A Label-Free Platform for Identification of Exosomes from Different Sources

Recent advances in optical label-free characterization of extracellular vesicles

Extracellular vesicles (EVs) are complex biological nanoparticles endogenously secreted by all eukaryotic cells. EVs carry a specific molecular cargo of proteins, lipids, and nucleic acids derived from cells of origin and play a significant role in the physiology and pathology of cells, organs, and organisms. Upon release, they may be found in different body fluids that can be easily accessed via noninvasive methodologies. Due to the unique information encoded in their molecular cargo, they may reflect the state of the parent cell and therefore EVs are recognized as a rich source of biomarkers for early diagnostics involving liquid biopsy. However, body fluids contain a mixture of EVs released by different types of healthy and diseased cells, making the detection of the EVs of interest very challenging. Recent research efforts have been focused on the detection and characterization of diagnostically relevant subpopulations of EVs, with emphasis on label-free methods that simplify sample preparation and are free of interfering signals. Therefore, in this paper, we review the recent progress of the label-free optical methods employed for the detection, counting, and morphological and chemical characterization of EVs. We will first briefly discuss the biology and functions of EVs, and then introduce different optical label-free techniques for rapid, precise, and nondestructive characterization of EVs such as nanoparticle tracking analysis, dynamic light scattering, atomic force microscopy, surface plasmon resonance spectroscopy, Raman spectroscopy, and SERS spectroscopy. In the end, we will discuss their applications in the detection of neurodegenerative diseases and cancer and provide an outlook on the future impact and challenges of these technologies to the field of liquid biopsy via EVs.

A Comprehensive Cancer-Associated MicroRNA Expression Profiling and Proteomic Analysis of Human Umbilical Cord Mesenchymal Stem Cell-Derived Exosomes

Background:

The mesenchymal stem cells (MSCs) have enormous therapeutic potential owing to their multi-lineage differentiation and self-renewal properties. MSCs express growth factors, cytokines, chemokines, and non-coding regulatory RNAs with immunosuppressive, anti-tumor, and migratory properties. MSCs also release several anti-cancer molecules via extracellular vesicles, that act as pro-apoptotic/tumor suppressor factors. This study aimed to identify the stem cell-derived secretome that could exhibit anti-cancer properties through molecular profiling of cargos in MSC-derived exosomes.

Methods:

Human umbilical cord mesenchymal stem cells (hUCMSCs) were isolated from umbilical cord tissues and culture expanded. Subsequently, exosomes were isolated from hUCMSC conditioned medium and characterized by DLS, electron microscopy. Western blot for exosome surface marker protein CD63 expression was performed. The miRNA profiling of hUCMSCs and hUCMSC-derived exosomes was performed, followed by functional enrichment analysis.

Results:

The tri-lineage differentiation potential, fibroblastic morphology, and strong expression of pluripotency genes indicated that isolated fibroblasts are MSCs. The isolated extracellular vesicles were 133.8 ± 42.49 nm in diameter, monodispersed, and strongly expressed the exosome surface marker protein CD63. The miRNA expression profile and gene ontology (GO) depicted the differential expression patterns of high and less-expressed miRNAs that are crucial to be involved in the regulation of apoptosis. The LCMS/MS data and GO analysis indicate that hUCMSC secretomes are involved in several oncogenic and inflammatory signaling cascades.

Conclusion:

Primary human MSCs released miRNAs and growth factors via exosomes that are increasingly implicated in intercellular communications, and hUCMSC-exosomal miRNAs have a critical influence in regulating cell death and apoptosis of cancer cells.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s13770-022-00450-8.

Exosome detection via surface-enhanced Raman spectroscopy for cancer diagnosis

As nanoscale extracellular vesicles, exosomes are secreted by various cell types, and they are widely distributed in multiple biological fluids. Studies have shown that tumor-derived exosomes can carry a variety of primary tumor-specific molecules, which may represent a novel tool for the early detection of cancer. However, the clinical translation of exosomes remains a challenge due to the requirement of large quantities of samples when enriching the cancer-related exosomes in biological fluids, the insufficiency of traditional techniques for exosome subpopulations, and the complex exosome isolation of the current commercially available exosome phenotype profiling approaches. The evolving surface-enhanced Raman scattering (SERS) technology, with properties of unique optoelectronics, easy functionalization, and the particular interaction between light and nanoscale metallic materials, can achieve sensitive detection of exosomes without large quantities of samples and multiplexed phenotype profiling, providing a new mode of real-time and noninvasive analysis for cancer patients. In the present review, we mainly discussed exosome detection based on SERS, especially SERS immunoassay. The basic structure and function of exosomes were firstly introduced. Then, recent studies using the SERS technique for cancer detection were critically reviewed, which mainly included various SERS substrates, biological modification of SERS substrates, SERS-based exosome detection, and the combination of SERS and other technologies for cancer diagnosis. This review systematically discussed the essential aspects, limitations, and considerations of applying SERS technology in the detection and analysis of cancer-derived exosomes, which could provide a valuable reference for the early diagnosis of cancer through SERS technology. STATEMENT OF SIGNIFICANCE: Surface-enhanced Raman scattering (SERS) has been applied to exosomes detection to obtain better diagnostic results. In past three years, several reviews have been published in exosome detection, which were narrowly focus on methods of exosome detection. Selection and surface functionalization of the substrate and the combination detection with different methods based on SERS will provide new strategies for the detection of exosomes. This review will focus on the above aspects. This emerging detection method is constantly evolving and contributing to the early discovery of diseases in the future.

Surface enhanced Raman scattering for probing cellular biochemistry

Surface enhanced Raman scattering (SERS) from biomolecules in living cells enables the sensitive, but also very selective, probing of their biochemical composition. This minireview discusses the developments of SERS probing in cells over the past years from the proof-of-principle to observe a biochemical status to the characterization of molecule-nanostructure and molecule-molecule interactions and cellular processes that involve a wide variety of biomolecules and cellular compartments. Progress in applying SERS as a bioanalytical tool in living cells, to gain a better understanding of cellular physiology and to harness the selectivity of SERS, has been achieved by a combination of live cell SERS with several different approaches. They range from organelle targeting, spectroscopy of relevant molecular models, and the optimization of plasmonic nanostructures to the application of machine learning and help us to unify the information from defined biomolecules and from the cell as an extremely complex system.

