None of us is the same as all of us: resolving the heterogeneity of extracellular vesicles using single-vesicle, nanoscale characterization with resonance enhanced atomic force microscope infrared spectroscopy (AFM-IR)

Observation of Ice-Like Two-Dimensional Flakes on Self-Assembled Protein Monolayer without Nanoconfinement under Ambient Conditions

Directly correlating the morphology and composition of interfacial water is vital not only for studying water icing under critical conditions but also for understanding the role of protein-water interactions in bio-relevant systems. In this study, we present a model system to study two-dimensional (2D) water layers under ambient conditions by using self-assembled monolayers (SAMs) supporting the physisorption of the Cytochrome C (Cyt C) protein layer. We observed that the 2D island-like water layers were uniformly distributed on the SAMs as characterized by atomic force microscopy, and their composition was confirmed by nano-atomic force microscopy-infrared spectroscopy and Raman spectroscopy. In addition, these 2D flakes could grow under high-humidity conditions or melt upon the introduction of a heat source. The formation of these flakes is attributed to the activation energy for water desorption from the Cyt C being nearly twofold high than that from the SAMs. Our results provide a new and effective method for further understanding the water-protein interactions.

Profiling the extracellular vesicles of two human placenta-derived mesenchymal stromal cell populations

Increasing evidence shows extracellular vesicles (EVs) are primarily responsible for the beneficial effects of cell-based therapies. EVs derived from mesenchymal stromal cells (MSCs) show promise as a source of EVs for cell-free therapies. The human placental fetal-maternal interface is a rich and abundant source of MSCs from which EVs can be isolated. This study focusses on chorionic MSCs (CMSC) located on the fetal aspect of the interface and decidual MSCs (DMSC) on the maternal aspect. This study used Ligand-based Exosome Affinity Purification (LEAP) chromatography to isolate EVs from well-characterized placental hTERT-transduced CMSC29 and DMSC23 cell lines, which retain many important stem cell-like properties of primary CMSC and DMSC, respectively. After initial biophysical characterization of the EVs isolated from each cell line, the biological activities and the protein, lipid and small RNA contents of CMSC29-EVs and DMSC23-EVs were compared and assessed. LEAP-purified EVs from both sources were validated at the biophysical level by Spectradyne, Cryo-Transmission Electron Microscopy (Cryo-TEM), and Western blot analysis. EVs from each type were labelled with the live cell stain PKH26 and their in vitro uptake and internalization by human dermal fibroblast cells was assessed, as well as their phosphorylation of the protein kinase B/AKT (AKT) pathway. The protein and lipid contents were analyzed by mass spectrometry and the nucleic acid content by RNA sequencing (RNA-seq). Lastly, the biological activities of the EVs were evaluated in a BioMAP® Diversity PLUS® screen system across a panel of 12 human primary cell-based systems and in vitro cell proliferation. EVs isolated from both DMSC23 and CMSC29 significantly increased proliferation of fibroblasts and showed phosphorylation of the AKT pathway. Protein mass spectrometry analysis identified a large number of proteins including cell surface receptors, cytokines, chemokines, matrix molecules and enzymes in both EV types. Lipidomic analysis identified species including phosphatidylcholine, triacylglycerides and diacylglycerides in both DMSC23 and CMSC29-derived EVs. There were some significant differences in identified microRNAs (miRNAs) between the two EV types. The top differentially expressed miRNAs between the two EV types show pathways association with matrix interaction, transcriptional regulation, proliferation, cellular protein modification processes, and vasculogenesis. Differences were also detected between DMSC23- and CMSC29-EVs in the biological activity they displayed in the BioMAP® Diversity PLUS® screen.

Single extracellular vesicle research: From cell population to a single cell

Extracellular vesicles (EVs) are secreted by cells with a membrane structure and complex components such as DNA, RNA and proteins. These biomolecules play an important role in cell communication, cell proliferation, cell migration, vascularization, immune response and other physiological and pathological processes. Most current research on EVs focused on populations of EVs. Heterogeneity of EVs is neglected. Considering the heterogeneity of single EVs may offer critical molecular insights into cell-cell interactions, it is necessary to enhance our understanding about molecular characteristics from EVs derived from cell population to a single EV of derived from a single cell. This transformation is expected to provide a new insight into the understanding of cellular biology and the accurate description of the law of disease progress. In this article, we review the current research progress of single EV analysis technology for single EVs derived from cell population (SECP) and discuss its main applications in biological and clinical medicine research. After that, we propose the development direction, main difficulties and application prospect of single EV analysis technology for single EVs derived from single cells (SESC) according to our own research work, to provide new perspectives for the field of EV research.

Exploring novel circulating biomarkers for liver cancer through extracellular vesicle characterization with infrared spectroscopy and plasmonics

BACKGROUND

Hepatocellular carcinoma (HCC) is the most common form of liver cancer, with cirrhosis being a major risk factor. Traditional blood markers like alpha-fetoprotein (AFP) demonstrate limited efficacy in distinguishing between HCC and cirrhosis, underscoring the need for more effective diagnostic methodologies. In this context, extracellular vesicles (EVs) have emerged as promising candidates; however, their practical diagnostic application is restricted by the current lack of label-free methods to accurately profile their molecular content. To address this gap, our study explores the potential of mid-infrared (mid-IR) spectroscopy, both alone and in combination with plasmonic nanostructures, to detect and characterize circulating EVs.

RESULTS

EVs were extracted from HCC and cirrhotic patients. Mid-IR spectroscopy in the Attenuated Total Reflection (ATR) mode was utilized to identify potential signatures for patient classification, highlighting significant changes in the Amide I-II region (1475-1700 cm-1). This signature demonstrated diagnostic performance comparable to AFP and surpassed it when the two markers were combined. Further investigations utilized a plasmonic metasurface suitable for ultrasensitive spectroscopy within this spectral range. This device consists of two sets of parallel rod-shaped gold nanoantennas (NAs); the longer NAs produced an intense near-field amplification in the Amide I-II bands, while the shorter NAs were utilized to provide a sharp reflectivity edge at 1800-2200 cm-1 for EV mass-sensing. A clinically relevant subpopulation of EVs was targeted by conjugating NAs with an antibody specific to Epithelial Cell Adhesion Molecule (EpCAM). This methodology enabled the detection of variations in the quantity of EpCAM-presenting EVs and revealed changes in the Amide I-II lineshape.

