Non-contact acoustic capture of microparticles from small plasma volumes

Small extracellular vesicles' enrichment from biological fluids using an acoustic trap

Small extracellular vesicles (sEVs), a form of extracellular vesicles, are lipid bilayered structures released by all cells. Large-scale studies on sEVs from clinical samples are necessary, but a major obstacle is the lack of rapid, reproducible, efficient, and low-cost methods to enrich sEVs. Acoustic microfluidics have the advantage of being label-free and biocompatible, which have been reported to successfully enrich sEVs. In this paper, we present a highly efficient acoustic microfluidic trap that can offer low and large volume compatible ways of enriching sEVs from biological fluids by flexible structure design. It uses the idea of pre-loading larger seed particles in the acoustic trap to enable sub-micron particle capturing. The microfluidic chip is actuated using a piezoelectric plate transducer attached to a silicon-glass bonding plate with circular cavities. Each cavity works as a resonant unit, excited at the frequency of both the half wave resonance in the main plane and inverted quarter wave resonance in the depth direction, which has the ability to strongly trap seed particles at the center, thereby improving the subsequent nanoparticle capture efficiency. Mean trapping efficiencies of 35.62% and 64.27% were obtained using 60 nm and 100 nm nanobeads, respectively. By the use of this technology, we have successfully enriched sEVs from cell culture conditioned media and blood plasma at a flow rate of 10 μL min-1. The isolated sEV subpopulations are characterized by NTA and TEM, and their protein cargo is determined by WB. This acoustic trapping chip provides a rapid and robust method to enrich sEVs from biofluids with high reproducibility and sufficient quantities. Therefore, it can serve as a new tool for biological and clinical research such as cancer diagnosis and drug delivery.

Enhanced immune capture of extracellular vesicles with gelatin nanoparticles and acoustic mixing

Extracellular vesicles (EVs) originating from cancer cells incorporate various critical biomolecules that can aid in early cancer diagnosis. However, the rapid analysis of these micro vesicles remains challenging due to their nano-scale size and overlapping dimensions, hindering sufficient capture in terms of quantity and purity. In this study, an acoustofluidic device was developed to enhance the yield of immune-captured EVs. The channel of the device was modified with degradable gelatin nanoparticles (∼220 nm) to increase the surface roughness, and subsequently treated with CD63 antibodies. The acoustic-induced streaming would prolong the rotation time of the EVs in the targeted continuous flow area, improving their aggregation towards the surrounding pillars and subsequent capture by the specific CD63 antibodies. Consequently, the capture efficiency of the device was improved when the signal was on, as evidenced by enhanced fluorescence intensity in the main channel. It is demonstrated that the acoustofluidic device could enhance the immune capture of EVs through acoustic mixing, showcasing great potential in the rapid and fast detection of EVs in liquid biopsy applications.

An overview of challenges associated with exosomal miRNA isolation toward liquid biopsy-based ovarian cancer detection

As one of the deadliest gynaecological cancers, ovarian cancer has been on the list. With lesser-known symptoms and lack of an accurate detection method, it is still difficult to catch it early. In terms of both the diagnosis and outlook for cancer, liquid biopsy has come a long way with significant advancements. Exosomes, extracellular components commonly shed by cancerous cells, are nucleic acid-rich particles floating in almost all body fluids and hold enormous promise, leading to minimallyinvasive molecular diagnostics. They have been shown as potential biomarkers in liquid biopsy, being implicated in tumour growth and metastasis. In order to address the drawbacks of ovarian cancer tumor heterogeneity, a liquid biopsy-based approach is being investigated by detecting cell-free nucleic acids, particularly non-coding RNAs, having the advantage of being less invasive and more prominent in nature. microRNAs are known to actively contribute to cancer development and their existence inside exosomes has also been made quite apparent which can be leveraged to diagnose and treat the disease. Extraction of miRNAs and exosomes is an arduous execution, and while other approaches have been investigated, none have produced results that are as encouraging due to limits in time commitment, yield, and, most significantly, damage to the exosomal structure resulting discrepancies in miRNA-based expression profiling for disease diagnosis. We have briefly outlined and reviewed the difficulties with exosome isolation techniques and the need for their standardization. The several widely used procedures and their drawbacks in terms of the exosomal purity they may produce have also been outlined.

Emerging Microfluidic Tools for Simultaneous Exosomes and Cargo Biosensing in Liquid Biopsy: New Integrated Miniaturized FFF-Assisted Approach for Colon Cancer Diagnosis

The early-stage diagnosis of cancer is a crucial clinical need. The inadequacies of surgery tissue biopsy have prompted a transition to a less invasive profiling of molecular biomarkers from biofluids, known as liquid biopsy. Exosomes are phospholipid bilayer vesicles present in many biofluids with a biologically active cargo, being responsible for cell-to-cell communication in biological systems. An increase in their excretion and changes in their cargo are potential diagnostic biomarkers for an array of diseases, including cancer, and they constitute a promising analyte for liquid biopsy. The number of exosomes released, the morphological properties, the membrane composition, and their content are highly related to the physiological and pathological states. The main analytical challenge to establishing liquid biopsy in clinical practice is the development of biosensors able to detect intact exosomes concentration and simultaneously analyze specific membrane biomarkers and those contained in their cargo. Before analysis, exosomes also need to be isolated from biological fluids. Microfluidic systems can address several issues present in conventional methods (i.e., ultracentrifugation, size-exclusion chromatography, ultrafiltration, and immunoaffinity capture), which are time-consuming and require a relatively high amount of sample; in addition, they can be easily integrated with biosensing systems. A critical review of emerging microfluidic-based devices for integrated biosensing approaches and following the major analytical need for accurate diagnostics is presented here. The design of a new miniaturized biosensing system is also reported. A device based on hollow-fiber flow field-flow fractionation followed by luminescence-based immunoassay is applied to isolate intact exosomes and characterize their cargo as a proof of concept for colon cancer diagnosis.

