Role of nanoscale antigen organization on B-cell activation probed using DNA origami

Functionalization of Nucleic Acid Molecular Machines under Physiological Conditions: A Review

In-situ fabrication of nucleic acid molecular machines in biological environments is desirable for smart theranostic applications. However, given the complex nature of biological environments, the integration of multiple functional modules into a coordinated machine remains challenging. Recent advances in nucleic acid nanotechnology offer solutions to these challenges. Here, we outline design principles for nucleic acid-based molecular machines tailored for physiological conditions, drawing on recent examples. We review cutting-edge technologies that facilitate their functionalization in physiological settings, particularly presynthesis modifications using unnatural bases and postsynthesis functionalization via bioorthogonal chemistry and noncovalent biological interactions. We discuss the advantages and limitations of these technologies and suggest future directions to overcome existing challenges.

Heterovalent Click Reactions on DNA Origami

Nucleic acid nanoparticles (NANPs) fabricated by using the DNA origami method have broad utility in materials science and bioengineering. Their site-specific, heterovalent functionalization with secondary molecules such as proteins or fluorophores is a unique feature of this technology that drives its utility. Currently, however, there are few chemistries that enable fast, efficient covalent functionalization of NANPs with a broad conjugate scope and heterovalency. To address this need, we introduce synthetic methods to access inverse electron-demand Diels-Alder chemistry on NANPs. We demonstrate a broad conjugate scope, characterize application-relevant kinetics, and integrate this new chemistry with strain-promoted azide-alkyne cycloaddition chemistry to enable heterovalent click reactions on NANPs. We applied these chemistries to formulate a prototypical chemical countermeasure against chemical nerve agents. We envision this additional chemistry finding broad utility in the synthetic toolkit accessible to the nucleic acid nanotechnology community.

DNA as a Promising Biomaterial for Bone Regeneration and Potential Mechanisms of Action

DNA nanotechnology has created new possibilities for the use of DNA in tissue regeneration - an important advance for DNA use beyond its paradigmatic role as the hereditary biomacromolecule. Biomaterials containing synthetic or natural DNA have been proposed for several applications including drug and gene delivery, and more recently, as osteoconductive biomaterials. This review provides an in-depth discussion of studies that have used DNA-based materials for biomineralization and/or bone repair, with expansion on the topic of DNA hydrogels specifically, and the advantages they offer for advancing the field of bone regeneration. Four mechanisms of action for the osteoconductive capabilities of DNA-based materials are discussed, and a proposed model for degradation of these materials and its link to their osteoconductive properties is later presented. Finally, the review considers current limitations of DNA-based materials and summarizes important aspects that need to be addressed for future application of DNA nanotechnology in tissue repair. STATEMENT OF SIGNIFICANCE: Herein we summarize the developing field of DNA-based materials for biomineralization and bone repair, with a focus on DNA hydrogels. We first provide a comprehensive review of different forms of DNA-based materials described thus far which have been shown to enhance bone repair and mineralization (namely DNA coatings, DNA-containing pastes, DNA nanostructures and DNA hydrogels). Next, we describe four different mechanisms by which DNA-based materials could be exerting their osteogenic effect. Then, we propose a novel model that links DNA degradation and osteoconductivity. Lastly, we suggest future research directions to enhance DNA-based materials for future clinical application. The suggested mechanisms and the proposed model can guide future research to better understand how DNA functions as a mineral- and bone-promoting molecule.

Logic-Gated Modulation of Cell Migration via Mesoscale Mechanical Uncaging Effects

Mesoscopic objects ranging from molecular machinery to cells are prevalent in nature. Unlike atomic and nanoscopic objects that do not have pronounced mechanical properties due to their small sizes, mesoscale substances demonstrate their unique mechanical features that can interfere with cell functions, particularly those with a mechanical nature such as cell migrations. Here, we demonstrate mechanical caging/uncaging effects in a DNA origami nanospring system that precisely controls cancer cell migrations. By leveraging DNA as a programming language, our work demonstrates the creation of logic gates (Boolean AND and OR gates) responsive to various miRNA inputs, resulting in mechanical and structural changes in DNA origami nanosprings serving as processors, which uncage the arginyl-glycyl-aspartate (RGD) ligands to interact with integrins on the cell membrane surface. The mechanical uncaging effect inhibits the migration of cancer cells. The strategy can be readily harnessed for targeted drug delivery with minimal off-target effects. Our proof-of-concept mesoscale DNA origami self-assembly highlights the potential for exquisite multimodal control of mechanical functions of cells with future applications in synthetic biology and precision medicine.

DNA origami vaccines program antigen-focused germinal centers

Recruitment and expansion of rare precursor B cells in germinal centers (GCs) is a central goal of vaccination to generate broadly neutralizing antibodies (bnAbs) against challenging pathogens such as HIV. Multivalent immunogen display is a well-established method to enhance vaccine-induced B cell responses, typically accomplished by using natural or engineered protein scaffolds. However, these scaffolds themselves are targets of antibody responses, with the potential to generate competitor scaffold-specific B cells that could theoretically limit expansion and maturation of "on-target" B cells in the GC response. Here, we rationally designed T-independent, DNA-origami based virus-like particles (VLPs) with optimal antigenic display of the germline targeting HIV Env immunogen, eOD-GT8, and appropriate T cell help to achieve a potent GC response. In preclinical mouse models, these DNA-VLPs expanded significantly higher frequencies of epitope-specific GC B cells compared with a state-of-the-art clinical protein nanoparticle. Optimized DNA-VLPs primed germinal centers focused on the target antigen and rapidly expanded subdominant broadly neutralizing antibody precursor B cells for HIV with a single immunization. Thus, avoiding scaffold-specific responses augments priming of bnAb precursor B cells, and DNA-VLPs are a promising platform for promoting B cell responses towards challenging subdominant epitopes.