SIGNIFICANCE

The presented results can positively impact the development of novel laboratory methods for the label-free characterization of EVs, based on the combination between mid-IR spectroscopy and plasmonics. Additionally, data obtained by using HCC and cirrhotic subjects as a model system, suggest that this approach could be adapted for monitoring these conditions.

Fast Nano-IR Hyperspectral Imaging Empowered by Large-Dataset-Free Miniaturized Spatial-Spectral Network

The emerging field of nanoscale infrared (nano-IR) offers label-free molecular contrast, yet its imaging speed is limited by point-by-point traverse acquisition of a three-dimensional (3D) data cube. Here, we develop a spatial-spectral network (SS-Net), a miniaturized deep-learning model, together with compressive sampling to accelerate the nano-IR imaging. The compressive sampling is performed in both the spatial and spectral domains to accelerate the imaging process. The SS-Net is trained to learn the mapping from small nano-IR image patches to the corresponding spectra. With this elaborated mapping strategy, the training can be finished quickly within several minutes using the subsampled data, eliminating the need for a large-labeled dataset of common deep learning methods. We also designed an efficient loss function, which incorporates the image and spectral similarity to enhance the training. We first validate the SS-Net on an open stimulated Raman-scattering dataset; the results exhibit the potential of 10-fold imaging speed improvement with state-of-the-art performance. We then demonstrate the versatility of this approach on atomic force microscopy infrared (AFM-IR) microscopy with 7-fold imaging speed improvement, even on nanoscale Fourier transform infrared (nano-FTIR) microscopy with up to 261.6 folds faster imaging speed. We further showcase the generalization of this method on AFM-force volume-based multiparametric nanoimaging. This method establishes a paradigm for rapid nano-IR imaging, opening new possibilities for cutting-edge research in materials, photonics, and beyond.

Extracellular vesicles in cancer therapy: Roles, potential application, and challenges

Extracellular vesicles (EVs) have emerged as a novel cell-free strategy for the treatment of many diseases including cancer as they play important roles in cancer development and progression. Considering their natural capacity to facilitate cell-to-cell communication as well as their high physiochemical stability and biocompatibility, EVs serve as superior delivery systems for a wide range of therapeutic agents, including medicines, nanomaterials, nucleic acids, and proteins. Therefore, EVs-based cancer therapy is of greater interest to researchers. Mounting studies indicate that EVs can be improved in efficiency, specificity, and safety for cancer therapy. However, their heterogeneity of physicochemical properties and functions is not fully understood, hindering the achievement of bioactive EVs with high yield and purity. Herein, we paid more attention to the EVs applications and their significance in cancer therapy.

Advancements in Mid-Infrared spectroscopy of extracellular vesicles

Extracellular vesicles (EVs) are lipid vesicles secreted by all cells into the extracellular space and act as nanosized biological messengers among cells. They carry a specific molecular cargo, composed of lipids, proteins, nucleic acids, and carbohydrates, which reflects the state of their parent cells. Due to their remarkable structural and compositional heterogeneity, characterizing EVs, particularly from a biochemical perspective, presents complex challenges. In this context, mid-infrared (IR) spectroscopy is emerging as a valuable tool, providing researchers with a comprehensive and label-free spectral fingerprint of EVs in terms of their specific molecular content. This review aims to provide an up-to-date critical overview of the major advancements in mid-IR spectroscopy of extracellular vesicles, encompassing both fundamental and applied research achievements. We also systematically emphasize the new possibilities offered by the integration of emerging cutting-edge IR technologies, such as tip-enhanced and surface-enhanced spectroscopy approaches, along with the growing use of machine learning for data analysis and spectral interpretation. Additionally, to assist researchers in navigating this intricate subject, our manuscript includes a wide and detailed collection of the spectral peaks that have been assigned to EV molecular constituents up to now in the literature.

AFM-IR for Nanoscale Chemical Characterization in Life Sciences: Recent Developments and Future Directions

Despite the ubiquitous absorption of mid-infrared (IR) radiation by virtually all molecules that belong to the major biomolecules groups (proteins, lipids, carbohydrates, nucleic acids), the application of conventional IR microscopy to the life sciences remained somewhat limited, due to the restrictions on spatial resolution imposed by the diffraction limit (in the order of several micrometers). This issue is addressed by AFM-IR, a scanning probe-based technique that allows for chemical analysis at the nanoscale with resolutions down to 10 nm and thus has the potential to contribute to the investigation of nano and microscale biological processes. In this perspective, in addition to a concise description of the working principles and operating modes of AFM-IR, we present and evaluate the latest key applications of AFM-IR to the life sciences, summarizing what the technique has to offer to this field. Furthermore, we discuss the most relevant current limitations and point out potential future developments and areas for further application for fruitful interdisciplinary collaboration.

Extracellular Vesicles: Techniques and Biomedical Applications Related to Single Vesicle Analysis

Extracellular vesicles (EVs) are extensively dispersed lipid bilayer membrane vesicles involved in the delivery and transportation of molecular payloads to certain cell types to facilitate intercellular interactions. Their significant roles in physiological and pathological processes make EVs outstanding biomarkers for disease diagnosis and treatment monitoring as well as ideal candidates for drug delivery. Nevertheless, differences in the biogenesis processes among EV subpopulations have led to a diversity of biophysical characteristics and molecular cargos. Additionally, the prevalent heterogeneity of EVs has been found to substantially hamper the sensitivity and accuracy of disease diagnosis and therapeutic monitoring, thus impeding the advancement of clinical applications. In recent years, the evolution of single EV (SEV) analysis has enabled an in-depth comprehension of the physical properties, molecular composition, and biological roles of EVs at the individual vesicle level. This review examines the sample acquisition tactics prior to SEV analysis, i.e., EV isolation techniques, and outlines the current state-of-the-art label-free and label-based technologies for SEV identification. Furthermore, the challenges and prospects of biomedical applications based on SEV analysis are systematically discussed.