Advancement and obstacles in microfluidics-based isolation of extracellular vesicles

There is a great need for techniques which enable reproducible separation of extracellular vesicles (EVs) from biofluids with high recovery, purity and throughput. The development of new techniques for isolation of EVs from minute sample volumes is instrumental in enabling EV-based biomarker profiling in large biobank cohorts and paves the way to improved diagnostic profiles in precision medicine. Recent advances in microfluidics-based devices offer a toolbox for separating EVs from small sample volumes. Microfluidic devices that have been used in EV isolation utilise different fundamental principles and rely largely on benefits of scaling laws as the biofluid processing is miniaturised to chip level. Here, we review the progress in the practicality and performance of both passive devices (such as mechanical filtering and hydrodynamic focusing) and active devices (using magnetic, electric or acoustic fields). As it stands, many microfluidic devices isolate intact EV populations at higher purities than centrifugation, precipitation or size-exclusion chromatography. However, this comes at a cost. We address challenges (in particular low throughput, clogging risks and ability to process biofluids) and highlight the need for more improvements in microfluidic devices. Finally, we conclude that there is a need to refine and standardise these lab-on-a-chip techniques to meet the growing interest in the diagnostic and therapeutic value of purified EVs.

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.

Microparticles in Autoimmunity: Cause or Consequence of Disease?

Microparticles (MPs) are small (100 nm - 1 um) extracellular vesicles derived from the plasma membrane of dying or activated cells. MPs are important mediators of intercellular communication, transporting proteins, nucleic acids and lipids from the parent cell to other cells. MPs resemble the state of their parent cells and are easily accessible when released into the blood or urine. MPs also play a role in the pathogenesis of different diseases and are considered as potential biomarkers. MP isolation and characterization is technically challenging and results in different studies are contradictory. Therefore, uniform guidelines to isolate and characterize MPs should be developed. Our understanding of MP biology and how MPs play a role in different pathological mechanisms has greatly advanced in recent years. MPs, especially if derived from apoptotic cells, possess strong immunogenic properties due to the presence of modified proteins and nucleic acids. MPs are often found in patients with autoimmune diseases where MPs for example play a role in the break of immunological tolerance and/or induction of inflammatory conditions. In this review, we describe the main techniques to isolate and characterize MPs, define the characteristics of MPs generated during cell death, illustrate different mechanism of intercellular communication via MPs and summarize the role of MPs in pathological mechanisms with a particular focus on autoimmune diseases.

Interparticle attraction along the direction of the pressure gradient in an acoustic standing wave

Scattering of an acoustic wave by particles gives rise to microstreaming, as well as to acoustic radiation and interaction forces on the particles. We numerically study these steady, nonlinear phenomena for a case of two elastic spheres in a standing wave. We show that if one or both spheres are smaller or comparable to the viscous boundary layer, the microstreaming close to the pressure node can lead to an interparticle attraction along the direction of the pressure gradient of the wave. Similar behavior is observed when, instead of size, density of one of the spheres is sufficiently larger relative to the other sphere. These findings could promote the acoustic manipulation of nanoparticles and bacteria.

Label-Free Isolation of Exosomes Using Microfluidic Technologies

Exosomes are cell-derived structures packaged with lipids, proteins, and nucleic acids. They exist in diverse bodily fluids and are involved in physiological and pathological processes. Although their potential for clinical application as diagnostic and therapeutic tools has been revealed, a huge bottleneck impeding the development of applications in the rapidly burgeoning field of exosome research is an inability to efficiently isolate pure exosomes from other unwanted components present in bodily fluids. To date, several approaches have been proposed and investigated for exosome separation, with the leading candidate being microfluidic technology due to its relative simplicity, cost-effectiveness, precise and fast processing at the microscale, and amenability to automation. Notably, avoiding the need for exosome labeling represents a significant advance in terms of process simplicity, time, and cost as well as protecting the biological activities of exosomes. Despite the exciting progress in microfluidic strategies for exosome isolation and the countless benefits of label-free approaches for clinical applications, current microfluidic platforms for isolation of exosomes are still facing a series of problems and challenges that prevent their use for clinical sample processing. This review focuses on the recent microfluidic platforms developed for label-free isolation of exosomes including those based on sieving, deterministic lateral displacement, field flow, and pinched flow fractionation as well as viscoelastic, acoustic, inertial, electrical, and centrifugal forces. Further, we discuss advantages and disadvantages of these strategies with highlights of current challenges and outlook of label-free microfluidics toward the clinical utility of exosomes.

Microfluidic device for one-step detection of breast cancer-derived exosomal mRNA in blood using signal-amplifiable 3D nanostructure

Metastasis attributed to approximately 90% of cancer-related deaths; hence, the detection of metastatic tumor-derived components in the blood assists in determining cancer recurrence and patient survival. Microfluidic-based sensors facilitate analysis of small fluid volumes and represent an accurate, rapid, and user-friendly method of field diagnoses. In this study, we have developed a microfluidic chip-based exosomal mRNA sensor (exoNA-sensing chip) for the one-step detection of exosomal ERBB2 in the blood by integrating a microfluidic chip and 3D-nanostructured hydrogels. The exoNA-sensing chip is a vacuum-driven power-free microfluidic chip that can accurately control the flow of trace fluids (<100 μL). The sensing part of the exoNA-sensing chip includes 3D-nanostructured hydrogels capable of detecting ERBB2 and a reference gene by amplifying a fluorescent signal via an enzyme-free catalytic hairpin assembly reaction at room temperature. This hydrogel offers a detection limit of 58.3 fM with good selectivity for target sequences. The performance of the exoNA-sensing chip was evaluated by testing in vitro and in vivo samples and was proven to be effective for cancer diagnosis and liquid biopsies.

