experiments to compare and reconcile the two schools are still lacking. Furthermore, recent investigations using compliant substrates have elucidated other intriguing aspects of T cell mechanics. Here we review experiments on interaction of T cells with planar artificial antigen presenting cells to explore the impact of mechanics on adhesion and actin morphodynamics during the spreading process. We enumerate a sequence tracing first contact to final spread state that is consistent with current understanding. Finally, we interpret the presented experimental results in light of a mechanical model that captures all the different morphodynamic states.
Collapse
Affiliation(s)
- Kheya Sengupta
- Aix-Marseille Université, CNRS, CINAM, Turing Centre for Living Systems, Marseille, France.
| | - Pierre Dillard
- Aix-Marseille Université, CNRS, CINAM, Turing Centre for Living Systems, Marseille, France; Aix-Marseille Université, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France
| | - Laurent Limozin
- Aix-Marseille Université, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France.
| |
Collapse
|
9
|
Mayer I, Karimian T, Gordiyenko K, Angelin A, Kumar R, Hirtz M, Mikut R, Reischl M, Stegmaier J, Zhou L, Ma R, Nienhaus GU, Rabe KS, Lanzerstorfer P, Domínguez CM, Niemeyer CM. Surface-Patterned DNA Origami Rulers Reveal Nanoscale Distance Dependency of the Epidermal Growth Factor Receptor Activation. NANO LETTERS 2024; 24:1611-1619. [PMID: 38267020 PMCID: PMC10853960 DOI: 10.1021/acs.nanolett.3c04272] [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: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The nanoscale arrangement of ligands can have a major effect on the activation of membrane receptor proteins and thus cellular communication mechanisms. Here we report on the technological development and use of tailored DNA origami-based molecular rulers to fabricate "Multiscale Origami Structures As Interface for Cells" (MOSAIC), to enable the systematic investigation of the effect of the nanoscale spacing of epidermal growth factor (EGF) ligands on the activation of the EGF receptor (EGFR). MOSAIC-based analyses revealed that EGF distances of about 30-40 nm led to the highest response in EGFR activation of adherent MCF7 and Hela cells. Our study emphasizes the significance of DNA-based platforms for the detailed investigation of the molecular mechanisms of cellular signaling cascades.
Collapse
Affiliation(s)
- Ivy Mayer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Tina Karimian
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Klavdiya Gordiyenko
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Alessandro Angelin
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ravi Kumar
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Michael Hirtz
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ralf Mikut
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Johannes Stegmaier
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute
of Imaging and Computer Vision, RWTH Aachen
University, 52074 Aachen, Germany
| | - Lu Zhou
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Rui Ma
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
- Institute
of Biological and Chemical Systems (IBCS) and Institute of Nanotechnology
(INT), Karlsruhe Institute of Technology
(KIT), 76021 Karlsruhe, Germany
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kersten S. Rabe
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Peter Lanzerstorfer
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Carmen M. Domínguez
- 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
| |
Collapse
|
10
|
Paloja K, Weiden J, Hellmeier J, Eklund AS, Reinhardt SCM, Parish IA, Jungmann R, Bastings MMC. Balancing the Nanoscale Organization in Multivalent Materials for Functional Inhibition of the Programmed Death-1 Immune Checkpoint. ACS NANO 2024; 18:1381-1395. [PMID: 38126310 PMCID: PMC10795474 DOI: 10.1021/acsnano.3c06552] [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: 07/17/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Dendritic cells (DCs) regulate immune priming by expressing programmed death ligand 1 (PD-L1) and PD-L2, which interact with the inhibitory receptor PD-1 on activated T cells. PD-1 signaling regulates T cell effector functions and limits autoimmunity. Tumor cells can hijack this pathway by overexpressing PD-L1 to suppress antitumor T cell responses. Blocking this inhibitory pathway has been beneficial for the treatment of various cancer types, although only a subset of patients responds. A deepened understanding of the spatial organization and molecular interplay between PD-1 and its ligands may inform the design of more efficacious nanotherapeutics. We visualized the natural molecular PD-L1 organization on DCs by DNA-PAINT microscopy and created a template to engineer DNA-based nanoclusters presenting PD-1 at defined valencies, distances, and patterns. These multivalent nanomaterials were examined for their cellular binding and blocking ability. Our data show that PD-1 nano-organization has profound effects on ligand interaction and that the valency of PD-1 molecules modulates the effectiveness in restoring T cell function. This work highlights the power of spatially controlled functional materials to unravel the importance of multivalent patterns in the PD-1 pathway and presents alternative design strategies for immune-engineering.
Collapse
Affiliation(s)
- Kaltrina Paloja
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale
de Lausanne, Lausanne 1015, Switzerland
| | - Jorieke Weiden
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale
de Lausanne, Lausanne 1015, Switzerland
| | | | | | - Susanne C. M. Reinhardt
- Max
Planck Institute of Biochemistry, Planegg 82152, Germany
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich 80539, Germany
| | - Ian A. Parish
- Peter
MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir
Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3128, Australia
| | - Ralf Jungmann
- Max
Planck Institute of Biochemistry, Planegg 82152, Germany
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich 80539, Germany
| | - Maartje M. C. Bastings
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, École Polytechnique Fédérale
de Lausanne, Lausanne 1015, Switzerland
- Interfaculty
Bioengineering Institute, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| |
Collapse
|
11
|
Aba G, Scheeren FA, Sharp TH. Design and Synthesis of DNA Origami Nanostructures to Control TNF Receptor Activation. Methods Mol Biol 2024; 2800:35-53. [PMID: 38709476 DOI: 10.1007/978-1-0716-3834-7_4] [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: 05/07/2024]
Abstract
Clustering of type II tumor necrosis factor (TNF) receptors (TNFRs) is essential for their activation, yet currently available drugs fail to activate signaling. Some strategies aim to cluster TNFR by using multivalent streptavidin or scaffolds based on dextran or graphene. However, these strategies do not allow for control of the valency or spatial organization of the ligands, and consequently control of the TNFR activation is not optimal. DNA origami nanostructures allow nanometer-precise control of the spatial organization of molecules and complexes, with defined spacing, number and valency. Here, we demonstrate the design and characterization of a DNA origami nanostructure that can be decorated with engineered single-chain TNF-related apoptosis-inducing ligand (SC-TRAIL) complexes, which show increased cell killing compared to SC-TRAIL alone on Jurkat cells. The information in this chapter can be used as a basis to decorate DNA origami nanostructures with various proteins, complexes, or other biomolecules.
Collapse
Affiliation(s)
- Göktuğ Aba
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands.
