Label-Free Multiple Reaction Monitoring-Mass Spectrometry for Quantifying Phosphopeptides from Extracellular Vesicles.

Increasing efforts have been made to develop proteins in circulating extracellular vesicles (EVs) as potential disease markers. It is in particular intriguing to measure post-translational modifications (PTMs) such as phosphorylation, preserved and stable in EVs. To facilitate the quantitative measurement of EV protein phosphorylation for potential clinical use, a label-free (LF) multiple reaction monitoring (MRM) strategy is introduced by utilizing a synthetic phosphopeptide set (phos-iRT) as the internal standards and a local normalization method. The quantitation method was investigated in terms of its linear dynamic range, sensitivity, accuracy, precision, and matrix effect, with a dynamic range spanning from 10 to 1000 ng/mL and an accuracy ranging from 82.4 to 116.8% for EV samples. Then, the LF-MRM-based local normalization method was utilized to evaluate and optimize our recently developed EVTOP method for the enrichment of phosphopeptides from EVs. Finally, we applied the optimized EV enrichment approach and the LF-MRM-based local normalization method to quantify phosphopeptides in urine EVs from patients with prostate cancer (PCa) and healthy individuals, showcasing the strategy's superiority in quantifying phosphopeptides without isotopic internal standards and validating that the method is generally applicable in MRM-based EV phosphopeptide quantification.

Targeted Phosphoproteomics of Human Saliva Extracellular Vesicles via Multiple Reaction Monitoring Cubed (MRM3).

Oral squamous cell carcinoma (OSCC) has become a global health problem due to its increasing incidence and high mortality rate. Early intervention through monitoring of the diagnostic biomarker levels during OSCC treatment is critical. Extracellular vesicles (EVs) are emerging surrogates in intercellular communication through transporting biomolecule cargo and have recently been identified as a potential source of biomarkers such as phosphoproteins for many diseases. Here, we developed a multiple reaction monitoring cubed (MRM3) method coupled with a novel sample preparation strategy, extracellular vesicles to phosphoproteins (EVTOP), to quantify phosphoproteins using a minimal amount of saliva (50 µL) samples from OSCC patients with high specificity and sensitivity. Our results established differential patterns in the phosphopeptide content of healthy, presurgery, and postsurgery OSCC patient groups. Notably, we discovered significantly increased salivary phosphorylated alpha-amylase (AMY) in the postsurgery group compared to the presurgery group. We hereby present the first targeted MS method with extremely high sensitivity for measuring endogenous phosphoproteins in human saliva EVs.

Assessment of urine sample collection and processing variables for extracellular vesicle-based proteomics.

Extracellular vesicles (EVs) in urine are a promising source for developing non-invasive biomarkers. However, urine concentration and content are highly variable and dynamic, and actual urine collection and handling often is nonideal. Furthermore, patients such as those with prostate diseases have challenges in sample collection due to difficulties in holding urine at designated time points. Here, we simulated the actual situation of clinical sample collection to examine the stability of EVs in urine under different circumstances, including urine collection time and temporary storage temperature, as well as daily urine sampling under different diet conditions. EVs were isolated using functionalized EVtrap magnetic beads and characterized by nanoparticle tracking analysis (NTA), western blotting, electron microscopy, and mass spectrometry (MS). EVs in urine remained relatively stable during temporary storage for 6 hours at room temperature and for 12 hours at 4 °C, while significant fluctuations were observed in EV amounts from urine samples collected at different time points from the same individuals, especially under certain diets. Sample normalization with creatinine reduced the coefficient of variation (CV) values among EV samples from 17% to approximately 6% and facilitated downstream MS analyses. Finally, based on the results, we applied them to evaluate potential biomarker panels in prostate cancer by data-independent acquisition (DIA) MS, presenting the recommendation that can facilitate biomarker discovery with nonideal handling conditions.

Research progress in the development of 3D skin models and their application to in vitro skin irritation testing.