Theory and simulation of electroosmotic suppression of acoustic streaming

Acoustic handling of nanoparticles in resonating acoustofluidic devices is often impeded by the presence of acoustic streaming. For micrometer-sized acoustic chambers, this acoustic streaming is typically driven by viscous shear in the thin acoustic boundary layer near the fluid-solid interface. Alternating current (ac) electroosmosis is another boundary-driven streaming phenomenon routinely used in microfluidic devices for the handling of particle suspensions in electrolytes. Here, we study how streaming can be suppressed by combining ultrasound acoustics and ac electroosmosis. Based on a theoretical analysis of the electrokinetic problem, we are able to compute numerically a form of the electrical potential at the fluid-solid interface, which is suitable for suppressing the typical acoustic streaming pattern associated with a standing acoustic half-wave. In the linear regime, we even derive an analytical expression for the electroosmotic slip velocity at the fluid-solid interface and use this as a guiding principle for developing models in the experimentally more relevant nonlinear regime that occurs at elevated driving voltages. We present simulation results for an acoustofluidic device, showing how implementing a suitable ac electroosmosis results in a suppression of the resulting electroacoustic streaming in the bulk of the device by 2 orders of magnitude.

Microvesicles in plasma reflect coronary flow reserve in patients with cardiovascular disease

High levels of microvesicles (MVs), a type of extracellular vesicles, are detected in several pathological conditions. We investigated the connection between coronary flow reserve (CFR), a prognostic clinical parameter that reflects blood flow in the heart, with levels of MVs and their cargo, from plasma of patients with cardiovascular disease. The PROFLOW study consists of 220 patients with prior myocardial infarction and measured CFR with transthoracic echocardiography. The patients were divided into high and low CFR groups. Plasma MVs were captured with acoustic trapping. Platelet- and endothelial-derived MVs were measured with flow cytometry, and vesicle lysates were analyzed with proteomic panels against cardiovascular biomarkers. Flow cytometry was further applied to identify cellular origin of biomarkers. Our data show a negative correlation between MV concentration and CFR values. Platelet and endothelial MV levels were significantly increased in plasma from the low CFR group. CFR negatively correlates with the levels of several proteomic biomarkers, and the low CFR group exhibited higher concentrations of these proteins in MVs. Focused analysis of one of the MV proteins, B cell activating factor (BAFF), revealed platelet and not leukocyte origin and release upon proinflammatory stimulus. Higher levels of MVs carrying an elevated concentration of proatherogenic proteins circulate in plasma in patients with low CFR, a marker of vascular dysfunction, reduced blood flow, and poor prognosis. Our findings demonstrate a potential clinical value of MVs as biomarkers and possible therapeutic targets against endothelial deterioration.

NEW & NOTEWORTHY We investigated how microvesicles (MVs) from patients with cardiovascular diseases are related to coronary flow reserve (CFR), a clinical parameter reflecting blood flow in the heart. Our results show a negative relationship between CFR and levels of platelet and endothelial MVs. The pattern of MV-enriched cardiovascular biomarkers differs between patients with high and low CFR. Our findings suggest a potential clinical value of MVs as biomarkers of reduced blood flow and proatherogenic status, additional to CFR.

Novel devices for isolation and detection of bacterial and mammalian extracellular vesicles

Extracellular vesicles are spherical nanoparticles inherently released by almost all cell types. They acquire the cell's membrane and cytoplasmic characteristics offering abundant identical units that can be captured to recognize the cell of origin. The abundance of vital cell information and multifunctional roles in cellular processes has rendered them attention, particularly as promising biomarkers for disease diagnosis and use in potential drug delivery systems. This review provides insights into standard approaches towards cultivation and isolation of mammalian and bacterial extracellular vesicles. We assess gaps in conventional separation and detection technologies while also tracking developments in ongoing research. The review focuses on highlighting alternative state-of-the-art microfluidic devices that offer avenues for fast, cost-effective, precision-oriented capture and sensing of extracellular vesicles. Combining different detection technologies on an integrated "lab-on-a-chip" system has the prospective to provide customizable opportunities for clinical use of extracellular vesicles in disease diagnostics and therapeutic applications.

High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer

Molecular profiling of extracellular vesicles (EVs) offers novel opportunities for diagnostic applications, but the current major obstacle for clinical translation is the lack of efficient, robust, and reproducible isolation methods. To bridge that gap, we developed a microfluidic, non-contact, and low-input volume compatible acoustic trapping technology for EV isolation that enabled downstream small RNA sequencing. In the current study, we have further automated the acoustic microfluidics-based EV enrichment technique that enables us to serially process 32 clinical samples per run. We utilized the system to enrich EVs from urine collected as the first morning void from 207 men referred to 10-core prostate biopsy performed the same day. Using automated acoustic trapping, we successfully enriched EVs from 199/207 samples (96%). After RNA extraction, size selection, and library preparation, a total of 173/199 samples (87%) provided sufficient materials for next-generation sequencing that generated an average of 2 × 10⁶ reads per sample mapping to the human reference genome. The predominant RNA species identified were fragments of long RNAs such as protein coding and retained introns, whereas small RNAs such as microRNAs (miRNA) accounted for less than 1% of the reads suggesting that partially degraded long RNAs out-competed miRNAs during sequencing. We found that the expression of six miRNAs was significantly different (P_adj < 0.05) in EVs isolated from patients found to have high grade prostate cancer [ISUP 2005 Grade Group (GG) 4 or higher] compared to those with GG3 or lower, including those with no evidence of prostate cancer at biopsy. These included miR-23b-3p, miR-27a-3p, and miR-27b-3p showing higher expression in patients with GG4 or high grade prostate cancer, whereas miR-1-3p, miR-10a-5p, and miR-423-3p had lower expression in the GG4 PCa cases. Cross referencing our differentially expressed miRNAs to two large prostate cancer datasets revealed that the putative tumor suppressors miR-1, miR-23b, and miR-27a are consistently deregulated in prostate cancer. Taken together, this is the first time that our automated microfluidic EV enrichment technique has been found to be capable of enriching EVs on a large scale from 900 μl of urine for small RNA sequencing in a robust and disease discriminatory manner.

