Infrared and Raman spectroscopy for purity assessment of extracellular vesicles

Illuminating extracellular nanovesicles through the spectroscopic lens: a mini review of cutting-edge insights and emerging applications

Extracellular vesicles (EVs) are cell-derived particles that facilitate intercellular communication by carrying bioactive molecules like proteins and RNA, impacting both health and disease. Herein, the EVs' significance in physiological and pathological processes is reviewed, emphasising their potential as biomarkers for diseases including for instance, cancer, neurodegenerative disorders and cardiovascular conditions. The principles and applications of Raman spectroscopy (RS) - a powerful tool offering detailed molecular insights into EVs, are further examined. The non-destructive nature of this spectroscopic technique renders it invaluable for studying the molecular composition, purity and concentration of EVs. When EVs are isolated from accessible biofluids such as blood, urine or saliva, the overall process remains minimally invasive, enhancing its clinical applicability. The review highlights Raman spectroscopy's role in identifying disease-related EVs, distinguishing subpopulations and enhancing our understanding of EVs in disease mechanisms and therapeutic applications.

Raman spectroscopy in extracellular vesicles analysis: Techniques, applications and advancements

Raman spectroscopy provides a robust approach for detailed analysis of the chemical and molecular profiles of extracellular vesicles (EVs). Recent advancements in Raman techniques have significantly enhanced the sensitivity and accuracy of EV characterization, enabling precise detection and profiling of molecular components within EV samples. This review introduces and compares various Raman-based techniques for EV characterization. These include Raman spectroscopy (RS), which provides fundamental molecular information; Raman trapping analysis (RTA), which combines optical trapping with Raman scattering for the manipulation and analysis of individual EVs; surface-enhanced Raman spectroscopy (SERS), which enhances the Raman signal through the use of metallic nanostructures, significantly improving sensitivity; and microfluidic SERS, which integrates SERS with microfluidic platforms to allow high-throughput, label-free analysis of EVs in biological fluids. In addition to comparing various Raman techniques, this review provides a comprehensive analysis that includes comparisons of machine learning methods, EV isolation techniques, and characterization strategies. By integrating these approaches, the review presents a holistic perspective on Raman-based EV analysis, covering profiling, purity, heterogeneity and size analysis as well as imaging. The combined assessment of Raman technologies with advanced computational and experimental methodologies supports the development of more robust diagnostic and therapeutic applications involving EVs.

Molecular profiling of blood plasma-derived extracellular vesicles derived from Duchenne muscular dystrophy patients through integration of FTIR spectroscopy and machine learning reveals disease signatures

PURPOSE

To identify and monitor the FTIR spectral signatures of plasma extracellular vesicles (EVs) from Duchenne Muscular Dystrophy (DMD) patients at different stages with Healthy controls using machine learning models.

MATERIALS AND METHODS

Whole blood samples were collected from the DMD (n = 30) and Healthy controls (n = 12). EVs were extracted by the Total Exosome Isolation (TEI) Method and resuspended in 1XPBS. We characterize the morphology, size, particle count, and surface markers (CD9, Alix, and Flotillin) by HR-TEM, NTA, and Western Blot analysis. The mid-IR spectra were recorded from (4000-400 cm-1) by Bruker ALPHA II FTIR spectrometer model, which was equipped with an attenuated total reflection (ATR) module. Machine learning algorithms like Principal Component Analysis (PCA) and Random Forest (RF) for dimensionality reduction and classifying the two study groups based on the FTIR spectra. The model performance was evaluated by a confusion matrix and the sensitivity, specificity, and Receiver Operating Characteristic Curve (ROC) was calculated respectively.

RESULTS

Alterations in Amide I & II (1700-1470 cm-1) and lipid (3000-2800 cm-1) regions in FTIR spectra of DMD compared with healthy controls. The PCA-RF model classified correctly the two study groups in the range of 4000-400 cm-1 with a sensitivity of 20 %, specificity of 87.50 %, accuracy of 71.43 %, precision of 33.33 %, and 5-fold cross-validation accuracy of 82 %. We analyzed the ten different spectral regions which showed statistically significant at P < 0.01 except the Ester Acyl Chain region.

CONCLUSION

Our proof-of-concept study demonstrated distinct infrared (IR) spectral signatures in plasma EVs derived from DMD. Consistent alterations in protein and lipid configurations were identified using a PCA-RF model, even with a small clinical dataset. This minimally invasive liquid biopsy method, combined with automated analysis, warrants further investigation for its potential in early diagnosis and monitoring of disease progression in DMD patients within clinical settings.

