Time-Resolved Proteomic Visualization of Dendrimer Cellular Entry and Trafficking

Diverse Approaches for the Difunctionalization of PPH Dendrimers, Precise Versus Stochastic: How Does this Influence Catalytic Performance?

Random difunctionalization of dendrimer surfaces, frequently employed in biological applications, provides the advantage of dual functional groups through a synthetic pathway that is simpler compared to precise difunctionalization. However, is the random difunctionalization as efficient as the precise difunctionalization on the surface of dendrimers? This question is unanswered to date because most dendrimer families face challenges in achieving precise functionalization. Polyphosphorhydrazone (PPH) dendrimers present a unique opportunity to obtain precise difunctionalization at each terminal branching point. The work concerning catalysis we report with PPH dendrimers, whether precisely or randomly functionalized, addresses this question. Across PPH dendrimers, from generations 1 to 3, precise functionalization consistently outperforms random functionalization in terms of efficiency. This finding introduces a novel concept in dendrimer science, emphasizing the superiority of precise over random functionalization methodologies. Introducing a groundbreaking concept in the field of dendrimers.

Proteomics reveals time-dependent protein corona changes in the intracellular pathway

The intracellular protein corona has not been fully investigated in the field of nanotechnology-biology (nano-bio) interactions. To effectively understand intracellular protein corona formation and dynamics, we established a workflow to isolate the intracellular protein corona at different uptake times of two nanoparticles - magnetic hydroxyethyl starch nanoparticles (HES-NPs) and magnetic human serum albumin nanocapsules (HSA-NCs). We performed label-free quantitative LC-MS proteomics to analyze the composition of the intracellular protein corona and correlated our findings with results from conventional methods for intracellular trafficking of nanocarriers, such as flow cytometry, transmission electron microscopy (TEM), and confocal microscopy (cLSM). We determined the evolution of the intracellular protein corona. At different time stages the protein corona of the HES-NPs with a slower uptake changed, but there were fewer changes in that of the HSA-NCs with a more rapid uptake. We identified proteins that are involved in macropinocytosis (RAC1, ASAP2) as well as caveolin. This was confirmed by blocking experiments and by TEM studies. The investigated nanocarrier predominantly trafficked from early endosomes as determined by RAB5 identification in proteomics and in cLSM to late endosomes/lysosomes (RAB7, LAMP1, cathepsin K and HSP 90-beta) We further demonstrated differences between nanoparticles with slower and faster uptake kinetics and determined the associated proteome at different time points. Analysis of the intracellular protein corona provides us with effective data to examine the intracellular trafficking of nanocarriers used in efficient drug delivery and intracellular applications. STATEMENT OF SIGNIFICANCE: Many research papers focus on the protein corona on nanoparticles formed in biological fluids, but there are hardly any articles dealing with proteins that come in contact with nanoparticles inside cells. The "intracellular protein corona" studied here is a far more complex and highly demanding field. Most nanocarriers are designed to be taken up into cells. Given this, we chose two different nanocarriers to reveal changes in the proteins in dendritic cells during contact at specific times. Further studies will allow us to examine molecular target proteins using these methods. Our research is a significant addition towards the goal of understanding and thus improving the efficacy of drug nanocarriers.

Synthetic receptors in medicine

Cellular signaling is controlled by ligand receptor interaction and subsequent biochemical changes inside the cell. Manipulating receptors as per need that can be a strategy to alter the disease pathologies in various conditions. With recent advances in synthetic biology, now it is possible to engineer the artificial receptor "synthetic receptors." Synthetic receptors are the engineering receptors that have potential to alter the disease pathology by altering/manipulating the cellular signaling. Several synthetic receptors are being engineered that have shown positive regulation in several disease conditions. Thus, synthetic receptor-based strategy opens a new avenue in the medical field to cope up with various health issues. The current chapter summarizes updated information about the synthetic receptors and their applications in the medical field.

Nanoprotein Interaction Atlas Reveals the Transport Pathway of Gold Nanoparticles across Epithelium and Its Association with Wnt/β-Catenin Signaling

A tremendous number of proteins participate in the delivery and transport process of nanomedicines. Nanoprotein interactions not only mediate drug delivery but also determine drug safety. In the field of biomedical sciences, the epithelial barrier is a huge challenge for gastrointestinal, intratracheal, intranasal, vaginal, and intrauterine delivery of nanomedicines. However, the molecular mechanisms by which nanomedicines cross tissue or cell barriers are not well understood. Here, we explored the nanoprotein interactions during the transcytosis of nanoparticles across the epithelial barrier by focusing on the transport pathway and mechanisms. Due to the limitations of traditional methods in resolving nanoprotein interactions, we developed a backward analysis strategy. By simultaneously analyzing the protein corona on the particle surface and the cellular response after transcytosis, we integrated the information on both directly and indirectly interacting proteins, establishing a holistic nanoprotein interaction atlas. It revealed the dominant role of the EV/ER/Golgi/SV pathway in the transcytosis of nanoparticles. More importantly, based on the established atlas, we discovered the association of Wnt/β-catenin signaling with nanoparticle transportation. The endocytosis for entering cells and exocytosis/transcytosis for leaving cells were differently regulated by the Wnt pathway. Notably, this regulatory effect was dependent on the particle size. Bigger nanoparticles departed from cells through the exocytosis pathway faster because of the specific bridging effect on the Wnt-Frizzled interaction and the feedback loop construction based on the exosomes. This mechanism gives an interpretation at the molecular level to the transcytosis dilemma of larger nanoparticles. Moreover, the size-dependent Wnt/β-catenin signaling pathway provides a promising regulatory and screening platform for the transportation of different nanomedicines through the epithelial barrier.