Multinodal Acoustic Trapping Enables High Capacity and High Throughput Enrichment of Extracellular Vesicles and Microparticles in miRNA and MS Proteomics Studies

We report a new design of an acoustophoretic trapping device with significantly increased capacity and throughput, compared to current commercial acoustic trapping systems. Acoustic trapping enables nanoparticle and extracellular vesicle (EV) enrichment without ultracentrifugation. Current commercial acoustic trapping technology uses an acoustic single-node resonance and typically operates at flow rates <50 μL/min, which limits the processing of the larger samples. Here, we use a larger capillary that supports an acoustic multinode resonance, which increased the seed particle capacity 40 times and throughput 25–40 times compared to single-node systems. The resulting increase in capacity and throughput was demonstrated by isolation of nanogram amounts of microRNA from acoustically trapped urinary EVs within 10 min. Additionally, the improved trapping performance enabled isolation of extracellular vesicles for downstream mass spectrometry analysis. This was demonstrated by the differential protein abundance profiling of urine samples (1–3 mL), derived from the non-trapped versus trapped urine samples.

Development of acoustically isolated extracellular plasma vesicles for biomarker discovery in allogeneic hematopoietic stem cell transplantation

Background

Infection and graft-versus-host disease (GvHD) are the major causes for mortality and morbidity of allogeneic hematopoietic stem cell transplantation (allo-HSCT). Plasma-derived extracellular vesicles (EVs) contain disease-related proteins, DNAs and RNAs, and have recently been suggested as potential biomarker candidates for transplantation complications. However, EV isolation from small plasma volumes in clinical biomarker studies using conventional methods is challenging. We therefore investigated if EVs isolated by novel automated acoustic trapping could be developed as potential biomarkers for allo-HSCT complications by performing a clinical proof-of-principle study.

Results

Plasma samples were collected from twenty consecutive patients with high-risk/relapsed hematologic malignancies undergoing allo-HSCT before transplantation and post-transplant up to 12 weeks. EVs were isolated from small plasma sample volumes (150 μl) by an automated, acoustofluidic-based particle trapping device, which utilizes a local λ/2 ultrasonic standing wave in a borosilicate glass capillary to capture plasma EVs among pre-seeded polystyrene microbeads through sound scatter interactions. We found that EVs could be reliably isolated from all plasma samples (n = 173) and that EV numbers increased more than 2-fold in the majority of patients after transplantation. Also, sufficient quantities of RNA for downstream microRNA (miRNA) analysis were obtained from all samples and EV miRNA profiles were found to differ from whole plasma profiles. As a proof of principle, expression of platelet-specific miR-142-3p in EVs was shown to correlate with platelet count kinetics after transplantation as expected. Importantly, we identified plasma EV miRNAs that were consistently positively correlated with infection and GvHD, respectively, as well as miRNAs that were consistently negatively correlated with these complications.

Conclusions

This study demonstrates that acoustic enrichment of EVs in a clinical biomarker study setting is feasible and that downstream analysis of acoustically-enriched EVs presents a promising tool for biomarker development in allo-HSCT. Certainly, these findings warrant further exploration in larger studies, which will have significant implications not only for biomarker studies in transplantation but also for the broad field of EV-based biomarker discovery.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40364-020-00259-4.

Trends in Research on Exosomes in Cancer Progression and Anticancer Therapy

Simple Summary

Intensive research in the field of cancer biology has discovered a unique mode of interplay between cells via extracellular bioactive vesicles called exosomes. Exosomes serve as intermediators among cells via their cargoes that, in turn, contribute in the progression of cancer. They are ubiquitously present in all body fluids as they are secreted from both normal and tumor cells. These minuscules exhibit multiple unique properties that facilitate their migration to distant locations and modulate the microenvironment for progression of cancer. This review summarizes the multifarious role of exosomes in various aspects of cancer research with its pros and cons. It discusses biogenesis of exosomes, their functional role in cancer metastasis, both protumorigenic and antitumorigenic, and also their applications in anticancer therapy.

Abstract

Exosomes, the endosome-derived bilayered extracellular nanovesicles with their contribution in many aspects of cancer biology, have become one of the prime foci of research. Exosomes derived from various cells carry cargoes similar to their originator cells and their mode of generation is different compared to other extracellular vesicles. This review has tried to cover all aspects of exosome biogenesis, including cargo, Rab-dependent and Rab-independent secretion of endosomes and exosomal internalization. The bioactive molecules of the tumor-derived exosomes, by virtue of their ubiquitous presence and small size, can migrate to distal parts and propagate oncogenic signaling and epigenetic regulation, modulate tumor microenvironment and facilitate immune escape, tumor progression and drug resistance responsible for cancer progression. Strategies improvised against tumor-derived exosomes include suppression of exosome uptake, modulation of exosomal cargo and removal of exosomes. Apart from the protumorigenic role, exosomal cargoes have been selectively manipulated for diagnosis, immune therapy, vaccine development, RNA therapy, stem cell therapy, drug delivery and reversal of chemoresistance against cancer. However, several challenges, including in-depth knowledge of exosome biogenesis and protein sorting, perfect and pure isolation of exosomes, large-scale production, better loading efficiency, and targeted delivery of exosomes, have to be confronted before the successful implementation of exosomes becomes possible for the diagnosis and therapy of cancer.

Contactless acoustic micro/nano manipulation: a paradigm for next generation applications in life sciences

Acoustic actuation techniques offer a promising tool for contactless manipulation of both synthetic and biological micro/nano agents that encompass different length scales. The traditional usage of sound waves has steadily progressed from mid-air manipulation of salt grains to sophisticated techniques that employ nanoparticle flow in microfluidic networks. State-of-the-art in microfabrication and instrumentation have further expanded the outreach of these actuation techniques to autonomous propulsion of micro-agents. In this review article, we provide a universal perspective of the known acoustic micromanipulation technologies in terms of their applications and governing physics. Hereby, we survey these technologies and classify them with regards to passive and active manipulation of agents. These manipulation methods account for both intelligent devices adept at dexterous non-contact handling of micro-agents, and acoustically induced mechanisms for self-propulsion of micro-robots. Moreover, owing to the clinical compliance of ultrasound, we provide future considerations of acoustic manipulation techniques to be fruitfully employed in biological applications that range from label-free drug testing to minimally invasive clinical interventions.

