Exosome Separation Research Articles

A DNA-based hydrogel for exosome separation and biomedical applications

Exosomes (EXOs) have been proven as biomarkers for disease diagnosis and agents for therapeutics. Great challenge remains in the separation of EXOs with high-purity and low-damage from complex biological media, which is critical for the downstream applications. Herein, we report a DNA-based hydrogel to realize the specific and nondestructive separation of EXOs from complex biological media. The separated EXOs were directly utilized in the detection of human breast cancer in clinical samples, as well as applied in the therapeutics of myocardial infarction in rat models. The materials chemistry basis of this strategy involved the synthesis of ultralong DNA chains via an enzymatic amplification, and the formation of DNA hydrogels through complementary base-pairing. These ultralong DNA chains that contained polyvalent aptamers were able to recognize and bind with the receptors on EXOs, and the specific and efficient binding ensured the selective separation of EXOs from media into the further formed networked DNA hydrogel. Based on this DNA hydrogel, rationally designed optical modules were introduced for the detection of exosomal pathogenic microRNA, which achieved the classification of breast cancer patients versus healthy donors with 100% precision. Furthermore, the DNA hydrogel that contained mesenchymal stem cell-derived EXOs was proved with significant therapeutic efficacy in repairing infarcted myocardium of rat models. We envision that this DNA hydrogel-based bioseparation system is promising as a powerful biotechnology, which will promote the development of extracellular vesicles in nanobiomedicine.

A double tangential flow filtration-based microfluidic device for highly efficient separation and enrichment of exosomes

Recently, exosomes have been recognized as important disease biomarkers due to the essential roles they played in disease development. Nevertheless, the highly efficient isolation and enrichment of exosomes from complex body fluids continues to hinder the research and application of exosomes for clinical use. In this work, we developed a double tangential flow filtration-based microfluidic device for exosome isolation from cell supernatants and human serum. The microfluidic device contained two modules. Each module included two polymethylmethacrylate (PMMA) plates with symmetrical serpentine channels and a nanoporous membrane with 200 nm or 30 nm pore diameter and was used to separate larger vesicles, exosomes and free biomolecules. The design of double tangential flow filtration in symmetrical serpentine channels largely increased the contact area between the filtrate and the nanoporous membranes, thus improved the separation efficiency and prevented the clogging of the membrane. Compared with standard separation method, i.e. ultracentrifugation (UC), the microfluidic chip-based separation (Chip) of exosomes showed the advantages of much lower instrumental cost, lower consumable cost, shorter time (<120 min), higher purity (82.8%) and significantly higher recovery rate (77.8%). In addition, due to the label-free separation, the microfluidic device-collected exosomes could be directly used for downstream analysis such as proteomics analysis. The proteomics analysis results of exosomes isolated from the sera of clinical patients with different diseases by the chip revealed richer disease-related information comparing with those exosomes isolated by UC, demonstrating the good practicability of this chip for future clinical research and applications.

Thermoresponsive bio-affinity interfaces for temperature-modulated selective capture and release of targeted exosomes.

The existing methods for exosome isolation, such as ultracentrifugation, size exclusion, and affinity separation, suffer from some limitations. Herein, we aimed to develop temperature-modulated exosome-capturing materials using thermoresponsive polymers and peptides with affinity for exosomes. Poly(2-hydroxyethyl methacrylate-co-propargyl acrylate)-b-poly(N-isopropylacrylamide) (P(HEMA-co-PgA)-b-PNIPAAm) was grafted on silica beads via a two-step process of activator regenerated by electron transfer atom transfer radical polymerization. Peptides with affinity for exosomes were conjugated to the propargyl group of the bottom P(HEMA-co-PgA) segment of the copolymer via a click reaction. The prepared copolymer-grafted beads were characterized by elemental analysis, X-ray photoelectron spectroscopy, scanning electron microscopy, transmission electron microscopy, gel permeation chromatography, and the turbidity of the polymer solution. Results indicated that the copolymer and peptide were successfully modified on the silica beads. Exosomes from SK-BR-3​cells, a human breast cancer cell line, were selectively captured on the prepared beads at 37​°C, as the upper PNIPAAm segment shrank and the affinity between the peptide and exosome was enhanced. Upon lowering the temperature to 4​°C, the captured exosomes were released from the copolymer brush because of the extension of the PNIPAAm segment that reduced the affinity between peptides and exosomes. These findings demonstrated that the prepared copolymer brush-grafted silica beads can capture and release targeted exosomes via temperature modulation. Taken together, the developed copolymer brush-grafted silica beads would be useful for the separation of exosomes using simple procedures such as temperature modulation.