- School of Biochemistry, University of Bristol, Bristol, UK.
| |
Collapse
|
12
|
Wang WX, Douglas TR, Zhang H, Bhattacharya A, Rothenbroker M, Tang W, Sun Y, Jia Z, Muffat J, Li Y, Chou LYT. Universal, label-free, single-molecule visualization of DNA origami nanodevices across biological samples using origamiFISH. NATURE NANOTECHNOLOGY 2024; 19:58-69. [PMID: 37500778 DOI: 10.1038/s41565-023-01449-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 07/29/2023]
Abstract
Structural DNA nanotechnology enables the fabrication of user-defined DNA origami nanostructures (DNs) for biological applications. However, the role of DN design during cellular interactions and subsequent biodistribution remain poorly understood. Current methods for tracking DN fates in situ, including fluorescent-dye labelling, suffer from low sensitivity and dye-induced artifacts. Here we present origamiFISH, a label-free and universal method for the single-molecule fluorescence detection of DNA origami nanostructures in cells and tissues. origamiFISH targets pan-DN scaffold sequences with hybridization chain reaction probes to achieve 1,000-fold signal amplification. We identify cell-type- and DN shape-specific spatiotemporal distribution patterns within a minute of uptake and at picomolar DN concentrations, 10,000× lower than field standards. We additionally optimize compatibility with immunofluorescence and tissue clearing to visualize DN distribution within tissue cryo-/vibratome sections, slice cultures and whole-mount organoids. Together, origamiFISH enables the accurate mapping of DN distribution across subcellular and tissue barriers for guiding the development of DN-based therapeutics.
Collapse
Affiliation(s)
- Wendy Xueyi Wang
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Travis R Douglas
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Haiwang Zhang
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Afrin Bhattacharya
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Wentian Tang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Yu Sun
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Zhengping Jia
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
13
|
Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
Collapse
Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
| |
Collapse
|
14
|
Platzer R, Hellmeier J, Göhring J, Perez ID, Schatzlmaier P, Bodner C, Focke‐Tejkl M, Schütz GJ, Sevcsik E, Stockinger H, Brameshuber M, Huppa JB. Monomeric agonist peptide/MHCII complexes activate T-cells in an autonomous fashion. EMBO Rep 2023; 24:e57842. [PMID: 37768718 PMCID: PMC10626418 DOI: 10.15252/embr.202357842] [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: 07/19/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular crowding of agonist peptide/MHC class II complexes (pMHCIIs) with structurally similar, yet per se non-stimulatory endogenous pMHCIIs is postulated to sensitize T-cells for the recognition of single antigens on the surface of dendritic cells and B-cells. When testing this premise with the use of advanced live cell microscopy, we observe pMHCIIs as monomeric, randomly distributed entities diffusing rapidly after entering the APC surface. Synaptic TCR engagement of highly abundant endogenous pMHCIIs is low or non-existent and affects neither TCR engagement of rare agonist pMHCII in early and advanced synapses nor agonist-induced TCR-proximal signaling. Our findings highlight the capacity of single freely diffusing agonist pMHCIIs to elicit the full T-cell response in an autonomous and peptide-specific fashion with consequences for adaptive immunity and immunotherapeutic approaches.
Collapse
Affiliation(s)
- René Platzer
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Joschka Hellmeier
- TU Wien, Institute of Applied PhysicsViennaAustria
- Present address:
Max Planck Institute of Biochemistry, Molecular Imaging and BionanotechnologyMartinsriedGermany
| | - Janett Göhring
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Iago Doel Perez
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
- Present address:
Takeda Manufacturing Austria AGViennaAustria
| | - Philipp Schatzlmaier
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Clara Bodner
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Margarete Focke‐Tejkl
- Center for Pathophysiology, Infectiology, Immunology, Institute for Pathophysiology and Allergy ResearchMedical University of ViennaViennaAustria
| | | | - Eva Sevcsik
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Hannes Stockinger
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | | | - Johannes B Huppa
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| |
Collapse
|
15
|
Hou Y, Treanor B. DNA origami: Interrogating the nano-landscape of immune receptor activation. Biophys J 2023:S0006-3495(23)00649-5. [PMID: 37838832 DOI: 10.1016/j.bpj.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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.
Collapse
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.
| |
Collapse
|
16
|
Toledo E, Iraqi M, Pandey A, Tzadka S, Le Saux G, Porgador A, Schvartzman M. Multifunctional Nanoscale Platform for the Study of T Cell Receptor Segregation. ACS OMEGA 2023; 8:28968-28975. [PMID: 37599975 PMCID: PMC10433356 DOI: 10.1021/acsomega.2c08194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/10/2023] [Indexed: 08/22/2023]
Abstract
T cells respond not only to biochemical stimuli transmitted through their activating, costimulatory, and inhibitory receptors but also to biophysical aspects of their environment, including the receptors' spatial arrangement. While these receptors form nanoclusters that can either colocalize or segregate, the roles of these colocalization and segregation remain unclear. Deciphering these roles requires a nanoscale platform with independent and simultaneous spatial control of multiple types of receptors. Herein, using a straightforward and modular fabrication process, we engineered a tunable nanoscale chip used as a platform for T cell stimulation, allowing spatial control over the clustering and segregation of activating, costimulatory, and inhibitory receptors. Using this platform, we showed that, upon blocked inhibition, cells became sensitive to changes in the nanoscale ligand configuration. The nanofabrication methodology described here opens a pathway to numerous studies, which will produce an important insight into the molecular mechanism of T cell activation. This insight is essential for the fundamental understanding of our immune system as well as for the rational design of future immunotherapies.
Collapse
Affiliation(s)
- Esti Toledo
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Muhammed Iraqi
- The
Shraga Segal Department of Microbiology, Immunology, and Genetics,
Faculty of Health Science, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
| | - Ashish Pandey
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Sivan Tzadka
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Guillaume Le Saux
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Angel Porgador
- The
Shraga Segal Department of Microbiology, Immunology, and Genetics,
Faculty of Health Science, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
| | - Mark Schvartzman
- Department
of Materials Engineering, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
- Ilse
Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| |
Collapse
|
17
|
Sun L, Shen F, Qu Y, Liu Z. Functional DNA as a Molecular Tool in Regulating Immunoreceptor-Ligand Interactions. JACS AU 2023; 3:1820-1834. [PMID: 37502159 PMCID: PMC10369416 DOI: 10.1021/jacsau.3c00291] [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: 06/07/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
During immune responses, activating ligands would trigger dynamic spatiotemporal organization of immunoreceptors at the cell interface, governing the fate and effector functions of immune cells. To understand the biophysical mechanisms of immunoreceptor signaling, diverse tools, including DNA technologies, have been developed to manipulate receptor-ligand interactions during the immune activation process. With great capability in the controllable assembly of biomolecules, functional DNA-based precise arrangement of immune molecules at cell interfaces has provided a powerful means in revealing the principles of immunoreceptor triggering, even at the single-molecule level. In addition, precisely regulating immunoreceptor-ligand interactions with functional DNA has been applied in immunotherapies of major diseases. This Perspective will focus on the recent advances in exploring immunoreceptor signaling with functional DNA as the molecular tool as well as the applications of functional DNA mediated regulation of immunoreceptor activation. We also outline the challenges and opportunities of applying functional DNA in immune modulation and immunotherapy.