Surface-enhanced infrared spectroscopic study of extracellular vesicles using plasmonic gold nanoparticles

Extracellular vesicles (EVs), sub-micrometer lipid-bound particles released by most cells, are considered a novel area in both biology and medicine. Among characterization methods, infrared (IR) spectroscopy, especially attenuated total reflection (ATR), is a rapidly emerging label-free tool for molecular characterization of EVs. The relatively low number of vesicles in biological fluids (∼1010 particle/mL), however, and the complex content of the EVs' milieu (protein aggregates, lipoproteins, buffer molecules) might result in poor signal-to-noise ratio in the IR analysis of EVs. Exploiting the increment of the electromagnetic field at the surface of plasmonic nanomaterials, surface-enhanced infrared spectroscopy (SEIRS) provides an amplification of characteristic IR signals of EV samples. Negatively charged citrate-capped and positively charged cysteamine-capped gold nanoparticles with around 10 nm diameter were synthesized and tested with blood-derived EVs. Both types of gold nanoparticles contributed to an enhancement of the EVs' IR spectroscopic signature. Joint evaluation of UV-Vis and IR spectroscopic results, supported by FF-TEM images, revealed that proper interaction of gold nanoparticles with EVs is crucial, and an aggregation or clustering of gold nanoparticles is necessary to obtain the SEIRS effect. Positively charged gold nanoparticles resulted in higher enhancement, probably due to electrostatic interaction with EVs, commonly negatively charged.

Urineprint of high-altitude: Insights from analyses of urinary biomarkers and bio-physical-chemical features of extracellular vesicles

Humans exposed to altitude hypoxia experience dysfunctions of the urinary system. As a non-invasive, easily manageable and informative biological sample, urine represents a relevant matrix for detecting clinical impairments of urinary system, as well as alterations of other systems and extracellular vesicles (EVs) biology during high-altitude expeditions. Nevertheless, gaps exist in the comprehensive assessment of dysfunction, molecular burden and EVs biology due to high-altitude acute exposure. This study aimed to find a biophysical and biochemical signature of urinary EVs for hypoxia-induced changes in urinary function, putatively accompanied by an oxinflammatory burden. Urine samples of 15 participants were sampled at low and high-altitude during an Alpine project (7 women and 8 men, aged 24-to-63 years and with BMI 17.93-to-30.76 kg/m2) and analysed for: creatinin and albumin, lipid peroxidation, IL6, NO derivatives; atomic force microscopy and Raman spectroscopy were carried out after urinary EVs were isolated through sucrose-gradient ultracentrifugation. Albumin-to-creatinin ratio increased at high altitude, as did IL6 and 8-isoprostane. AFM showed a globular and flattened shape of EVs, although several samples were characterized by a lot of contaminants and EVs lost their prototypal spherical shape; EVs comprehensively maintained their morphology at high altitude. Raman spectroscopy revealed some typical phospholipidic-like pattern, often masked by contaminants of spectra that most often refer to high-altitude samples. Collectively, short-term exposure to altitude hypoxia increased renal concentrating ability, produced non-pathological impairment or renal function, and triggered an oxyinflammatory burden with heterogeneous response of NO system. The combination of AFM and Raman spectroscopy revealed that EVs collected at high altitude more likely are fused together and incorporated into a sediment matrix, and contain contaminants peaks that make the purification process less efficient. The combination of analytical procedures as in the present study offers novel possibilities to detect the biological and clinical effects of high altitude on renal system.

Raman spectroscopy of large extracellular vesicles derived from human microvascular endothelial cells to detect benzo[a]pyrene exposure

Extracellular vesicles (EVs) have shown great potential as biomarkers since they reflect the physio-pathological status of the producing cell. In the context of cytotoxicity, it has been found that exposing cells to toxicants leads to changes in protein expression and the cargo of the EVs they produce. Here, we studied large extracellular vesicles (lEVs) derived from human microvascular endothelial cells (HMEC-1) to detect the modifications induced by cell exposure to benzo[a]pyrene (B[a]P). We used a custom CaF2-based biochip which allowed hyphenated techniques of investigation: surface plasmon resonance imaging (SPRi) to monitor the adsorption of objects, atomic force microscopy (AFM) to characterise EVs' size and morphology, and Raman spectroscopy to detect molecular modifications. Results obtained on EVs by Raman microscopy and tip-enhanced Raman spectroscopy (TERS) showed significant differences induced by B[a]P in the high wavenumber region of Raman spectra (2800 to 3000 cm-1), corresponding mainly to lipid modifications. Two types of spectra were detected in the control sample. A support vector machine (SVM) model was trained on the pre-processed spectral data to differentiate between EVs from cells exposed or not to B[a]P at the spectrum level; this model could achieve a sensitivity of 88% and a specificity of 99.5%. Thus, this experimental setup facilitated the distinction between EVs originating from two cell culture conditions and enabled the discrimination of EV subsets within one cell culture condition.

