Protein-Corona-by-Design in 2D: A Reliable Platform to Decode Bio-Nano Interactions for the Next-Generation Quality-by-Design Nanomedicines

Enhancing RNA-lipid nanoparticle delivery: Organ- and cell-specificity and barcoding strategies

Recent advancements in RNA therapeutics highlight the critical need for precision gene delivery systems that target specific organs and cells. Lipid nanoparticles (LNPs) have emerged as key vectors in delivering mRNA and siRNA, offering protection against enzymatic degradation, enabling targeted delivery and cellular uptake, and facilitating RNA cargo release into the cytosol. This review discusses the development and optimization of organ- and cell-specific LNPs, focusing on their design, mechanisms of action, and therapeutic applications. We explore innovations such as DNA/RNA barcoding, which facilitates high-throughput screening and precise adjustments in formulations. We address major challenges, including improving endosomal escape, minimizing off-target effects, and enhancing delivery efficiencies. Notable clinical trials and recent FDA approvals illustrate the practical applications and future potential of LNP-based RNA therapies. Our findings suggest that while considerable progress has been made, continued research is essential to resolve existing limitations and bridge the gap between preclinical and clinical evaluation of the safety and efficacy of RNA therapeutics. This review highlights the dynamic progress in LNP research. It outlines a roadmap for future advancements in RNA-based precision medicine.

Graphene Oxide Nanosheets Toxicity in Mice Is Dependent on Protein Corona Composition and Host Immunity

Two-dimension graphene oxide (GO) nanosheets with high and low serum protein binding profiles (high/low hard-bound protein corona/HChigh/low) are used in this study as model materials and screening tools to investigate the underlying roles of the protein corona on nanomaterial toxicities in vivo. We proposed that the in vivo biocompatibility/nanotoxicity of GO is protein corona-dependent and host immunity-dependent. The hypothesis was tested by injecting HChigh/low GO nanosheets in immunocompetent ICR/CD1 and immunodeficient NOD-scid II2rγnull mice and performed histopathological and hematological evaluation studies on days 1 and 14 post-injection. HClow GO induced more severe acute lung injury compared to HChigh GO in both immunocompetent and immunodeficient mice, with the effect being particularly pronounced in immunocompetent animals. Additionally, HClow GO caused more significant liver injury in both types of mice, with immunodeficient mice being more susceptible to its hepatotoxic effects. Moreover, administration of HClow GO resulted in increased hematological toxicity and elevated levels of serum pro-inflammatory cytokines in immunocompromised and immunocompetent mice, respectively. Correlation studies were conducted to explore the impact of distinct protein corona compositions on resulting toxicities in both immunocompetent and immunodeficient mice. This facilitated the identification of consistent patterns, aligning with those observed in vitro, thus indicating a robust in vitro-in vivo correlation. This research will advance our comprehension of how hard corona proteins interact with immune cells, leading to toxicity, and will facilitate the development of improved immune-modulating nanomaterials for therapeutic purposes.

Calreticulin P-domain-derived "Eat-me" peptides for enhancing liposomal uptake in dendritic cells

Discovering new ligands for enhanced drug uptake and delivery has been the core interest of the drug delivery field. This study capitalizes on the natural "eat-me" signal of calreticulin (CRT), proposing a novel strategy for functionalizing liposomes to improve cellular uptake. CRT is presented on the surfaces of apoptotic cells, and it plays a crucial role in immunogenic cell death (ICD). This is because it is essential for antigen uptake via low-density lipoprotein (LDL) receptor-mediated phagocytosis. Inspired by this mechanism, we interrogated CRT's "eat-me" feature using CRT-derived peptides to functionalize liposomes. We studied liposomal formulation stability, properties, cellular uptake, toxicity, and intracellular trafficking in dendritic cells. We identified key peptide fragments of CRT, specifically from the hydrophilic P-domain, that are compatible with liposomal formulations. Contrary to the more hydrophobic N-domain peptides, the P-domain peptides induced significantly higher liposomal uptake in DC2.4 dendritic cells than cationic DOTAP and anionic DPPG liposomes without inducing toxicity. The P-domain-derived peptides led to enhanced liposomal uptake into DC2.4 dendritic cells compared to the standard DPPC liposomes. The uptake can be partially blocked by the receptor-associated protein (RAP). Upon internalization, P-domain-peptide-decorated liposomes showed higher co-localization with lysosomes compared to the standard DPPC liposomes. Our findings illuminate CRT's operational role and identify P-domain peptides as promising agents for developing biomimetic drug delivery systems that can potentially replicate CRT's "eat-me" function.