There and back again: a dendrimer's tale

The development of molecular nanostructures with well-defined particle size and shape is of eminent interest in biomedicine. Among many studied nanostructures, dendrimers represent the group of those most thoroughly characterized ones. Due to their unique structure and properties, dendrimers are very attractive for medical and pharmaceutical applications. Owing to the controllable cavities inside the dendrimer, guest molecules may be encapsulated, and highly reactive terminal groups are susceptible to further modifications, e.g., to facilitate target delivery. To understand the potential of these nanoparticles and to predict and avoid any adverse cellular reactions, it is necessary to know the mechanisms responsible for an efficient dendrimer uptake and the destination of their intracellular journey. In this article, we summarize the results of studies describing the dendrimer uptake, traffic, and efflux mechanisms depending on features of specific nanoparticles and cell types. We also present mechanisms of dendrimers responsible for toxicity and alteration in signal transduction pathways at the cellular level.

Composition of Intracellular Protein Corona around Nanoparticles during Internalization

It has been well established that the early-stage interactions of nanoparticles with cells are governed by the extracellular protein corona. However, after entering into the cells, the evolving protein corona is the key to subsequent processing of nanoparticles by cells. To identify the protein corona around intracellular nanoparticles, it is essential to maintain its original compositions during cell treatment. Herein, we develop a paraformaldehyde (PFA) cross-linking strategy to stabilize corona compositions when extracting protein coronas from cells, providing original information on protein coronas around intercellular gold nanoparticles (AuNPs). The stability of the protein corona after PFA cross-linking was carefully investigated with several characterization methods, and the results demonstrate that PFA cross-linking successfully prevents the dissociation and exchange of corona proteins. Then the recovered intracellular protein corona around AuNPs from living HepG2 cells with a PFA cross-linking strategy was subjected to nanoHPLC-MS/MS for proteomic analysis. It was found that the compositions of intracellular protein coronas are dominated by cell-derived proteins and undergo significant variation of protein species and amounts over time during internalization. Time-resolved analysis provides relevant proteins involved in nanoparticle cellular uptake and transportation, indicating that AuNPs are endocytosed mainly by a clathrin-mediated uptake mechanism and directed into an endolysosomal pathway toward their final destination. Such proteomic-based results are verified by pharmacological inhibition and TEM imaging analysis. This work provides a universal strategy to study compositions of protein corona around intercellular nanoparticles and could be a footstone to link the formation of protein corona around nanoparticles to their biological function in cells.

Recent Progresses in Organic-Inorganic Nano Technological Platforms for Cancer Therapeutics

Nanotechnology offers promising tools in interdisciplinary research areas and getting an upsurge of interest in cancer therapeutics. Organic nanomaterials and inorganic nanomaterials bring revolutionary advancement in cancer eradication process. Oncology is achieving new heights under nano technological platform by expediting chemotherapy, radiotherapy, photo thermodynamic therapy, bio imaging and gene therapy. Various nanovectors have been developed for targeted therapy which acts as "Nano-bullets" for tumor cells selectively. Recently combinational therapies are catching more attention due to their enhanced effect leading towards the use of combined organicinorganic nano platforms. The current review covers organic, inorganic and their hybrid nanomaterials for various therapeutic action. The technological aspect of this review emphasizes on the use of inorganic-organic hybrids and combinational therapies for better results and also explores the future opportunities in this field.

Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor

The outbreak of Zika virus (ZIKV) in 2016 created worldwide health emergency which demand urgent research efforts on understanding the virus biology and developing therapeutic strategies. Here, we present a time-resolved chemical proteomic strategy to track the early-stage entry of ZIKV into host cells. ZIKV was labeled on its surface with a chemical probe, which carries a photocrosslinker to covalently link virus-interacting proteins in living cells on UV exposure at different time points, and a biotin tag for subsequent enrichment and mass spectrometric identification of the receptor or other host proteins critical for virus internalization. We identified Neural Cell Adhesion Molecule (NCAM1) as a potential ZIKV receptor and further validated it through overexpression, knockout, and inhibition of NCAM1 in Vero cells and human glioblastoma cells U-251 MG. Collectively, the strategy can serve as a universal tool to map virus entry pathways and uncover key interacting proteins.