Anti-Metastatic Function of Extracellular Vesicles Derived from Nanog-Overexpressing Melanoma

A metastatic melanoma cell line B16-F10 (F10) was modified to a more undifferentiated state by Nanog overexpression. The produced cell line Nanog⁺F10 showed a higher metastatic potential than F10. Instead of whole cells, the extracellular vesicles (EVs) therefrom were investigated about their possible role as an autovaccine against metastasis. EVs from Nanog⁺F10 cells (Nanog⁺F10-EVs) could suppress the metastasis, contrasting the EVs from less metastatic F10 cells (F10-EVs) enhanced metastasis. The involvement of TGF-β1 in the role of Nanog⁺F10-EVs was analyzed, as TGF-β1 was a secretory cytokine being affected most intensively by Nanog overexpression. It was suggested to be crucial that the TGF-β1 concentration in Nanog⁺F10-EVs should be as low as 1.6 pg/μg for its metastasis-suppressive role. In response to Nanog⁺F10-EVs, immunoreaction was observed in liver, indicating the specific decrease in the number of tumor-promotive CD163-positive macrophages. These indicate a possibility of Nanog⁺F10-EVs as a novel autovaccine candidate against melanoma metastasis.

Plasma Small Extracellular Vesicles with Complement Alterations in GRN/C9orf72 and Sporadic Frontotemporal Lobar Degeneration

Cutting-edge research suggests endosomal/immune dysregulation in GRN/C9orf72-associated frontotemporal lobar degeneration (FTLD). In this retrospective study, we investigated plasma small extracellular vesicles (sEVs) and complement proteins in 172 subjects (40 Sporadic FTLD, 40 Intermediate/Pathological C9orf72 expansion carriers, and 49 Heterozygous/Homozygous GRN mutation carriers, 43 controls). Plasma sEVs (concentration, size) were analyzed by nanoparticle tracking analysis; plasma and sEVs C1q, C4, C3 proteins were quantified by multiplex assay. We demonstrated that genetic/sporadic FTLD share lower sEV concentrations and higher sEV sizes. The diagnostic performance of the two most predictive variables (sEV concentration/size ratio) was high (AUC = 0.91, sensitivity 85.3%, specificity 81.4%). C1q, C4, and C3 cargo per sEV is increased in genetic and sporadic FTLD. C4 (cargo per sEV, total sEV concentration) is increased in Sporadic FTLD and reduced in GRN+ Homozygous, suggesting its specific unbalance compared with Heterozygous cases. C3 plasma level was increased in genetic vs. sporadic FTLD. Looking at complement protein compartmentalization, in control subjects, the C3 and C4 sEV concentrations were roughly half that in respect to those measured in plasma; interestingly, this compartmentalization was altered in different ways in patients. These results suggest sEVs and complement proteins as potential therapeutic targets to mitigate neurodegeneration in FTLD.

Advances in the Application of Exosomes Identification Using Surface-Enhanced Raman Spectroscopy for the Early Detection of Cancers

Exosomes are small nanoscale vesicles with a double-layered lipid membrane structure secreted by cells, and almost all types of cells can secrete exosomes. Exosomes carry a variety of biologically active contents such as nucleic acids and proteins, and play an important role not only in intercellular information exchange and signal transduction, but also in various pathophysiological processes in the human body. Surface-enhanced Raman Spectroscopy (SERS) uses light to interact with nanostructured materials such as gold and silver to produce a strong surface plasmon resonance effect, which can significantly enhance the Raman signal of molecules adsorbed on the surface of nanostructures to obtain a rich fingerprint of the sample itself or Raman probe molecules with ultra-sensitivity. The unique advantages of SERS, such as non-invasive and high sensitivity, good selectivity, fast analysis speed, and low water interference, make it a promising technology for life science and clinical testing applications. In this paper, we briefly introduce exosomes and the current main detection methods. We also describe the basic principles of SERS and the progress of the application of unlabeled and labeled SERS in exosome detection. This paper also summarizes the value of SERS-based exosome assays for early tumor diagnosis.

A systematic review on the modifications of extracellular vesicles: a revolutionized tool of nano-biotechnology

Background

Tailoring extracellular vesicles (EVs) can bequeath them with diverse functions and efficient performance in nano-biotechnology. Engineering and modification of EVs improves the targeted drug delivery efficiency. Here, we performed systematic review of various methods for EVs modifications.

Methods

PubMed, Scopus, ISI Web of Science, EMBASE, and Google Scholar were searched for available articles on EVs modifications (up to March 2021). In total, 1208 articles were identified and assessed, and then only 36 articles were found eligible and included.

Results

Six studies demonstrate the application of click chemistry, seven studies used co-incubation, two studies used chemical transfection, four studies implicated electroporation and sonication approach for modification of EVs. Moreover, two studies utilized microfluidics as suitable approach for loading cargo into EVs, while eight studies showed freeze–thaw method as feasible for these biological nanoparticles.

Conclusion

Freeze–thaw approach is found to be convenient and popular among researchers for performing modifications in EVs for the purpose of targeted drug delivery loading. Clinical-grade EVs production with good clinical practices (GCPs) is challenging in the current scenario. More studies are needed to determine the best suitable approach for cargo loading of EVs that may be exploited for research and therapeutic use.

Graphical Abstract

Extracellular vesicles (EVs) can be modified using various methods available including physical, chemical and engineering based. These tailoring methods are helpful in targeting drug delivery to treat various diseases. Moreover, EVs have the ability to modify that’s due to presence of lipid bilayer membrane, that’s effectively participate in loading and unloading of desired drug.

EVs expressed from the specific cell types can give useful information about the pathogenesis of a particular disease in the form of unique nucleic acids, protein and lipid sequences and therefore, EVs derived from these cells can be used as specific diagnostic biomarker for diagnosis of diseases.

Modified EVs using various drugs or miRNAs can be used for targeted drug delivery to specific cells.

A sandwich-based evanescent wave fluorescent biosensor for simple, real-time exosome detection†

Exosomes are regarded as a promising biomarker for the noninvasive diagnosis and treatment of diseases. The value of exosomes for medical research has promoted the search for a fast, efficient, and sensitive detection method. This study reported a sandwich-based evanescent wave fluorescent biosensor (S-EWFB) for exosome detection. A two-step strategy was implemented to take advantages of the simple binding of fluorescent probes with exosomes via the hydrophobic interaction between the cholesteryl and phospholipid bilayer membrane, as well as real-time detection on an evanescent wave liquid-solid interface based on CD63 aptamer-specific capture to form an exosome@fluorescence probe/aptamer sandwich structure. The one-to-many connection between exosomes and signal molecules and the aptamer-modified evanescent wave optical fiber detection platform reduced the detection limit of exosomes to 7.66 particles/mL, with a linear range of 47.5-4.75 × 10⁶ particles/mL. The entire detection process was simple, rapid, and real-time and lasted about 1 h while requiring no separation and purification. Additionally, this platform showed excellent surface regeneration capability and exhibited good performance during the analysis of tumor and non-tumor-derived exosomes.