Modulating the toxicity of engineered nanoparticles by controlling protein corona formation: Recent advances and future prospects

With the rapid development and widespread application of engineered nanoparticles (ENPs), understanding the fundamental interactions between ENPs and biological systems is essential to assess and predict the fate of ENPs in vivo. When ENPs are exposed to complex physiological environments, biomolecules quickly and inevitably adsorb to ENPs to form a biomolecule corona, such as a protein corona (PC). The formed PC has a significant effect on the physicochemical properties of ENPs and gives them a brand new identity in the biological environment, which determines the subsequent ENP-cell/tissue/organ interactions. Controlling the formation of PCs is therefore of utmost importance to accurately predict and optimize the behavior of ENPs within living organisms, as well as ensure the safety of their applications. In this review, we provide an overview of the fundamental aspects of the PC, including the formation mechanism, composition, and frequently used characterization techniques. We comprehensively discuss the potential impact of the PC on ENP toxicity, including cytotoxicity, immune response, and so on. Additionally, we summarize recent advancements in manipulating PC formation on ENPs to achieve the desired biological outcomes. We further discuss the challenges and prospects, aiming to provide valuable insights for a better understanding and prediction of ENP behaviors in vivo, as well as the development of low-toxicity ENPs.

Adhesion States Greatly Affect Cellular Susceptibility to Graphene Oxide: Therapeutic Implications for Cancer Metastasis

Graphene oxide (GO) has received increasing attention in the life sciences because of its potential for various applications. Although GO is generally considered biocompatible, it can negatively impact cell physiology under some circumstances. Here, we demonstrate that the cytotoxicity of GO greatly varies depending on the cell adhesion states. Human HCT-116 cells in a non-adhered state were more susceptible to GO than those in an adherent state. Apoptosis was partially induced by GO in both adhered and non-adhered cells to a similar extent, suggesting that apoptosis induction does not account for the selective effects of GO on non-adhered cells. GO treatment rapidly decreased intracellular ATP levels in non-adhered cells but not in adhered ones, suggesting ATP depletion as the primary cause of GO-induced cell death. Concurrently, autophagy induction, a cellular response for energy homeostasis, was more evident in non-adhered cells than in adhered cells. Collectively, our observations provide novel insights into GO's action with regard to cell adhesion states. Because the elimination of non-adhered cells is important in preventing cancer metastasis, the selective detrimental effects of GO on non-adhered cells suggest its therapeutic potential for use in cancer metastasis.

The Hybrid Nano-Biointerface between Proteins/Peptides and Two-Dimensional Nanomaterials

In typical protein-nanoparticle surface interactions, the biomolecule surface binding and consequent conformational changes are intermingled with each other and are pivotal to the multiple functional properties of the resulting hybrid bioengineered nanomaterial. In this review, we focus on the peculiar properties of the layer formed when biomolecules, especially proteins and peptides, face two-dimensional (2D) nanomaterials, to provide an overview of the state-of-the-art knowledge and the current challenges concerning the biomolecule coronas and, in general, the 2D nano-biointerface established when peptides and proteins interact with the nanosheet surface. Specifically, this review includes both experimental and simulation studies, including some recent machine learning results of a wide range of nanomaterial and peptide/protein systems.