Collapse
Affiliation(s)
- Lele Sun
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Fengyun Shen
- School
of Chemistry and Chemical Engineering, Shanghai
Jiao Tong University, Shanghai 201240, China
| | - Yanfei Qu
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Zhuang Liu
- Institute
of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Lab
Carbon Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| |
Collapse
|
18
|
Hu Y, Duan Y, Velusamy A, Narum S, Rogers J, Salaita K. DNA Origami Tension Sensors (DOTS) to study T cell receptor mechanics at membrane junctions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.09.548279. [PMID: 37503090 PMCID: PMC10369911 DOI: 10.1101/2023.07.09.548279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The T cell receptor (TCR) is thought to be a mechanosensor, meaning that it transmits mechanical force to its antigen and leverages the force to amplify the specificity and magnitude of TCR signaling. The past decade has witnessed the development of molecular probes which have revealed many aspects of receptor mechanotransduction. However, most force probes are immobilized on hard substrates, thus failing to reveal mechanics in the physiological context of cell membranes. In this report, we developed DNA origami tension sensors (DOTS) which bear force sensors on a DNA origami breadboard and allow mapping of TCR mechanotransduction at dynamic intermembrane junctions. We demonstrate that TCR-antigen bonds experience 5-10 pN forces, and the mechanical events are dependent on cell state, antigen mobility, antigen potency, antigen height and F-actin activity. We tethered DOTS onto a microparticle to mechanically screen antigen in high throughput using flow cytometry. Finally, DOTS were anchored onto live B cell membranes thus producing the first quantification of TCR mechanics at authentic immune cell-cell junctions.
Collapse
Affiliation(s)
- Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Arventh Velusamy
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Steven Narum
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Jhordan Rogers
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| |
Collapse
|
19
|
Tian R, Shang Y, Wang Y, Jiang Q, Ding B. DNA Nanomaterials-Based Platforms for Cancer Immunotherapy. SMALL METHODS 2023; 7:e2201518. [PMID: 36651129 DOI: 10.1002/smtd.202201518] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Indexed: 05/17/2023]
Abstract
The past few decades have witnessed the evolving paradigm for cancer therapy from nonspecific cytotoxic agents to selective, mechanism-based therapeutics, especially immunotherapy. In particular, the integration of nanomaterials with immunotherapy is proven to improve the therapeutic outcome and minimize off-target toxicity in the treatment. As a novel nanomaterial, DNA-based self-assemblies featuring uniform geometries, feasible modifications, programmability, surface addressability, versatility, and intrinsic biocompatibility, are extensively exploited for innovative and effective cancer immunotherapy. In this review, the successful employment of DNA nanoplatforms for cancer immunotherapy, including the delivery of immunogenic cell death inducers, adjuvants and vaccines, immune checkpoint blockers as well as the application in immune cell engineering and adoptive cell therapy is summarized. The remaining challenges and future perspectives regarding the pharmacokinetics/pharmacodynamics, in vivo fate and immunogenicity of DNA materials, and the design of intelligent DNA nanomedicine for individualized cancer immunotherapy are also discussed.
Collapse
Affiliation(s)
- Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| |
Collapse
|
20
|
Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
Collapse
Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| |
Collapse
|
21
|
Schneider L, Rabe KS, Domínguez CM, Niemeyer CM. Hapten-Decorated DNA Nanostructures Decipher the Antigen-Mediated Spatial Organization of Antibodies Involved in Mast Cell Activation. ACS NANO 2023; 17:6719-6730. [PMID: 36990450 PMCID: PMC10100567 DOI: 10.1021/acsnano.2c12647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The immunological response of mast cells is controlled by the multivalent binding of antigens to immunoglobulin E (IgE) antibodies bound to the high-affinity receptor FcεRI on the cell membrane surface. However, the spatial organization of antigen-antibody-receptor complexes at the nanometer scale and the structural constraints involved in the initial events at the cell surface are not yet fully understood. For example, it is unclear what influence the affinity and nanoscale distance between the binding partners involved have on the activation of mast cells to degranulate inflammatory mediators from storage granules. We report the use of DNA origami nanostructures (DON) functionalized with different arrangements of the haptenic 2,4-dinitrophenyl (DNP) ligand to generate multivalent artificial antigens with full control over valency and nanoscale ligand architecture. To investigate the spatial requirements for mast cell activation, the DNP-DON complexes were initially used in surface plasmon resonance (SPR) analysis to study the binding kinetics of isolated IgE under physiological conditions. The most stable binding was observed in a narrow window of approximately 16 nm spacing between haptens. In contrast, affinity studies with FcεRI-linked IgE antibodies on the surface of rat basophilic leukemia cells (RBL-2H3) indicated virtually no distance-dependent variations in the binding of the differently structured DNP-DON complexes but suggested a supramolecular oligovalent nature of the interaction. Finally, the use of DNP-DON complexes for mast cell activation revealed that antigen-directed tight assembly of antibody-receptor complexes is the critical factor for triggering degranulation, even more critical than ligand valence. Our study emphasizes the significance of DNA nanostructures for the study of fundamental biological processes.
Collapse
|
22
|
Banerjee A, Anand M, Ganji M. Labeling approaches for DNA-PAINT super-resolution imaging. NANOSCALE 2023; 15:6563-6580. [PMID: 36942769 DOI: 10.1039/d2nr06541j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.
Collapse
Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| |
Collapse
|
23
|
Ding F, Zhang S, Chen Q, Feng H, Ge Z, Zuo X, Fan C, Li Q, Xia Q. Immunomodulation with Nucleic Acid Nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206228. [PMID: 36599642 DOI: 10.1002/smll.202206228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
The precise regulation of interactions of specific immunological components is crucial for controllable immunomodulation, yet it remains a great challenge. With the assistance of advanced computer design, programmable nucleic acid nanotechnology enables the customization of synthetic nucleic acid nanodevices with unprecedented geometrical and functional precision, which have shown promising potential for precise immunoengineering. Notably, the inherently immunologic functions of nucleic acids endow these nucleic acid-based assemblies with innate advantages in immunomodulatory engagement. In this review, the roles of nucleic acids in innate immunity are discussed, focusing on the definition, immunologic modularity, and enhanced bioavailability of structural nucleic acid nanodevices. In light of this, molecular programming and precise organization of functional modules with nucleic acid nanodevices for immunomodulation are emphatically reviewed. At last, the present challenges and future perspectives of nucleic acid nanodevices for immunomodulation are discussed.
Collapse
Affiliation(s)
- Fei Ding
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Shuangye Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Qian Chen
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Hao Feng
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xiaolei Zuo
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- WLA Laboratories, World Laureates Association, Shanghai, 201203, P. R. China
| | - Qiang Xia
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| |
Collapse
|
24
|
Kocabey S, Chiarelli G, Acuna GP, Ruegg C. Ultrasensitive and multiplexed miRNA detection system with DNA-PAINT. Biosens Bioelectron 2023; 224:115053. [PMID: 36608362 DOI: 10.1016/j.bios.2022.115053] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
MiRNAs hold great potential as biomarkers for the early detection and monitoring of diseases based on their differential expression profiles. Therefore, the sensitive, specific and accurate detection of miRNAs represents an emerging new tool to improve diagnosis and treatment of several diseases, cancer in particular. DNA origami-based miRNA detection is particularly advantageous as it allows to incorporate multiple attachment sites to capture different target miRNAs at the nanoscale. In this work, we present a DNA origami nanoarray system providing distance-dependent recognition of miRNAs by applying super-resolution microscopy technique; DNA-PAINT (point accumulation for imaging in nanoscale topography). The sensor can detect up to 4 miRNAs either separately or in combination based on the relative distance to the boundary markers on the structure using a single imager strand. The detection is highly sensitive, with a limit of detection down to the low femtomolar range (11 fM - 388 fM) and has a large dynamic range up to 10 nM without need for amplification. Moreover, our detection system can discriminate single base mismatches with low false positive rates. Using our strategy, we demonstrate the detection of endogenous miRNAs from cell extracts of cancer cell lines and plasma from breast cancer patients. Overall, we developed an ultrasensitive and amplification-free, DNA-PAINT imaging-based miRNA detection method using DNA origami nanoarray system for the detection of breast-cancer associated miRNAs which potentially provides a sensitive and accurate alternative to the current multiplexed diagnostic technologies.
