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.

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.

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.

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.

Imaging cellular forces with photonic crystals.

Current techniques for visualizing and quantifying cellular forces have limitations in live cell imaging, throughput, and multi-scale analysis, which impede progress in cell force research and its practical applications. We developed a photonic crystal cellular force microscopy (PCCFM) to image vertical cell forces over a wide field of view (1.3 mm ⨯ 1.0 mm, a 10 ⨯ objective image) at high speed (about 20 frames per second) without references. The photonic crystal hydrogel substrate (PCS) converts micro-nano deformations into perceivable color changes, enabling in situ visualization and quantification of tiny vertical cell forces with high throughput. It enabled long-term, cross-scale monitoring from subcellular focal adhesions to tissue-level cell sheets and aggregates.

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.

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.

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.

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.

Macrophage-Derived Exosomal miR-31-5p Promotes Oral Squamous Cell Carcinoma Tumourigenesis Through the Large Tumor Suppressor 2-Mediated Hippo Signalling Pathway.

Tumour-associated macrophages (TAMs) are thought to contribute to oral squamous cell carcinoma (OSCC) initiation and progression. However, the underlying mechanism through which TAMs foster OSCC progression is still unclear. This study intended to determine whether there are exclusively exosomal miRNAs-derived macrophages that are functionally necessary for OSCC progression. The phenotype of TAM recruitment in OSCC tissue samples was assessed, subsequently identifying the influence of M2 macrophages and exosomes derived from M2 macrophages on OSCC proliferation and tumorigenesis in vitro and in vivo. CD68 and CD163, the specific markers of M2 type macrophages, were upregulated in TAMs presented in intra-cancer tissues. M2 macrophages and M2 macrophage-derived exosomes (M2 exos) both can promote OSCC growth and tumorigenicity. An exosomal RNA-seq analysis was conducted to predict regulatory exosomal miRNAs related to OSCC growth, which determined miR-31-5p and LATS2 for subsequent experiments. Mechanistically, miR-31-5p was delivered to recipient OSCC cells through M2 exos and complementary pairing with the large tumor suppressor 2 (LATS2) coding sequence, thus suppressing the expression of LATS2 and inactivation the Hippo signaling pathway to support OSCC growth. Collectively, our findings demonstrate that M2 macrophage-derived exosomal miR- 31-5p can make tumor suppressor LATS2 gene inhibited and facilitate the progression of OSCC via inhibiting the Hippo signaling pathway, which possibly provides new targets for the molecular therapy of OSCC.

Robust Carbonated Structural Color Barcodes with Ultralow Ontology Fluorescence as Biomimic Culture Platform.

Photonic crystal (PC) barcodes are a new type of spectrum-encoding microcarriers used in multiplex high-throughput bioassays, such as broad analysis of biomarkers for clinical diagnosis, gene expression, and cell culture. Unfortunately, most of these existing PC barcodes suffered from undesired features, including difficult spectrum-signal acquisition, weak mechanical strength, and high ontology fluorescence, which limited their development to real applications. To address these limitations, we report a new type of structural color-encoded PC barcodes. The barcodes are fabricated by the assembly of monodisperse polydopamine- (PDA-) coated silica (PDA@SiO2) nanoparticles using a droplet-based microfluidic technique and followed by pyrolysis of PDA@SiO2 (C@SiO2) barcodes. Because of the templated carbonization of adhesive PDA, the prepared C@SiO2 PC beads were endowed with simultaneous easy-to-identify structural color, high mechanical strength, and ultralow ontology fluorescence. We demonstrated that the structural colored C@SiO2 barcodes not only maintained a high structural stability and good biocompatibility during the coculturing with fibroblasts and tumor cells capture but also achieved an enhanced fluorescent-reading signal-to-noise ratio in the fluorescence-reading detection. These features make the C@SiO2 PC barcodes versatile for expansive application in fluorescence-reading-based multibioassays.

Radiotherapy Enhancement for Human Pancreatic Carcinoma Using a Peptide-Gold Nanoparticle Hybrid.

Pancreatic ductal adenocarcinoma (PDAC) is radioresistant. Due to their strong X-ray absorption capacity, gold nanoparticles (AuNPs) have been used as radiosensitizers for cancer therapeutics. Herein, we describe a novel conjugate complex consisting of a peptide for targeting plectin-1 (PTP) specifically expressed on the PDAC cell membrane and AuNPs, termed AuNP-PTP, to be used for PDAC radiotherapy in vitro and in vivo. Previous studies revealed that compared with unmodified AuNPs, AuNP-PTP along with relevant low-energy X-ray irradiation of 6 MV at a dose of 2 Gy (RF) increased the targeting efficiency and induced apoptosis in treated PANC-1 cells and tumours. Importantly, extensive histopathological examination did not reveal evidence of acute or chronic injury in mice due to AuNPs or AuNP-PTP for up to six weeks despite the presence of X-ray exposure. The delicate AuNP-PTP hybrid provides a novel strategy to enhance radiotherapy efficiency in PDAC treatment.