Exosome trapping and enrichment using a sound wave activated nano-sieve (SWANS)

Exosomes, a form of extracellular vesicle, are an important precursor in regenerative medicine. Microfluidic methods exist to capture these sub-micrometer sized objects from small quantities of sample, ideal for multiple diagnostic applications. To address the challenge of extraction from large volumes, we use the visual access offered by microfluidic techniques to probe the physical mechanisms behind a method which is compatible with future upscaling. The sound wave actuated nano-sieve uses resonant modes in a packed bed of microparticles to exert trapping forces on nanoparticles. Here, we examine the role of the microparticle size, demonstrating better performance from 15 μm particles than 7 μm particles. When applied to biological samples, we demonstrate for the first time that a packed bed of these larger particles is capable of capturing exosomes and liposomes, the captured particles being on average 20 to 40 times smaller than the pores within the trapped bed.

MicroRNAs from Liquid Biopsy Derived Extracellular Vesicles: Recent Advances in Detection and Characterization Methods

Liquid biopsies have become a convenient tool in cancer diagnostics, real-time disease monitoring, and evaluation of residual disease. Yet, the information still encrypted in the variety of tumor-derived molecules identified in biofluids has proven difficult to decipher due to the technological limitations imposed by their biological nature. Such is the case of extracellular vesicle (EV) encapsulated ncRNAs, which have gained traction in recent years as biomarkers. Due to their resilience towards degrading factors they may act as suitable disease indicators. This review addresses the less described issues in this context. We present an overview of less investigated biofluids that can be used for EV isolation in addition to different isolation approaches to overcome the technical challenges these specimens harbor. Furthermore, we summarize the latest technological advances providing improvement to ncRNA detection and analysis. Thereby, this review summarizes the current state-of-the-art methodologies regarding EV and EV derived miRNA analysis and how they compare to current approaches.

Toward optimal acoustophoretic microparticle manipulation by exploiting asymmetry

The performance of a micro-acousto-fluidic device designed for microparticle trapping is simulated using a three-dimensional (3D) numerical model. It is demonstrated by numerical simulations that geometrically asymmetric architecture and actuation can increase the acoustic radiation forces in a liquid-filled cavity by almost 2 orders of magnitude when setting up a standing pressure half wave in a microfluidic chamber. Similarly, experiments with silicon-glass devices show a noticeable improvement in acoustophoresis of 20-μm silica beads in water when asymmetric devices are used. Microparticle acoustophoresis has an extensive array of applications in applied science fields ranging from life sciences to 3D printing. A more efficient and powerful particle manipulation system can boost the overall effectiveness of an acoustofluidic device. The numerical simulations are developed in the COMSOL Multiphysics^® software package (COMSOL AB, Stockholm, Sweden). By monitoring the modes and magnitudes of simulated acoustophoretic fields in a relatively wide range of ultrasonic frequencies, a map of device performance is obtained. 3D resonant acoustophoretic fields are identified to quantify the improved performance of the chips with an asymmetric layout. Four different device designs are analyzed experimentally, and particle tracking experimental data qualitatively supports the numerical results.

Theory of acoustic trapping of microparticles in capillary tubes

We present a semianalytical theory for the acoustic fields and particle-trapping forces in a viscous fluid inside a capillary tube with arbitrary cross section and ultrasound actuation at the walls. We find that the acoustic fields vary axially on a length scale proportional to the square root of the quality factor of the two-dimensional (2D) cross-section resonance mode. This axial variation is determined analytically based on the numerical solution to the eigenvalue problem in the 2D cross section. The analysis is developed in two steps: First, we generalize a recently published expression for the 2D standing-wave resonance modes in a rectangular cross section to arbitrary shapes, including the viscous boundary layer. Second, based on these 2D modes, we derive analytical expressions in three dimensions for the acoustic pressure, the acoustic radiation and trapping force, as well as the acoustic energy flux density. We validate the theory by comparison to three-dimensional numerical simulations.

Microparticle Acoustophoresis in Aluminum-Based Acoustofluidic Devices with PDMS Covers

We present a numerical model for the recently introduced simple and inexpensive micromachined aluminum devices with a polydimethylsiloxane (PDMS) cover for microparticle acoustophoresis. We validate the model experimentally for a basic design, where a microchannel is milled into the surface of an aluminum substrate, sealed with a PDMS cover, and driven at MHz frequencies by a piezoelectric lead-zirconate-titanate (PZT) transducer. Both experimentally and numerically we find that the soft PDMS cover suppresses the Rayleigh streaming rolls in the bulk. However, due to the low transverse speed of sound in PDMS, such devices are prone to exhibit acoustic streaming vortices in the corners with a relatively large velocity. We predict numerically that in devices, where the microchannel is milled all the way through the aluminum substrate and sealed with a PDMS cover on both the top and bottom, the Rayleigh streaming is suppressed in the bulk thus enabling focusing of sub-micrometer-sized particles.

Sound wave activated nano-sieve (SWANS) for enrichment of nanoparticles

Acoustic actuation is widely used in microfluidic systems as a method of controlling the behaviour of suspended matter. When acoustic waves impinge on particles, a radiation force is exerted which can cause migration over multiple acoustic time periods; in addition the scattering of the wave by the particle will affect the behaviour of nearby particles. This interparticle effect, or Bjerknes force, tends to attract particles together. Here, instead of manipulating a dilute sample of particles, we examine the acoustic excitation of a packed bed. We fill a microfluidic channel with microparticles, such that they form a closely packed structure and then excite them at the particle's resonant frequency. In this scenario, each particle acts as a source of scattered waves and we show that these waves are highly effective at attracting nanoparticles onto the surface of the microparticles, and nanoparticle collection characterises the performance of this mechanically activated packed bed.