Collapse
Affiliation(s)
- Samet Kocabey
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700, Fribourg, Switzerland.
| | - Germán Chiarelli
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700, Fribourg, Switzerland
| | - Guillermo P Acuna
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700, Fribourg, Switzerland
| | - Curzio Ruegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700, Fribourg, Switzerland
| |
Collapse
|
25
|
Yu L, Ma Z, He Q. Dynamic DNA Nanostructures for Cell Manipulation. ACS Biomater Sci Eng 2023; 9:562-576. [PMID: 36592368 DOI: 10.1021/acsbiomaterials.2c01204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Dynamic DNA nanostructures are DNA nanostructures with reconfigurable elements that can undergo structural transformations in response to specific stimuli. Thus, anchoring dynamic DNA nanostructures on cell membranes is an attractive and promising strategy for well-controlled cell manipulation. Here, we review the latest progress in dynamic DNA nanostructures for cell manipulation. Commonly used mechanisms for dynamic DNA nanostructures are first introduced. Subsequently, we summarize the anchoring strategies for dynamic DNA nanostructures on cell membranes and list possible applications (including programming cell membrane receptors, controlling ligand activity and drug delivery, capturing and releasing cells, and assembling cells into clusters). Finally, insights into the remaining challenges are presented.
Collapse
Affiliation(s)
- Lu Yu
- Department of Endocrinology and Metabolism, The First People's Hospital of Changde City, Renmin Middle Road 818, Changde, Hunan 415000, P. R. China
| | - Zongrui Ma
- Department of Ophthalmology, The First People's Hospital of Changde City, Renmin Middle Road 818, Changde, Hunan 415000, P. R. China
| | - Qunye He
- School of Pharmacy, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200000, P. R. China
| |
Collapse
|
26
|
Mathur D, Galvan AR, Green CM, Liu K, Medintz IL. Uptake and stability of DNA nanostructures in cells: a cross-sectional overview of the current state of the art. NANOSCALE 2023; 15:2516-2528. [PMID: 36722508 PMCID: PMC10407680 DOI: 10.1039/d2nr05868e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The physical and chemical properties of synthetic DNA have transformed this prototypical biopolymer into a versatile nanoscale building block material in the form of DNA nanotechnology. DNA nanotechnology is, in turn, providing unprecedented precision bioengineering for numerous biomedical applications at the nanoscale including next generation immune-modulatory materials, vectors for targeted delivery of nucleic acids, drugs, and contrast agents, intelligent sensors for diagnostics, and theranostics, which combines several of these functionalities into a single construct. Assembling a DNA nanostructure to be programmed with a specific number of targeting moieties on its surface to imbue it with concomitant cellular uptake and retention capabilities along with carrying a specific therapeutic dose is now eminently feasible due to the extraordinary self-assembling properties and high formation efficiency of these materials. However, what remains still only partially addressed is how exactly this class of materials is taken up into cells in both the native state and as targeted or chemically facilitated, along with how stable they are inside the cellular cytosol and other cellular organelles. In this minireview, we summarize what is currently reported in the literature about how (i) DNA nanostructures are taken up into cells along with (ii) what is understood about their subsequent stability in the complex multi-organelle environment of the cellular milieu along with biological fluids in general. This allows us to highlight the many challenges that still remain to overcome in understanding DNA nanostructure-cellular interactions in order to fully translate these exciting new materials.
Collapse
Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Angelica Rose Galvan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Kevin Liu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| |
Collapse
|
27
|
Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
Collapse
Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| |
Collapse
|
28
|
Sterling S, Ke Y. Unraveling mechanotransduction in T cells with DNA nanotechnology. TRENDS IN CHEMISTRY 2023. [DOI: 10.1016/j.trechm.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
29
|
Hellmeier J, Platzer R, Huppa JB, Sevcsik E. A DNA Origami-Based Biointerface to Interrogate the Spatial Requirements for Sensitized T-Cell Antigen Recognition. Methods Mol Biol 2023; 2654:277-302. [PMID: 37106189 DOI: 10.1007/978-1-0716-3135-5_18] [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] [Indexed: 04/29/2023]
Abstract
When T cells scan the surface of antigen-presenting cells (APCs), they can detect the presence of just a few antigenic peptide/MHC complexes (pMHCs), in some cases even a single agonist pMHC. These are typically vastly outnumbered by structurally similar yet non-stimulatory endogenous pMHCs. How T cells achieve this enormous sensitivity and selectivity is still not clear, in particular in view of the rather moderate (1-100 μM) affinity that T-cell receptors (TCRs) typically exert for antigenic pMHCs. Experimental approaches that enable the control and quantification of physical input parameters within the context of the immunological synapse to precisely interrogate the molecular consequences of TCR-engagement, appear highly advantageous when searching for better answers.We here describe the implementation of a biointerface that allows to experimentally define molecular distances between T-cell ligands as a means to correlate them with molecular dynamics of antigen engagement, downstream signaling, and the overall T-cell response. The basis of this biointerface is DNA origami nanostructures, which are (i) rigid and highly versatile platforms that can (ii) be embedded as laterally mobile entities within supported lipid bilayers and functionalized (iii) in a site-specific and orthogonal manner with (iv) one or more proteins of choice.
Collapse
Affiliation(s)
- Joschka Hellmeier
- Institute of Applied Physics, TU Wien, Vienna, Austria
- Max Planck Institute of Biochemistry, Planegg, Germany
| | - René Platzer
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Johannes B Huppa
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria.
| |
Collapse
|
30
|
Xu F, Xia Q, Ye J, Dong L, Yang D, Xue W, Wang P. Programming DNA Aptamer Arrays of Prescribed Spatial Features with Enhanced Bioavailability and Cell Growth Modulation. NANO LETTERS 2022; 22:9935-9942. [PMID: 36480429 DOI: 10.1021/acs.nanolett.2c03377] [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: 06/17/2023]
Abstract
Epithelial cell adhesion molecules (EpCAMs) play pivotal roles in tumorigenesis in many cancer types, which is reported to reside within nano- to microscale membrane domains, forming small clusters. We propose that building multivalent ligands that spatially patch to EpCAM clusters may largely enhance their targeting capability. Herein, we assembled EpCAM aptamers into nanoscale arrays of prescribed valency and spatial arrangements by using a rectangular DNA pegboard. Our results revealed that EpCAM aptamer arrays exhibited significantly higher binding avidity to MCF-7 cells than free monovalent aptamers, which was affected by both valency and spatial arrangement of aptamers. Furthermore, EpCAM aptamer arrays showed improved tolerance against competing targets in an extracellular environment and potent bioavailability and targeting specificity in a xenograft tumor model in mice. This work may shed light on rationally designing multivalent ligand complexes of defined parameters with optimized binding avidity and targeting capability toward various applications in the biomedical fields.