Single Particle Automated Raman Trapping Analysis of Breast Cancer Cell-Derived Extracellular Vesicles as Cancer Biomarkers

Extracellular vesicles (EVs) secreted by cancer cells provide an important insight into cancer biology and could be leveraged to enhance diagnostics and disease monitoring. This paper details a high-throughput label-free extracellular vesicle analysis approach to study fundamental EV biology, toward diagnosis and monitoring of cancer in a minimally invasive manner and with the elimination of interpreter bias. We present the next generation of our single particle automated Raman trapping analysis─SPARTA─system through the development of a dedicated standalone device optimized for single particle analysis of EVs. Our visualization approach, dubbed dimensional reduction analysis (DRA), presents a convenient and comprehensive method of comparing multiple EV spectra. We demonstrate that the dedicated SPARTA system can differentiate between cancer and noncancer EVs with a high degree of sensitivity and specificity (>95% for both). We further show that the predictive ability of our approach is consistent across multiple EV isolations from the same cell types. Detailed modeling reveals accurate classification between EVs derived from various closely related breast cancer subtypes, further supporting the utility of our SPARTA-based approach for detailed EV profiling.

Characterization of ovarian cancer-derived extracellular vesicles by surface-enhanced Raman spectroscopy

Ovarian cancer is the most lethal gynecological malignancy, owing to the fact that most cases are diagnosed at a late stage. To improve prognosis and reduce mortality, we must develop methods for the early diagnosis of ovarian cancer. A step towards early and non-invasive cancer diagnosis is through the utilization of extracellular vesicles (EVs), which are nanoscale, membrane-bound vesicles that contain proteins and genetic material reflective of their parent cell. Thus, EVs secreted by cancer cells can be thought of as cancer biomarkers. In this paper, we present gold nanohole arrays for the capture of ovarian cancer (OvCa)-derived EVs and their characterization by surface-enhanced Raman spectroscopy (SERS). For the first time, we have characterized EVs isolated from two established OvCa cell lines (OV-90, OVCAR3), two primary OvCa cell lines (EOC6, EOC18), and one human immortalized ovarian surface epithelial cell line (hIOSE) by SERS. We subsequently determined their main compositional differences by principal component analysis and were able to discriminate the groups by a logistic regression-based machine learning method with ∼99% accuracy, sensitivity, and specificity. The results presented here are a great step towards quick, facile, and non-invasive cancer diagnosis.

Human umbilical vein endothelial cells derived-exosomes promote osteosarcoma cell stemness by activating Notch signaling pathway

Osteosarcoma is one of the most common primary malignant tumors of bone in adolescents. Human umbilical vein endothelial cells (HUVECs) derived exosomes are associated with osteosarcoma cell stemness. Little is known about the function of HUVECs-exosomes in osteosarcoma cell stemness. This work aimed to investigate the mechanism of action of HUVECs-exosomes in regulating stem cell-like phenotypes of osteosarcoma cells. HUVECs were treated with GW4869 (exosome inhibitor). Human osteosarcoma cells (U2OS and 143B) were treated with HUVECs supernatant, HUVECs-exosomes with or without RO4929097 (γ secretase inhibitor, used to block Notch signaling pathway). We found that HUVECs supernatant and HUVECs-exosomes enhanced the proportions of STRO-1⁺CD117⁺ cells and the expression of stem cell-related proteins Oct4 and Sox2. Both HUVECs supernatant and HUVECs-exosomes promoted the sarcosphere formation efficiency of U2OS and 143B cells. These stem-like phenotypes of U2OS and 143B cells conferred by HUVECs-exosomes were repressed by GW4869. Moreover, HUVECs-exosomes promoted the expression of Notch1, Hes1 and Hey1 in the U2OS and 143B cells. RO4929097 treatment reversed the impact of HUVECs-exosomes on Notch1, Hes1, and Hey1 expression by inhibiting Notch1 signaling pathway. In conclusion, this work demonstrated that HUVECs-exosomes promoted cell stemness in osteosarcoma through activating Notch signaling pathway. Thus, our data reveal the mechanism of HUVECs-exosomes in regulating cell stemness of osteosarcoma, and provide a theoretical basis for osteosarcoma treatment by exosomes.

Progress in Nanomaterials-Based Optical and Electrochemical Methods for the Assays of Exosomes

Exosomes with diameters of 30-150 nm are small membrane-bound vesicles secreted by a variety of cells. They play an important role in many biological processes, such as tumor-related immune response and intercellular signal transduction. Exosomes have been considered as emerging and noninvasive biomarkers for cancer diagnosis. Recently, a large number of optical and electrochemical biosensors have been proposed for sensitive detection of exosomes. To meet the increasing demands for ultrasensitive detection, nanomaterials have been integrated with various techniques as powerful components. Because of their intrinsic merits of biological compatibility, excellent physicochemical features and unique catalytic ability, nanomaterials have significantly improved the analytical performances of exosome biosensors. In this review, we summarized the recent progress in nanomaterials-based biosensors for the detection of cancer-derived exosomes, including fluorescence, colorimetry, surface plasmon resonance spectroscopy, surface enhanced Raman scattering spectroscopy, electrochemistry, electrochemiluminescence and so on.

SERS and MALDI-TOF MS based plasma exosome profiling for rapid detection of osteosarcoma

Osteosarcoma is the most frequent primary bone cancer, particularly among children and adolescents. The early diagnosis of osteosarcoma is significant for timely clinical treatment to reduce the mortality of patients. Exosomes play a significant role in intercellular communication and serve as promising biomarkers in liquid biopsy for the diagnosis and monitoring of tumors. Herein, we report the utility of surface-enhanced Raman scattering (SERS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of osteosarcoma. We firstly profiled the intrinsic SERS signals and MALDI-TOF mass fingerprints of different subgroups of extracellular vesicles (EVs) and the corresponding cells, demonstrating that the SERS signals and MALDI-TOF mass spectra of exosomes from different types of cells were more discriminative compared to those of large and medium EVs and the cells themselves. Then, we characterized plasma-derived exosomes of 15 osteosarcoma patients and 15 healthy volunteers using SERS and MALDI-TOF MS, revealing distinctive biochemical differences in the spectra. We further utilized a data fusion approach to combine the two types of spectroscopic techniques, differentiating osteosarcoma patients from healthy controls with higher precision than either technique. The results reveal that the non-invasive liquid biopsy method using SERS and MALDI-TOF MS fingerprinting of exosomes has great potential for rapid diagnosis of osteosarcoma.

Advanced Nanotechnologies for Extracellular Vesicle-Based Liquid Biopsy

Extracellular vesicles (EVs) are emerging as a new source of biomarkers in liquid biopsy because of their wide presence in most body fluids and their ability to load cargoes from disease-related cells. Owing to the crucial role of EVs in disease diagnosis and treatment, significant efforts have been made to isolate, detect, and analyze EVs with high efficiency. A recent overview of advanced EV detection nanotechnologies is discussed here. First, several key challenges in EV-based liquid biopsies are introduced. Then, the related pivotal advances in nanotechnologies for EV isolation based on physical features, chemical affinity, and the combination of nanostructures and chemical affinity are summarized. Next, a summary of high-sensitivity sensors for EV detection and advanced approaches for single EV detection are provided. Later, EV analysis is introduced in practical clinical scenarios, and the application of machine learning in this field is highlighted. Finally, future opportunities for the development of next-generation nanotechnologies for EV detection are presented.