Bulk-driven acoustic streaming at resonance in closed microcavities

Bulk-driven acoustic (Eckart) streaming is the steady flow resulting from the time-averaged acoustic energy flux density in the bulk of a viscous fluid. In simple cases, like the one-dimensional single standing-wave resonance, this energy flux is negligible, and therefore the bulk-driven streaming is often ignored relative to the boundary-driven (Rayleigh) streaming in the analysis of resonating acoustofluidic devices with length scales comparable to the acoustic wavelength. However, in closed acoustic microcavities with viscous dissipation, two overlapping resonances may be excited at the same frequency as a double mode. In contrast to single modes, the double modes can support a steady rotating acoustic energy flux density and thus a corresponding rotating bulk-driven acoustic streaming. We derive analytical solutions for the double modes in a rectangular-box-shaped cavity including the viscous boundary layers, and use them to map out possible rotating patterns of bulk-driven acoustic streaming. Remarkably, the rotating bulk-driven streaming may be excited by a nonrotating actuation, and we determine the optimal geometry that maximizes this excitation. In the optimal geometry, we finally simulate a horizontal 2×2, 4×4, and 6×6 streaming-roll pattern in a shallow square cavity. We find that the high-frequency 6×6 streaming-roll pattern is dominated by the bulk-driven streaming as opposed to the low-frequency 2×2 streaming pattern, which is dominated by the boundary-driven streaming.

An acoustofluidic platform for non-contact trapping of cell-laden hydrogel droplets compatible with optical microscopy

Production of cell-laden hydrogel droplets as miniaturized niches for 3D cell culture provides a new route for cell-based assays. Such production can be enabled by droplet microfluidics and here we present a droplet trapping system based on bulk acoustic waves for handling hydrogel droplets in a continuous flow format. The droplet trapping system consists of a glass capillary equipped with a small piezoelectric transducer. By applying ultrasound (4 MHz), a localized acoustic standing wave field is generated in the capillary, trapping the droplets in a well-defined cluster above the transducer area. The results show that the droplet cluster can be retained at flow rates of up to 76 μl/min, corresponding to an average flow speed of 3.2 mm/s. The system allows for important operations such as continuous perfusion and/or addition of chemical reagents to the encapsulated cells with in situ optical access. This feature is demonstrated by performing on-chip staining of the cell nuclei. The key advantages of this trapping method are that it is label-free and gentle and thus well-suited for biological applications. Moreover, the droplets can easily be released on-demand, which facilitates downstream analysis. It is envisioned that the presented droplet trapping system will be a valuable tool for a wide range of multistep assays as well as long-term monitoring of cells encapsulated in gel-based droplets.

Proteomic profiling of extracellular vesicles reveals additional diagnostic biomarkers for myocardial infarction compared to plasma alone

Extracellular vesicles (EVs) are submicron, membrane-enclosed particles that are released from cells in various pathophysiological states. The molecular cargo of these vesicles is considered to reflect the composition of the cell of origin, and the EV proteome is therefore a potential source of biomarkers for various diseases. Our aim was to determine whether EVs isolated from plasma provide additional diagnostic value or improved pathophysiological understanding compared to plasma alone in the context of myocardial infarction (MI). A panel of proximity extension assays (n = 92) was employed to analyze EV lysates and plasma from patients with MI (n = 60) and healthy controls (n = 22). After adjustment for multiple comparisons, a total of 11 dysregulated proteins were identified in EVs of MI patients compared to the controls (q < 0.01). Three of these proteins: chymotrypsin C (CTRC), proto-oncogene tyrosine-protein kinase SRC (SRC) and C-C motif chemokine ligand 17 (CCL17) were unaltered in the corresponding plasma samples. As biomarkers for MI, rudimentary to no evidence exists for these proteins. In a separate group of patients with varying degrees of coronary artery disease, the decrease in EV-associated (but not plasma-related) SRC levels was confirmed by ELISA. Confirmation of the presence of SRC on EVs of different sizes and cellular origins was performed with ELISA, flow cytometry and nanoparticle tracking analysis. In conclusion, the data revealed that despite a similarity in the EV and plasma proteomes, analysis of isolated EVs does indeed provide additional diagnostic information that cannot be obtained from plasma alone.

Application of Microfluidic Chips in Separation and Analysis of Extracellular Vesicles in Liquid Biopsy for Cancer

Extracellular vesicles (EVs) are becoming a promising biomarker in liquid biopsy of cancer. Separation EV from cell culture medium or biofluids with high purity and quality remains a technique challenge. EV manipulation techniques based on microfluidics have been developed in the last decade. Microfluidic-based EV separation techniques developed so far can be classified into two categories: surface biomarker-dependent and size-dependent approaches. Microfluidic techniques allow the integration of EV separation and analysis on a single chip. Integrated EV separation and on-chip analysis have shown great potential in cancer diagnosis and monitoring treatment of responses. In this review, we discuss the development of microfluidic chips for EV separation and analysis. We also detail the clinical application of these microfluidic chips in the liquid biopsy of various cancers.

Acoustofluidic separation of cells and particles

Acoustofluidics, the integration of acoustics and microfluidics, is a rapidly growing research field that is addressing challenges in biology, medicine, chemistry, engineering, and physics. In particular, acoustofluidic separation of biological targets from complex fluids has proven to be a powerful tool due to the label-free, biocompatible, and contact-free nature of the technology. By carefully designing and tuning the applied acoustic field, cells and other bioparticles can be isolated with high yield, purity, and biocompatibility. Recent advances in acoustofluidics, such as the development of automated, point-of-care devices for isolating sub-micron bioparticles, address many of the limitations of conventional separation tools. More importantly, advances in the research lab are quickly being adopted to solve clinical problems. In this review article, we discuss working principles of acoustofluidic separation, compare different approaches of acoustofluidic separation, and provide a synopsis of how it is being applied in both traditional applications, such as blood component separation, cell washing, and fluorescence activated cell sorting, as well as emerging applications, including circulating tumor cell and exosome isolation.