SARS-CoV-2 B Epitope-Guided Neoantigen NanoVaccines Enhance Tumor-Specific CD4/CD8 T Cell Immunity through B Cell Antigen Presentation

Current neoantigen cancer vaccines activate T cell immunity through dendritic cell/macrophage-mediated antigen presentation. It is unclear whether incorporating B cell-mediated antigen presentation into current neoantigen vaccines could enhance CD4/CD8 T cell immunity to improve their anticancer efficacy. We developed SARS-CoV-2 B cell epitope-guided neoantigen peptide/mRNA cancer nanovaccines (BSARSTNeoAgVax) to improve anticancer efficacy by enhancing tumor-specific CD4/CD8 T cell antitumor immunity through B cell-mediated antigen presentation. BSARSTNeoAgVax cross-linked with B cell receptor, promoted SARS-CoV-2 B cell-mediated antigen presentation to tumor-specific CD4 T cells, increased tumor-specific follicular/nonfollicular CD4 T cells, and enhanced B cell-dependent tumor-specific CD8 T cell immunity. BSARSTNeoAgVax achieved superior efficacy in melanoma, pancreatic, and breast cancer models compared with the current neoantigen vaccines. Our study provides a universal platform, SARS-CoV-2 B epitope-guided neoantigen nanovaccines, to improve anticancer efficacy against various cancer types by enhancing CD4/CD8 T cell antitumor immunity through viral-specific B cell-mediated antigen presentation.

Dynamics and activation of membrane-bound B cell receptor assembly

B-cell receptor (BCR) complexes are expressed on the surface of a B-cell and are critical in antigen recognition and modulating the adaptive immune response. Even though the relevance of antibodies has been known for almost a hundred years, the antigen-dependent activation mechanism of B-cells has remained elusive. Several models have been proposed for BCR activation, including cross-linking, conformation-induced oligomerization, and dissociation activation models. Recently, the first cryo-EM structures of the human B-cell antigen receptor of the IgM and IgG isotypes have been published that validates the asymmetric organization of the BCR complex. Here, we carry out extensive molecular dynamics simulations to probe the conformational changes upon antigen binding and the influence of the membrane lipids. We identify two critical dynamical events that could be associated with antigen-dependent activation of BCR. First, antigen binding causes increased flexibility in regions distal to the antigen binding site. Second, antigen binding alters the rearrangement of IgM transmembrane helices, including the relative interaction of Igα/Igβ that mediates intracellular signaling. Furthermore, these transmembrane rearrangements lead to changes in localized lipid composition. Our work indirectly supports the conformational-change induced models of BCR activation and contributes to the understanding of the antigen-dependent activation mechanism of BCRs.

Tailoring DNA Origami Protection: A Study of Oligolysine-PEG Coatings for Improved Colloidal, Structural, and Functional Integrity

Application of protective polymer coatings to enhance the biostability of DNA-based nanomaterials (DONs) has become common practice in in vitro and in vivo experiments. While the functional effect of these coatings is obvious, a detailed molecular picture of what is protected and for how long remains unclear. Additionally, the use of the oligolysine-1kPEG protective polymer has been limited due to aggregation issues. In this study, we evaluated the colloidal stability, structural integrity, and functional preservation of DONs coated with oligolysine (K)-1k/5kPEG block copolymers. Dynamic light scattering and transmission electron microscopy were employed to assess colloidal stability before and after degradation. A FRET-based assay was developed to monitor the directionality of degradation, while quantitative PCR measured the protection of functional DNA handles, crucial for the design of ligand-functionalized DONs. Our results show that K10-1kPEG, while prone to aggregation, can offer similar protection against nucleases as K10-5kPEG, provided buffer conditions are carefully chosen. Maintaining the colloidal, structural, and functional stability before and after nuclease exposure supports DON applications, particularly at the biointerface. These insights provide valuable guidelines for selecting the most effective protection strategy and enhancing DON functionality across diverse biological environments.

Fully addressable designer superstructures assembled from one single modular DNA origami

DNA nanotechnology and especially the DNA origami method are primal tools to create precise nanoscale objects. For DNA origami, a long ssDNA scaffold strand is folded by a multitude of smaller staple strands into base-pair accurate shapes, allowing for precise modification and incorporation of guest molecules. However, DNA origami are limited in size, and thus is the area that can be controlled with nanoscale precision. Prior methods of creating larger assemblies were either costly or lacked structural control. Here, we incorporate two methods of modularity into one exemplary modular DNA origami (moDON). The modularity allows for the creation of over 50,000 diverse monomers and subsequently the assembly of a plethora of fully addressable designer superstructures while keeping the construction cost very low. The here-introduced methods for modularity in DNA origami design offer an efficient, cost-effective solution for constructing precisely organized, and fully addressable structures on a variety of scales.

Recent Advances in DNA-Templated Protein Patterning

In recent decades, the advancement of DNA nanotechnology enables precise nanoscale organization of diverse functional materials with DNA templates. Particularly, a variety of DNA-templated protein patterns are constructed as powerful tools for programming biomimetic protein complexes. In this review, recent progress in DNA-templated protein patterning, including cutting-edge methods for arranging proteins with DNA templates, and protein patterns across varying dimensions are briefly summarized. Representative applications in biological analysis and biomedicine are discussed. DNA-protein patterns with programmable dynamics, which hold promise in precision diagnosis and therapeutics are highlighted. Finally, current challenges and opportunities in the fabrication and application of DNA-templated protein pattering are discussed.

Longitudinal phage-bacteria dynamics in the early life gut microbiome

Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.

Towards a unifying model for B-cell receptor triggering

Antibodies are exceptionally versatile molecules with remarkable flexibility in their binding properties. Their natural targets range from small-molecule toxins, across viruses of different sizes, to bacteria and large multicellular parasites. The molecular determinants bound by antibodies include proteins, peptides, carbohydrates, nucleic acids, lipids and even synthetic molecules that have never existed in nature. Membrane-anchored antibodies also serve as receptors on the surface of the B cells that produce them. Despite recent structural insights, there is still no unifying molecular mechanism to explain how antibody targets (antigens) trigger the activation of these B-cell receptors (BCRs). After cognate antigen encounter, somatic hypermutation and class-switch recombination allow BCR affinity maturation and immunoglobulin class-specific responses, respectively. This raises the fundamental question of how one receptor activation mechanism can accommodate a plethora of variant receptors and ligands, and how it can ensure that individual B cells remain responsive to antigen after somatic hypermutation and class switching. There is still no definite answer. Here we give a brief historical account of the different models proposed to explain BCR triggering and discuss their merit in the context of the current knowledge of the structure of BCRs, their dynamic membrane distribution, and recent biochemical and cell biological insights.