Treatment of Cardiac Fibrosis with Extracellular Vesicles: What Is Missing for Clinical Translation?

Heart failure is the leading cause of morbidity and mortality and currently affects more than 60 million people worldwide. A key feature in the pathogenesis of almost all forms of heart failure is cardiac fibrosis, which is characterized by excessive accumulation of extracellular matrix components in the heart. Although cardiac fibrosis is beneficial in the short term after acute myocardial injury to preserve the structural and functional integrity of the heart, persistent cardiac fibrosis contributes to pathological cardiac remodeling, leading to mechanical and electrical dysfunction of the heart. Despite its high prevalence, standard therapies specifically targeting cardiac fibrosis are not yet available. Cell-based approaches have been extensively studied as potential treatments for cardiac fibrosis, but several challenges have been identified during clinical translation. The observation that extracellular vesicles (EVs) derived from stem and progenitor cells exhibit some of the therapeutic effects of the parent cells has paved the way to overcome limitations associated with cell therapy. However, to make EV-based products a reality, standardized methods for EV production, isolation, characterization, and storage must be established, along with concrete evidence of their safety and efficacy in clinical trials. This article discusses EVs as novel therapeutics for cardiac fibrosis from a translational perspective.

Nanostructures and Nanotechnologies for the Detection of Extracellular Vesicle

Liquid biopsy has been taken as a minimally invasive examination and a promising surrogate to the clinically applied tissue-based test for the diagnosis and molecular analysis of cancer. Extracellular vesicles (EVs) carry complex molecular information from the tumor, allowing for the multicomponent analysis of cancer and would be beneficial to personalized medicine. In this review, the advanced nanomaterials and nanotechniques for the detection and molecular profiling of EVs, highlight the advantages of nanotechnology in the high-purity isolation and the high-sensitive and high-specific identification of EVs, are summarized. An outlook on the clinical application of nanotechnology-based liquid biopsy in the diagnosis, prognostication, and surveillance of cancer is also provided. It provides information for developing liquid biopsy based on EVs by discussing the advantages and challenges of functionalized nanomaterials and various nanotechnologies.

Progress of Endogenous and Exogenous Nanoparticles for Cancer Therapy and Diagnostics

The focus of this brief review is to describe the application of nanoparticles, including endogenous nanoparticles (e.g., extracellular vesicles, EVs, and virus capsids) and exogenous nanoparticles (e.g., organic and inorganic materials) in cancer therapy and diagnostics. In this review, we mainly focused on EVs, where a recent study demonstrated that EVs secreted from cancer cells are associated with malignant alterations in cancer. EVs are expected to be used for cancer diagnostics by analyzing their informative cargo. Exogenous nanoparticles are also used in cancer diagnostics as imaging probes because they can be easily functionalized. Nanoparticles are promising targets for drug delivery system (DDS) development and have recently been actively studied. In this review, we introduce nanoparticles as a powerful tool in the field of cancer therapy and diagnostics and discuss issues and future prospects.

Current Advances in Technologies for Single Extracellular Vesicle Analysis and Its Clinical Applications in Cancer Diagnosis

Extracellular vesicles (EVs) have been regarded as one of the most potential diagnostic biomarkers for different cancers, due to their unique physiological and pathological functions. However, it is still challenging to precisely analyze the contents and sources of EVs, due to their heterogeneity. Herein, we summarize the advances in technologies for a single EV analysis, which may provide new strategies to study the heterogeneity of EVs, as well as their cargo, more specifically. Furthermore, the applications of a single EV analysis on cancer early diagnosis are also discussed.

The Convergence of FTIR and EVs: Emergence Strategy for Non-Invasive Cancer Markers Discovery

In conjunction with imaging analysis, pathology-based assessments of biopsied tissue are the gold standard for diagnosing solid tumors. However, the disadvantages of tissue biopsies, such as being invasive, time-consuming, and labor-intensive, have urged the development of an alternate method, liquid biopsy, that involves sampling and clinical assessment of various bodily fluids for cancer diagnosis. Meanwhile, extracellular vesicles (EVs) are circulating biomarkers that carry molecular profiles of their cell or tissue origins and have emerged as one of the most promising biomarkers for cancer. Owing to the biological information that can be obtained through EVs' membrane surface markers and their cargo loaded with biomolecules such as nucleic acids, proteins, and lipids, EVs have become useful in cancer diagnosis and therapeutic applications. Fourier-transform infrared spectroscopy (FTIR) allows rapid, non-destructive, label-free molecular profiling of EVs with minimal sample preparation. Since the heterogeneity of EV subpopulations may result in complicated FTIR spectra that are highly diverse, computational-assisted FTIR spectroscopy is employed in many studies to provide fingerprint spectra of malignant and non-malignant samples, allowing classification with high accuracy, specificity, and sensitivity. In view of this, FTIR-EV approach carries a great potential in cancer detection. The progression of FTIR-based biomarker identification in EV research, the rationale of the integration of a computationally assisted approach, along with the challenges of clinical translation are the focus of this review.

Nanoscale biophysical properties of small extracellular vesicles from senescent cells using atomic force microscopy, surface potential microscopy, and Raman spectroscopy

Cells secrete extracellular vesicles (EVs) carrying cell-of-origin markers to communicate with surrounding cells. EVs regulate physiological processes ranging from intercellular signaling to waste management. However, when senescent cells (SnCs) secrete EVs, the EVs, which are newly regarded as senescence-associated secretory phenotype (SASP) factors, can evoke inflammation, senescence induction, and metabolic disorders in neighboring cells. Unlike other soluble SASP factors, the biophysical properties of EVs, including small EVs (sEVs), derived from SnCs have not yet been investigated. In this study, sEVs were extracted from a human IMR90 lung fibroblast in vitro senescence model. Their biomechanical properties were mapped using atomic force microscopy-based quantitative nanomechanical techniques, surface potential microscopy, and Raman spectroscopy. The surfaces of sEVs derived from SnCs are slightly stiffer but their cores are softer than those of sEVs secreted from non-senescent cells (non-SnCs). This inversely proportional relationship between deformation and stiffness, attributed to a decrease in the concentration of genetic and protein materials inside the vesicles and the adsorption of positively charged SASP factors onto the vesicle surfaces, respectively, was found to be a peculiar characteristic of SnC-derived sEVs. Our results demonstrate that the biomechanical properties of SnC-derived sEVs differ from those of non-SnC-derived sEVs and provide insight into the mechanisms underlying their formation and composition.