Differential modulation of endothelial cytoplasmic protrusions after exposure to graphene-family nanomaterials

Engineered nanomaterials offer the benefit of having systematically tunable physicochemical characteristics (e.g., size, dimensionality, and surface chemistry) that highly dictate the biological activity of a material. Among the most promising engineered nanomaterials to date are graphene-family nanomaterials (GFNs), which are 2-D nanomaterials (2DNMs) with unique electrical and mechanical properties. Beyond engineering new nanomaterial properties, employing safety-by-design through considering the consequences of cell-material interactions is essential for exploring their applicability in the biomedical realm. In this study, we asked the effect of GFNs on the endothelial barrier function and cellular architecture of vascular endothelial cells. Using micropatterned cell pairs as a reductionist in vitro model of the endothelium, the progression of cytoskeletal reorganization as a function of GFN surface chemistry and time was quantitatively monitored. Here, we show that the surface oxidation of GFNs (graphene, reduced graphene oxide, partially reduced graphene oxide, and graphene oxide) differentially affect the endothelial barrier at multiple scales; from the biochemical pathways that influence the development of cellular protrusions to endothelial barrier integrity. More oxidized GFNs induce higher endothelial permeability and the increased formation of cytoplasmic protrusions such as filopodia. We found that these changes in cytoskeletal organization, along with barrier function, can be potentiated by the effect of GFNs on the Rho/Rho-associated kinase (ROCK) pathway. Specifically, GFNs with higher surface oxidation elicit stronger ROCK2 inhibitory behavior as compared to pristine graphene sheets. Overall, findings from these studies offer a new perspective towards systematically controlling the surface-dependent effects of GFNs on cytoskeletal organization via ROCK2 inhibition, providing insight for implementing safety-by-design principles in GFN manufacturing towards their targeted biomedical applications.

Nanoparticles Surface Chemistry Influence on Protein Corona Composition and Inflammatory Responses

Nanoparticles are widely used for biomedical applications such as vaccine, drug delivery, diagnostics, and therapeutics. This study aims to reveal the influence of nanoparticle surface functionalization on protein corona formation from blood serum and plasma and the subsequent effects on the innate immune cellular responses. To achieve this goal, the surface chemistry of silica nanoparticles of 20 nm diameter was tailored via plasma polymerization with amine, carboxylic acid, oxazolines, and alkane functionalities. The results of this study show significant surface chemistry-induced differences in protein corona composition, which reflect in the subsequent inflammatory consequences. Nanoparticles rich with carboxylic acid surface functionalities increased the production of pro-inflammatory cytokines in response to higher level of complement proteins and decreased the number of lipoproteins found in their protein coronas. On another hand, amine rich coatings led to increased expressions of anti-inflammatory markers such as arginase. The findings demonstrate the potential to direct physiological responses to nanomaterials via tailoring their surface chemical composition.

Development of Graphene-Based Materials in Bone Tissue Engineaering

Bone regeneration-related graphene-based materials (bGBMs) are increasingly attracting attention in tissue engineering due to their special physical and chemical properties. The purpose of this review is to quantitatively analyze mass academic literature in the field of bGBMs through scientometrics software CiteSpace, to demonstrate the rules and trends of bGBMs, thus to analyze and summarize the mechanisms behind the rules, and to provide clues for future research. First, the research status, hotspots, and frontiers of bGBMs are analyzed in an intuitively and vividly visualized way. Next, the extracted important subjects such as fabrication techniques, cytotoxicity, biodegradability, and osteoinductivity of bGBMs are presented, and the different mechanisms, in turn, are also discussed. Finally, photothermal therapy, which is considered an emerging area of application of bGBMs, is also presented. Based on this approach, this work finds that different studies report differing opinions on the biological properties of bGBMS due to the lack of consistency of GBMs preparation. Therefore, it is necessary to establish more standards in fabrication, characterization, and testing for bGBMs to further promote scientific progress and clinical translation.

Evolution of the protein corona affects macrophage polarization

When nanoparticles (NPs) come into contact with bioenvironments, a protein corona forms on the NP surface. Previous reports showed that the constituents of the corona change with time. However, how different protein corona compositions influence cells, especially immune cells, has received less attention. Macrophages are important immune cells that can be polarized into a pro-inflammatory (M1) or anti-inflammatory (M2) phenotype. In this study, AuNPs were incubated with human plasma for different periods to obtain time-related AuNP-coronas, and the influences of time-related AuNP-coronas on macrophage polarization were investigated. The macrophage morphology, biomarkers, cytokine secretion studies show that the pristine AuNPs and 4 h-AuNP-corona induced macrophage cells into M2 phenotype, while the co-incubation of 12 h-AuNP-corona and macrophage cells result in M1 phenotype. Further proteomic analysis showed that the compositions of protein corona were changing constantly after AuNPs contacted with plasma. When the incubation time increased to 12 h, the immune proteins in protein corona were increased significantly, which play a key role in modulation of the different macrophages polarization. Our findings demonstrated that plasma incubation time is an important parameter that needs to be taken into account in the study of nano-immune interactions and safe use of NPs in biological systems. Moreover, our finding can be a new efficient strategy for activating inflammatory or anti-inflammatory in medical treatment.