Dean-Flow-Coupled Elasto-Inertial Focusing Accelerates Exosome Purification to Facilitate Single Vesicle Profiling.

Exosomes are recognized as noteworthy biomarkers playing unprecedented roles in intercellular communication and disease diagnosis and treatment. It is a prerequisite to obtain high-purity exosomes for the comprehension of exosome biochemistry and further illustration of their functionality/mechanisms. However, the isolation of nanoscale exosomes from endogenous proteins is particularly challenging for small-volume biological samples. Herein, a Dean-flow-coupled elasto-inertial microfluidic chip (DEIC) was developed. It consists of a spiral microchannel with dimensional confined concave structures and facilitates elasto-inertial separation of exosomes with lower protein contaminants from cell culture medium and human serum. The presence of 0.15% (w/v) poly-(oxyethylene) controls the elastic lift force acting on suspended nanoscale particles and makes it feasible for field-free purification of integrity exosomes with a 70.6% recovery and a 91.4% removal rate for proteins. As a proof of concept, the technique demonstrated the individual-vesicle-level biomarker (EpCAM and PD-L1) profiling in combination with simultaneous aptamer-mediated analysis to disclose the sensibility for immune response. Overall, DEIC enables the collection of high-purity exosomes and exhibits potential in integration with downstream analyses of exosomes.

A facile method based on a superabsorbent polymer composite for concentration and separation of exosomes from cell culture media

A method using superabsorbent polymers of alginate and poly(acrylamide-co-acrylic acid) composites for concentration and purification of exosomes from cell culture media is reported, and it is efficient, facile and equipment-free.

Integrated separation and detection of exosomes via a label-free magnetic SERS platform.

A label-free magnetic surface enhanced Raman scattering (SERS) platform was constructed, which was composed of superparamagnetic Fe3O4 nanoparticles as cores for separation and Au layers as shells for label-free SERS detection. Our method could effectively distinguish exosomes from different cell sources for cancer diagnosis and showed high sensitivity and specificity within a 95% confidence interval. As a low-cost and efficient exosome analysis method, the designed integrated platform for separation and detection has promising applicability in clinical diagnostics.

Convenient exosome separation by phosphatidylserine targeting polymer brush materials.

We report phosphatidylserine targeting polymer brush materials to selectively separate exosomes. This method provides an efficient separation strategy with ordinary centrifuge force, which improves the integrity and purity of the exosomes. Compared with the common methods, the content of contaminated lipoprotein in the resulting exosomes decreased obviously.

A Modified Method for the Quantification of Immune Checkpoint Ligands on Exosomes from Human Serum using Flow Cytometry.