Infrared nanospectroscopic imaging of DNA molecules on mica surface

Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying IR-AFM technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the AFM-IR investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of AFM-IR mapping modalities with corresponding absorption spectra based on two different DNA deposition protocols on spermidine and Ni²⁺ pretreated mica surface. The nanoscale IR absorbance of distinctly formed DNA morphologies on mica are demonstrated through series of AFM-IR absorption maps with corresponding IR spectrum. Our results thus demonstrate the sensitivity of AFM-IR nanospectroscopy for a nucleic acid research with an open potential to be employed in further investigation of nucleoprotein complexes.

An immunogold single extracellular vesicular RNA and protein (Au SERP) biochip to predict responses to immunotherapy in non-small cell lung cancer patients

Conventional PD-L1 immunohistochemical tissue biopsies only predict 20%-40% of non-small cell lung cancer (NSCLC) patients that will respond positively to anti-PD-1/PD-L1 immunotherapy. Herein, we present an immunogold biochip to quantify single extracellular vesicular RNA and protein (Au SERP) as a non-invasive alternative. With only 20 μl of purified serum, PD-1/PD-L1 proteins on the surface of extracellular vesicles (EVs) and EV PD-1/PD-L1 messenger RNA (mRNA) cargo were detected at a single-vesicle resolution and exceeded the sensitivities of their bulk-analysis conventional counterparts, ELISA and qRT-PCR, by 1000 times. By testing a cohort of 27 non-responding and 27 responding NSCLC patients, Au SERP indicated that the single-EV mRNA biomarkers surpass the single-EV protein biomarkers in predicting patient responses to immunotherapy. Dual single-EV PD-1/PD-L1 mRNA detection differentiated responders from non-responders with an accuracy of 72.2% and achieved an NSCLC diagnosis accuracy of 93.2%, suggesting the potential for Au SERP to provide enhanced immunotherapy predictions and cancer diagnoses within the clinical setting.

Machine Learning-Assisted FTIR Analysis of Circulating Extracellular Vesicles for Cancer Liquid Biopsy

Extracellular vesicles (EVs) are abundantly released into the systemic circulation, where they show remarkable stability and harbor molecular constituents that provide biochemical information about their cells of origin. Due to this characteristic, EVs are attracting increasing attention as a source of circulating biomarkers for cancer liquid biopsy and personalized medicine. Despite this potential, none of the discovered biomarkers has entered the clinical practice so far, and novel approaches for the label-free characterization of EVs are highly demanded. In this regard, Fourier Transform Infrared Spectroscopy (FTIR) has great potential as it provides a quick, reproducible, and informative biomolecular fingerprint of EVs. In this pilot study, we investigated, for the first time in the literature, the capability of FTIR spectroscopy to distinguish between EVs extracted from sera of cancer patients and controls based on their mid-IR spectral response. For this purpose, EV-enriched suspensions were obtained from the serum of patients diagnosed with Hepatocellular Carcinoma (HCC) of nonviral origin and noncancer subjects. Our data point out the presence of statistically significant differences in the integrated intensities of major mid-IR absorption bands, including the carbohydrate and nucleic acids band, the protein amide I and II bands, and the lipid CH stretching band. Additionally, we used Principal Component Analysis combined with Linear Discriminant Analysis (PCA-LDA) for the automated classification of spectral data according to the shape of specific mid-IR spectral signatures. The diagnostic performances of the proposed spectral biomarkers, alone and combined, were evaluated using multivariate logistic regression followed by a Receiving Operator Curve analysis, obtaining large Areas Under the Curve (AUC = 0.91, 95% CI 0.81–1.0). Very interestingly, our analyses suggest that the discussed spectral biomarkers can outperform the classification ability of two widely used circulating HCC markers measured on the same groups of subjects, namely alpha-fetoprotein (AFP), and protein induced by the absence of vitamin K or antagonist-II (PIVKA-II).

Correlated mechanochemical maps of Arabidopsis thaliana primary cell walls using atomic force microscope infrared spectroscopy

Spatial heterogeneity in composition and organisation of the primary cell wall affects the mechanics of cellular morphogenesis. However, directly correlating cell wall composition, organisation and mechanics has been challenging. To overcome this barrier, we applied atomic force microscopy coupled with infrared (AFM-IR) spectroscopy to generate spatially correlated maps of chemical and mechanical properties for paraformaldehyde-fixed, intact Arabidopsis thaliana epidermal cell walls. AFM-IR spectra were deconvoluted by non-negative matrix factorisation (NMF) into a linear combination of IR spectral factors representing sets of chemical groups comprising different cell wall components. This approach enables quantification of chemical composition from IR spectral signatures and visualisation of chemical heterogeneity at nanometer resolution. Cross-correlation analysis of the spatial distribution of NMFs and mechanical properties suggests that the carbohydrate composition of cell wall junctions correlates with increased local stiffness. Together, our work establishes new methodology to use AFM-IR for the mechanochemical analysis of intact plant primary cell walls.

Made by cells for cells - extracellular vesicles as next-generation mainstream medicines

Current medicine has only taken us so far in reducing disease and tissue damage. Extracellular vesicles (EVs), which are membranous nanostructures produced naturally by cells, have been hailed as a next-generation medicine. EVs deliver various biomolecules, including proteins, lipids and nucleic acids, which can influence the behaviour of specific target cells. Since EVs not only mirror composition of their parent cells but also modify the recipient cells, they can be used in three key areas of medicine: regenerative medicine, disease detection and drug delivery. In this Review, we discuss the transformational and translational progress witnessed in EV-based medicine to date, focusing on two key elements: the mechanisms by which EVs aid tissue repair (for example, skin and bone tissue regeneration) and the potential of EVs to detect diseases at an early stage with high sensitivity and specificity (for example, detection of glioblastoma). Furthermore, we describe the progress and results of clinical trials of EVs and demonstrate the benefits of EVs when compared with traditional medicine, including cell therapy in regenerative medicine and solid biopsy in disease detection. Finally, we present the challenges, opportunities and regulatory framework confronting the clinical application of EV-based products.