Self-assembled colloidal arrays for structural color.

Structural color materials that are colloidally assembled as inspired by nature are attracting increased interest in a wide range of research fields. The assembly of colloidal particles provides a facile and cost-effective strategy for fabricating three-dimensional structural color materials. In this review, the generation mechanisms of structural colors from colloidally assembled photonic crystalline structures (PCSs) and photonic amorphous structures (PASs) are first presented, followed by the state-of-the-art and detailed technologies for their fabrication. The variable optical properties of PASs and PCSs are then discussed, focusing on their spatial long- and short-order structures and surface topography, followed by a detailed description of the modulation of structural color by refractive index and lattice distance. Finally, the current applications of structural color materials colloidally assembled in various fields including biomaterials, microfluidic chips, sensors, displays, and anticounterfeiting are reviewed, together with future applications and tasks to be accomplished.

Photonic crystal enhanced laser desorption and ionization substrate for detection of stress biomarkers under atmospheric pressure.

Enhanced efficiency for generating molecular ions is essential for high-throughput and sensitive detection using mass spectrometry in clinical diagnostics and biomarker discovery. In this study, we developed a novel strategy to promote laser desorption and ionization by using photonic crystals as substrates. The WO3-TiO2 inverse opal photonic crystal, with a coupling stop band and laser wavelength, significantly enhanced the efficiency of laser desorption and ionization owing to the slow light effect and the porous structure of the inverse opal, which increased the interaction between the laser and WO3-TiO2. Furthermore, stress biomarkers were conveniently measured under atmospheric pressure by using WO3-TiO2 inverse opal as an enhanced substrate to evaluate the impact of chronic unpredictable mild stress. The universal and highly sensitive substrate has promised for application in the highly sensitive detection and quantification of biomarkers.

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.

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.

Self-Reporting Colorimetric Analysis of Drug Release by Molecular Imprinted Structural Color Contact Lens.

As a prospective ophthalmic drug delivery device, contact lenses attract a lot of attention because of the improved drug residence time and bioavailability. Herein, we proposed and fabricated a molecular imprinted structural color contact lens for sustained timolol release which could self-report the release process by color change. The specific recognition of target timolol by molecular imprinted sites can not only increase the loading amount and the residence time of the drug but also endow the structure color of lens remarkable blue shift with the accumulative release of timolol. The fascinating contact lens can be further used for controlling release of a large number of ophthalmic drugs and has high potential to be a new generation of functional contact lenses.

Robust, Highly Visible, and Facile Bioconjugation Colloidal Crystal Beads for Bioassay.

High mechanical strength, highly visible, and admirable grafting molecular ability is the key challenge for colloidal photonic crystal (CPC) barcode beads in multiplex analysis fields. To achieve this goal, we proposed self-adhesion particles, polydopamine-coated SiO2 nanoparticles (PDA@SiO2), to construct CPC barcode beads by droplet-based microfluidic approach. Because of the adhesion, broad absorption of light, and "active" functional groups of PDA, the beads are endowed with high robustness, visibility, and excellent biomolecule immobilization. Ultrasonic treatment and compression experiments demonstrated that PDA@SiO2 CPC barcode beads have a high mechanical strength. Color analysis illustrated that PDA@SiO2 CPC beads exhibited a high visibility in color. The verification of fluorescent-tagged biomolecule conjugation together with the antigen detection stated that PDA@SiO2 CPC beads are capable of immobilizing biomolecule by covalent binding. With a sandwich format, the beads were applied to analyze the tumor makers including alpha fetal protein, carcinoembryonic antigen, and prostate specific antigen from practical clinical serum. The proposed suspension arrays using PDA@SiO2 CPC beads as a barcode showed acceptable accuracy and detection reproducibility.

Morphology, Migration, and Transcriptome Analysis of Schwann Cell Culture on Butterfly Wings with Different Surface Architectures.

It has been shown that material surface topography greatly affects cell attachment, growth, proliferation, and differentiation. However, the underlying molecular mechanisms for cell-material interactions are still not understood well. Here, two kinds of butterfly wings with different surface architectures were employed for addressing such an issue. Papilio ulysses telegonus (P.u.t.) butterfly wing surface is composed of micro/nanoconcaves, whereas Morpho menelaus (M.m.) butterfly wings are decorated with grooves. RSC96 cells grown on M.m. wings showed a regular sorting pattern along with the grooves. On the contrary, the cells seeded on P.u.t. wings exhibited random arrangement. Transcriptome sequencing and bioinformatics analysis revealed that huntingtin (Htt)-regulated lysosome activity is a potential key factor for determining cell growth behavior on M.m. butterfly wings. Gene silence further confirmed this notion. In vivo experiments showed that the silicone tubes fabricated with M.m. wings markedly facilitate rat sciatic nerve regeneration after injury. Lysosome activity and Htt expression were greatly increased in the M.m. wing-fabricated graft-bridged nerves. Collectively, our data provide a theoretical basis for employing butterfly wings to construct biomimetic nerve grafts and establish Htt lysosome as a crucial regulator for cell-material interactions.