DNA Nanostructures-Based In Situ Cancer Vaccines: Mechanisms and Applications

Current tumor vaccines suffer from inadequate immune responsive due to the insufficient release of tumor antigens, low tumor infiltration, and immunosuppressive microenvironment. DNA nanostructures with their ability to precisely engineer, controlled release, biocompatibility, and the capability to augment the immunogenicity of tumor microenvironment, have gained significant attention for their potential to revolutionize vaccine designing. This review summarizes various applications of DNA nanostructures in the construction of in situ cancer vaccines, which can generate tumor-associated antigens directly from damaged tumors for cancer immune-stimulation. The mechanisms and components of cancer vaccines are listed, the specific strategies for constructing in situ vaccines using DNA nanostructures are explored and their underlying mechanisms of action are elucidated. The immunogenic cell death (ICD) induced by chemotherapeutic agents, photothermal therapy (PTT), photodynamic therapy (PDT), and radiation therapy (RT) and the related cancer vaccines building strategies are systematically summarized. The applications of different DNA nanostructures in various cancer immunotherapy are elaborated, which exerts precise, long-lasting, and robust immune responses. The current challenges and future prospectives are proposed. This review provides a holistic understanding of the evolving role of DNA nanostructures for in situ vaccine development.

Patterned Antigens on DNA Origami Controls the Structure and Cellular Uptake of Immune Complexes

Immune complexes (ICs), formed via antibody (Ab)-antigen (Ag) binding, trigger diverse immune responses, which are critical for natural immunity and have uses for vaccines and immunotherapies. While IC-elicited immune responses depend on its structure, existing methods for IC synthesis produce heterogeneous assemblies, which limits control over their cellular interactions and pharmacokinetics. In this study, we demonstrate the use of DNA origami to create synthetic ICs with defined shape, size, and solubility by displaying Ags in prescribed spatial patterns. We find that Ag arrangement relative to the spatial tolerance of IgG Fab arms (∼13-18 nm) determines IC formation into "monomeric" versus "multimeric" regimes. When Ag spacing matches Fab arm tolerance, ICs are exclusively monomeric, while spacing mismatches favor the formation of multimeric ICs. Within each IC regime, parameters such as the number of Ags and Ab-Ag ratios, as well as DNA origami shape, further fine-tune IC size, shape, and Fc valency. These parameters influenced IC interactions with FcγR-expressing immune cells, with uptake by macrophages showing greater sensitivity to IC cross-linking while dendritic cells were more responsive to Ab valency. Our findings thus provide design principles for controlling the structure and cellular interactions of synthetic ICs and highlight DNA origami-scaffolded ICs as a programmable platform for investigating IC immunology and developing FcγR-targeted therapeutics and vaccines.

Genetically Encoded Nucleic Acid Nanostructures for Biological Applications

Nucleic acid, as a carrier of genetic information, has been widely employed as a building block for the construction of versatile nanostructures with pre-designed sizes and shapes through complementary base pairing. With excellent programmability, addressability, and biocompatibility, nucleic acid nanostructures are extensively applied in biomedical researches, such as bio-imaging, bio-sensing, and drug delivery. Notably, the original gene-encoding capability of the nucleic acids themselves has been utilized in these structurally well-defined nanostructures. In this review, we will summarize the recent progress in the design of double-stranded DNA and mRNA-encoded nanostructures for various biological applications, such as gene regulation, gene expression, and mRNA transcription. Furthermore, the challenges and future opportunities of genetically encoded nucleic acid nanostructures in biomedical applications will be discussed.

Noncovalently Bridging Cell-Surface Proteins Using Synthetic Peptides to Modulate Cell Apoptosis

Controlled high-order clustering of cell-surface proteins is an essential but unmatched regulatory mechanism in living systems for the modulation of cell behavior. Here, we present a strategy for generating extended and tunable one-dimensional clusters of death receptors on live cell surfaces by employing synthetic peptides to noncovalently bridging the proteins. The on-cell assembly process is validated through super-resolution fluorescence imaging and fluorescence lifetime imaging analyses. By adjusting the number of spacing peptides between the receptors before and even after the cluster formation, receptor separation can be precisely varied at nanoscale to drive cells into apoptotic or antiapoptotic states. Remarkably, this approach results in higher levels of cell apoptosis compared to the conventional practice of using preformed ligand-appended peptide coassemblies. These results demonstrate that in situ fabrication of cell-interfacing materials with compositional control permits robust and effective manipulation of high-order clustering of cell-surface proteins, advancing our ability to regulate cell behavior.

A Highly Tumor-Permeating DNA Nanoplatform for Efficient Remodeling of Immunosuppressive Tumor Microenvironments

The immunosuppressive tumor microenvironment and limited intratumoral permeation have largely constrained the outcome of tumor therapy. Herein, we report a tailored DNA structure-based nanoplatform with striking tumor-penetrating capability for targeted remodeling of the immunosuppressive tumor microenvironment in vivo. In our design, chemo-immunomodulator (gemcitabine) can be precisely grafted on DNA sequences through a reactive oxygen species (ROS)-sensitive linker. After self-assembly, the gemcitabine-grafted DNA structure can site-specifically organize legumain-activatable melittin pro-peptide (promelittin) on each vertex for intratumoral delivery and further function as the template to load photosensitizers (methylene blue) for ROS production. The tailored DNA nanoplatform can achieve targeted accumulation, highly improved intratumoral permeation, and efficient immunogenic cell death of tumor cells by laser irradiation. Finally, the immunosuppressive tumor microenvironment can be successfully remodeled by reducing multi-type immunosuppressive cells and enhancing the infiltration of cytotoxic lymphocytes in the tumor. This rationally developed multifunctional DNA nanoplatform provides a new avenue for the development of tumor therapy.

Nanoparticles in Subunit Vaccines: Immunological Foundations, Categories, and Applications

Subunit vaccines, significant in next-generation vaccine development, offer precise targeting of immune responses by focusing on specific antigens. However, this precision often comes at the cost of eliciting strong and durable immunity, posing a great challenge to vaccine design. To address this limitation, recent advancements in nanoparticles (NPs) are utilized to enhance antigen delivery efficiency and boost vaccine efficacy. This review examines how the physicochemical properties of NPs influence various stages of the immune response during vaccine delivery and analyzes how different NP types contribute to immune activation and enhance vaccine performance. It then explores the unique characteristics and immune activation mechanisms of these NPs, along with their recent advancements, and highlights their application in subunit vaccines targeting infectious diseases and cancer. Finally, it discusses the challenges in NP-based vaccine development and proposes future directions for innovation in this promising field.