Tracking Pathogen Infections by Time-Resolved Chemical Proteomics

Studying the dynamic interaction between host cells and pathogen is vital but remains technically challenging. We describe herein a time-resolved chemical proteomics strategy enabling host and pathogen temporal interaction profiling (HAPTIP) for tracking the entry of a pathogen into the host cell. A novel multifunctional chemical proteomics probe was introduced to label living bacteria followed by in vivo crosslinking of bacteria proteins to their interacting host-cell proteins at different time points initiated by UV for label-free quantitative proteomics analysis. We observed over 400 specific interacting proteins crosslinked with the probe during the formation of Salmonella-containing vacuole (SCV). This novel chemical proteomics approach provides a temporal interaction profile of host and pathogen in high throughput and would facilitate better understanding of the infection process at the molecular level.

Proteomic analysis of intracellular protein corona of nanoparticles elucidates nano-trafficking network and nano-bio interactions

The merits of nanomedicines are significantly impacted by the surrounding biological environment. Similar to the protein corona generated on the surface of nanoparticles in the circulation system, the intracellular protein corona (IPC) might be formed on nanoparticles when transported inside the cells. However, little is known currently about the formation of IPC and its possible biological influence.

Methods: Caco-2 cells, a classical epithelial cell line, were cultured in Transwell plates to form a monolayer. Gold nanoparticles (AuNPs) were prepared as the model nanomedicine due to their excellent stability. Here we focused on identifying IPC formed on the surface of AuNPs during cell transport. The nanoparticles in the basolateral side of the Caco-2 monolayer were collected and analyzed by multiple techniques to verify IPC formation. High-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics was utilized to analyze the composition of IPC proteins. In particular, we established a dual-filtration strategy to exclude various interference in IPC identification. Based on the subcellular localization of specific IPC proteins, we elicited the nano-trafficking network of AuNPs. The transport pathways of AuNPs identified by proteomic analysis were also verified by various conventional technologies. Finally, we explored the influence of IPC on the uptake and stress response of endothelium.

Results: The existence of IPC was demonstrated on the surface of AuNPs, in which 227 proteins were identified. Among them, 40 proteins were finally ascertained as the specific IPC proteins. The subcellular location analysis indicated that these “specific” IPC proteins could back-track the transport pathways of nanoparticles in the epithelial cell monolayer. According to the subcellular distribution of IPC proteins and co-localization, we discovered a new pathway of nanoparticles from endosomes to secretory vesicles which was dominant during the transcytosis. After employing conventional imageology and pharmacology strategies to verify the result of proteomic analysis, we mapped a comprehensive intracellular transport network. Our study also revealed the merits of IPC analysis, which could readily elucidate the molecular mechanisms of transcytosis. Besides, the IPC proteins increased the uptake and stress response of endothelium, which was likely mediated by extracellular matrix and mitochondrion-related IPC proteins.

Conclusion: The comprehensive proteomic analysis of IPC enabled tracing of transport pathways in epithelial cells as well as revealing the biological impact of nanoparticles on endothelium.

A near-infrared light-controlled, ultrasensitive one-step photoelectrochemical detection of dual cell apoptosis indicators in living cancer cells

The proposed near-infrared (NIR) light-controlled, one-step photoelectrochemical (PEC) strategy could simultaneously detect cell apoptosis indicators, phosphatidylserine (Pho) and sodium potassium adenosine triphosphatase (Sat), on living cancer cells.

Size changeable nanosystems for precise drug controlled release and efficient overcoming of cancer multidrug resistance

Herein we demonstrate the rational design of a size changeable nanosystem for precise drug controlled release and efficient overcoming of cancer multidrug resistance in cancer cells by enhancing the cellular uptake and inhibiting the expression of ABC family proteins.

Quantification of tunicamycin-induced protein expression and N-glycosylation changes in yeast

Tunicamycin is a potent protein N-glycosylation inhibitor that has frequently been used to manipulate protein glycosylation in cells. However, protein expression and glycosylation changes as a result of tunicamycin treatment are still unclear. Using yeast as a model system, we systematically investigated the cellular response to tunicamycin at the proteome and N-glycoproteome levels. By utilizing modern mass spectrometry-based proteomics, we quantified 4259 proteins, which nearly covers the entire yeast proteome. After the three-hour tunicamycin treatment, more than 5% of proteins were down-regulated by at least 2 fold, among which proteins related to several glycan metabolism and glycolysis-related pathways were highly enriched. Furthermore, several proteins in the canonical unfolded protein response pathway were up-regulated because the inhibition of protein N-glycosylation impacts protein folding and trafficking. We also comprehensively quantified protein glycosylation changes in tunicamycin-treated cells, and more than one third of quantified unique glycopeptides (168 of 465 peptides) were down-regulated. Proteins containing down-regulated glycopeptides were related to glycosylation, glycoprotein metabolic processes, carbohydrate processes, and cell wall organization according to gene ontology clustering. The current results provide the first global view of the cellular response to tunicamycin at the proteome and glycoproteome levels.