Collapse
Affiliation(s)
- Fan Xu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qing Xia
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jing Ye
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liang Dong
- Department of Urology, 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, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Xue
- Department of Urology, 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, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| |
Collapse
|
31
|
Sun Y, Sun J, Xiao M, Lai W, Li L, Fan C, Pei H. DNA origami-based artificial antigen-presenting cells for adoptive T cell therapy. SCIENCE ADVANCES 2022; 8:eadd1106. [PMID: 36459554 PMCID: PMC10936057 DOI: 10.1126/sciadv.add1106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Nanosized artificial antigen-presenting cells (aAPCs) with efficient signal presentation hold great promise for in vivo adoptive cell therapy. Here, we used DNA origami nanostructures as two-dimensional scaffolds to regulate the spatial presentation of activating ligands at nanoscale to construct high-effective aAPCs. The DNA origami-based aAPC comprises costimulatory ligands anti-CD28 antibody anchored at three vertices and T cell receptor (TCR) ligands peptide-major histocompatibility complex (pMHC) anchored at three edges with varying density. The DNA origami scaffold enables quantitative analysis of ligand-receptor interactions in T cell activation at the single-particle, single-molecule resolution. The pMHC-TCR-binding dwell time is increased from 9.9 to 12.1 s with increasing pMHC density, driving functional T cell responses. In addition, both in vitro and in vivo assays demonstrate that the optimized DNA origami-based aAPCs show effective tumor growth inhibiting capability in adoptive immunotherapy. These results provide important insights into the rational design of molecular vaccines for cancer immunotherapy.
Collapse
Affiliation(s)
- Yueyang Sun
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jiajia Sun
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| |
Collapse
|
32
|
Buchberger A, Riker K, Bernal-Chanchavac J, Narayanan RP, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N. Bioactive Fibronectin-III 10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. ACS APPLIED BIO MATERIALS 2022; 5:10.1021/acsabm.2c00303. [PMID: 36108278 PMCID: PMC10014493 DOI: 10.1021/acsabm.2c00303] [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] [Indexed: 11/30/2022]
Abstract
The integration of proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for the incorporation of bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading with the nanofibers showing enhanced bioactivity compared to that of the monomeric protein.
Collapse
Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Kyle Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Chad R Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Nour Eddine Fahmi
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| |
Collapse
|
33
|
Domínguez CM, García-Chamé M, Müller U, Kraus A, Gordiyenko K, Itani A, Haschke H, Lanzerstorfer P, Rabe KS, Niemeyer CM. Linker Engineering of Ligand-Decorated DNA Origami Nanostructures Affects Biological Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202704. [PMID: 35934828 DOI: 10.1002/smll.202202704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/11/2022] [Indexed: 06/15/2023]
Abstract
News from an old acquaintance: The streptavidin (STV)-biotin binding system is frequently used for the decoration of DNA origami nanostructures (DON) to study biological systems. Here, a surprisingly high dynamic of the STV/DON interaction is reported, which is affected by the structure of the DNA linker system. Analysis of different mono- or bi-dentate linker architectures on DON with a novel high-speed atomic force microscope (HS-AFM) enabling acquisition times as short as 50 ms per frame gave detailed insights into the dynamics of the DON/STV interaction, revealing dwell times in the sub-100 millisecond range. The linker systems are also used to present biotinylated epidermal growth factor on DON to study the activation of the epidermal growth factor receptor signaling cascade in HeLa cells. The studies confirm that cellular activation correlated with the binding properties of linker-specific STV/DON interactions observed by HS-AFM. This work sheds more light on the commonly used STV/DON system and will help to further standardize the use of DNA nanostructures for the study of biological processes.
Collapse
Affiliation(s)
- Carmen M Domínguez
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Miguel García-Chamé
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ulrike Müller
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Andreas Kraus
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Klavdiya Gordiyenko
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Ahmad Itani
- Institute for Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Heiko Haschke
- Bruker Nano GmbH, JPK BioAFM, Am Studio 2D, 12489, Berlin, Germany
| | - Peter Lanzerstorfer
- School of Engineering, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Kersten S Rabe
- 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
| |
Collapse
|
34
|
Nanoscale organization of two-dimensional multimeric pMHC reagents with DNA origami for CD8 + T cell detection. Nat Commun 2022; 13:3916. [PMID: 35798752 PMCID: PMC9263106 DOI: 10.1038/s41467-022-31684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/23/2022] [Indexed: 11/08/2022] Open
Abstract
Peptide-MHC (pMHC) multimers have excelled in the detection of antigen-specific T cells and have allowed phenotypic analysis using other reagents, but their use for detection of low-affinity T cells remains a challenge. Here we develop a multimeric T cell identifying reagent platform using two-dimensional DNA origami scaffolds to spatially organize pMHCs (termed as dorimers) with nanoscale control. We show that these dorimers enhance the binding avidity for low-affinity antigen-specific T cell receptors (TCRs). The dorimers are able to detect more antigen-specific T cells in mouse CD8+ T cells and early-stage CD4+CD8+ double-positive thymocytes that express less dense TCRs, compared with the equivalent tetramers and dextramers. Moreover, we demonstrate dorimer function in the analysis of autoimmune CD8+ T cells that express low-affinity TCRs, which are difficult to detect using tetramers. We anticipate that dorimers could contribute to the investigation of antigen-specific T cells in immune T cell function or immunotherapy applications. MHC-peptide multimers are important reagents for detecting antigen specific T cells. Here the authors show that DNA scaffolds can be used to make MHC-peptide multimers and the avidity controlled so that low abundance or T cells with low affinity TCR can be detected using these reagents.
Collapse
|
35
|
Wang C, Chen X, Su Y, Wang H, Li D. Precise Regulating T Cell Activation Signaling with Spatial Controllable Positioning of Receptors on DNA Origami. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
36
|
Comberlato A, Koga MM, Nüssing S, Parish IA, Bastings MMC. Spatially Controlled Activation of Toll-like Receptor 9 with DNA-Based Nanomaterials. NANO LETTERS 2022; 22:2506-2513. [PMID: 35266392 PMCID: PMC8949768 DOI: 10.1021/acs.nanolett.2c00275] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
First evidence of geometrical patterns and defined distances of biomolecules as fundamental parameters to regulate receptor binding and cell signaling have emerged recently. Here, we demonstrate the importance of controlled nanospacing of immunostimulatory agents for the activation of immune cells by exploiting DNA-based nanomaterials and pre-existing crystallography data. We created DNA origami nanoparticles that present CpG-motifs in rationally designed spatial patterns to activate Toll-like Receptor 9 in RAW 264.7 macrophages. We demonstrated that stronger immune activation is achieved when active molecules are positioned at the distance of 7 nm, matching the active dimer structure of the receptor. Moreover, we show how the introduction of linkers between particle and ligand can influence the spatial tolerance of binding. These findings are fundamental for a fine-tuned manipulation of the immune system, considering the importance of spatially controlled presentation of therapeutics to increase efficacy and specificity of immune-modulating nanomaterials where multivalent binding is involved.