Extracellular vesicles may provide an alternative detoxification pathway during skeletal muscle myoblast ageing

Skeletal muscle (SM) acts as a secretory organ, capable of releasing myokines and extracellular vesicles (SM-EVs) that impact myogenesis and homeostasis. While age-related changes have been previously reported in murine SM-EVs, no study has comprehensively profiled SM-EV in human models. To this end, we provide the first comprehensive comparison of SM-EVs from young and old human primary skeletal muscle cells (HPMCs) to map changes associated with SM ageing. HPMCs, isolated from young (24 ± 1.7 years old) and older (69 ± 2.6 years old) participants, were immunomagnetically sorted based on the presence of the myogenic marker CD56 (N-CAM) and cultured as pure (100% CD56+) or mixed populations (MP: 90% CD56+). SM-EVs were isolated using an optimised protocol combining ultrafiltration and size exclusion chromatography (UF + SEC) and their biological content was extensively characterised using Raman spectroscopy (RS) and liquid chromatography mass spectrometry (LC-MS). Minimal variations in basic EV parameters (particle number, size, protein markers) were observed between young and old populations. However, biochemical fingerprinting by RS highlighted increased protein (amide I), lipid (phospholipids and phosphatidylcholine) and hypoxanthine signatures for older SM-EVs. Through LC-MS, we identified 84 shared proteins with functions principally related to cell homeostasis, muscle maintenance and transcriptional regulation. Significantly, SM-EVs from older participants were comparatively enriched in proteins involved in oxidative stress and DNA/RNA mutagenesis, such as E3 ubiquitin-protein ligase TTC3 (TTC3), little elongation complex subunit 1 (ICE1) and Acetyl-CoA carboxylase 1 (ACACA). These data suggest SM-EVs could provide an alternative pathway for homeostasis and detoxification during SM ageing.

Inline Raman Spectroscopy Provides Versatile Molecular Monitoring for Platelet Extracellular Vesicle Purification with Anion-Exchange Chromatography

Extracellular vesicles (EVs) are relatively recently discovered biological nanoparticles that mediate intercellular communication. The development of new methods for the isolation and characterization of EVs is crucial to support further studies on these small and structurally heterogenous vesicles. New scalable production methods are also needed to meet the needs of future therapeutic applications. A reliable inline detection method for the EV manufacturing process is needed to ensure reproducibility and to identify any possible variations in real time. Here, we demonstrate the use of an inline Raman detector in conjunction with anion exchange chromatography for the isolation of EVs from human platelets. Anion-exchange chromatography can be easily coupled with multiple inline detectors and provides an alternative to size-based methods for separating EVs from similar-sized impurities, such as lipoprotein particles. Raman spectroscopy enabled us to identify functional groups in EV samples and trace EVs and impurities in different stages of the process. Our results show a notable separation of impurities from the EVs during anion-exchange chromatography and demonstrate the power of inline Raman spectroscopy. Compared to conventional EV analysis methods, the inline Raman approach does not require hands-on work and can provide detailed, real-time information about the sample and the purification process.

Toward the nanoscale chemical and physical probing of milk-derived extracellular vesicles using Raman and tip-enhanced Raman spectroscopy

Tip-enhanced Raman spectroscopy (TERS) is an advanced technique to perform local chemical analysis of the surface of a sample through the improvement of the sensitivity and the spatial resolution of Raman spectroscopy by plasmonic enhancement of the electromagnetic signal in correspondence with the nanometer-sized tip of an atomic force microscope (AFM). In this work, TERS is demonstrated to represent an innovative and powerful approach for studying extracellular vesicles, in particular bovine milk-derived extracellular vesicles (mEVs), which are nanostructures with considerable potential in drug delivery and therapeutic applications. Raman spectroscopy has been used to analyze mEVs at the micrometric and sub-micrometric scales to obtain a detailed Raman spectrum in order to identify the 'signature' of mEVs in terms of their characteristic molecular vibrations and, therefore, their chemical compositions. With the ability to improve lateral resolution, TERS has been used to study individual mEVs, demonstrating the possibility of investigating a single mEV selected on the surface of the sample and, moreover, analyzing specific locations on the selected mEV with nanometer lateral resolution. TERS potentially allows one to reveal local differences in the composition of mEVs providing new insights into their structure. Also, thanks to the intrinsic properties of TERS to acquire the signal from only the first few nanometers of the surface, chemical investigation of the lipid membrane in correspondence with the various locations of the selected mEV could be performed by analyzing the peaks of the Raman shift in the relevant range of the spectrum (2800-3000 cm-1). Despite being limited to mEVs, this work demonstrates the potential of TERS in the analysis of extracellular vesicles.