Raman Imaging of Targeted Drug Delivery with DNA-Based Nano-Optical Devices

Raman spectroscopy (RS) has emerged as a novel optical imaging modality by identifying molecular species through their bond vibrations, offering high specificity and sensitivity in molecule detection. However, its application in intracellular molecular probing has been limited due to challenges in combining vibrational tags with functional probes. DNA nanostructures, known for their high programmability, have been instrumental in fields like biomedicine and nanofabrication. So far, their ability to customize Raman signals remains largely untapped. In this study, a new class of Raman active DNA origami-based hybrid nanodevice (ND) for targeted cancer cell drug delivery and imaging is engineered. The ND is specifically engineered for metastatic prostate cancer treatment, featuring a legumain enzyme-responsive sequence for the controlled release of the chemotherapeutic agent doxorubicin. Integrating RS with precise targeting, the ND enables imaging of aggressive cancer cells and efficient drug delivery with minimal off-target effects. The developed device offers stimuli-responsive behavior, enhanced stability, exceptional tunability, and potent targeting abilities, positioning it as a highly promising strategy for advancing precision cancer imaging and therapy.

Plugging synthetic DNA nanoparticles into the central dogma of life

Synthetic DNA nanotechnology has emerged as a powerful tool for creating precise nanoscale structures with diverse applications in biotechnology and materials science. Recently, it has evolved to include gene-encoded DNA nanoparticles, which have potentially unique advantages compared to alternative gene delivery platforms. In exciting new developments, we and others have shown how the long single strand within DNA origami nanoparticles, the scaffold strand, can be customized to encode protein-expressing genes and engineer nanoparticles that interface with the transcription-translation machinery for protein production. Remarkably, therefore, DNA nanoparticles - despite their complex three-dimensional shapes - can function as canonical genes. Characteristics such as potentially unlimited gene packing size and low immunogenicity make DNA-based platforms promising for a variety of gene therapy applications. In this review, we first outline various techniques for the isolation of the gene-encoded scaffold strand, a crucial precursor for building protein-expressing DNA nanoparticles. Next, we highlight how features such as sequence design, staple strand optimization, and overall architecture of gene-encoded DNA nanoparticles play a key role in the enhancement of protein expression. Finally, we discuss potential applications of these DNA origami structures to provide a comprehensive overview of the current state of gene-encoded DNA nanoparticles and motivate future directions.

Constructing protein-functionalized DNA origami nanodevices for biological applications

In living systems, proteins participate in various physiological processes and the clustering of multiple proteins is essential for efficient signaling. Therefore, understanding the effects of the number, distance and orientation of proteins is of great significance. With programmability and addressability, DNA origami technology has enabled fabrication of sophisticated nanostructures with precise arrangement and orientation control of proteins to investigate the effects of these parameters on protein-involved cellular processes. Herein, we highlight the construction and applications of protein-functionalized DNA origami nanodevices. After the introduction of the structural design principles of DNA origami and the strategies of protein-DNA conjugation, the emerging applications of protein-functionalized DNA origami nanodevices with controlled key parameters are mainly discussed, including the regulation of enzyme cascade reactions, modulation of cellular behaviours, drug delivery therapy and protein structural analysis. Finally, the current challenges and potential directions of protein-functionalized DNA origami nanodevices are also presented, advancing their applications in biomedicine, cell biology and structural biology.

Cargo Quantification of Functionalized DNA Origami for Therapeutic Application

In recent years, notable advances in nanotechnology-based drug delivery have emerged. A particularly promising platform in this field is DNA origami-based nanoparticles, which offer highly programmable surfaces, providing precise control over the nanoscale spacing and stoichiometry of various cargo. These versatile particles are finding diverse applications ranging from basic molecular biology to diagnostics and therapeutics. This growing interest creates the need for effective methods to quantify cargo on DNA origami nanoparticles. The study consolidates several previously validated methods focusing on gel-based and fluorescence-based techniques, including multiplexed quantification of protein, peptide, and nucleic acid cargo on these nanoparticles. In this work, how gel band intensity and nanodrop fluorescence readings can be used to quantify protein, peptide, and RNA cargo on a DNA origami nanoparticle is demonstrated. This work may serve as a valuable resource for groups of researchers keen on utilizing DNA origami-based nanoparticles in therapeutic applications.

Toward Precise Fabrication of Finite-Sized DNA Origami Superstructures

DNA origami enables the precise construction of 2D and 3D nanostructures with customizable shapes and the high-resolution organization of functional materials. However, the size of a single DNA origami is constrained by the length of the scaffold strand, and since its inception, scaling up the size and complexity has been a persistent pursuit. Hierarchical self-assembly of DNA origami units offers a feasible approach to overcome the limitation. Unlike periodic arrays, finite-sized DNA origami superstructures feature well-defined structural boundaries and uniform dimensions. In recent years, increasing attention has been directed toward precise control over the hierarchical self-assembly of DNA origami structures and their applications in fields such as nanophotonics, biophysics, and material science. This review summarizes the strategies for fabricating finite-sized DNA origami superstructures, including heterogeneous self-assembly, self-limited self-assembly, and templated self-assembly, along with a comparative analysis of the advantages and limitations of each approach. Subsequently, recent advancements in the application of these structures are discussed from a structure design perspective. Finally, an outlook on the current challenges and potential future directions is provided, highlighting opportunities for further research and development in this rapidly evolving field.