A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing

Development of a robust automated platform for enrichment of extracellular vesicles from low sample volume that matches the needs for next-generation sequencing could remove major hurdles for genomic biomarker discovery. Here, we document a protocol for urinary EVs enrichment by utilizing an automated microfluidic system, termed acoustic trap, followed by next-generation sequencing of microRNAs (miRNAs) for biomarker discovery. Specifically, we compared the sequencing output from two small RNA library preparations, NEXTFlex and CATS, using only 130 pg of input total RNA. The samples prepared using NEXTflex was found to contain larger number of unique miRNAs that was the predominant RNA species whereas rRNA was the dominant RNA species in CATS prepared samples. A strong correlation was found between the miRNA expressions of the acoustic trap technical replicate in the NEXTFlex prepared samples, as well as between the acoustic trap and ultracentrifugation enrichment methods. Together, these results demonstrate a robust and automated strategy for biomarker discovery from small volumes of urine.

Applications of Acoustofluidics in Bioanalytical Chemistry

Acoustics has a broad spectrum of applications, ranging from noise cancelation to ultrasonic imaging. In the past decade, there has been increasing interest in developing acoustic-based methods for biological and biomedical applications. This Perspective summarizes the recent progress in applying acoustofluidic methods (i.e., the fusion of acoustics and microfluidics) to bioanalytical chemistry. We describe the concepts of acoustofluidics and how it can be tailored to different types of bioanalytical applications, including sample concentration, fluorescence-activated cell sorting, label-free cell/particle separation, and fluid manipulation. Examples of each application are given, and the benefits and limitations of these methods are discussed. Finally, our perspectives on the directions that developing solutions should take to address the bottlenecks in the acoustofluidic applications in bioanalytical chemistry are presented.

Effect of exercise on the plasma vesicular proteome: a methodological study comparing acoustic trapping and centrifugation

Extracellular vesicles (EVs) are a heterogeneous group of actively released vesicles originating from a wide range of cell types. Characterization of these EVs and their proteomes in the human plasma provides a novel approach in clinical diagnostics, as they reflect physiological and pathological states. However, EV isolation is technically challenging with the current methods having several disadvantages, requiring large sample volumes, and resulting in loss of sample and EV integrity. Here, we use an alternative, non-contact method based on a microscale acoustic standing wave technology. Improved coupling of the acoustic resonator increased the EV recovery from 30% in earlier reports to 80%, also displaying long term stability between experiment days. We report a pilot study, with 20 subjects who underwent physical exercise. Plasma samples were obtained before and 1 h after the workout. Acoustic trapping was compared to a standard high-speed centrifugation protocol, and the method was validated by flow cytometry (FCM). To monitor the device stability, the pooled frozen plasma from volunteers was used as an internal control. A key finding from the FCM analysis was a decrease in CD62E+ (E-selectin) EVs 1 h after exercise that was consistent for both methods. Furthermore, we report the first data that analyse differential EV protein expression before and after physical exercise. Olink-based proteomic analysis showed 54 significantly changed proteins in the EV fraction in response to physical exercise, whereas the EV-free plasma proteome only displayed four differentially regulated proteins, thus underlining an important role of these vesicles in cellular communication, and their potential as plasma derived biomarkers. We conclude that acoustic trapping offers a fast and efficient method comparable with high-speed centrifugation protocols. Further, it has the advantage of using smaller sample volumes (12.5 μL) and rapid contact-free separation with higher yield, and can thus pave the way for future clinical EV-based diagnostics.

Acoustic Enrichment of Extracellular Vesicles from Biological Fluids

Extracellular vesicles (EVs) have emerged as a rich source of biomarkers providing diagnostic and prognostic information in diseases such as cancer. Large-scale investigations into the contents of EVs in clinical cohorts are warranted, but a major obstacle is the lack of a rapid, reproducible, efficient, and low-cost methodology to enrich EVs. Here, we demonstrate the applicability of an automated acoustic-based technique to enrich EVs, termed acoustic trapping. Using this technology, we have successfully enriched EVs from cell culture conditioned media and urine and blood plasma from healthy volunteers. The acoustically trapped samples contained EVs ranging from exosomes to microvesicles in size and contained detectable levels of intravesicular microRNAs. Importantly, this method showed high reproducibility and yielded sufficient quantities of vesicles for downstream analysis. The enrichment could be obtained from a sample volume of 300 μL or less, an equivalent to 30 min of enrichment time, depending on the sensitivity of downstream analysis. Taken together, acoustic trapping provides a rapid, automated, low-volume compatible, and robust method to enrich EVs from biofluids. Thus, it may serve as a novel tool for EV enrichment from large number of samples in a clinical setting with minimum sample preparation.

Isolation of Extracellular Vesicles: General Methodologies and Latest Trends

BACKGROUND

Extracellular vesicles (EVs) play an essential role in the communication between cells and transport of diagnostically significant molecules. A wide diversity of approaches utilizing different biochemical properties of EVs and a lack of accepted protocols make data interpretation very challenging.

SCOPE OF REVIEW

This review consolidates the data on the classical and state-of-the-art methods for isolation of EVs, including exosomes, highlighting the advantages and disadvantages of each method. Various characteristics of individual methods, including isolation efficiency, EV yield, properties of isolated EVs, and labor consumption are compared.

MAJOR CONCLUSIONS

A mixed population of vesicles is obtained in most studies of EVs for all used isolation methods. The properties of an analyzed sample should be taken into account when planning an experiment aimed at studying and using these vesicles. The problem of adequate EVs isolation methods still remains; it might not be possible to develop a universal EV isolation method but the available protocols can be used towards solving particular types of problems.

GENERAL SIGNIFICANCE

With the wide use of EVs for diagnosis and therapy of various diseases the evaluation of existing methods for EV isolation is one of the key problems in modern biology and medicine.