Converging 2D Nanomaterials and 3D Bioprinting Technology: State-of-the-Art, Challenges, and Potential Outlook in Biomedical Applications

The development of next-generation of bioinks aims to fabricate anatomical size 3D scaffold with high printability and biocompatibility. Along with the progress in 3D bioprinting, 2D nanomaterials (2D NMs) prove to be emerging frontiers in the development of advanced materials owing to their extraordinary properties. Harnessing the properties of 2D NMs in 3D bioprinting technologies can revolutionize the development of bioinks by endowing new functionalities to the current bioinks. First the main contributions of 2D NMS in 3D bioprinting technologies are categorized here into six main classes: 1) reinforcement effect, 2) delivery of bioactive molecules, 3) improved electrical conductivity, 4) enhanced tissue formation, 5) photothermal effect, 6) and stronger antibacterial properties. Next, the recent advances in the use of each certain 2D NMs (1) graphene, 2) nanosilicate, 3) black phosphorus, 4) MXene, 5) transition metal dichalcogenides, 6) hexagonal boron nitride, and 7) metal-organic frameworks) in 3D bioprinting technology are critically summarized and evaluated thoroughly. Third, the role of physicochemical properties of 2D NMSs on their cytotoxicity is uncovered, with several representative examples of each studied 2D NMs. Finally, current challenges, opportunities, and outlook for the development of nanocomposite bioinks are discussed thoroughly.

Profiling and Regulating Proteins That Adsorb to DNA Materials in Human Serum

DNA aptamers and framework DNA nanostructures are emerging DNA materials with many appealing biological applications including biosensing, bioimaging, drug delivery, and so forth. When placed in physiological fluids, they inevitably encounter biomolecules (majorly proteins) and form complexes that largely affect their biological fate. Nevertheless, little is known regarding the quantitative profile of proteins that adsorb to DNA aptamers and DNA nanostructures in biological environments, and there are no potent strategies to regulate protein profiles. Herein, we performed a proteomic analysis to profile proteins that bind to DNA aptamers (Sgc8c and SYLC3) and nanostructures (a tetrahedral DNA nanostructure and a DNA origami rod) in human serum using liquid chromatography-mass spectrometry (LC-MS). Dozens to hundreds of proteins were identified with each DNA material exhibiting highly distinctive profiles. It was also revealed that the origin of serum (from healthy donor vs from prostate cancer patients) causes significant differences in profiles of bound proteins. Furthermore, we demonstrated that the protein profile may be regulated by tethering a layer of single-stranded DNA (polythymine) onto the DNA origami rod to alleviate the adsorption of complement-associated proteins, which significantly reduced its sequestration by macrophages. Taken together, this study has provided qualitative and quantitative proteomic profiles regarding serum proteins that adsorb to various DNA materials and have demonstrated that the composition of interacted proteins may be regulated toward better biological performances.

Comparative study on formation of protein coronas under three different serum origins

Nanomaterials form a complex called "protein corona" by contacting with protein-containing biological fluids such as serum when they are exposed to physiological environments. The characteristics of these proteins, which are one of the substantial factors in cellular response, are affected by the interactions between the nanomaterials and the biological systems. Many studies have investigated the biological behaviors of nanomaterials by conducting experiments in vitro and in vivo; however, the origin of the biological materials used is rather inconsistent. This is due to the fact that the composition of the protein coronas may differ depending on the animal origin, not on the composition or size of the nanoparticles. The resulting differences in the composition of the protein coronas can lead to different conclusions. To identify the differences in protein corona formation among sera of different species, we investigated protein coronas of gold and silica nanoparticles in serum obtained from various species. Using comparative proteomic analysis, common proteins adsorbed onto each nanoparticle among the three different sera were identified as highly abundant proteins in the serum. These findings indicate that protein corona formation is dependent on the serum population rather than the size or type of the nanoparticles. Additionally, in the physiological classification of protein coronas, human serum (HS) was found to be rich in apolipoproteins. In conclusion, our data indicate that HS components are different from those of bovine or mouse, indicating that the serum species origin should be carefully considered when selecting a biological fluid.