DNA Nanostructures: Advancing Cancer Immunotherapy

Cancer immunotherapy is a groundbreaking medical revolution and a paradigm shift from traditional cancer treatments, harnessing the power of the immune system to target and destroy cancer cells. In recent years, DNA nanostructures have emerged as prominent players in cancer immunotherapy, exhibiting immense potential due to their controllable structure, surface addressability, and biocompatibility. This review provides an overview of the various applications of DNA nanostructures, including scaffolded DNA, DNA hydrogels, tetrahedral DNA nanostructures, DNA origami, spherical nucleic acids, and other DNA-based nanostructures in cancer immunotherapy. These applications explore their roles in vaccine development, immune checkpoint blockade therapies, adoptive cellular therapies, and immune-combination therapies. Through rational design and optimization, DNA nanostructures significantly bolster the immunogenicity of the tumor microenvironment by facilitating antigen presentation, T-cell activation, tumor infiltration, and precise immune-mediated tumor killing. The integration of DNA nanostructures with cancer therapies ushers in a new era of cancer immunotherapy, offering renewed hope and strength in the battle against this formidable foe of human health.

Advanced technologies for the development of infectious disease vaccines

Vaccines play a critical role in the prevention of life-threatening infectious disease. However, the development of effective vaccines against many immune-evading pathogens such as HIV has proven challenging, and existing vaccines against some diseases such as tuberculosis and malaria have limited efficacy. The historically slow rate of vaccine development and limited pan-variant immune responses also limit existing vaccine utility against rapidly emerging and mutating pathogens such as influenza and SARS-CoV-2. Additionally, reactogenic effects can contribute to vaccine hesitancy, further undermining the ability of vaccination campaigns to generate herd immunity. These limitations are fuelling the development of novel vaccine technologies to more effectively combat infectious diseases. Towards this end, advances in vaccine delivery systems, adjuvants, antigens and other technologies are paving the way for the next generation of vaccines. This Review focuses on recent advances in synthetic vaccine systems and their associated challenges, highlighting innovation in the field of nano- and nucleic acid-based vaccines.

Navarro E, Fong N, Douglas SM. Design principles for accurate folding of DNA origami

We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate design rules, we reduced the problem of DNA strand routing to the known problem of shortest-path finding in a weighted graph. To score candidate DNA strand routes we used a thermodynamic model that accounts for enthalpic and entropic contributions of initial binding, hybridization, and DNA loop closure. We encoded and analyzed new and previously reported design heuristics. Using design principles emerging from this analysis, we redesigned and fabricated multiple shapes and compared their folding accuracy using electrophoretic mobility analysis and electron microscopy imaging. Redesigned shapes showed 6- to 30-fold improvements in yield compared to original designs. We demonstrate accurate folding can be achieved by optimizing staple routes using our model and provide a computational framework for applying our methodology to any design.

Anti-HIV-1 B cell antigen receptor signaling and structure

The B cell antigen receptor (BCR) complex, comprised of antigen recognition and signaling components, functions in initiating B cell activation. While structural studies have described BCR domain organization, gaps remain in our understanding of its antigen binding domain (Fab, fragment antigen-binding) disposition, and how antigen binding is sensed to initiate signaling. Here, we report antigen affinity and signaling of the immunoglobulin (Ig) class IgM and IgG BCRs and define conformational states of full-length BCRs of two human broadly neutralizing antibodies, the glycan-specific, heavy chain domain-swapped, I-shaped 2G12, and a canonical Y-shaped antibody, CH31, that recognizes the CD4-binding site on the HIV-1 Envelope protein (Env). The BCRs adopted the shapes (I or Y) of their respective soluble antibodies, and both Ig class of BCRs of the same specificity bound Env trimers with similar affinities. We observed antigen-valenc y dependent differential signaling by the 2G12 IgM and IgG BCRs with trimeric Envs. Cryo-electron microscopy of the 2G12 IgG and CH31 IgM BCRs revealed varied Fab orientations. Structural comparisons revealed hinge points and regions of flexibility in the BCRs suggesting a highly dynamic structure of the BCR complex. Taken together, our results provide an integrated understanding of BCR structure, conformation, antigen recognition and signaling, and provide the basis for understanding antigen induced BCR signal transmission.

One Sentence Summary

Cryo-electron microscopy structures of full-length B cell antigen receptor complex provide a novel dynamic BCR model and a basis for understanding antigen binding induced signal transmission.

Rationally designed multimeric nanovaccines using icosahedral DNA origami for display of SARS-CoV-2 receptor binding domain

Multivalent antigen display on nanoparticles can enhance the immunogenicity of nanovaccines targeting viral moieties, such as the receptor binding domain (RBD) of SARS-CoV-2. However, particle morphology and size of current nanovaccines are significantly different from those of SARS-CoV-2. Additionally, surface antigen patterns are not controllable to enable the optimization of B cell activation. Herein, we employ an icosahedral DNA origami (ICO) as a display particle for RBD nanovaccines, achieving morphology and diameter like the virus (91 ± 11 nm). The surface addressability of DNA origami permits facile modification of the ICO surface with numerous RBD antigen clusters (ICO-RBD) to form various antigen patterns. Using an in vitro screening system, we demonstrate that the antigen spacing, antigen copies within clusters and cluster number parameters of the surface antigen pattern all impact the ability of the nanovaccines to activate B cells. Importantly, the optimized ICO-RBD nanovaccines evoke stronger and more enduring humoral and T cell immune responses in female mouse models compared to soluble RBD antigens, and the multivalent display broaden the protection range of B cell responses to more mutant strains. Our vaccines activate similar humoral immunity, observable stronger cellular immunity and more memory immune cells compared to trimeric mRNA vaccines.

Bottom-up synthetic immunology

Infectious diseases and cancer evade immune surveillance using similar mechanisms. Targeting immune mechanisms using common strategies thus represents a promising avenue to improve prevention and treatment. Synthetic immunology can provide such strategies by applying engineering principles from synthetic biology to immunology. Synthetic biologists engineer cells by top-down genetic manipulation or bottom-up assembly from nanoscale building blocks. Recent successes in treating advanced tumours and diseases using genetically engineered immune cells highlight the power of the top-down synthetic immunology approach. However, genetic immune engineering is mostly limited to ex vivo applications and is subject to complex counter-regulation inherent to immune functions. Bottom-up synthetic biology can harness the rich nanotechnology toolbox to engineer molecular and cellular systems from scratch and equip them with desired functions. These are beginning to be tailored to perform targeted immune functions and should hence allow intervention strategies by rational design. In this Perspective we conceptualize bottom-up synthetic immunology as a new frontier field that uses nanotechnology for crucial innovations in therapy and the prevention of infectious diseases and cancer.