Toxicological assessment of chemicals is crucial for safeguarding human health and the environment. However, traditional animal experiments are associated with ethical, technical, and predictive limitations in assessing the toxicity of chemicals to the skin. With the recent development of bioengineering and tissue engineering, three-dimensional (3D) skin models have been commonly used as an alternative for toxicological studies. The skin consists of the subcutaneous, dermis, and epidermis. All these layers have crucial functions such as physical and biological protection and thermoregulation. The epidermis is the shallowest layer protecting against external substances and media. Because the skin is the first contact point for many substances, this organ is very significant for assessing local toxicity following skin exposure. According to the classification of the United Nations Global Harmonized System, skin irritation is a major potentially hazardous characteristic of chemicals, and this characteristic must be accurately assessed and classified for enhancing chemical safety management and preventing and reducing chemical accidents. This review discusses the research progress of 3D skin models and introduces their application in assessing chemical skin irritation.

Proteomic and phosphoproteomic landscape of salivary extracellular vesicles to assess OSCC therapeutical outcomes.

Circulating extracellular vesicles (EVs) have emerged as an appealing source for surrogates to evaluate the disease status. Herein, we present a novel proteomic strategy to identify proteins and phosphoproteins from salivary EVs to distinguish oral squamous cell carcinoma (OSCC) patients from healthy individuals and explore the feasibility to evaluate therapeutical outcomes. Bi-functionalized magnetic beads (BiMBs) with Ti (IV) ions and a lipid analog, 1,2-Distearoyl-3-sn-glycerophosphoethanolamine (DSPE) are developed to efficiently isolate EVs from small volume of saliva. In the discovery stage, label-free proteomics and phosphoproteomics quantification showed 315 upregulated proteins and 132 upregulated phosphoproteins in OSCC patients among more than 2500 EV proteins and 1000 EV phosphoproteins, respectively. We further applied targeted proteomics by coupling parallel reaction monitoring with parallel accumulation-serial fragmentation (prm-PASEF) to measure panels of proteins and phosphoproteins from salivary EVs collected before and after surgical resection. A panel of three total proteins and three phosphoproteins, most of which have previously been associated with OSCC and other cancer types, show sensitive response to the therapy in individual patients. Our study presents a novel strategy to the discovery of effective biomarkers for non-invasive assessment of OSCC surgical outcomes with small amount of saliva.

Phosphoproteome analysis of cerebrospinal fluid extracellular vesicles in primary central nervous system lymphoma.

Primary central nervous system lymphoma (PCNSL) is a rare but highly aggressive extra-nodal non-Hodgkin's lymphoma, mostly of the diffuse large B-cell lymphoma (DLBCL) type. The present invasive diagnosis and poor prognosis of PCNSL propose an urgent need to develop molecular markers for early detection, real-time monitoring and treatment evaluation. Cerebrospinal fluid (CSF)-derived extracellular vesicles (EVs) are promising biomarker carriers for liquid biopsy of CNS diseases and brain tumors; however, research remains challenging due to the low concentration of EVs in the limited available volume of CSF from each individual patient and the low efficiency of existing methods for EV enrichment. Here, we introduce functionalized magnetic beads called EVTRAP (extracellular vesicles total recovery and purification) for rapid and efficient EV isolation from CSF. By coupling with high-performance mass spectrometry, over 19 000 peptides representing 1841 proteins were identified from just 30 µL of CSF. Furthermore, up to 3000 phosphopeptides representing over 1000 phosphoproteins were identified from about 2 mL of CSF. Finally, we analyzed the EV phosphoproteomics of CSF samples from PCNSL patients and non-PCNSL controls. Among them, multiple phosphoproteins related to PCNSL, including SPP1, MARCKS, NPM1 and VIM, were shown to be up-regulated in the PCNSL group. These results demonstrated the feasibility of the EVTRAP-based analytical strategy in CSF EV phosphoproteomic analysis of PCNSL molecular markers.