Collapse
Affiliation(s)
- Alice Comberlato
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Marianna M. Koga
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Simone Nüssing
- Peter
MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir
Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ian A. Parish
- Peter
MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir
Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Maartje M. C. Bastings
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
- Interfaculty
Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| |
Collapse
|
37
|
Hoffecker IT, Shaw A, Sorokina V, Smyrlaki I, Högberg B. Stochastic modeling of antibody binding predicts programmable migration on antigen patterns. NATURE COMPUTATIONAL SCIENCE 2022; 2:179-192. [PMID: 36311262 PMCID: PMC7613752 DOI: 10.1038/s43588-022-00218-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Viruses and bacteria commonly exhibit spatial repetition of surface molecules that directly interface with the host immune system. However the complex interaction of patterned surfaces with immune molecules containing multiple binding domains is poorly understood. We developed a pipeline for constructing mechanistic models of antibody interactions with patterned antigen substrates. Our framework relies on immobilized DNA origami nanostructures decorated with precisely placed antigens. The results revealed that antigen spacing is a spatial control parameter that can be tuned to influence antibody residence time and migration speed. The model predicts that gradients in antigen spacing can drive persistent, directed antibody migration in the direction of more stable spacing. These results depict antibody-antigen interactions as a computational system wherein antigen geometry constrains and potentially directs antibody movement. We propose that this form of molecular programmability could be exploited during co-evolution of pathogens and immune systems or in the design of molecular machines.
Collapse
Affiliation(s)
- Ian T. Hoffecker
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
- Dept. of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23a, 17165 Solna, Sweden
- ,
| | - Alan Shaw
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
- Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720-3220
| | - Viktoria Sorokina
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
| | - Ioanna Smyrlaki
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
| | - Björn Högberg
- Division of Biomaterials, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 16, 17165 Solna, Sweden
- ,
| |
Collapse
|
38
|
Dam T, Chouliara M, Junghans V, Jönsson P. Supported Lipid Bilayers and the Study of Two-Dimensional Binding Kinetics. Front Mol Biosci 2022; 9:833123. [PMID: 35252352 PMCID: PMC8896763 DOI: 10.3389/fmolb.2022.833123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Binding between protein molecules on contacting cells is essential in initiating and regulating several key biological processes. In contrast to interactions between molecules in solution, these events are restricted to the two-dimensional (2D) plane of the meeting cell surfaces. However, converting between the more commonly available binding kinetics measured in solution and the so-called 2D binding kinetics has proven a complicated task since for the latter several factors other than the protein-protein interaction per se have an impact. A few important examples of these are: protein density, membrane fluctuations, force on the bond and the use of auxiliary binding molecules. The development of model membranes, and in particular supported lipid bilayers (SLBs), has made it possible to simplify the studied contact to analyze these effects and to measure 2D binding kinetics of individual protein-protein interactions. We will in this review give an overview of, and discuss, how different SLB systems have been used for this and compare different methods to measure binding kinetics in cell-SLB contacts. Typically, the SLB is functionalized with fluorescently labelled ligands whose interaction with the corresponding receptor on a binding cell can be detected. This interaction can either be studied 1) by an accumulation of ligands in the cell-SLB contact, whose magnitude depends on the density of the proteins and binding affinity of the interaction, or 2) by tracking single ligands in the SLB, which upon interaction with a receptor result in a change of motion of the diffusing ligand. The advantages and disadvantages of other methods measuring 2D binding kinetics will also be discussed and compared to the fluorescence-based methods. Although binding kinetic measurements in cell-SLB contacts have provided novel information on how ligands interact with receptors in vivo the number of these measurements is still limited. This is influenced by the complexity of the system as well as the required experimental time. Moreover, the outcome can vary significantly between studies, highlighting the necessity for continued development of methods to study 2D binding kinetics with higher precision and ease.
Collapse
Affiliation(s)
- Tommy Dam
- Department of Chemistry, Lund University, Lund, Sweden
| | | | - Victoria Junghans
- Nuffield Department of Medicine, CAMS Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Peter Jönsson
- Department of Chemistry, Lund University, Lund, Sweden
- *Correspondence: Peter Jönsson,
| |
Collapse
|
39
|
Egan JR, Abu-Shah E, Dushek O, Elliott T, MacArthur BD. Fluctuations in T cell receptor and pMHC interactions regulate T cell activation. J R Soc Interface 2022; 19:20210589. [PMID: 35135295 PMCID: PMC8833104 DOI: 10.1098/rsif.2021.0589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adaptive immune responses depend on interactions between T cell receptors (TCRs) and peptide major histocompatibility complex (pMHC) ligands located on the surface of T cells and antigen presenting cells (APCs), respectively. As TCRs and pMHCs are often only present at low copy numbers their interactions are inherently stochastic, yet the role of stochastic fluctuations on T cell function is unclear. Here, we introduce a minimal stochastic model of T cell activation that accounts for serial TCR-pMHC engagement, reversible TCR conformational change and TCR aggregation. Analysis of this model indicates that it is not the strength of binding between the T cell and the APC cell per se that elicits an immune response, but rather the information imparted to the T cell from the encounter, as assessed by the entropy rate of the TCR-pMHC binding dynamics. This view provides an information-theoretic interpretation of T cell activation that explains a range of experimental observations. Based on this analysis, we propose that effective T cell therapeutics may be enhanced by optimizing the inherent stochasticity of TCR-pMHC binding dynamics.
Collapse
Affiliation(s)
- Joseph R Egan
- Mathematical Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Institute for Life Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology, University Hospital Southampton, Southampton SO16 6YD, UK.,Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Enas Abu-Shah
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.,Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Tim Elliott
- Institute for Life Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology, University Hospital Southampton, Southampton SO16 6YD, UK.,Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Ben D MacArthur
- Mathematical Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Institute for Life Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Alan Turing Institute, London NW1 2DB, UK
| |
Collapse
|
40
|
Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
Collapse
Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| |
Collapse
|
41
|
Schoenit A, Lo Giudice C, Hahnen N, Ollech D, Jahnke K, Göpfrich K, Cavalcanti-Adam EA. Tuning Epithelial Cell-Cell Adhesion and Collective Dynamics with Functional DNA-E-Cadherin Hybrid Linkers. NANO LETTERS 2022; 22:302-310. [PMID: 34939414 PMCID: PMC8759084 DOI: 10.1021/acs.nanolett.1c03780] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/12/2021] [Indexed: 06/14/2023]
Abstract
The binding strength between epithelial cells is crucial for tissue integrity, signal transduction and collective cell dynamics. However, there is no experimental approach to precisely modulate cell-cell adhesion strength at the cellular and molecular level. Here, we establish DNA nanotechnology as a tool to control cell-cell adhesion of epithelial cells. We designed a DNA-E-cadherin hybrid system consisting of complementary DNA strands covalently bound to a truncated E-cadherin with a modified extracellular domain. DNA sequence design allows to tune the DNA-E-cadherin hybrid molecular binding strength, while retaining its cytosolic interactions and downstream signaling capabilities. The DNA-E-cadherin hybrid facilitates strong and reversible cell-cell adhesion in E-cadherin deficient cells by forming mechanotransducive adherens junctions. We assess the direct influence of cell-cell adhesion strength on intracellular signaling and collective cell dynamics. This highlights the scope of DNA nanotechnology as a precision technology to study and engineer cell collectives.