Engineered protein subunit COVID19 vaccine is as immunogenic as nanoparticles in mouse and hamster models

Initial studies on the immunogenicity of SARS-CoV-2 (CoV-2) S glycoprotein ("spike") as a protein subunit vaccine suggested sub-optimal efficacy in mammals. Although protein engineering efforts have produced CoV-2 spike protein sequences with greatly improved immunogenicity, additional strategies for improving the immunogenicity of CoV-2 protein subunit vaccines are scaffolding and the use of adjuvants. Comparisons of the effectiveness of engineered protein-only and engineered protein-nanoparticles vaccines have been rare. To explore this knowledge gap, we inoculated mice with two doses of either sequence-optimized trimeric spike protein or one of several sequence-optimized spike nanoparticles. We measured their immune response up to two months after the first dose. We also measured the immune response and protection against live virus in hamsters inoculated with either sequence-optimized trimeric spike protein or a liposome-based sequence-optimized spike nanoparticle. We found that in the presence of adjuvant, the antibody and neutralization titers elicited by spike-nanoparticles were not significantly greater than those elicited by spike-only in mice, even at doses as low as 0.1 µg/animal. Hamsters vaccinated with spike-only or spike-nanoparticles were equally protected from live virus one month after their first inoculation. These results suggest that sequence-optimized protein subunit vaccines in the form of individual prefusion-stabilized trimers can be as effective in improving immunogenicity as scaffolded forms.

Coupling of Spectrin Repeat Modules for the Assembly of Nanorods and Presentation of Protein Domains

Modular protein engineering is a powerful approach for fabricating high-molecular-weight assemblies and biomaterials with nanoscale precision. Herein, we address the challenge of designing an extended nanoscale filamentous architecture inspired by the central rod domain of human dystrophin, which protects sarcolemma during muscle contraction and consists of spectrin repeats composed of three-helical bundles. A module of three tandem spectrin repeats was used as a rigid building block self-assembling via coiled-coil (CC) dimer-forming peptides. CC peptides were precisely integrated to maintain the spectrin α-helix continuity in an appropriate frame to form extended nanorods. An orthogonal set of customizable CC heterodimers was harnessed for modular rigid domain association, which could be additionally regulated by metal ions and chelators. We achieved a robust assembly of rigid rods several micrometers in length, determined by atomic force microscopy and negative stain transmission electron microscopy. Furthermore, these rigid rods can serve as a scaffold for the decoration of diverse proteins or biologically active peptides along their length with adjustable spacing up to tens of nanometers, as confirmed by the DNA-PAINT super-resolution microscopy. This demonstrates the potential of modular bottom-up protein engineering and tunable CCs for the fabrication of functionalized protein biomaterials.

Domínguez C. Fluidic Interface for Surface-based DNA Origami Studies

Traditionally, the use of DNA origami nanostructures (DONs) to study early cell signaling processes has been conducted using standard laboratory equipment with DONs typically utilized in solution. Surface-based technologies simplify the microscopic analysis of cells treated with DON agents by anchoring them to solid substrates, thus avoiding the complications of receptor-mediated endocytosis. A robust microfluidic platform for real-time monitoring and precise functionalization of surfaces with DONs was developed here. The combination of controlled flow conditions with an upright total internal reflection fluorescence microscope enabled the kinetic analysis of the immobilization of DONs on DNA-functionalized surfaces. The results revealed that DON morphology and binding tags influence the binding kinetics and that DON hybridization on surfaces is more effective in microfluidic devices with larger-than-standard dimensions, addressing the low diffusivity challenge of DONs. The platform enabled the decoration of DONs with protein-binding ligands and in situ investigation of ligand occupancy on DONs to produce high-quality bioactive surfaces. These surfaces were used to recruit and activate the epidermal growth factor receptor (EGFR) through clustering in the membranes of living cancer cells (MCF-7) using an antagonistic antibody (Panitumumab). The activation was quantified depending on the interligand distances of the EGFR-targeting antibody.

Conversion of vaccines from low to high immunogenicity by antibodies with epitope complementarity

Existing antibodies (Abs) have varied effects on humoral immunity during subsequent infections. Here, we leveraged in vivo systems that allow precise control of antigen-specific Abs and B cells to examine the impact of Ab dose, affinity, and specificity in directing B cell activation and differentiation. Abs competing with the B cell receptor (BCR) epitope showed affinity-dependent suppression. By contrast, Abs targeting a complementary epitope, not overlapping with the BCR, shifted B cell differentiation toward Ab-secreting cells. Such Abs allowed for potent germinal center (GC) responses to otherwise poorly immunogenic sites by promoting antigen capture and presentation by low-affinity B cells. These mechanisms jointly diversified the B cell repertoire by facilitating the recruitment of high- and low-affinity B cells into Ab-secreting cell, GC, and memory B cell fates. Incorporation of small amounts of monoclonal Abs into protein- or mRNA-based vaccines enhanced immunogenicity and facilitated sustained immune responses, with implications for vaccine design and our understanding of protective immunity.

DNA Origami - Lipid Membrane Interactions Controlled by Nanoscale Sterics

DNA nanostructures designed to interact with bilayer membranes are of fundamental interest as they mimic biological cytoskeletons and other membrane-associated proteins for applications in synthetic biology, biosensing, and biological research. Yet, there is limited insight into how the binary interactions are influenced by steric effects produced by 3D geometries of DNA structures and membranes. This work uses a 3D DNA nanostructure with membrane anchors in four different steric environments to elucidate the interaction with membrane vesicles of varying sizes and different local bilayer morphology. It is found that interactions are significantly affected by the steric environments of the anchors -often against predicted accessibility- as well as local nanoscale morphology of bilayers rather than on the usually considered global vesicle size. Furthermore, anchor-mediated bilayer interactions are co-controlled by weak contacts with non-lipidated DNA regions, as showcased by pioneering size discrimination between 50 and 200 nm vesicles. This study extends DNA nanotechnology to controlled bilayer interactions and can facilitate the design of nanodevices for vesicle-based diagnostics, biosensing, and protocells.