Objectives: Exosomes are the smallest of the extracellular vesicles and can contain a variety of different cargos, including nucleic acids, lipids, and proteins. Ultracentrifugation followed by electron microscopy has historically been used for the isolation and visualization of exosomes; Western blot and ELISA have also been used, but these techniques are only semiquantitative and are unable to distinguish different exosome markers in the same sample. To resolve some of these issues, we propose a modification of a bead-based flow cytometry method. Methods: Peripheral blood serum was mixed with a commercial exosome separation reagent and incubated for 30 min at 4°, centrifuged, exosome pellet was isolated and resuspended in PBS. Exosomes were then added to magnetic beads, incubated 18 h, then incubated with exosome-specific antibodies for 1 h. The resulting bead:exosome complexes were centrifuged and then washed, then washed again using a magnetic separator, resuspended in PBS, and analyzed via flow cytometry. Results: Using commercial magnetic beads bound with anti-CD63, our protocol modifies starting conditions, washing steps, and magnetic separation and uses the FSC and SSC determination of the flow cytometer to result in increased yield and identification of the exosome populations of interest. Our modified protocol increased the yield of specific populations approximately 10-fold. Conclusion: The new protocol was used to identify exosomes positive for 2 immune checkpoint ligands in serum-derived exosomes from cervical cancer patients. We suspect that this protocol can also be used for the identification of other exosome proteins since we also quantified the exosome membrane-enriched tetraspanins CD9 and CD81. Identification of proteins rarely expressed in exosomes is complicated in this technique as serum is an inherently dirty source of exosomes, and great care must be taken in the washing and gating of the exosome:bead populations.

Nickel-Doped Microfluidic Chip for Rapid and Efficient Immunomagnetic Separation and Detection of Breast Cancer Cell-Derived Exosomes.

Breast cancer cell-derived exosomes have high potential as biomarkers for continuous biopsies and longitudinal monitoring in breast cancer. However, it is extremely difficult to separate exosomes with high recovery and high purity from complex media, such as urine, plasma, saliva and cell culture supernatants. Here, we designed a flexible and simple microfluidic chip for exosome separation. The capture zone of the chip is a three-dimensional structure of interlaced cylinders doped with nickel powder. Exosomes were separated from cell culture supernatant by the immunomagnetic separation method in continuous flow mode and were detected by fluorescence imaging with high sensitivity. The chip achieved a high exosome recovery rate (> 74%) and purity (> 67%) at an injection rate of 3.6 mL/h. Thus, this chip was demonstrated to be a cutting-edge platform for the separation and detection of exosomes. It could also be applied to separate and detect other types of exosomes, microbubbles and cells.

A Breast Cancer Prediction Model Based on a Panel from Circulating Exosomal miRNAs.

Breast cancer (BC) has been a serious threat to women's health. Exosomes contain a variety of biomolecules, which is an excellent choice as disease diagnostic markers, but whether it could be applied as a noninvasive biomarker for BC diagnosis demands to be additional studied. In this study, we aimed at creating a predictive model and reveal the value of plasma exosomal miRNA (exo-miRNA) in early diagnosis of BC. Firstly, exosomes isolated from plasma were identified by Nanoparticle Tracking Analysis (NTA), Transmission Electron Microscope (TEM), and Western Blot. miRNA expression in plasma samples from 56 BC patients and 40 normal controls was analyzed by high-throughput sequencing. miRNAs with strong correlation characteristics were selected by Lasso logistic regression. Then, we built the training set and test set, evaluated the Lasso regression accuracy, and evaluated the performance of different models in the training set and test set. Finally, GO analysis, KEGG, and Reactome pathway enrichment analysis were used to understand the biological significance of 16 characteristic miRNAs. The successful separation of exosomes in serum was identified by NTA, TEM, and Western Blot. The training set data matrix containing 1962 miRNAs was obtained by sequencing for model construction, and 16 strongly correlated miRNAs were selected by Lasso logistic regression. The accuracy of Lasso regression in training set and test set were 97.22% and 95.83%, respectively. We built different models and evaluated the performance of each model in the training set and test set. The results showed that the AUC values of Lasso, SVM, GBDT, and Random Forest model in the training set were 1, and the AUC values in the test set were 0.979, 0.936, 0.971, and 0.979, respectively. Bioinformatics analysis showed that 16 signature miRNAs were significantly enriched in cancer-related pathways such as herpes simplex virus 1 infection, TGF-β signaling, and Toll-like receptor family. The results of this study suggest that the 16 characteristic miRNAs screened from plasma exosomes can be used as a group of biomarkers, and the prediction model constructed based on this set of markers is expected to be used in the early diagnosis of BC.