Bifunctional Microbead Carriers with Magnetic Response and Plasmonic Fluorescence Enhancement.

In this work, we combine the magnetic microbeads fabricated by microfluidics with nanoplasmonic-assisted fluorescence enhancement for the first time. These bifunctional microbeads not only have high fluorescence enhancement factor but also have magnetic response. The magnetic polymer microbeads were generated by capillary microfluidic device and then coated uniformly by the gold nano-islands layer. By enhancing the electric field and improving the quantum yield of the fluorescent dye, the fluorescence intensity of Dylight 800 dye has increased about 121 fold. These results demonstrate that these fluorescence enhancement magnetic microbeads have potential for developing high sensitively automatic detection systems.

Effect of verbascoside on apoptosis and metastasis in human oral squamous cell carcinoma.

Despite significant advances in therapy, the 5-year survival rates for patients with advanced stage oral cancers still remains poor as an appropriate treatment has not been found yet, due to side effects of chemo/radiotherapy. Verbascoside (VB), a major bioactive constituent of the Tsoong herb, displays pharmacological properties by exhibiting anti-oxidative, anti-inflammatory and anti-cancer activities. However, the underlining function and mechanism of VB in human oral squamous cell carcinoma (OSCC) remains unclear. In this study, we show that VB significantly decreased the viability and metastasis of HN4 and HN6 tumor cells, while promoting apoptosis. A xenograft OSCC mouse model further showed that intraperitoneal injection of VB strongly inhibited growth and lung metastasis of implanted tumor cells. Immunoblot analysis confirmed that VB effectively suppressed nuclear factor (NF)-κB activation and downstream Bcl-2/Bcl-XL expression, resulting in increased OSCC cell apoptosis. In addition, VB suppressed mRNA and protein expression of matrix metalloproteinase-9 via suppression of NF-κB activation, thereby inhibiting tumor cell metastasis. Inspiringly, compared to cisplatin-treated group, VB is a biocompatible agent without signficant side effects in vivo. Collectively, our results demonstrate that VB effectively inhibits OSCC tumor cell growth and metastasis via suppression of IκB kinase complex (IKK)/NF-κB-related signaling activation, suggesting that VB has potential use as a potent anticancer agent in OSCC therapeutic strategies.

Clickable Colloidal Photonic Crystals for Structural Color Pattern.

Patterning colloidal photonic crystals have broad important applications in optical devices, functional coatings, full color displays, and colorimetric sensors. In this paper, a clickable colloidal photonic crystal using vinyl-modified sub-micrometer silica particles as building blocks was proposed to pattern photonic crystals. By click chemistry, different chemical groups were simply grafted to the clickable photonic crystals film and obtained wettability-encoded structure color patterns. The clickable photonic crystals provide a simple, controllable, and rapid path to pattern photonic crystals.

Carbon Inverse Opal Rods for Nonenzymatic Cholesterol Detection.

Carbon inverse opal rods made from silica photonic crystal rods are used for nonenzymatic cholesterol sensing. The characteristic reflection peak originating from the physical periodic structure works as sensing signals for quantitatively estimating cholesterol concentrations. Carbon inverse opal rods work both in cholesterol standard solutions and human serum. They are suitable for practical use in clinical diagnose.

Microfluidic synthesis of barcode particles for multiplex assays.

The increasing use of high-throughput assays in biomedical applications, including drug discovery and clinical diagnostics, demands effective strategies for multiplexing. One promising strategy is the use of barcode particles that encode information about their specific compositions and enable simple identification. Various encoding mechanisms, including spectroscopic, graphical, electronic, and physical encoding, have been proposed for the provision of sufficient identification codes for the barcode particles. These particles are synthesized in various ways. Microfluidics is an effective approach that has created exciting avenues of scientific research in barcode particle synthesis. The resultant particles have found important application in the detection of multiple biological species as they have properties of high flexibility, fast reaction times, less reagent consumption, and good repeatability. In this paper, research progress in the microfluidic synthesis of barcode particles for multiplex assays is discussed. After introducing the general developing strategies of the barcode particles, the focus is on studies of microfluidics, including their design, fabrication, and application in the generation of barcode particles. Applications of the achieved barcode particles in multiplex assays will be described and emphasized. The prospects for future development of these barcode particles are also presented.