Insight into the Exosomal Membrane: From Viewpoints of Membrane Fluidity and Polarity

Numerous research studies have been done for exosomes, particularly focusing on membrane proteins and included nucleic acids, and the volume of the knowledge about the lipids in the exosomal membrane has been increasing. However, the dynamic property of the exosomal membrane is hardly studied. By employing milk exosome as an example, herein the exosomal membrane was characterized focusing on the membrane fluidity and polarity. The lipid composition and phase state of milk exosome (exosome from bovine milk) were estimated. The milk exosome contained enriched Chol (43.6 mol % in total lipid extracts), which made the membrane in the liquid-ordered (l_o) phase by interacting with phospholipids. To suggest a model of exosomal vesicle cargo, the liposome compositions that mimic milk exosome were studied: liposomes were made of cholesterol (Chol), milk sphingomyelin (milk SM), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). By using fluorescent probes 1,6-diphenyl-1,3,5-hexatriene and 6-dodecanoyl-2-dimethylaminonaphthalene, the microenvironments of submicron-sized membranes of exosome and model liposomes were investigated. The membrane fluidity of milk exosome was slightly higher than those of Chol/milk SM/POPC liposomes with a similar content of Chol, suggesting the presence of enriched unsaturated lipids. The most purposeful membrane property was obtained by the liposome composition of Chol/milk SM/POPC = 40/15/45. From the above, it is concluded that Chol is a fundamental component of the milk exosomal membrane to construct the enriched l_o phase, which could increase the membrane rigidity and contribute to the function of exosome.

Recent Progress in Detection and Profiling of Cancer Cell-Derived Exosomes

Exosomes, known as nanometer-sized vesicles (30-200 nm), are secreted by many types of cells. Cancer-derived exosomes have great potential to be biomarkers for early clinical diagnosis and evaluation of cancer therapeutic efficacy. Conventional detection methods are limited to low sensitivity and reproducibility. There are hundreds of papers published with different detection methods in recent years to address these challenges. Therefore, in this review, pioneering researches about various detection strategies are comprehensively summarized and the analytical performance of these tests is evaluated. Furthermore, the exosome molecular composition (protein and nucleic acid) profiling, a single exosome profiling, and their application in clinical cancer diagnosis are reviewed. Finally, the principles and applications of machine learning method in exosomes researches are presented.

Mesenchymal Stromal Cell-Derived Tailored Exosomes Treat Bacteria-Associated Diabetes Foot Ulcers: A Customized Approach From Bench to Bed

Exosomes are nano-vesicles of endosomal origin inherited with characteristics of drug delivery and cargo loading. Exosomes offer a diverse range of opportunities that can be exploited in the treatment of various diseases post-functionalization. This membrane engineering is recently being used in the management of bacteria-associated diabetic foot ulcers (DFUs). Diabetes mellitus (DM) is among the most crippling disease of society with a large share of its imposing economic burden. DM in a chronic state is associated with the development of micro- and macrovascular complications. DFU is among the diabetic microvascular complications with the consequent occurrence of diabetic peripheral neuropathy. Mesenchymal stromal cell (MSC)-derived exosomes post-tailoring hold promise to accelerate the diabetic wound repair in DFU associated with bacterial inhabitant. These exosomes promote the antibacterial properties with regenerative activity by loading bioactive molecules like growth factors, nucleic acids, and proteins, and non-bioactive substances like antibiotics. Functionalization of MSC-derived exosomes is mediated by various physical, chemical, and biological processes that effectively load the desired cargo into the exosomes for targeted delivery at specific bacterial DFUs and wound. The present study focused on the application of the cargo-loaded exosomes in the treatment of DFU and also emphasizes the different approaches for loading the desired cargo/drug inside exosomes. However, more studies and clinical trials are needed in the domain to explore this membrane engineering.

Current strategies in tailoring methods for engineered exosomes and future avenues in biomedical applications

Exosomes are naturally occurring nanovesicles of endosomal origin, responsible for cellular communication. Depending on the cell type, exosomes display disparity in the cargo and are involved in up/down regulation of different biological pathways. Naturally secreted exosomes, owing to their inherent delivery potential, non-immunogenic nature and limited structural resemblance to the cells have emerged as ideal candidates for various drug delivery and therapeutic applications. Moreover, the structural versatility of exosomes provides greater flexibility for surface modifications to be made in the native configuration, by different methods, like genetic-engineering, chemical procedures, physical methods and microfluidic-technology, to enhance the cargo quality for expanded biomedical applications. Post isolation and prior to engineering exosomes for various applications, the internal and external structural compositions of exosomes are studied via different techniques. Efficiency and scalability of the exosome modification methods are pivotal in determining the scope of the technique for clinical applications. This review majorly focuses on different methods employed for engineering exosomes, and advantages/disadvantages associated with different tailoring approaches, along with the efficacy of engineered exosomes in biomedical applications. Further, the review highlights the importance of a relatively recent avenue for delivery of exosomes via scaffold-based delivery of naïve/engineered exosomes for regenerative medicine and tissue engineering. This review is based on the recent knowledge generated in this field and our comprehension in this domain.

A Holistic Review of the State-of-the-Art Microfluidics for Exosome Separation: An Overview of the Current Status, Existing Obstacles, and Future Outlook

Exosomes, a class of small extracellular vesicles (30-150 nm), are secreted by almost all types of cells into virtually all body fluids. These small vesicles are attracting increasing research attention owing to their potential for disease diagnosis and therapy. However, their inherent heterogeneity and the complexity of bio-fluids pose significant challenges for their isolation. Even the "gold standard," differential centrifugation, suffers from poor yields and is time-consuming. In this context, recent developments in microfluidic technologies have provided an ideal system for exosome extraction and these devices exhibit some fascinating properties such as high speeds, good portability, and low sample volumes. In this review, the focus is on the state-of-the-art microfluidic technologies for exosome isolation and highlight potential directions for future research and development by analyzing the challenges faced by the current strategies.