Preparation of viromimetic rod-like nanoparticle vaccines (RLNVax) and study of their humoral immune activation efficacy

Virus-like nanoparticle vaccines can efficiently activate the humoral immune response by cross-linking B cell receptors with their surface multivalent antigen arrays. This structurally dependent mechanism makes it crucial to regulate and optimize structural parameters to enhance the efficacy of nanoparticle vaccines. In this study, we prepared nanoparticle vaccines with different aspect ratios by chemically modifying antigen proteins onto the surfaces of poly(amino acid) nanoparticles of various shapes (spherical, ellipsoidal, and rod-like). This allowed us to investigate the impact of structural anisotropy on the humoral immune activation efficacy of nanoparticle vaccines. Furthermore, the end-group molecules of poly(amino acid) materials possess aggregation-induced emission (AIE) properties, which facilitate monitoring the dynamics of nano-assemblies within the body. Results showed that rod-like nanoparticle vaccines (RLNVax) with a higher aspect ratio (AR = 5) exhibited greater lymph node draining efficiency and could elicit more effective B cell activation compared to conventional isotropic spherical nanoparticle vaccines. In a murine subcutaneous immunization model using ovalbumin (OVA) as a model antigen, RLNVax elicited antigen-specific antibody titers that were about 64 times and 4.6 times higher than those induced by free antigen proteins and spherical nanoparticle vaccines, respectively. Additionally, when combined with an aluminum adjuvant, antibody titers elicited by RLNVax were further enhanced by 4-fold. These findings indicate that the anisotropic rod-like structure is advantageous for improving the humoral immune activation efficacy of nanoparticle vaccines, providing significant insights for the design and optimization of next-generation nanoparticle vaccines.

Programming DNA Nanoassemblies into Polyvalent Lysosomal Degraders for Potent Degradation of Pathogenic Membrane Proteins

Lysosome-targeting chimera (LYTAC) shows great promise for protein-based therapeutics by targeted degradation of disease-associated membrane or extracellular proteins, yet its efficiency is constrained by the limited binding affinity between LYTAC reagents and designated proteins. Here, we established a programmable and multivalent LYTAC system by tandem assembly of DNA into a high-affinity protein degrader, a heterodimer aptamer nanostructure targeting both pathogenic membrane protein and lysosome-targeting receptor (insulin-like growth factor 2 receptor, IGF2R) with adjustable spatial distribution or organization pattern. The DNA-based multivalent LYTACs showed enhanced efficacy in removing immune-checkpoint protein programmable death-ligand 1 (PD-L1) and vascular endothelial growth factor receptor 2 (VEGFR2) in tumor cell membrane that respectively motivated a significant increase in T cell activity and a potent effect on cancer cell growth inhibition. With high programmability and versatility, this multivalent LYTAC system holds considerable promise for realizing protein therapeutics with enhanced activity.

DNA-Origami-Based Precise Molecule Assembly and Their Biological Applications

Inspired by efficient natural biomolecule assembly with precise control on key parameters such as distance, number, orientation, and pattern, the constructions and applications of artificial precise molecule assembly are highly important in many research areas including chemistry, biology, and medicine. DNA origami, a sophisticated DNA nanotechnology with rational design, can offer a predictable, programmable, and addressable nanoscale scaffold for the precise assembly of various kinds of molecules. Herein, we summarize recent progress, particularly in the last three years, in DNA-origami-based precise molecule assembly and their emerging biological applications. We first introduce DNA origami and the progress on DNA-origami-based precise molecule assembly, including assembly of various kinds of molecules (e.g., nucleic acids, proteins, organic molecules, nanoparticles), and precise control of important parameters (e.g., distance, number, orientation, pattern). Their biological applications in sensing, imaging, therapy, bionics, biophysics, and chemical biology are then summarized, and current challenges and opportunities are finally discussed.

Cargo quantification of functionalized DNA origami for therapeutic application

In recent years, notable advances in nanotechnology-based drug delivery have emerged. A particularly promising platform in this field is DNA origami-based nanoparticles, which offer highly programmable surfaces, providing precise control over the nanoscale spacing and stoichiometry of various cargo. These versatile particles are finding diverse applications ranging from basic molecular biology to diagnostics and therapeutics. This growing interest creates the need for effective methods to quantify cargo on DNA origami nanoparticles. Our study consolidates several previously validated methods focusing on gel-based and fluorescence-based techniques, including multiplexed quantification of protein, peptide, and nucleic acid cargo on these nanoparticles. This work may serve as a valuable resource for groups researchers keen on utilizing DNA origami-based nanoparticles in therapeutic applications.

Unravelling the contribution of lymph node fibroblasts to vaccine responses

Vaccination is one of the most effective medical interventions, saving millions of lives and reducing the morbidity of infections across the lifespan, from infancy to older age. The generation of plasma cells and memory B cells that produce high affinity class switched antibodies is central to this protection, and these cells are the ultimate output of the germinal centre response. Optimal germinal centre responses require different immune cells to interact with one another in the right place and at the right time and this delicate cellular ballet is coordinated by a network of interconnected stromal cells. In this review we will discuss the various types of lymphoid stromal cells and how they coordinate immune cell homeostasis, the induction and maintenance of the germinal centre response, and how this is disorganised in older bodies.

Both sides now: evolutionary traits of antigens and B cells in tolerance and activation

B cells are the cornerstone of our body's defense system, producing precise antibodies and safeguarding immunological memory for future protection against pathogens. While we have a thorough understanding of how naïve B cells differentiate into plasma or memory B cells, the early B cell response to various antigens-whether self or foreign-remains a thrilling and evolving area of study. Advances in imaging have illuminated the molecular intricacies of B cell receptor (BCR) signaling, yet the dynamic nature of B cell activation continues to reveal new insights based on the nature of antigen exposure. This review explores the evolutionary journey of B cells as they adapt to the unique challenges presented by pathogens. We begin by examining the specific traits of antigens that influence their pathogenic potential, then shift our focus to the distinct characteristics of B cells that counteract these threats. From foundational discoveries to the latest cutting-edge research, we investigate how B cells are effectively activated and distinguish between self and non-self antigens, ensuring a balanced immune response that defends against pathogenic diseases but not self-antigens.