A Raman spectral marker for the iso-octyl chain structure of cholesterol

Raman spectroscopy provides label-free, specific analysis of biomolecular structure and interactions. It could have a greater impact with improved characterization of complex fingerprint vibrations. Many Raman peaks have been assigned to cholesterol, for example, but the molecular vibrations associated with those peaks are not known. In this report, time-dependent density functional theory calculations of the Raman spectrum of cholesterol are compared to measurements on microcrystalline powder to identify 23 peaks in the Raman spectrum. Among them, a band of six peaks is found to be sensitive to the conformational structure of cholesterol's iso-octyl chain. Calculations on 10 conformers in this spectral band are fit to experimental spectra to probe the cholesterol chain structure in purified powder and in phospholipid vesicles. In vesicles, the chain is found to bend perpendicular to the steroid rings, supporting the case that the chain is a dynamic structure that contributes to lipid condensation and other effects of cholesterol in biomembranes. Statement of Significance: Here we use density functional theory to identify a band of six peaks in cholesterol's Raman spectrum that is sensitive to the conformational structure of cholesterol's chain. Raman spectra were analyzed to show that in fluid-phase lipid membranes, about half of the cholesterol chains point perpendicular to the steroid rings. This new method of label-free structural analysis could make significant contributions to our understanding of cholesterol's critical role in biomembrane structure and function. More broadly, the results show that computational quantum chemistry Raman spectroscopy can make significant new contributions to molecular structure when spectra are interpreted with computational quantum chemistry.

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.

Strategies and Progress of Raman Technologies for Cellular Uptake Analysis of the Drug Delivery Systems

Nanoparticle (NP)-based drug delivery systems have the potential to significantly enhance the pharmacological and therapeutic properties of drugs. These systems enhance the bioavailability and biocompatibility of pharmaceutical agents via enabling targeted delivery to specific tissues or organs. However, the efficacy and safety of these systems are largely dependent on the cellular uptake and intracellular transport of NPs. Thus, it is crucial to monitor the intracellular behavior of NPs within a single cell. Yet, it is challenging due to the complexity and size of the cell. Recently, the development of the Raman instrumentation offers a versatile tool to allow noninvasive cellular measurements. The primary objective of this review is to highlight the most recent advancements in Raman techniques (spontaneous Raman scattering, bioorthogonal Raman scattering, coherence Raman scattering, and surface-enhanced Raman scattering) when it comes to assessing the internalization of NP-based drug delivery systems and their subsequent movement within cells.

Extracellular vesicles and their non-coding RNA cargos: Emerging players in cardiovascular disease

Extracellular vesicles (EVs), including exosomes, microvesicles and apoptotic bodies, have recently received attention as essential mechanisms for cell-to-cell communication in cardiovascular disease. EVs can be released from different types of cells, including endothelial cells, smooth muscle cells, cardiac cells, fibroblasts, platelets, adipocytes, immune cells and stem cells. Non-coding (nc)RNAs as EV cargos have recently been investigated in the cardiovascular system. Up- or downregulated ncRNAs in EVs have been shown to play a crucial role in various cardiovascular diseases. Communication via EV-derived ncRNAs can occur between cells of the same type and between different types of cells involved in the pathophysiology of cardiovascular disease. In the present review, we highlight the important aspects of diverse cell-derived EVs and their ncRNA cargos as disease mediators and potential therapeutic targets in atherosclerosis, coronary artery disease, ischaemic heart disease and cardiac fibrosis. In addition, we summarize the potential of EV-derived ncRNAs in the treatment of cardiovascular disease. Finally, we discuss the different methods for EV isolation and characterization. A better understanding of the specific role of EVs and their ncRNA cargos in the regulation of cardiovascular (dys)function will be of importance for the development of diagnostic and therapeutic tools for cardiovascular disease.

Introduction of Nanomaterials to Biosensors for Exosome Detection: Case Study for Cancer Analysis

Exosomes have been gaining attention for early cancer diagnosis owing to their biological functions in cells. Several studies have reported the relevance of exosomes in various diseases, including pancreatic cancer, retroperitoneal fibrosis, obesity, neurodegenerative diseases, and atherosclerosis. Particularly, exosomes are regarded as biomarkers for cancer diagnosis and can be detected in biofluids, such as saliva, urine, peritoneal fluid, and blood. Thus, exosomes are advantageous for cancer liquid biopsies as they overcome the current limitations of cancer tissue biopsies. Several studies have reported methods for exosome isolation, and analysis for cancer diagnosis. However, further clinical trials are still required to determine accurate exosome concentration quantification methods. Recently, various biosensors have been developed to detect exosomal biomarkers, including tumor-derived exosomes, nucleic acids, and proteins. Among these, the exact quantification of tumor-derived exosomes is a serious obstacle to the clinical use of liquid biopsies. Precise detection of exosome concentration is difficult because it requires clinical sample pretreatment. To solve this problem, the use of the nanobiohybrid material-based biosensor provides improved sensitivity and selectivity. The present review will discuss recent progress in exosome biosensors consisting of nanomaterials and biomaterial hybrids for electrochemical, electrical, and optical-based biosensors.