Space curvature-inspired nanoplasmonic sensor for breast cancer extracellular vesicle fingerprinting and machine learning classification

Extracellular vesicles (EVs) are micro and nanoscale lipid-enclosed packages that have shown potential as liquid biopsy targets for cancer because their structure and contents reflect their cell of origin. However, progress towards the clinical applications of EVs has been hindered due to the low abundance of disease-specific EVs compared to EVs from healthy cells; such applications thus require highly sensitive and adaptable characterization tools. To address this obstacle, we designed and fabricated a novel space curvature-inspired surfaced-enhanced Raman spectroscopy (SERS) substrate and tested its capabilities using bioreactor-produced and size exclusion chromatography-purified breast cancer EVs of three different subtypes. Our findings demonstrate the platform's ability to effectively fingerprint and efficiently classify, for the first time, three distinct subtypes of breast cancer EVs following the application of machine learning algorithms on the acquired spectra. This platform and characterization approach will enhance the viability of EVs and nanoplasmonic sensors towards clinical utility for breast cancer and many other applications to improve human health.

Characterization of extracellular vesicles derived from mesenchymal stromal cells by surface-enhanced Raman spectroscopy

Extracellular vesicles (EVs) are secreted by all cells into bodily fluids and play an important role in intercellular communication through the transfer of proteins and RNA. There is evidence that EVs specifically released from mesenchymal stromal cells (MSCs) are potent cell-free regenerative agents. However, for MSC EVs to be used in therapeutic practices, there must be a standardized and reproducible method for their characterization. The detection and characterization of EVs are a challenge due to their nanoscale size as well as their molecular heterogeneity. To address this challenge, we have fabricated gold nanohole arrays of varying sizes and shapes by electron beam lithography. These platforms have the dual purpose of trapping single EVs and enhancing their vibrational signature in surface-enhanced Raman spectroscopy (SERS). In this paper, we report SERS spectra for MSC EVs derived from pancreatic tissue (Panc-MSC) and bone marrow (BM-MSC). Using principal component analysis (PCA), we determined that the main compositional differences between these two groups are found at 1236, 761, and 1528 cm^-1, corresponding to amide III, tryptophan, and an in-plane -C=C- vibration, respectively. We additionally explored several machine learning approaches to distinguish between BM- and Panc-MSC EVs and achieved 89 % accuracy, 89 % sensitivity, and 88 % specificity using logistic regression.

Non-invasive SERS serum detection technology combined with multivariate statistical algorithm for simultaneous screening of cervical cancer and breast cancer

Surface-enhanced Raman scattering (SERS), as a rapid, reliable and non-destructive spectral detection technology, has made a series of breakthrough achievements in screening and pre-diagnosis of various cancerous tumors. In this paper, high-performance gold nanoparticles/785 porous silicon photonic crystals (Au NPs/785 PSi PhCs) active SERS substrates were specially designed for serum testing, and realized highly sensitive detection of serum from healthy people, patients with cervical cancer and breast cancer. Based on the SERS spectra of the three groups of serum, the significant differences between the healthy group and cancer group at 1030 cm^-1 and 1051 cm^-1 were analyzed, and the similar but different serum SERS spectra of cervical cancer and breast cancer patients were compared. In addition, the spectral difference detected by SERS technology combined with a multivariate statistical algorithm was used to distinguish three kinds of serum. The serum SERS spectral sensitive bands were extracted by recursive weighted partial least squares (rPLS), and the three classification diagnosis models were established by combining orthogonal partial least squares discriminant analysis (OPLS-DA), linear discriminant analysis (LDA) and principal component analysis support vector machine (PCA-SVM) for synchronous classification and discrimination of the three groups of serum. The diagnostic results showed that the overall screening accuracy of three models were 93.28%, 97.77% and 94.78%, respectively. These above results confirmed that the Au NPs/785 PSi PhCs can realize super-sensitive detection of serum, and the established diagnostic model has great potential for pre-diagnosis and simultaneous screening of cervical cancer and breast cancer.

Recent Advances in the Label-Free Characterization of Exosomes for Cancer Liquid Biopsy: From Scattering and Spectroscopy to Nanoindentation and Nanodevices

Exosomes (EXOs) are nano-sized vesicles secreted by most cell types. They are abundant in bio-fluids and harbor specific molecular constituents from their parental cells. Due to these characteristics, EXOs have a great potential in cancer diagnostics for liquid biopsy and personalized medicine. Despite this unique potential, EXOs are not yet widely applied in clinical settings, with two main factors hindering their translational process in diagnostics. Firstly, conventional extraction methods are time-consuming, require large sample volumes and expensive equipment, and often do not provide high-purity samples. Secondly, characterization methods have some limitations, because they are often qualitative, need extensive labeling or complex sampling procedures that can induce artifacts. In this context, novel label-free approaches are rapidly emerging, and are holding potential to revolutionize EXO diagnostics. These methods include the use of nanodevices for EXO purification, and vibrational spectroscopies, scattering, and nanoindentation for characterization. In this progress report, we summarize recent key advances in label-free techniques for EXO purification and characterization. We point out that these methods contribute to reducing costs and processing times, provide complementary information compared to the conventional characterization techniques, and enhance flexibility, thus favoring the discovery of novel and unexplored EXO-based biomarkers. In this process, the impact of nanotechnology is systematically highlighted, showing how the effectiveness of these techniques can be enhanced using nanomaterials, such as plasmonic nanoparticles and nanostructured surfaces, which enable the exploitation of advanced physical phenomena occurring at the nanoscale level.

Progress in the research of nanomaterial-based exosome bioanalysis and exosome-based nanomaterials tumor therapy

Exosomes and their internal components have been proven to play critical roles in cell-cell interactions and intrinsic cellular regulations, showing promising prospects in both biomedical and clinical fields. Although conventional methods have so far been utilized to great effect, accurate bioanalysis remains a major challenge. In recent years, the fast-paced development of nanomaterials with unique physiochemical properties has led to a boom in the potential bioapplications of such materials. In particular, the application of nanomaterials in exosome bioanalysis provides a great opportunity to overcome the current challenges and limitations of conventional methods. A timely review of the research progress in this field is thus of great significance to the continued development of new methods. This review outlines the properties and potential uses of exosomes, and discusses the conventional methods currently used for their analysis. We then focus on exploring the current state of the art regarding the use of nanomaterials for the isolation, detection and even the subsequent profiling of exosomes. The main methods are based on principles including fluorescence, surface-enhanced Raman spectroscopy, colorimetry, electrochemistry, and surface plasmon resonance. Additionally, research on exosome-based nanomaterials tumor therapy is also promising from a clinical perspective, so the research progress in this branch is also summarized. Finally, we look at ways in which the field might develop in the future.

Surface-Enhanced Raman Scattering (SERS) Spectroscopy for Sensing and Characterization of Exosomes in Cancer Diagnosis

Simple Summary

The distinct molecular and biological properties of exosomes, together with their abundance and stability, make them an ideal target in liquid biopsies for early diagnosis and disease monitoring. On the other hand, in recent years, nanomaterial-based optical biosensors have been extensively investigated as novel, rapid and sensitive tools for exosome detection and discrimination. The scope of this review is to summarize and coherently discussed the diverse applications, challenges and limitations of nanosensors based on surface-enhanced Raman spectroscopy (SERS) as the optosensing technique.