Presence of Intact Hepatitis B Virions in Exosomes

Hepatitis B virus (HBV) was identified as an enveloped DNA virus with a diameter of 42 nm. Multivesicular bodies play a central role in HBV egress and exosome biogenesis. In light of this, it was studied whether intact virions wrapped in exosomes are released by HBV-producing cells. Robust methods for efficient separation of exosomes from virions were established. Exosomes were subjected to limited detergent treatment for release of viral particles. Electron microscopy of immunogold labeled ultrathin sections of purified exosomes was performed for characterization of exosomal HBV. Exosome formation/release was affected by inhibitors or Crispr/Cas-mediated gene silencing. Infectivity/uptake of exosomal HBV was investigated in susceptible and non-susceptible cells. Exosomes could be isolated from supernatants of HBV-producing cells, which are characterized by the presence of exosomal and HBV markers. These exosomal fractions could be separated from the fractions containing free virions. Limited detergent treatment of exosomes causes stepwise release of intact HBV virions and naked capsids. Inhibition of exosome morphogenesis impairs the release of exosome-wrapped HBV. Electron microscopy confirmed the presence of intact virions in exosomes. Moreover, the presence of large hepatitis B virus surface antigen on the surface of exosomes derived from HBV expressing cells was observed, which conferred exosome-encapsulated HBV initiating infection in susceptible cells in a , large hepatitis B virus surface antigen/Na+-taurocholate co-transporting polypeptide-dependent manner. The uptake of exosomal HBV with low efficiency was also observed in non-permissive cells. These data indicate that a fraction of intact HBV virions can be released as exosomes. This reveals a so far not described release pathway for HBV.

Microfluidic Technology for the Isolation and Analysis of Exosomes.

Exosomes are lipid-bilayer enclosed vesicles with diameters of 30–150 nm, which play a pivotal role in cell communication by transporting their cargoes such as proteins, lipids, and genetic materials. In recent years, exosomes have been under intense investigation, as they show great promise in numerous areas, especially as bio-markers in liquid biopsies. However, due to the high heterogeneity and the nano size of exosomes, the separation of exosomes is not easy. This review will deliver an outline of the conventional methods and the microfluidic-based technologies for exosome separation. Particular attention is devoted to microfluidic devices, highlighting the efficiency of exosome isolation by these methods. Additionally, this review will introduce advances made in the integrated microfluidics technologies that enable the separation and analysis of exosomes.

Research Development on Exosome Separation Technology.

Exosomes are special extracellular vesicles secreted by cells, which are of great significance in the basic research of life science and clinical application and has become a hot research field with rapid development in recent 10years. Therefore, the isolation and separation of exosomes is particularly important for the research and application of exosomes. This paper aims to review the research progress of exosome isolation and separation methods in recent years, including ultracentrifugation, ultrafiltration, size‑exclusion chromatography, precipitation, immunomagnetic bead capture method, aptamer-based isolation, and isolation methods based on microfluidic technology. It is generally accepted that most of the existing methods have limitations, for example, ultracentrifugation is time-consuming and laborious, and immunomagnetic bead capture method and aptamer-based separation method have small sample processing capacity and high cost. As a result, we also introduce some common situations in which two or more methods are combined for use. Finally, the separation and isolation methods including all those presented in this review were compared and summarized.

Current status and outlook of advances in exosome isolation.

Exosomes are extracellular vesicles with a diameter ranging from 30 to 150 nm, which are an important medium for intercellular communication and are closely related to the progression of certain diseases. Therefore, exosomes are considered promising biomarkers for the diagnosis of specific diseases, and thereby, treatments based on exosomes are being widely examined. For exosome-related research, a rapid, simple, high-purity, and recovery isolation method is the primary prerequisite for exosomal large-scale application in medical practice. Although there are no standardized methods for exosome separation and analysis, various techniques have been established to explore their biochemical and physicochemical properties. In this review, we analyzed the progress in exosomal isolation strategies and proposed our views on the development prospects of various exosomal isolation techniques.Graphical abstract

Microfluidic Approaches for Affinity-Based Exosome Separation.