SKP-SC-EVs Mitigate Denervated Muscle Atrophy by Inhibiting Oxidative Stress and Inflammation and Improving Microcirculation

Denervated muscle atrophy is a common clinical disease that has no effective treatments. Our previous studies have found that oxidative stress and inflammation play an important role in the process of denervated muscle atrophy. Extracellular vesicles derived from skin precursor-derived Schwann cells (SKP-SC-EVs) contain a large amount of antioxidants and anti-inflammatory factors. This study explored whether SKP-SC-EVs alleviate denervated muscle atrophy by inhibiting oxidative stress and inflammation. In vitro studies have found that SKP-SC-EVs can be internalized and caught by myoblasts to promote the proliferation and differentiation of myoblasts. Nutrient deprivation can cause myotube atrophy, accompanied by oxidative stress and inflammation. However, SKP-SC-EVs can inhibit oxidative stress and inflammation caused by nutritional deprivation and subsequently relieve myotube atrophy. Moreover, there is a remarkable dose-effect relationship. In vivo studies have found that SKP-SC-EVs can significantly inhibit a denervation-induced decrease in the wet weight ratio and myofiber cross-sectional area of target muscles. Furthermore, SKP-SC-EVs can dramatically inhibit highly expressed Muscle RING Finger 1 and Muscle Atrophy F-box in target muscles under denervation and reduce the degradation of the myotube heavy chain. SKP-SC-EVs may reduce mitochondrial vacuolar degeneration and autophagy in denervated muscles by inhibiting autophagy-related proteins (i.e., PINK1, BNIP3, LC3B, and ATG7). Moreover, SKP-SC-EVs may improve microvessels and blood perfusion in denervated skeletal muscles by enhancing the proliferation of vascular endothelial cells. SKP-SC-EVs can also significantly inhibit the production of reactive oxygen species (ROS) in target muscles after denervation, which indicates that SKP-SC-EVs elicit their role by upregulating Nrf2 and downregulating ROS production-related factors (Nox2 and Nox4). In addition, SKP-SC-EVs can significantly reduce the levels of interleukin 1β, interleukin-6, and tumor necrosis factor α in target muscles. To conclude, SKP-SC-EVs may alleviate the decrease of target muscle blood perfusion and passivate the activities of ubiquitin-proteasome and autophagy-lysosome systems by inhibiting oxidative stress and inflammatory response, then reduce skeletal muscle atrophy caused by denervation. This study not only enriches the molecular regulation mechanism of denervated muscle atrophy, but also provides a scientific basis for SKP-SC-EVs as a protective drug to prevent and treat muscle atrophy.

Nanoarrays of Individual Liposomes and Bacterial Outer Membrane Vesicles by Liftoff Nanocontact Printing

Analytical characterization of small biological particles, such as extracellular vesicles (EVs), is complicated by their extreme heterogeneity in size, lipid, membrane protein, and cargo composition. Analysis of individual particles is essential for illuminating particle property distributions that are obscured by ensemble measurements. To enable high-throughput analysis of individual particles, liftoff nanocontact printing (LNCP) is used to define hexagonal antibody and toxin arrays that have a 425 nm dot size, on average, and 700 nm periodicity. The LNCP process is rapid, simple, and does not require access to specialized nanofabrication tools. These densely packed, highly ordered arrays are used to capture liposomes and bacterial outer membrane vesicles on the basis of their surface biomarkers, with a maximum of one particle per array dot, resulting in densely packed arrays of particles. Despite the high particle density, the underlying antibody or toxin array ensured that neighboring individual particles are optically resolvable. Provided target particle biomarkers and suitable capture molecules are identified, this approach can be used to generate high density arrays of a wide variety of small biological particles, including other types of EVs like exosomes.

Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles

Extracellular vesicles (EVs) are heterogeneous lipid containers with a complex molecular cargo comprising several populations with unique roles in biological processes. These vesicles are closely associated with specific physiological features, which makes them invaluable in the detection and monitoring of various diseases. EVs play a key role in pathophysiological processes by actively triggering genetic or metabolic responses. However, the heterogeneity of their structure and composition hinders their application in medical diagnosis and therapies. This diversity makes it difficult to establish their exact physiological roles, and the functions and composition of different EV (sub)populations. Ensemble averaging approaches currently employed for EV characterization, such as western blotting or 'omics' technologies, tend to obscure rather than reveal these heterogeneities. Recent developments in single-vesicle analysis have made it possible to overcome these limitations and have facilitated the development of practical clinical applications. In this review, we discuss the benefits and challenges inherent to the current methods for the analysis of single vesicles and review the contribution of these approaches to the understanding of EV biology. We describe the contributions of these recent technological advances to the characterization and phenotyping of EVs, examination of the role of EVs in cell-to-cell communication pathways and the identification and validation of EVs as disease biomarkers. Finally, we discuss the potential of innovative single-vesicle imaging and analysis methodologies using microfluidic devices, which promise to deliver rapid and effective basic and practical applications for minimally invasive prognosis systems.

New Multiscale Characterization Methodology for Effective Determination of Isolation-Structure-Function Relationship of Extracellular Vesicles

Extracellular vesicles (EVs) have been lauded as next-generation medicines, but very few EV-based therapeutics have progressed to clinical use. Limited clinical translation is largely due to technical barriers that hamper our ability to mass produce EVs, i.e., to isolate, purify, and characterize them effectively. Technical limitations in comprehensive characterization of EVs lead to unpredicted biological effects of EVs. Here, using a range of optical and non-optical techniques, we showed that the differences in molecular composition of EVs isolated using two isolation methods correlated with the differences in their biological function. Our results demonstrated that the isolation method determines the composition of isolated EVs at single and sub-population levels. Besides the composition, we measured for the first time the dry mass and predicted sedimentation of EVs. These parameters were likely to contribute to the biological and functional effects of EVs on single cell and cell cultures. We anticipate that our new multiscale characterization approach, which goes beyond traditional experimental methodology, will support fundamental understanding of EVs as well as elucidate the functional effects of EVs in in vitro and in vivo studies. Our findings and methodology will be pivotal for developing optimal isolation methods and establishing EVs as mainstream therapeutics and diagnostics. This innovative approach is applicable to a wide range of sectors including biopharma and biotechnology as well as to regulatory agencies.