Abstract

Exosomes are emerging as one of the most intriguing cancer biomarkers in modern oncology for early cancer diagnosis, prognosis and treatment monitoring. Concurrently, several nanoplasmonic methods have been applied and developed to tackle the challenging task of enabling the rapid, sensitive, affordable analysis of exosomes. In this review, we specifically focus our attention on the application of plasmonic devices exploiting surface-enhanced Raman spectroscopy (SERS) as the optosensing technique for the structural interrogation and characterization of the heterogeneous nature of exosomes. We summarized the current state-of-art of this field while illustrating the main strategic approaches and discuss their advantages and limitations.

Superhydrophobic bowl-like SERS substrates patterned from CMOS sensors for extracellular vesicle characterization

Using a regular CMOS sensor as a template, we are able to fabricate a simple but highly effective superhydrophobic SERS substrate. Specifically, we decorated the microlens layer of the sensor with 7 μm polystyrene beads to obtain a PDMS patterned replica. The process resulted in a uniform pattern of voids in the PDMS (denoted nanobowls) that are intercalated with a few larger voids (denoted here microbowls). The voids act as superhydrophobic substrates with analyte concentration capabilities in bigger bowl-like structures. Silver nanoparticles were directly grown on the patterned PDMS substrate inside both the nano- and microbowls, and serve as strong electromagnetic field enhancers for the SERS substrate. After systematic characterization of the fabricated SERS substrate by atomic force microscopy and scanning electron microscopy, we demonstrated its SERS performance using 4-aminothiophenol as a reporter molecule. Finally, we employed this innovative substrate to concentrate and analyze extracellular vesicles (EVs) isolated from an MC65 neural cell line in an ultralow sample volume. This substrate can be further exploited for the investigation of various EV biomarkers for early diagnosis of different diseases using liquid biopsy.

Single plasmonic nanostructures for biomedical diagnosis

The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.

Microfluidic-Based Exosome Analysis for Liquid Biopsy

Liquid biopsy offers non-invasive and real-time molecular profiling of individual patients, and is thus considered a revolutionary technology in precision medicine. Exosomes have been acknowledged as significant biomarkers in liquid biopsy, as they play a central role in cell-cell communication and are closely related to the pathogenesis of most human malignancies. Nevertheless, in biofluids exosomes always co-exist with other particles, and the cargo components of exosomes are highly heterogeneous. Thus, the isolation and molecular characterization of exosomes are still technically challenging. Microfluidics technology effectively addresses this challenge by virtue of its inherent advantages, such as precise manipulation of fluids, low consumption of samples and reagents, and a high level of integration. Recent advances in microfluidics allow in situ exosome capture and molecular detection with unprecedented selectivity and sensitivity. In this review, the state-of-the-art developments in microfluidics-based exosome research, including exosome isolation approaches and molecular detection strategies, with highlights of the characterization of exosomal biomarkers in cancer liquid biopsy is summarized. The major challenges are also discussed and some perspectives for the future directions of exosome-based liquid biopsy in microfluidic systems are presented.

Immunoassay-aptasensor for the determination of tumor-derived exosomes based on the combination of magnetic nanoparticles and hybridization chain reaction

The detection of tumor-related exosomes is of great significance. In this work, a fluorescence aptasensor was designed for the determination of tumor-related exosomes based on the capture of magnetic nanoparticles (MNPs) and specific recognition of an aptamer. MNPs were used as substrates to capture the exosomes by modifying the CD63 antibody on the MNP surface. Probe 1 consists of PDL-1 aptamer sequence and a section of other sequences. PDL-1 expression was observed on the surface of exosomes; the aptamer of PDL-1 could combine with PDL-1 with high affinity. Thus, the immunoassay-type compounds of "MNPs-exosomes-probe 1" were formed. The other section of probe 1 triggered the HCR with probe 2 and probe 3 and formed the super-long dsDNA. The addition of GelRed resulted in the generation of an amplified fluorescence signal. The proposed design demonstrated a good linearity with the exosome concentration ranging from 300 to 107 particles per mL and with a low detection limit of 100 particles per mL. This aptasensor also exhibited high specificity for tumor-related exosomes, and was successfully applied in biological samples.

Analysis of urinary exosomes applications for rare kidney disorders

Introduction: Exosomes are nanovesicles that play important functions in a variety of physiological and pathological conditions. They are powerful cell-to-cell communication tool thanks to the protein, mRNA, miRNA, and lipid cargoes they carry. They are also emerging as valuable diagnostic and prognostic biomarker sources. Urinary exosomes carry information from all the cells of the urinary tract, downstream of the podocyte. Rare kidney diseases are a subset of an inherited diseases whose genetic diagnosis can be unclear, and presentation can vary due to genetic, epigenetic, and environmental factors. Areas covered: In this review, we focus on a group of rare and often neglected kidney diseases, for which we have sufficient available literature data on urinary exosomes. The analysis of their content can help to comprehend pathological mechanisms and to identify biomarkers for diagnosis, prognosis, and therapeutic targets. Expert opinion: The foreseeable large-scale application of system biology approach to the profiling of exosomal proteins as a source of renal disease biomarkers will be also useful to stratify patients with rare kidney diseases whose penetrance, phenotypic presentation, and age of onset vary sensibly. This can ameliorate the clinical management.

Positively charged gold-silver nanostar enabled molecular characterization of cancer associated extracellular vesicles

Direct surface-enhanced Raman scattering (SERS) has contributed to characterizing extracellular vesicles (EVs) by providing molecular signatures. However, little work has been carried out to understand the heterogeneity of EVs created by different methods or from different biological sources. Herein, we pioneered the use of positively charged gold-silver nanostars to explore the SERS profiles of different EVs. The physical features of EVs from cancer cells including the size, concentration, morphology and surface potential have been characterized via nanoparticle tracking analysis, transmission electron microscopy and zeta potential analysis. The results show that negatively charged EVs are attracted to positively charged gold-silver nanostar surfaces via electrostatic forces resulting in SERS spectra showing characteristic vibrational modes of the different components of EVs (i.e. proteins, lipids and nucleic acids). SERS data were complemented by other spectroscopic techniques including atomic force microscopy-infrared spectroscopy, UV-visible absorbance spectroscopy and fluorescence spectroscopy providing a more complete molecular picture of EVs. SERS signatures of EVs from different origins, batches, and isolation approaches were compared and analyzed. A statistical method (principal component analysis-linear discriminant analysis) was utilized to differentiate EV subtypes. Consequently, a desirable discrimination outcome for blind samples was obtained. This study provides novel insights to deepen our understanding of EV heterogeneity.