As a subspecies of extracellular vesicles (EVs), exosomes have provided promising results in diagnostic and theranostic applications in recent years. The nanometer-sized exosomes can be extracted by liquid biopsy from almost all body fluids, making them especially suitable for mainly non-invasive point-of-care (POC) applications. To achieve this, exosomes must first be separated from the respective biofluid. Impurities with similar properties, heterogeneity of exosome characteristics, and time-related biofouling complicate the separation. This practical review presents the state-of-the-art methods available for the separation of exosomes. Furthermore, it is shown how new separation methods can be developed. A particular focus lies on the fabrication and design of microfluidic devices using highly selective affinity separation. Due to their compactness, quick analysis time and portable form factor, these microfluidic devices are particularly suitable to deliver fast and reliable results for POC applications. For these devices, new manufacturing methods (e.g., laminating, replica molding and 3D printing) that use low-cost materials and do not require clean rooms are presented. Additionally, special flow routes and patterns that increase contact surfaces, as well as residence time, and thus improve affinity purification are displayed. Finally, various analyses are shown that can be used to evaluate the separation results of a newly developed device. Overall, this review paper provides a toolbox for developing new microfluidic affinity devices for exosome separation.

Self-adaptive virtual microchannel for continuous enrichment and separation of nanoparticles.

The transport, enrichment, and purification of nanoparticles are fundamental activities in the fields of biology, chemistry, material science, and medicine. Here, we demonstrate an approach for manipulating nanospecimens in which a virtual channel with a diameter that can be spontaneously self-adjusted from dozens to a few micrometers based on the concentration of samples is formed by acoustic waves and streams that are triggered and stabilized by a gigahertz bulk acoustic resonator and microfluidics, respectively. By combining a specially designed arc-shaped resonator and lateral flow, the in situ enrichment, focusing, displacement, and continuous size-based separation of nanoparticles were achieved, with the ability to capture 30-nm polystyrene nanoparticles and continuously focus 150-nm polystyrene nanoparticles. Furthermore, exosome separation was also demonstrated. This technology overcomes the limitation of continuously manipulating particles under 200 nm and has the potential to be useful for a wide range of applications in chemistry, life sciences, and medicine.

Size Separation of Exosomes and Microvesicles Using Flow Field-Flow Fractionation/Multiangle Light Scattering and Lipidomic Comparison

Extracellular vesicles (EVs) are cell-derived membrane-bound particles, including exosomes and microvesicles that differ in cellular origin, content, and lipid composition. This study reports that exosomes and microvesicles can be simultaneously separated by size using flow field-flow fractionation (FlFFF) employed with field programming and that the detection of low-concentration EV species can be significantly improved using multiangle light scattering (MALS). The efficiency of ultracentrifugation (UC) and ultrafiltration (UF) in isolating EVs from the culture media of DU145 cells was compared, and the results showed that UF retrieves more EVs than UC. Two size fractions (small and large) of both exosomes and microvesicles were collected during the FlFFF runs and examined using Western blotting to confirm each EV, and transmission electron microscopy was performed for size analysis. Sizes were compared using the root-mean-square radius obtained from the MALS calculation. The collected fractions were further examined using nanoflow ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry for the size-dependent lipidomic profiles of exosomes and microvesicles, showing that lipids were more enriched in the fraction containing large exosomes than in that containing small exosomes; however, an opposite trend was observed with microvesicles. The present study demonstrated that UF followed by FlFFF-MALS can be utilized for the size separation of exosomes and microvesicles without sequential centrifugation, which is useful for monitoring the changes in the size distribution of EVs depending on the biological status along with generating size-dependent lipidomic profiles.

U6/miR-211 expression ratio as a purity parameter for HEK293 cell-derived exosomes.