Extracellular Vesicles as an Emerging Frontier in Spinal Cord Injury Pathobiology and Therapy

Extracellular vesicles (EVs) are membrane-delimited particles that are secreted by nearly all cell types. EVs mediate crucial physiological functions and pathophysiological processes in the CNS. As carriers of diverse bioactive cargoes (e.g., proteins, lipids, and nucleic acids) that can be modified in response to external stimuli, EVs have emerged as pathological mediators following neurotrauma such as spinal cord injury (SCI). We discuss the roles of endogenous EVs in the CNS as well as crosstalk with peripheral EVs in relation to neurotrauma, with a particular focus on SCI. We then summarize the status of EV-based therapeutic advances in preclinical animal models for these conditions. Finally, we discuss new bioengineering strategies that are poised to enhance CNS-specific therapeutic capabilities of EVs.

SP, N. M, Barik AK, Pai KM, Unnikrishnan VK, George SD, Kartha VB, Chidangil S. Photonics of human saliva: potential optical methods for the screening of abnormal health conditions and infections

Human saliva can be treated as a pool of biological markers able to reflect on the state of personal health. Recent years have witnessed an increase in the use of optical devices for the analysis of body fluids. Several groups have carried out studies investigating the potential of saliva as a non-invasive and reliable clinical specimen for use in medical diagnostics. This brief review aims to highlight the optical technologies, mainly surface plasmon resonance (SPR), Raman, and Fourier transform infrared (FTIR) spectroscopy, which are being used for the probing of saliva for diverse biomedical applications. Advances in bio photonics offer the promise of unambiguous, objective and fast detection of abnormal health conditions and viral infections (such as COVID-19) from the analysis of saliva.

Extracellular-Vesicle-Based Coatings Enhance Bioactivity of Titanium Implants-SurfEV

Extracellular vesicles (EVs) are nanoparticles released by cells that contain a multitude of biomolecules, which act synergistically to signal multiple cell types. EVs are ideal candidates for promoting tissue growth and regeneration. The tissue regenerative potential of EVs raises the tantalizing possibility that immobilizing EVs on implant surfaces could potentially generate highly bioactive and cell-instructive surfaces that would enhance implant integration into the body. Such surfaces could address a critical limitation of current implants, which do not promote bone tissue formation or bond bone. Here, we developed bioactive titanium surface coatings (SurfEV) using two types of EVs: secreted by decidual mesenchymal stem cells (DEVs) and isolated from fermented papaya fluid (PEVs). For each EV type, we determined the size, morphology, and molecular composition. High concentrations of DEVs enhanced cell proliferation, wound closure, and migration distance of osteoblasts. In contrast, the cell proliferation and wound closure decreased with increasing concentration of PEVs. DEVs enhanced Ca/P deposition on the titanium surface, which suggests improvement in bone bonding ability of the implant (i.e., osteointegration). EVs also increased production of Ca and P by osteoblasts and promoted the deposition of mineral phase, which suggests EVs play key roles in cell mineralization. We also found that DEVs stimulated the secretion of secondary EVs observed by the presence of protruding structures on the cell membrane. We concluded that, by functionalizing implant surfaces with specialized EVs, we will be able to enhance implant osteointegration by improving hydroxyapatite formation directly at the surface and potentially circumvent aseptic loosening of implants.

Dry powder pharmaceutical biologics for inhalation therapy

Therapeutic biologics such as genes, peptides, proteins, virus and cells provide clinical benefits and are becoming increasingly important tools in respiratory medicine. Pulmonary delivery of therapeutic biologics enables the potential for safe and effective treatment option for respiratory diseases due to high bioavailability while minimizing absorption into the systemic circulation, reducing off-target toxicity to other organs. Development of inhalable powder formulation requires stabilization of complex biological materials, and each type of biologics may present unique challenges and require different formulation strategy combined with manufacture process to ensure biological and physical stabilities during production and over shelf-life. This review examines key formulation strategies for stabilizing proteins, nucleic acids, virus (bacteriophages) and bacterial cells in inhalable powders. It also covers characterization methods used to assess physicochemical properties and aerosol performance of the powders, biological activity and structural integrity of the biologics, and chemical analysis at the nanoscale. Furthermore, the review includes manufacture technologies which are based on lyophilization and spray-drying as they have been applied to manufacture Food and Drug Administration (FDA)-approved protein powders. In perspective, formulation and manufacture of inhalable powders for biologic are highly challenging but attainable. The key requirements are the stability of both the biologics and the powder, along with the powder dispersibility. The formulation to be developed depends on the manufacture process as it will subject the biologics to different stresses (temperature, mechanical and chemical) which could lead to degradation by different pathways. Stabilizing excipients coupled with the suitable choice of process can alleviate the stability issues of inhaled powders of biologics.

Nanoscale Infrared Spectroscopy and Chemometrics Enable Detection of Intracellular Protein Distribution

Determination of the intracellular location of proteins is one of the fundamental tasks of microbiology. Conventionally, label-based microscopy and super-resolution techniques are employed. In this work, we demonstrate a new technique that can determine intracellular protein distribution at nanometer spatial resolution. This method combines nanoscale spatial resolution chemical imaging using the photothermal-induced resonance (PTIR) technique with multivariate modeling to reveal the intracellular distribution of cell components. Here, we demonstrate its viability by imaging the distribution of major cellulases and xylanases in Trichoderma reesei using the colocation of a fluorescent label (enhanced yellow fluorescence protein, EYFP) with the target enzymes to calibrate the chemometric model. The obtained partial least squares model successfully shows the distribution of these proteins inside the cell and opens the door for further studies on protein secretion mechanisms using PTIR.