Acoustofluidics-Assisted Fluorescence-SERS Bimodal Biosensors

Acoustofluidics, the fusion of acoustics and microfluidic techniques, has recently seen increased research attention across multiple disciplines due in part to its capabilities in contactless, biocompatible, and precise manipulation of micro-/nano-objects. Herein, a bimodal signal amplification platform which relies on acoustofluidics-induced enrichment of nanoparticles is introduced. The dual-function biosensor can perform sensitive immunofluorescent or surface-enhanced Raman spectroscopy (SERS) detection. The platform functions by using surface acoustic waves to concentrate nanoparticles at either the center or perimeter of a glass capillary; the concentration location is adjusted simply by varying the input frequency. The immunofluorescence assay is achieved by concentrating fluorescent analytes and functionalized nanoparticles at the center of the microchannel, thereby improving the visibility of the fluorescent output. By modifying the inner wall of the glass capillary with plasmonic Ag nanoparticle-deposited ZnO nanorod arrays and focusing analytes toward the perimeter of the microchannel, SERS sensing using the same device setup is achieved. Nanosized exosomes are used as a proof-of-concept to validate the performance of the acoustofluidic bimodal biosensor. With its sample-enrichment functionality, bimodal sensing, short processing time, and minute sample consumption, the acoustofluidic chip holds great potential for the development of lab-on-a-chip based analysis systems in many real-world applications.

Plasmonic Sensors for Extracellular Vesicle Analysis: From Scientific Development to Translational Research

Extracellular vesicles (EVs), actively shed from a variety of neoplastic and host cells, are abundant in blood and carry molecular markers from parental cells. For these reasons, EVs have gained much interest as biomarkers of disease. Among a number of different analytical methods that have been developed, surface plasmon resonance (SPR) stands out as one of the ideal techniques given its sensitivity, robustness, and ability to miniaturize. In this Review, we compare different SPR platforms for EV analysis, including conventional SPR, nanoplasmonic sensors, surface-enhanced Raman spectroscopy, and plasmonic-enhanced fluorescence. We discuss different surface chemistries used to capture targeted EVs and molecularly profile their proteins and RNAs. We also highlight these plasmonic platforms' clinical applications, including cancers, neurodegenerative diseases, and cardiovascular diseases. Finally, we discuss the future perspective of plasmonic sensing for EVs and their potentials for commercialization and clinical translation.

Extracellular Vesicle Identification Using Label-Free Surface-Enhanced Raman Spectroscopy: Detection and Signal Analysis Strategies

Extracellular vesicles (EVs) have been widely investigated as promising biomarkers for the liquid biopsy of diseases, owing to their countless roles in biological systems. Furthermore, with the notable progress of exosome research, the use of label-free surface-enhanced Raman spectroscopy (SERS) to identify and distinguish disease-related EVs has emerged. Even in the absence of specific markers for disease-related EVs, label-free SERS enables the identification of unique patterns of disease-related EVs through their molecular fingerprints. In this review, we describe label-free SERS approaches for disease-related EV pattern identification in terms of substrate design and signal analysis strategies. We first describe the general characteristics of EVs and their SERS signals. We then present recent works on applied plasmonic nanostructures to sensitively detect EVs and notable methods to interpret complex spectral data. This review also discusses current challenges and future prospects of label-free SERS-based disease-related EV pattern identification.

Applications of surface-enhanced Raman spectroscopy in detection fields

Surface-enhanced Raman spectroscopy (SERS) is a Raman spectroscopy technique that has been widely used in food safety, environmental monitoring, medical diagnosis and treatment and drug monitoring because of its high selectivity, sensitivity, rapidness, simplicity and specificity in identifying molecular structures. This review introduces the detection mechanism of SERS and summarizes the most recent progress concerning the use of SERS for the detection and characterization of molecules, providing references for the later research of SERS in detection fields.

Liquid biopsy technologies based on membrane microfluidics: High-yield purification and selective quantification of biomarkers in nanocarriers

Liquid biopsy, screening cancer non-invasively and frequently by detecting and quantifying molecular markers in physiological fluids, would significantly improve cancer survival rate but it remains a distant goal. The key obstacles presented by the highly heterogeneous samples are rapid/high-yield purification and precise/selective marker capture by their antibody and oligo probes. As irregular expressions of these molecular biomarkers are the key signals, quantifying only those from the cancer cells would greatly enhance the performance of the screening tests. The recent discovery that the biomarkers are carried by nanocarriers, such as exosomes, with cell-specific membrane proteins suggests that such selection may be possible, although a new suite of fractionation and quantification technologies would need to be developed. Although under-appreciated, membrane microfluidics has made considerable contributions to resolving these issues. We review the progress made so far, based on ion-selective, track-etched, and gel membranes and advanced electrophoretic and nano-filtration designs, in this perspective and suggest future directions.

Recent advances in surface-enhanced Raman spectroscopy based liquid biopsy for colorectal cancer (Review)

As colorectal cancer (CRC) is one of the forms of cancer with the highest prevalence globally and with a high mortality, screening and early detection remains a major issue. Colonoscopy is still the gold standard for detecting premalignant lesions, but it is burdened by some complications. For instance, it is laborious, with some difficulties of acceptance for some patients, and is ultimately an imperfect standard, given that some premalignant lesions or incipient malignancies can be missed by colonoscopic evaluation. In this context, new non-invasive approaches such as surface-enhanced Raman spectroscopy (SERS) based liquid biopsy have gained ground in recent years, showing promising results in oncological pathology diagnosis. These new methods have enabled the detection of subtle molecular profile alterations prior to any macroscopic morphological changes, thus providing a useful tool for early CRC detection. In the present review, we provide a summary of published studies applying SERS in CRC detection, along with our personal experience in using SERS in the diagnosis of different oncological pathologies, including CRC.

Applications of Bionano Sensor for Extracellular Vesicles Analysis

Recently, extracellular vesicles (EVs) and their contents have been revealed to play crucial roles in the intrinsic intercellular communications and have received extensive attention as next-generation biomarkers for diagnosis of diseases such as cancers. However, due to the structural nature of the EVs, the precise isolation and characterization are extremely challenging. To this end, tremendous efforts have been made to develop bionano sensors for the precise and sensitive characterization of EVs from a complex biologic fluid. In this review, we will provide a detailed discussion of recently developed bionano sensors in which EVs analysis applications were achieved, typically in optical and electrochemical methods. We believe that the topics discussed in this review will be useful to provide a concise guideline in the development of bionano sensors for EVs monitoring in the future. The development of a novel strategy to monitor various bio/chemical materials from EVs will provide promising information to understand cellular activities in a more precise manner and accelerates research on both cancer and cell-based therapy.