Exosome Theranostics: Biology and Translational Medicine

Exosomes are common membrane-bound nanovesicles that contain diverse biomolecules, such as lipids, proteins, and nucleic acids. Exosomes are derived from cells through exocytosis, are ingested by target cells, and can transfer biological signals between local or distant cells. Exosome secretion is a constitutive phenomenon that is involved in both physiological and pathological processes and determines both the exosomal surface molecules and the contents. Hence, we can exploit exosomes as biomarkers, vaccines and drug carriers and modify them rationally for therapeutic interventions. However, it is still a challenge to identify, isolate and quantify exosomes accurately, efficiently and selectively. Further studies on exosomes will explore their potential in translational medicine and provide new avenues for the creation of effective clinical diagnostics and therapeutic strategies; the use of exosomes in these applications can be called exosome theranostics. This review describes the fundamental processes of exosome formation and uptake. In addition, the physiological and pathological roles of exosomes in biology are also illustrated with a focus on how exosomes can be exploited or engineered as powerful tools in translational medicine.

Microfluidics for exosome isolation and analysis: enabling liquid biopsy for personalized medicine

Exosomes, the smallest sized extracellular vesicles (∽30-150 nm) packaged with lipids, proteins, functional messenger RNAs and microRNAs, and double-stranded DNA from their cells of origin, have emerged as key players in intercellular communication. Their presence in bodily fluids, where they protect their cargo from degradation, makes them attractive candidates for clinical application as innovative diagnostic and therapeutic tools. But routine isolation and analysis of high purity exosomes in clinical settings is challenging, with conventional methods facing a number of drawbacks including low yield and/or purity, long processing times, high cost, and difficulties in standardization. Here we review a promising solution, microfluidic-based technologies that have incorporated a host of separation and sensing capabilities for exosome isolation, detection, and analysis, with emphasis on point-of-care and clinical applications. These new capabilities promise to advance fundamental research while paving the way toward routine exosome-based liquid biopsy for personalized medicine.

Microfluidic approaches for isolation, detection, and characterization of extracellular vesicles: Current status and future directions

Extracellular vesicles (EVs) are cell-derived vesicles present in body fluids that play an essential role in various cellular processes, such as intercellular communication, inflammation, cellular homeostasis, survival, transport, and regeneration. Their isolation and analysis from body fluids have a great clinical potential to provide information on a variety of disease states such as cancer, cardiovascular complications and inflammatory disorders. Despite increasing scientific and clinical interest in this field, there are still no standardized procedures available for the purification, detection, and characterization of EVs. Advances in microfluidics allow for chemical sampling with increasingly high spatial resolution and under precise manipulation down to single molecule level. In this review, our objective is to give a brief overview on the working principle and examples of the isolation and detection methods with the potential to be used for extracellular vesicles. This review will also highlight the integrated on-chip systems for isolation and characterization of EVs.

Modeling of Microdevices for SAW-Based Acoustophoresis - A Study of Boundary Conditions

We present a finite-element method modeling of acoustophoretic devices consisting of a single, long, straight, water-filled microchannel surrounded by an elastic wall of either borosilicate glass (pyrex) or the elastomer polydimethylsiloxane (PDMS) and placed on top of a piezoelectric transducer that actuates the device by surface acoustic waves (SAW). We compare the resulting acoustic fields in these full solid-fluid models with those obtained in reduced fluid models comprising of only a water domain with simplified, approximate boundary conditions representing the surrounding solids. The reduced models are found to only approximate the acoustically hard pyrex systems to a limited degree for large wall thicknesses and but not very well for acoustically soft PDMS systems shorter than the PDMS damping length of 3 mm.

Acoustic Force Density Acting on Inhomogeneous Fluids in Acoustic Fields

We present a theory for the acoustic force density acting on inhomogeneous fluids in acoustic fields on time scales that are slow compared to the acoustic oscillation period. The acoustic force density depends on gradients in the density and compressibility of the fluid. For microfluidic systems, the theory predicts a relocation of the inhomogeneities into stable field-dependent configurations, which are qualitatively different from the horizontally layered configurations due to gravity. Experimental validation is obtained by confocal imaging of aqueous solutions in a glass-silicon microchip.

Comparative Proteomic Analysis of Extracellular Vesicles Isolated by Acoustic Trapping or Differential Centrifugation

Extracellular vesicles (ECVs), including microparticles and exosomes, are submicrometer membrane vesicles released by diverse cell types upon activation or stress. Circulating ECVs are potential reservoirs of disease biomarkers, and the complexity of these vesicles is significantly lower compared to their source, blood plasma, which makes ECV-based biomarker studies more promising. Proteomic profiling of ECVs is important not only to discover new diagnostic or prognostic markers but also to understand their roles in biological function. In the current study, we investigated the protein composition of plasma-derived ECVs isolated by acoustic seed trapping. Additionally, the protein composition of ECVs isolated with acoustic trapping was compared to that isolated with a conventional differential centrifugation protocol. Finally, the proteome of ECVs originating from ST-elevation myocardial infarction patients was compared with that of healthy controls using label-free LC-MS quantification. The acoustic trapping platform allows rapid and automated preparation of ECVs from small sample volumes, which are therefore well-suited for biobank repositories. We found that the protein composition of trapped ECVs is very similar to that isolated by the conventional differential centrifugation method.

Forces acting on a small particle in an acoustical field in a thermoviscous fluid

We present a theoretical analysis of the acoustic radiation force on a single small spherical particle, either a thermoviscous fluid droplet or a thermoelastic solid particle, suspended in a viscous and heat-conducting fluid medium. Within the perturbation assumptions, our analysis places no restrictions on the length scales of the viscous and thermal boundary-layer thicknesses δ(s) and δ(t) relative to the particle radius a, but it assumes the particle to be small in comparison to the acoustic wavelength λ. This is the limit relevant to scattering of ultrasound waves from nanometer- and micrometer-sized particles. For particles of size comparable to or smaller than the boundary layers, the thermoviscous theory leads to profound consequences for the acoustic radiation force. Not only do we predict forces orders of magnitude larger than expected from ideal-fluid theory, but for certain relevant choices of materials, we also find a sign change in the acoustic radiation force on different-sized but otherwise identical particles. These findings lead to the concept of a particle-size-dependent acoustophoretic contrast factor, highly relevant to acoustic separation of microparticles in gases, as well as to handling of nanoparticles in lab-on-a-chip systems.