Extracellular vesicles from skin precursor-derived Schwann cells promote axonal outgrowth and regeneration of motoneurons via Akt/mTOR/p70S6K pathway

Background

Skin precursor-derived Schwann cells (SKP-SCs) have been shown to benefit the recovery of spinal cord injury (SCI) and peripheral nerve injury (PNI) with motor dysfunction. However, the effect of extracellular vesicles (EVs) from SKP-SCs responsible for neuroregeneration remains unknown.

Methods

Based on the obtainment and identification of rat SKP-SCs and their derived EVs, the primary rat injury model of motoneurons resulting from axotomy in vitro or nerve crush in vivo, as well as the secondary rat ischemic hypoxic injury model of motoneuron exposure to oxygen-glucose-deprivation (OGD) in vitro, were treated with EVs from skin precursor-derived Schwann cells (SKP-SC-EVs), respectively. Then, the axonal outgrowth and regrowth was observed and compared, and cell viability as well as the protein kinase B/mammalian target of rapamycin/p70 S6 kinase (Akt/mTOR/p70S6K) signaling pathway was detected, moreover, rapamycin (an mTOR inhibitor) was used to further reveal the underlying molecular mechanism.

Results

The internalization of SKP-SC-EVs by neuronal cells was identified in vitro and in vivo. Besides the pro-axonal outgrowth effect of SKP-SC-EVs, prospectively, the treatment of OGD-injured motoneurons with SKP-SC-EVs potentiated the restoration of neuronal viability and axonal regrowth. Furthermore, the axotomizing injury could be improved with SKP-SC-EVs treatment in vitro and in vivo. Finally, it was shown that the application of SKP-SC-EVs could activate the Akt/mTOR/p70S6K signaling pathway that can be abolished by rapamycin.

Conclusions

In summary, the addition of SKP-SC-EVs could regulate the cell growth and death signaling pathway mediated by Akt/mTOR/p70S6K, owing to the transmission of cargos in EVs to damaged motoneurons, which leads to axonal regrowth and neuronal resurrection. Thus, SKP-SC-EVs treatment could be a novel promising strategy for improving the axonal outgrowth and regeneration of motoneurons.

Closed-loop atomic force microscopy-infrared spectroscopic imaging for nanoscale molecular characterization

Atomic force microscopy-infrared (AFM-IR) spectroscopic imaging offers non-perturbative, molecular contrast for nanoscale characterization. The need to mitigate measurement artifacts and enhance sensitivity, however, requires narrowly-defined and strict sample preparation protocols. This limits reliable and facile characterization; for example, when using common substrates such as Silicon or glass. Here, we demonstrate a closed-loop (CL) piezo controller design for responsivity-corrected AFM-IR imaging. Instead of the usual mode of recording cantilever deflection driven by sample expansion, the principle of our approach is to maintain a zero amplitude harmonic cantilever deflection by CL control of a subsample piezo. We show that the piezo voltage used to maintain a null deflection provides a reliable measure of the local IR absorption with significantly reduced noise. A complete analytical description of the CL operation and characterization of the controller for achieving robust performance are presented. Accurate measurement of IR absorption of nanothin PMMA films on glass and Silicon validates the robust capability of CL AFM-IR in routine mapping of nanoscale molecular information.

Placenta Stem/Stromal Cell-Derived Extracellular Vesicles for Potential Use in Lung Repair

Many acute and chronic lung injuries are incurable and rank as the fourth leading cause of death globally. While stem cell treatment for lung injuries is a promising approach, there is growing evidence that the therapeutic efficacy of stem cells originates from secreted extracellular vesicles (EVs). Consequently, EVs are emerging as next-generation therapeutics. While EVs are extensively researched for diagnostic applications, their therapeutic potential to promote tissue repair is not fully elucidated. By housing and delivering tissue-repairing cargo, EVs refine the cellular microenvironment, modulate inflammation, and ultimately repair injury. Here, the potential use of EVs derived from two placental mesenchymal stem/stromal cell (MSC) lines is presented; a chorionic MSC line (CMSC29) and a decidual MSC cell line (DMSC23) for applications in lung diseases. Functional analyses using in vitro models of injury demonstrate that these EVs have a role in ameliorating injuries caused to lung cells. It is also shown that EVs promote repair of lung epithelial cells. This study is fundamental to advancing the field of EVs and to unlock the full potential of EVs in regenerative medicine.

Bulk to Nanometer-Scale Infrared Spectroscopy of Pharmaceutical Dry Powder Aerosols

Solid state chemical analysis of pharmaceutical inhalation aerosols at the individual particle level has been an analytical challenge. These particles can range from a few nanometers to micrometers and are a complex mixture of drugs and excipients. Conventional analytical techniques cannot resolve the distribution of excipients and drugs at the submicrometer scale. Understanding the nanochemical composition of individual particles can be critical for pharmaceutical scientists to evaluate drug and excipient stability as well as the drug-drug or drug-excipient interactions that affect the aerosol performance of powders. Herein, we show the novel application of a combination of optical photothermal infrared (O-PTIR) spectroscopy and atomic force microscopy infrared (AFM-IR) spectroscopy to probe nanochemical domains of powders containing the inhaled corticosteroid fluticasone propionate and long-acting β2-agonist salmeterol xinafoate, which are widely used to treat asthma and chronic obstructive pulmonary disease. Three types of powder formulation were analyzed, including the commercial product Seretide, which is a physical mixture of the drugs with crystalline lactose, and two spray-dried powders containing the drugs along with either amorphous or crystalline lactose. We obtained spatially resolved O-PTIR and AFM-IR spectra confirming the presence of peaks related to fluticasone propionate at 1743, 1661, and 1700 cm^-1, salmeterol xinafoate at 1580 cm^-1, and lactose at 1030 and 1160 cm^-1. The location of the drugs and lactose among the particles varied significantly, depending on the formulation type. For the first time, it was possible to map the drug distribution in individual aerosol particles. This is significant as such information has been lacking, and it will open an exciting research direction on how drug distribution affects the aerosol performance of powders and the consistency of dose uniformity. Further, these advanced spectroscopic techniques can be applied to study a wide range of pharmaceutical formulations.

Nanoscale chemical and mechanical heterogeneity of human dentin characterized by AFM-IR and bimodal AFM

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AFM-IR technique was used to detect the chemical heterogeneity of human dentin for the first time.