Self-assembled coffee-ring colloidal crystals for structurally colored contact lenses.

A circlular structural-colored contact lens is reported, which is fabricated by replicating self-assembled colloidal photonic crystal templates. The structural-colored contact lenses not only display variable and brilliant color under light illumination, but also avoid the addition of any colorants to the hydrogel lenses and prevent the potential harm posed by traditional colored contact lenses.

New strategy for surface functionalization of periodic mesoporous silica based on meso-HSiO1.5.

Organic functionalization of periodic mesoporous silicas (PMSs) offers a way to improve their excellent properties and wide applications owing to their structural superiority. In this study, a new strategy for organic functionalization of PMSs is demonstrated by hydrosilylation of the recently discovered "impossible" periodic mesoporous hydridosilica, meso-HSiO1.5. This method overcomes the disadvantages of present pathways for organic functionalization of PMSs with organosilica. Moreover, compared to the traditional functionalization on the surface of porous silicon by hydrosilylation, the template-synthesized meso-HSiO1.5 is more flexible to access functional-groups-loaded PMSs with adjustable microstructures. The new method and materials will have wider applications based on both the structure and surface superiorities.

MiRS-HF: A Novel Deep Learning Predictor for Cancer Classification and miRNA Expression Patterns.

Cancer classification and biomarker identification are crucial for guiding personalized treatment. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. We propose an approach for cancer classification called MiRNA Selection and Hybrid Fusion (MiRS-HF), which consists of early fusion and intermediate fusion. The early fusion involves applying a Layer Attention Graph Convolutional Network (LAGCN) to a miRNA-disease heterogeneous network, resulting in a miRNA-disease association degree score matrix. The intermediate fusion employs a Graph Convolutional Network (GCN) in the classification tasks, weighting the expression data based on the miRNA-disease association degree score. Furthermore, MiRS-HF can identify the important miRNA biomarkers and their expression patterns. The proposed method demonstrates superior performance in the classification tasks of six cancers compared to other methods. Simultaneously, we incorporated the feature weighting strategy into the comparison algorithm, leading to a significant improvement in the algorithm's results, highlighting the extreme importance of this strategy.

Hierarchical Dendritic Photonic Crystal Beads for Efficient Isolation and Proteomic Analysis of Multiple Cell Types.

Cell types with different morphology, and function collaborate to maintain organ function. As such, analyzing proteomic differences and connections between different types of cells forms the foundation for establishing functional connectomes and developing in vitro organoid simulation experiments. However, the efficiency of cell type isolation from organs is limited by time, equipment, and cost. Here, hierarchical dendritic photonic crystal beads (HDPCBs) featuring high-density functional groups via the self-assembly of dendritic mesoporous structure SiO2 nanoparticles (DM-SiO2) and grafting dendrimers onto the surface of dendritic mesoporous photonic crystal beads (DMPCBs) is developed. This platform integrates multitype cell separation with in situ protein cleavage processes. Efficient simultaneous isolation of Kupffer cells and Liver Sinusoidal Endothelial cells (LSECs) from liver, with high specificity and convenient operation in a short separation time are demonstrated. The results reveal 2832 and 3442 unique proteins identified in Kupffer cells and LSECs using only 50 HDPCBs, respectively. 764 and 629 over-expressed proteins associated with the function of Kupffer cells and LSECs are found, respectively. The work offers a new method for efficiently isolating multiple cell types from tissues and downstream proteomic analysis, ultimately facilitating the identification of primary cell compositions and functions.

Bioinspired multifunctional Janus particles for droplet manipulation.