Biomaterial Surface Hydrophobicity-Mediated Serum Protein Adsorption and Immune Responses

The nature of the protein corona forming on biomaterial surfaces can affect the performance of implanted devices. This study investigated the role of surface chemistry and wettability on human serum-derived protein corona formation on biomaterial surfaces and the subsequent effects on the cellular innate immune response. Plasma polymerization, a substrate-independent technique, was employed to create nanothin coatings with four specific chemical functionalities and a spectrum of surface charges and wettability. The amount and type of protein adsorbed was strongly influenced by surface chemistry and wettability but did not show any dependence on surface charge. An enhanced adsorption of the dysopsonin albumin was observed on hydrophilic carboxyl surfaces while high opsonin IgG2 adsorption was seen on hydrophobic hydrocarbon surfaces. This in turn led to a distinct immune response from macrophages; hydrophilic surfaces drove greater expression of anti-inflammatory cytokines by macrophages, whilst surface hydrophobicity caused increased production of proinflammatory signaling molecules. These findings map out a unique relationship between surface chemistry, hydrophobicity, protein corona formation, and subsequent cellular innate immune responses; the potential outcomes of these studies may be employed to tailor biomaterial surface modifications, to modulate serum protein adsorption and to achieve the desirable innate immune response to implanted biomaterials and devices.

Application of carbon nanotubes in cancer vaccines: Achievements, challenges and chances

Tumour-specific, immuno-based therapeutic interventions can be considered as safe and effective approaches for cancer therapy. Exploitation of nano-vaccinology to intensify the cancer vaccine potency may overcome the need for administration of high vaccine doses or additional adjuvants and therefore could be a more efficient approach. Carbon nanotube (CNT) can be described as carbon sheet(s) rolled up into a cylinder that is nanometers wide and nanometers to micrometers long. Stemming from the observed capacities of CNTs to enter various types of cells via diversified mechanisms utilising energy-dependent and/or passive routes of cell uptake, the use of CNTs for the delivery of therapeutic agents has drawn increasing interests over the last decade. Here we review the previous studies that demonstrated the possible benefits of these cylindrical nano-vectors as cancer vaccine delivery systems as well as the obstacles their clinical application is facing.

Interaction of graphene oxide with cell culture medium: Evaluating the fetal bovine serum protein corona formation towards in vitro nanotoxicity assessment and nanobiointeractions

The interaction of single-layer graphene oxide (SLGO) and multi-layered graphene oxide (MLGO) with a cell culture medium (i.e. DMEM) was studied by evaluating fetal bovine serum (FBS) protein corona formation towards in vitro nanotoxicity assessment and nanobiointeractions. SLGO and MLGO exhibited different colloidal behavior in the culture medium, which was visualized by cryogenic transmission electron microscopy in situ analysis. Exploring proteomics and bioinformatics tools, 394 and 290 proteins were identified on the SLGO and MLGO hard corona compositions, respectively. From this amount, 115 proteins were exclusively detected on the SLGO and merely 11 on MLGO. SLGO enriched FBS proteins involved in metabolic processes and signal transduction, while MLGO enriched proteins involved in cellular development/structure, and lipid transport/metabolic processes. Such a distinct corona profile is due to differences on surface chemistry, aggregation behavior and the surface area of GO materials. Hydrophilic interactions were found to play a greater role in protein adsorption by MLGO than SLGO. Our results point out implications for in vitro studies of graphene oxide materials concerning the effective dose delivered to cells and corona bioactivity. Finally, we demonstrated the importance of integrating conventional and modern techniques thoroughly to understand the GO-FBS complexes towards more precise, reliable and advanced in vitro nanotoxicity assessment.