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The heterogeneity of mechanical properties of human dentin was explored by AFM AM-FM technique.

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A band at 1336 cm⁻¹ assigned to S Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]>O stretching vibrations was found only in peritubular dentin.

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Peritubular dentin had a higher Young’s modulus (32.25 ± 4.67 GPa) than intertubular dentin.

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AFM-IR and AFM AM-FM are useful for understanding the mineral deposition mechanisms of dentin.

Human dentin, as an important calcified tissue in the body, plays significant roles in withstanding masticatory forces and has a complex hierarchical organization. Understanding the composition and ultrastructure of dentin is critical for elucidating mechanisms of biomineralization under healthy and pathological states. Here, atomic force microscope infrared spectroscopy (AFM-IR) and AFM-based amplitude modulation-frequency modulation (AM-FM) techniques were utilized to detect the heterogeneity in chemical composition and mechanical properties between peritubular and intertubular dentin at the nanoscale. AFM-IR spectra collected from peritubular and intertubular dentin contained similar vibrational bands in the amide regions (I, II and III), suggesting that collagen may exist in both structures. A distinctive band at 1336 cm⁻¹ indicative of SO stretching vibrations was detected only in peritubular dentin. AFM-IR imaging showed an uneven distribution of chemical components at different locations, confirming the heterogeneity of dentin. The Young’s modulus of peritubular dentin was higher, and was associated to a higher mineral content. This study demonstrated distinctive chemical and mechanical properties of peritubular dentin, implying the different development and mineralization processes between peritubular and intertubular dentin. AFM-IR is useful to provide compositional information on the heterogeneity of human dentin, helping to understand the mineral deposition mechanisms of dentin.

Nanoscale AFM-IR spectroscopic imaging of lipid heterogeneity and effect of irradiation in prostate cancer cells

The recent development of the AFM-IR technique, which combines nanoscale imaging with chemical contrast through infrared spectroscopy, opened up new fields for exploration, which were out of reach for other modalities, e.g. Raman spectroscopy. Lipid droplets (LDs) are key organelles, which are associated with stress response mechanisms in cells and their size falls into that niche. LDs composition is heterogeneous and varies depending on cancer cell type and the tumor microenvironment. Prostate cancer cells show a unique lipid metabolism manifested by an increased requirement for lipid accumulation in cytosolic LDs. In the current work, AFM-IR nanoimaging was undertaken to analyze lipids in untreated and x-ray irradiated PC-3 prostate cancer cells. Cells poor in LDs showed slightly increased lipid signal in cytoplasm close to the nucleus. On the other hand, high lipid signal coming from LDs accumulation could be found in any part of the cytoplasmic region. The observed behavior was found to be independent from irradiation and its dose. According to the band assignment of the collected AFM-IR spectra, the main components of LDs were assigned to cholesteryl esters. The size of LDs present in cells poor in lipids was found to be of less than 1 μm, whereas LDs aggregates spread out over a few microns. Analysis of AFM-IR spectra shows relative homogeneity of LDs composition in single cells and heterogeneity of LDs content within the PC-3 cell population.

High-fidelity probing of the structure and heterogeneity of extracellular vesicles by resonance-enhanced atomic force microscopy infrared spectroscopy

Extracellular vesicles (EVs) are highly specialized nanoscale assemblies that deliver complex biological cargos to mediate intercellular communication. EVs are heterogeneous, and characterization of this heterogeneity is paramount to understanding EV biogenesis and activity, as well as to associating them with biological responses and pathologies. Traditional approaches to studying EV composition generally lack the resolution and/or sensitivity to characterize individual EVs, and therefore the assessment of EV heterogeneity has remained challenging. We have recently developed an atomic force microscope IR spectroscopy (AFM-IR) approach to probe the structural composition of single EVs with nanoscale resolution. Here, we provide a step-by-step procedure for our approach and show its power to reveal heterogeneity across individual EVs, within the same population of EVs and between different EV populations. Our approach is label free and able to detect lipids, proteins and nucleic acids within individual EVs. After isolation of EVs from cell culture medium, the protocol involves incubation of the EV sample on a suitable substrate, setup of the AFM-IR instrument and collection of nano-IR spectra and nano-IR images. Data acquisition and analyses can be completed within 24 h, and require only a basic knowledge of spectroscopy and chemistry. We anticipate that new understanding of EV composition and structure through AFM-IR will contribute to our biological understanding of EV biology and could find application in disease diagnosis and the development of EV therapies.

Isolation and Characterization of Extracellular Vesicles from Mesenchymal Stromal Cells

Extracellular vesicles (EVs) have received immense attention in the past decade for their diverse use in diagnosis and therapeutics. Enhancing our understanding of EVs and increasing the reliability and reproducibility of EV research demands the use of standard isolation procedures and multiple characterization methods. Here we describe the most commonly used EV isolation method involving ultracentrifugation, and various characterization methods that include nanoparticle tracking analysis, atomic force microscopy and electron microscopy, which measure the size, concentration, and morphology of EVs.

Improved bioactivity of GUMMETAL®, Ti59Nb36Ta2Zr3O0.3, via formation of nanostructured surfaces

The leading reason for implant revision surgery globally is lack of implant integration with surrounding bone. A new titanium alloy GUMMETAL^® (Ti₅₉Nb₃₆Ta₂Zr₃O_0.3) is currently used in biomedical devices and has a Young’s modulus that is better matched to bone. The surface was subject to NaOH, CaCl₂, heat and water treatment (BioGum) after which the surfaces were evaluated using atomic force microscope, scanning electron microscope, X-ray diffractometer and elemental analysis using energy dispersive X-ray. To demonstrate enhanced bone bonding ability and cytocompatibility, apatite formation in simulated body fluid and in vitro stem cell attachment, proliferation and cytoskeleton organisation were examined. The formation of a ~200 nm nanoscale needle-like calcium titanate network on the surface following treatment was revealed and upon soaking in simulated body fluid, the formation of a ~5 µm layer of apatite. Metabolic activity of rat bone marrow stem cells on BioGum was increased in comparison to control and the cell number appeared greater, with more elongated morphology as early as 2 h post-seeding. This positions the modification as a simple and potentially universal technology for the improvement of implant integration.