Collapse
Affiliation(s)
- Andreas Schoenit
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Cellular Biophysics, Growth Factor Mechanobiology Group, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Cristina Lo Giudice
- Department
of Cellular Biophysics, Growth Factor Mechanobiology Group, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Nina Hahnen
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Cellular Biophysics, Growth Factor Mechanobiology Group, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Dirk Ollech
- Department
of Cellular Biophysics, Growth Factor Mechanobiology Group, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Kevin Jahnke
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Kerstin Göpfrich
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Elisabetta Ada Cavalcanti-Adam
- Department
of Cellular Biophysics, Growth Factor Mechanobiology Group, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| |
Collapse
|
42
|
Winterwerber P, Whitfield CJ, Ng DYW, Weil T. Multi‐Wellenlängen‐Photopolymerisation von stabilen Poly(katecholamin)‐DNA‐Origami‐Nanostrukturen**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Pia Winterwerber
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Colette J. Whitfield
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - David Y. W. Ng
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| |
Collapse
|
43
|
Chen Y, Tian R, Shang Y, Jiang Q, Ding B. Regulation of Biological Functions at the Cell Interface by DNA Nanostructures. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yongjian Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Sino-Danish College Sino-Danish Center for Education and Research University of Chinese Academy of Sciences 100049 Beijing China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience 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 CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
| |
Collapse
|
44
|
Li Y, Avis SJ, Zhang T, Kusumaatmaja H, Wang X. Tailoring the multistability of origami-inspired, buckled magnetic structures via compression and creasing. MATERIALS HORIZONS 2021; 8:3324-3333. [PMID: 34528049 DOI: 10.1039/d1mh01152a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Origami-inspired multistable structures are gaining increasing interest because of their potential applications in fields ranging from deployable structures to reconfigurable microelectronics. The multistability of such structures is critical for their applications but is challenging to manipulate due to the highly nonlinear deformations and complex configurations of the structures. Here, a comprehensive experimental and computational study is reported to tailor the multistable states of origami-inspired, buckled ferromagnetic structures and their reconfiguration paths. Using ribbon structures as an example, a design phase diagram is constructed as a function of the crease number and compressive strain. As the crease number increases from 0 to 7, the number of distinct stable states first increases and then decreases. The multistability is also shown to be actively tuned by varying the strain from 0% to 40%. Furthermore, analyzing energy barriers for reconfiguration among the stable states reveals dynamic changes in reconfiguration paths with increasing strains. Guided by studies above, diverse examples are designed and demonstrated, from programmable structure arrays to a soft robot. These studies lay out the foundation for the rational design of functional, multistable structures.
Collapse
Affiliation(s)
- Yi Li
- Department of Materials Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Samuel J Avis
- Department of Physics, Durham University, Durham, DH1 3LE, UK.
| | - Teng Zhang
- Department of Mechanical and Aerospace Engineering, BioInspired Syracuse, Syracuse University, Syracuse, NY, 13244, USA.
| | | | - Xueju Wang
- Department of Materials Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA.
- Polymer program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
45
|
Winterwerber P, Whitfield CJ, Ng DYW, Weil T. Multi-Wavelength Photopolymerization of Stable Poly(Catecholamines)-DNA Origami Nanostructures. Angew Chem Int Ed Engl 2021; 61:e202111226. [PMID: 34813135 PMCID: PMC9303804 DOI: 10.1002/anie.202111226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 11/23/2022]
Abstract
The synthesis of multicomponent polymer hybrids with nanometer precision is chemically challenging in the bottom‐up synthesis of complex nanostructures. Here, we leverage the fidelity of the DNA origami technique to install a multiple wavelength responsive photopolymerization system with nanometer resolution. By precisely immobilizing various photosensitizers on the origami template, which are only activated at their respective maximum wavelength, we can control sequential polymerization processes. In particular, the triggered photosensitizers generate reactive oxygen species that in turn initiate the polymerization of the catecholamines dopamine and norepinephrine. We imprint polymeric layers at designated positions on DNA origami, which modifies the polyanionic nature of the DNA objects, thus promoting their uptake into living cells while preserving their integrity. Our herein proposed method provides a rapid platform to access complex 3D nanostructures by customizing material and biological interfaces.
Collapse
Affiliation(s)
- Pia Winterwerber
- Max Planck Institute for Polymer Research: Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, GERMANY
| | - Colette J Whitfield
- Max Planck Institute for Polymer Research: Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, GERMANY
| | - David Y W Ng
- Max Planck Institute for Polymer Research: Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, GERMANY
| | - Tanja Weil
- Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, Ackermannweg 10, 55128, Mainz, GERMANY
| |
Collapse
|
46
|
Velas L, Brameshuber M, Huppa JB, Kurz E, Dustin ML, Zelger P, Jesacher A, Schütz GJ. Three-Dimensional Single Molecule Localization Microscopy Reveals the Topography of the Immunological Synapse at Isotropic Precision below 15 nm. NANO LETTERS 2021; 21:9247-9255. [PMID: 34709845 PMCID: PMC8587899 DOI: 10.1021/acs.nanolett.1c03160] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
T-cells engage with antigen-presenting cells in search for antigenic peptides and form transient interfaces termed immunological synapses. Synapse topography affects receptor binding rates and the mutual segregation of proteins due to size exclusion effects. It is hence important to determine the 3D topography of the immunological synapse at high precision. Current methods provide only rather coarse images of the protein distribution within the synapse. Here, we applied supercritical angle fluorescence microscopy combined with defocused imaging, which allows three-dimensional single molecule localization microscopy (3D-SMLM) at an isotropic localization precision below 15 nm. Experiments were performed on hybrid synapses between primary T-cells and functionalized glass-supported lipid bilayers. We used 3D-SMLM to quantify the cleft size within the synapse by mapping the position of the T-cell receptor (TCR) with respect to the supported lipid bilayer, yielding average distances of 18 nm up to 31 nm for activating and nonactivating bilayers, respectively.