Mixed-Dimensional Heterostructure Material-Based SERS for Trace Level Identification of Breast Cancer-Derived Exosomes

Raman spectroscopy has capability for fingerprint molecular identification with high sensitivity if weak Raman scattering signal can be enhanced by several orders of magnitudes. Herein, we report a heterostructure-based surface-enhanced Raman spectroscopy (SERS) platform using 2D graphene oxide (GO) and 0D plasmonic gold nanostar (GNS), with capability of Raman enhancement factor (EF) in the range of ∼1010 via light-matter and matter-matter interactions. The current manuscript reveals huge Raman enhancement for heterostructure materials occurring via both electromagnetic enhancement mechanism though plasmonic GNS nanoparticle (EF ∼107) and chemical enhancement mechanism through 2D-GO material (EF ∼102). Finite-difference time-domain (FDTD) simulation data and experimental investigation indicate that GNS allows light to be concentrated into nanoscale "hotspots" formed on the heterostructure surface, which significantly enhanced Raman efficiency via a plasmon-exciton light coupling process. Notably, we have shown that mixed-dimensional heterostructure-based SERS can be used for tracking of cancer-derived exosomes from triple-negative breast cancer and HER2(+) breast cancer with a limit of detection (LOD) of 3.8 × 102 exosomes/mL for TNBC-derived exosomes and 4.4 × 102 exosomes/mL for HER2(+) breast cancer-derived exosomes.

Early-Stage Lung Cancer Diagnosis by Deep Learning-Based Spectroscopic Analysis of Circulating Exosomes

Lung cancer has a high mortality rate, but an early diagnosis can contribute to a favorable prognosis. A liquid biopsy that captures and detects tumor-related biomarkers in body fluids has great potential for early-stage diagnosis. Exosomes, nanosized extracellular vesicles found in blood, have been proposed as promising biomarkers for liquid biopsy. Here, we demonstrate an accurate diagnosis of early-stage lung cancer, using deep learning-based surface-enhanced Raman spectroscopy (SERS) of the exosomes. Our approach was to explore the features of cell exosomes through deep learning and figure out the similarity in human plasma exosomes, without learning insufficient human data. The deep learning model was trained with SERS signals of exosomes derived from normal and lung cancer cell lines and could classify them with an accuracy of 95%. In 43 patients, including stage I and II cancer patients, the deep learning model predicted that plasma exosomes of 90.7% patients had higher similarity to lung cancer cell exosomes than the average of the healthy controls. Such similarity was proportional to the progression of cancer. Notably, the model predicted lung cancer with an area under the curve (AUC) of 0.912 for the whole cohort and stage I patients with an AUC of 0.910. These results suggest the great potential of the combination of exosome analysis and deep learning as a method for early-stage liquid biopsy of lung cancer.

Acoustofluidics-Assisted Engineering of Multifunctional Three-Dimensional Zinc Oxide Nanoarrays

The integration of acoustics and microfluidics (termed acoustofluidics) presents a frontier in the engineering of functional micro-/nanomaterials. Acoustofluidic techniques enable active and precise spatiotemporal control of matter, providing great potential for the design of advanced nanosystems with tunable material properties. In this work, we introduce an acoustofluidic approach for engineering multifunctional three-dimensional nanostructure arrays and demonstrate their potential in enrichment and biosensing applications. In particular, our acoustofluidic device integrates an acoustic transducer with a sharp-edge-based acoustofluidic reactor that enables uniform patterning of zinc oxide (ZnO) nanoarrays with customizable lengths, densities, diameters, and other properties. The resulting ZnO nanoarray-coated glass capillaries can rapidly and efficiently capture and enrich biomolecules with sizes ranging from a few nanometers to several hundred nanometers. In order to enable the detection of these biomolecules, silver (Ag) nanoparticles are deposited onto the ZnO nanoarrays, and the integrated ZnO-Ag capillary device functions as a label-free plasmonic biosensing system for surface-enhanced Raman spectroscopy (SERS) based detection of exosomes, DNA oligonucleotides, and E. coli bacteria. The optical sensing enhancement of ZnO-Ag capillary is further validated through finite-difference time-domain (FDTD) simulations. These findings not only provide insights into the engineering of functional micro/nanomaterials using acoustofluidics but also shed light onto the development of portable microanalytical devices for point-of-care applications.

CNS-Derived Blood Exosomes as a Promising Source of Biomarkers: Opportunities and Challenges

Eukaryotic cells release different types of extracellular vesicles (EVs) including exosomes, ectosomes, and microvesicles. Exosomes are nanovesicles, 30–200 nm in diameter, that carry cell- and cell-state-specific cargo of proteins, lipids, and nucleic acids, including mRNA and miRNA. Recent studies have shown that central nervous system (CNS)-derived exosomes may carry amyloidogenic proteins and facilitate their cell-to-cell transfer, thus playing a critical role in the progression of neurodegenerative diseases, such as tauopathies and synucleinopathies. CNS-derived exosomes also have been shown to cross the blood-brain-barrier into the bloodstream and therefore have drawn substantial attention as a source of biomarkers for various neurodegenerative diseases as they can be isolated via a minimally invasive blood draw and report on the biochemical status of the CNS. However, although isolating specific brain-cell-derived exosomes from the blood is theoretically simple and the approach has great promise, practical details are of crucial importance and may compromise the reproducibility and utility of this approach, especially when different laboratories use different protocols. In this review we discuss the role of exosomes in neurodegenerative diseases, the usefulness of CNS-derived blood exosomes as a source of biomarkers for these diseases, and practical challenges associated with the methodology of CNS-derived blood exosomes and subsequent biomarker analysis.

Variability in protein cargo detection in technical and biological replicates of exosome-enriched extracellular vesicles

Exosomes are extracellular vesicles (EVs) of ~20-200 nm diameter that shuttle DNAs, RNAs, proteins and other biomolecules between cells. The large number of biomolecules present in exosomes demands the frequent use of high-throughput analysis. This, in turn, requires technical replicates (TRs), and biological replicates (BRs) to produce accurate results. As the number and abundance of identified biomolecules varies between replicates (Rs), establishing the replicate variability predicted for the event under study is essential in determining the number of Rs required. Although there have been few reports of replicate variability in high throughput biological data, none of them focused on exosomes. Herein, we determined the replicate variability in protein profiles found in exosomes released from 3 lung adenocarcinoma cell lines, H1993, A549 and H1975. Since exosome isolates are invariably contaminated by a small percentage of ~200-300 nm microvesicles, we refer to our samples as exosome-enriched EVs (EE-EVs). We generated BRs of EE-EVs from each cell line, and divided each group into 3 TRs. All Rs were analyzed by liquid chromatography/mass spectrometry (LC/MS/MS) and customized bioinformatics and biostatistical workflows (raw data available via ProteomeXchange: PXD012798). We found that the variability among TRs as well as BRs, was largely qualitative (protein present or absent) and higher among BRs. By contrast, the quantitative (protein abundance) variability was low, save for the H1975 cell line where the quantitative variability was significant. Importantly, our replicate strategy identified 90% of the most abundant proteins, thereby establishing the utility of our approach.