Modulated Cell Internalization Behavior of Icosahedral DNA Framework with Programmable Surface Modification

Surface modification could enhance the cell internalization efficiency of nanovehicles for targeted gene or drug delivery. However, the influence of surface modification parameters, including recognition manners, valences, and patterns, is often clouded, especially for the endocytosis of DNA nanostructures in customized shapes. Focusing on an icosahedral DNA framework, we systematically programmed three distinct types of ligands with diverse valence and spatial distribution on their outer surface to study the internalization efficiency, endocytic pathways, and postinternalization fate. The comparison in different aspects of parameters deepens our understanding of the intricate relationship between surface modification and cell entry behavior, offering insights crucial for designing and optimizing DNA framework nanostructures for potent cell-targeted purposes.

Extracellular matrix rigidity modulates physical properties of subcapsular sinus macrophage-B cell immune synapses

Subcapsular sinus macrophages (SSMs) play a key role in immune defense by forming immunological barriers that control the transport of antigens from lymph into lymph node follicles. SSMs participate in antibody responses by presenting antigens directly to naive B cells and by supplying antigens to follicular dendritic cells to propagate germinal center reactions. Despite the prominent roles that SSMs play during immune responses, little is known about their cell biology because they are technically challenging to isolate and study in vitro. Here, we used multicolor fluorescence microscopy to identify lymph node-derived SSMs in culture. We focused on the role of SSMs as antigen-presenting cells, and found that their actin cytoskeleton regulates the spatial organization and mobility of multivalent antigens (immune complexes [ICs]) displayed on the cell surface. Moreover, we determined that SSMs are mechanosensitive cells that respond to changes in extracellular matrix rigidity by altering the architecture of the actin cytoskeleton, leading to changes in cell morphology, membrane topography, and IC mobility. Changes to extracellular matrix rigidity also modulate actin remodeling by both SSMs and B cells when they form an immune synapse. This alters synapse duration but not IC internalization nor NF-κB activation in the B cell. Taken together, our data reveal that the mechanical microenvironment may influence B cell responses by modulating physical characteristics of antigen presentation by SSMs.

DNA origami: Interrogating the nano-landscape of immune receptor activation

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.

Mechanical control of antigen detection and discrimination by T and B cell receptors

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.

Enzyme-Programmed Self-Assembly of Nanoparticles

Nanoparticles are a hot topic in the field of nanomaterial research due to their excellent physical and chemical properties. In recent years, DNA-directed nanoparticle self-assembly technology has been widely applied to the development of numerous complex nanoparticle superstructures. Due to the inherent stability and surface electric repulsion of nanoparticles, it is difficult to make nanoparticle superstructures respond to molecular signals in the external environment. In fact, enzyme-programmed molecular systems are developed to allow diverse functions, including logical operations, signal amplification, and dynamic assembly control. Therefore, combining enzyme-controlled DNA systems may endow nanoparticle assembly systems with more flexibility in program design, allowing them to respond to a variety of external signals. In this review, we summarize the basic principles of enzyme-controlled DNA/nanoparticle self-assembly and introduce its applications in heavy metal detection, gene expression, proteins inside living cells, cancer cell therapy, and drug delivery. With the continuous development of new nanoparticle materials and the increasing functionality of enzyme DNA circuits, enzyme-directed DNA/nanoparticle self-assembled probe technology is expected to see significant future development.

Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses

Defending against future pandemics requires vaccine platforms that protect across a range of related pathogens. Nanoscale patterning can be used to address this issue. Here, we produce quartets of linked receptor-binding domains (RBDs) from a panel of SARS-like betacoronaviruses, coupled to a computationally designed nanocage through SpyTag/SpyCatcher links. These Quartet Nanocages, possessing a branched morphology, induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented in the vaccine. Equivalent antibody responses are raised to RBDs close to the nanocage or at the tips of the nanoparticle's branches. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increase the strength and breadth of an otherwise narrow immune response. A Quartet Nanocage including the Omicron XBB.1.5 'Kraken' RBD induced antibodies with binding to a broad range of sarbecoviruses, as well as neutralizing activity against this variant of concern. Quartet nanocages are a nanomedicine approach with potential to confer heterotypic protection against emergent zoonotic pathogens and facilitate proactive pandemic protection.

Computationally designed mRNA-launched protein nanoparticle vaccines

Both protein nanoparticle and mRNA vaccines were clinically de-risked during the COVID-19 pandemic1-6. These vaccine modalities have complementary strengths: antigen display on protein nanoparticles can enhance the magnitude, quality, and durability of antibody responses7-10, while mRNA vaccines can be rapidly manufactured11 and elicit antigen-specific CD4 and CD8 T cells12,13. Here we leverage a computationally designed icosahedral protein nanoparticle that was redesigned for optimal secretion from eukaryotic cells14 to develop an mRNA-launched nanoparticle vaccine for SARS-CoV-2. The nanoparticle, which displays 60 copies of a stabilized variant of the Wuhan-Hu-1 Spike receptor binding domain (RBD)15, formed monodisperse, antigenically intact assemblies upon secretion from transfected cells. An mRNA vaccine encoding the secreted RBD nanoparticle elicited 5- to 28-fold higher levels of neutralizing antibodies than an mRNA vaccine encoding membrane-anchored Spike, induced higher levels of CD8 T cells than the same immunogen when delivered as an adjuvanted protein nanoparticle, and protected mice from vaccine-matched and -mismatched SARS-CoV-2 challenge. Our data establish that delivering protein nanoparticle immunogens via mRNA vaccines can combine the benefits of each modality and, more broadly, highlight the utility of computational protein design in genetic immunization strategies.

Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity

A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.

A Versatile Microfluidic Platform for Extravasation Studies Based on DNA Origami-Cell Interactions

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.

Virus-like Particles as Vaccines for Allergen-Specific Therapy: An Overview of Current Developments

Immune engineering and modulation are the basis of a novel but powerful tool to treat immune diseases using virus-like particles (VLPs). VLPs are formed by the viral capsid without genetic material making them non-infective. However, they offer a wide variety of possibilities as antigen-presenting platforms, resulting in high immunogenicity and high efficacy in immune modulation, with low allergenicity. Both animal and plant viruses are being studied for use in the treatment of food allergies. These formulations are combined with adjuvants, T-stimulatory epitopes, TLR ligands, and other immune modulators to modulate or enhance the immune response toward the presented allergen. Here, the authors present an overview of VLP production systems, their immune modulation capabilities, and the applicability of actual VLP-based formulations targeting allergic diseases.