Collapse
Affiliation(s)
- Lukas Velas
- Institute
of Applied Physics, TU Wien, 1040 Vienna, Austria
| | | | - Johannes B. Huppa
- Institute
for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology
and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elke Kurz
- Kennedy
Institute of Rheumatology, University of
Oxford, OX3 7FY Oxford, United Kingdom
| | - Michael L. Dustin
- Kennedy
Institute of Rheumatology, University of
Oxford, OX3 7FY Oxford, United Kingdom
| | - Philipp Zelger
- Division
for Biomedical Physics, Medical University
of Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Jesacher
- Division
for Biomedical Physics, Medical University
of Innsbruck, 6020 Innsbruck, Austria
| | | |
Collapse
|
47
|
DNA origami patterning of synthetic T cell receptors reveals spatial control of the sensitivity and kinetics of signal activation. Proc Natl Acad Sci U S A 2021; 118:2109057118. [PMID: 34588308 DOI: 10.1073/pnas.2109057118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 12/27/2022] Open
Abstract
Receptor clustering plays a key role in triggering cellular activation, but the relationship between the spatial configuration of clusters and the elicitation of downstream intracellular signals remains poorly understood. We developed a DNA-origami-based system that is easily adaptable to other cellular systems and enables rich interrogation of responses to a variety of spatially defined inputs. Using a chimeric antigen receptor (CAR) T cell model system with relevance to cancer therapy, we studied signaling dynamics at single-cell resolution. We found that the spatial arrangement of receptors determines the ligand density threshold for triggering and encodes the temporal kinetics of signaling activities. We also showed that signaling sensitivity of a small cluster of high-affinity ligands is enhanced when surrounded by nonstimulating low-affinity ligands. Our results suggest that cells measure spatial arrangements of ligands, translate that information into distinct signaling dynamics, and provide insights into engineering immunotherapies.
Collapse
|
48
|
Fischer LS, Schlichthaerle T, Chrostek‐Grashoff A, Grashoff C. Peptide-PAINT Enables Investigation of Endogenous Talin with Molecular Scale Resolution in Cells and Tissues. Chembiochem 2021; 22:2872-2879. [PMID: 34286903 PMCID: PMC8518977 DOI: 10.1002/cbic.202100301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/16/2021] [Indexed: 11/12/2022]
Abstract
Talin is a cell adhesion molecule that is indispensable for the development and function of multicellular organisms. Despite its central role for many cell biological processes, suitable methods to investigate the nanoscale organization of talin in its native environment are missing. Here, we overcome this limitation by combining single-molecule resolved PAINT (points accumulation in nanoscale topography) imaging with the IRIS (image reconstruction by integrating exchangeable single-molecule localization) approach, enabling the quantitative analysis of genetically unmodified talin molecules in cells. We demonstrate that a previously reported peptide can be utilized to specifically label the two major talin isoforms expressed in mammalian tissues with a localization precision of <10 nm. Our experiments show that the methodology performs equally well as state-of-the-art single-molecule localization techniques, and the first applications reveal a thus far undescribed cell adhesion structure in differentiating stem cells. Furthermore, we demonstrate the applicability of this peptide-PAINT technique to mouse tissues paving the way to single-protein imaging of endogenous talin proteins under physiologically relevant conditions.
Collapse
Affiliation(s)
- Lisa S. Fischer
- Department of Quantitative Cell BiologyInstitute of Molecular Cell BiologyUniversity of MünsterSchlossplatz 5Münster48149Germany
| | - Thomas Schlichthaerle
- Department of BiochemistryUniversity of WashingtonSeattleWA 98195USA
- Institute for Protein DesignUniversity of WashingtonSeattleWA 98195USA
| | - Anna Chrostek‐Grashoff
- Department of Quantitative Cell BiologyInstitute of Molecular Cell BiologyUniversity of MünsterSchlossplatz 5Münster48149Germany
| | - Carsten Grashoff
- Department of Quantitative Cell BiologyInstitute of Molecular Cell BiologyUniversity of MünsterSchlossplatz 5Münster48149Germany
| |
Collapse
|
49
|
Knappe GA, Wamhoff EC, Read BJ, Irvine DJ, Bathe M. In Situ Covalent Functionalization of DNA Origami Virus-like Particles. ACS NANO 2021; 15:14316-14322. [PMID: 34490781 PMCID: PMC8628367 DOI: 10.1021/acsnano.1c03158] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DNA origami is a powerful nanomaterial for biomedical applications due in part to its capacity for programmable, site-specific functionalization. To realize these applications, scalable and efficient conjugation protocols are needed for diverse moieties ranging from small molecules to biomacromolecules. Currently, there are no facile and general methods for in situ covalent modification and label-free quantification of reaction conversion. Here, we investigate the postassembly functionalization of DNA origami and the subsequent high-performance liquid chromatography-based characterization of these nanomaterials. Following this approach, we developed a versatile DNA origami functionalization and characterization platform. We observed quantitative in situ conversion using widely accessible click chemistry for carbohydrates, small molecules, peptides, polymers, and proteins. This platform should provide broader access to covalently functionalized DNA origami, as illustrated here by PEGylation for passivation and HIV antigen decoration to construct virus-like particle vaccines.
Collapse
Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Benjamin J. Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Darrell J. Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States of America
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to
| |
Collapse
|
50
|
Hellmeier J, Platzer R, Mühlgrabner V, Schneider MC, Kurz E, Schütz GJ, Huppa JB, Sevcsik E. Strategies for the Site-Specific Decoration of DNA Origami Nanostructures with Functionally Intact Proteins. ACS NANO 2021; 15:15057-15068. [PMID: 34463486 PMCID: PMC8482763 DOI: 10.1021/acsnano.1c05411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/26/2021] [Indexed: 05/14/2023]
Abstract
DNA origami structures provide flexible scaffolds for the organization of single biomolecules with nanometer precision. While they find increasing use for a variety of biological applications, the functionalization with proteins at defined stoichiometry, high yield, and under preservation of protein function remains challenging. In this study, we applied single molecule fluorescence microscopy in combination with a cell biological functional assay to systematically evaluate different strategies for the site-specific decoration of DNA origami structures, focusing on efficiency, stoichiometry, and protein functionality. Using an activating ligand of the T-cell receptor (TCR) as the protein of interest, we found that two commonly used methodologies underperformed with regard to stoichiometry and protein functionality. While strategies employing tetravalent wildtype streptavidin for coupling of a biotinylated TCR-ligand yielded mixed populations of DNA origami structures featuring up to three proteins, the use of divalent (dSAv) or DNA-conjugated monovalent streptavidin (mSAv) allowed for site-specific attachment of a single biotinylated TCR-ligand. The most straightforward decoration strategy, via covalent DNA conjugation, resulted in a 3-fold decrease in ligand potency, likely due to charge-mediated impairment of protein function. Replacing DNA with charge-neutral peptide nucleic acid (PNA) in a ligand conjugate emerged as the coupling strategy with the best overall performance in our study, as it produced the highest yield with no multivalent DNA origami structures and fully retained protein functionality. With our study we aim to provide guidelines for the stoichiometrically defined, site-specific functionalization of DNA origami structures with proteins of choice serving a wide range of biological applications.
Collapse
Affiliation(s)
| | - René Platzer
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Vanessa Mühlgrabner
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | | | - Elke Kurz
- Kennedy
Institute of Rheumatology, University of
Oxford, Oxford, OX3 7FY, U.K.
| | | | - Johannes B. Huppa
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Eva Sevcsik
- Institute
of Applied Physics, TU Wien, Vienna, 1060, Austria
| |
Collapse
|