Inspired by the nipple arrays covering mosquitoes' eyes and the heterogeneous textured bumps on beetles' backs, we have developed a new kind of Janus particle with multiplexed features, such as different boss arrays and wettability compartmentalized on the same surface, and an anisotropic color and magnetic properties. The prepared Janus particles can be anchored at the air-water interface and act as a highly flexible barrier for preventing coalescence of water droplets. The incorporation of magnetic nanoparticles can give the Janus particles magnetic responsiveness for controlled transportation and coalescence of liquid marbles, while the structural colors in the Janus particles can be employed for barcoding of the encapsulated liquid marbles. We believe that these small Janus particles have great potential as components for constructing intelligent interfacial objects.

Tailoring colloidal photonic crystals with wide viewing angles.

Photonic crystal materials are developed from colloidal crystal fibers or beads. As the fibers have cylindrical symmetry, the fiber-composed PhCs show anisotropic angle independence. By contrast, the bead-composed PhCs display angle-independent structural colors because of the spherical symmetry of their bead elements.

Bio-inspired variable structural color materials.

Natural structural color materials, especially those that can undergo reversible changes, are attracting increasing interest in a wide variety of research fields. Inspired by the natural creatures, many elaborately nanostructured photonic materials with variable structural colors were developed. These materials have found important applications in switches, display devices, sensors, and so on. In this critical review, we will provide up-to-date research concerning the natural and bio-inspired photonic materials with variable structural colors. After introducing the variable structural colors in natural creatures, we will focus on the studies of artificial variable structural color photonic materials, including their bio-inspired designs, fabrications and applications. The prospects for the future development of these fantastic variable structural color materials will also be presented. We believe this review will promote the communications among biology, bionics, chemistry, optical physics, and material science (196 references).

3D gradient printing based on digital light processing.

3D gradient printing is a type of fabrication technique that builds three-dimensional objects with gradually changing properties. Gradient digital light processing based 3D printing has garnered considerable attention in recent years. This function-oriented technology precisely manipulates the performance of different positions of materials and prints them as a monolithic structure to realize specific functions. This review presents a conceptual understanding of gradient properties, covering an overview of current techniques and materials that can produce gradient structures, as well as their limitations and challenges. The principle of digital light processing (DLP) technology and feasible strategies for 3D gradient printing to overcome any barriers are also presented. Additionally, this review discusses the promising future of 4D bioprinting systems based on DLP printing.

A small pore black TiO2/-large pore Fe3O4 cascade nanoreactor for chemodynamic/photothermal synergetic tumour therapy.

Various unique spatial structures are often found in the enzymes of biological systems. From the consideration of bionics, it is challenging but meaningful to design nanozymes with distinctive structures to enhance their bioactivities. To explore the relationship between the structure and activity of nanozymes, in this work, a special structural nanoreactor, namely small pore black TiO2 coated/doped large pore Fe3O4 (TiO2/-Fe3O4) loaded with lactate oxidase (LOD), was constructed for chemodynamic and photothermal synergistic therapy. Specifically, LOD loaded on the surface of the TiO2/-Fe3O4 nanozyme alleviates the low level of H2O2 in the tumour microenvironment (TME); the black TiO2 shell with multiple pinhole channels and a large specific surface area not only facilitates LOD loading, but also enhances the affinity of the nanozyme for H2O2; H2O2 is continuously enriched on the surface of the TiO2/-Fe3O4 nanozyme and transmitted to mesoporous Fe3O4, in turn efficiently producing abundant toxic hydroxyl radicals (˙OH) for chemodynamic therapy. Meanwhile, the TiO2/-Fe3O4 nanozyme under 1120 nm laser irradiation has excellent photothermal conversion efficiency (η = 41.9%), and further accelerates the production of ˙OH for amplifying the chemodynamic therapy efficiency. This self-cascading, special structure nanozyme provides a novel strategy for application in highly efficient tumour synergetic therapy.