Small extracellular vesicles (sEVs) including exosomes are produced by all cell types and can be isolated from biological fluids and cell culture supernatants. The separation of exosomes with high purity from protein-rich media remains challenging. Besides contaminating proteins, small microvesicles (MVs) and apoptotic bodies are usually co-isolated with exosomes. The optimization of exosome separation and purification depends on reliable methods for the determination of the purity of the preparation, but no standard measurement has been defined so far. We tried to advance purity assessment. sEVs were isolated from HEK293 cell culture supernatants by various combinations of centrifugation, precipitation and size exclusion chromatography. sEVs with a diameter within the size range of 30-150 nm, typical for exosomes, were obtained with all tested isolation methods as shown by electron microscopy. To estimate the levels of protein contamination, flow cytometric analysis of the obtained vesicles was used. Based on the controlled preferential loading and enrichment of miR-211 into exosomes, a novel approach for the estimation of the fraction of HEK293 derived exosomes as opposed to MVs and apoptotic bodies in sEV mixtures was developed. This novel approach represents a simple qRT-PCR-based approach to improve the precise characterization of sEV isolates that is necessary for the usage of exosomes as carriers for therapeutic nucleic acids. Compared to the precipitation and size exclusion chromatography, the differential ultracentrifugation turned out to give sEVs with fairly intact shape and the highest purity according to the novel qRT-PCR-based approach, as well as to other established methods for purification assessment.

Rapid On-Chip Isolation of Cancer-Associated Exosomes and Combined Analysis of Exosomes and Exosomal Proteins.

Exosomes are lipid bilayer extracellular vesicles secreted by various types of cells and inherit abundant molecular information from parental cells. Tumor-derived exosomes have been widely recognized as noninvasive biomarkers for early cancer diagnosis and surveillance, but the separation of intact exosomes and detection of exosomal proteins remain challenging. Herein, we proposed a microfluidic chip for specific exosome isolation, integrated with sensitive quantification by a novel PTCDI-aptamer signal switch strategy. To enhance the capture efficiency, an alternating drop-shaped micropillar array was designed to assist the capture of tumor-derived exosomes by Tim4-modified magnetic beads (Tim4 beads) on the chip. Following capture, a chelating agent can easily elute intact exosomes which were further used for profiling exosomal surface proteins by the multiplexed fluorescence turn-on approach. Profiting from the efficient on-chip enrichment of the Tim4 beads and superior fluorescence signal transduction strategy, the detection limit of the analysis platform for HepG2 exosomes is as low as 8.69 × 103 particles/mL with a wide linear range spanning 6 orders of magnitude. Meanwhile, the proposed platform could recognize subtle changes in protein levels on the exosomal surface from various cell lines. More importantly, this strategy is successfully applied to analyze exosomes in human serum to distinguish liver cancer patients from healthy individuals. Combined analysis of different types of biomarkers on the exosomal membrane surface can greatly improve the accuracy of cancer type identification and disease monitoring. We hope that this convenient, rapid, and sensitive platform may become a powerful tool in the field of exosome analysis and early cancer screening.

Effective Separation of Cancer-Derived Exosomes in Biological Samples for Liquid Biopsy: Classic Strategies and Innovative Development.

Liquid biopsy has remarkably facilitated clinical diagnosis and surveillance of cancer via employing a non‐invasive way to detect cancer‐derived components, such as circulating tumor DNA and circulating tumor cells from biological fluid samples. The cancer‐derived exosomes, which are nano‐sized vesicles secreted by cancer cells have been investigated in liquid biopsy as their important roles in intracellular communication and disease development have been revealed. Given the challenges posed by the complicated humoral microenvironment, which contains a variety of different cells and macromolecular substances in addition to the exosomes, it has attracted a large amount of attention to effectively isolate exosomes from collected samples. In this review, the authors aim to analyze classic strategies for separation of cancer‐derived exosomes, giving an extensive discussion of advantages and limitations of these methods. Furthermore, the innovative multi‐strategy methods to realize efficient isolation of cancer‐derived exosomes in practical applications are also presented. Additionally, the possible development trends of exosome separation in to the future is discussed in this review.