Immunoaffinity based methods are superior to kits for purification of prostate derived extracellular vesicles from plasma samples

Recent advances and challenges in the recovery and purification of cellular exosomes

Exosomes are nanovesicles secreted by most cellular types that carry important biochemical compounds throughout the body with different purposes, playing a preponderant role in cellular communication. Because of their structure, physicochemical properties and stability, recent studies are focusing in their use as nanocarriers for different therapeutic compounds for the treatment of different diseases ranging from cancer to Parkinson's disease. However, current bioseparation protocols and methodologies are selected based on the final exosome application or intended use and present both advantages and disadvantages when compared among them. In this context, this review aims to present the most important technologies available for exosome isolation while discussing their advantages and disadvantages and the possibilities of being combined with other strategies. This is critical since the development of novel exosome-based therapeutic strategies will be constrained to the effectiveness and yield of the selected downstream purification methodologies for which a thorough understanding of the available technological resources is needed.

Insights into the Secretome of Mesenchymal Stem Cells and Its Potential Applications

Mesenchymal stem cells (MSCs) have regenerative, immunoregulatory properties and can be easily isolated and expanded in vitro. Despite being a powerful tool for clinical applications, they present limitations in terms of delivery, safety, and variability of therapeutic response. Interestingly, the MSC secretome composed by cytokines, chemokines, growth factors, proteins, and extracellular vesicles, could represent a valid alternative to their use. It is noteworthy that MSC-derived extracellular vesicles (MSC-EVs) have the same effect and could be advantageous compared to the parental cells because of their specific miRNAs load. MiRNAs could be useful both in diagnostic procedures such as “liquid biopsy” to identify early pathologies and in the therapeutic field. Not only are MSC-EVs’ preservation, transfer, and production easier, but their administration is also safer, hence some clinical trials are ongoing. However, much effort is required to improve the characterization of EVs to avoid artifacts and guarantee reproducibility of the studies.

Extracellular Vesicles in Mycobacterial Infections: Their Potential as Molecule Transfer Vectors

Extracellular vesicles are membrane-bound structures released by living cells and present in body fluids. Their composition includes proteins, lipids, carbohydrates, and nucleic acids and are involved in transfers between cells. Extracellular vesicles can deliver molecules to cells and tissues even if distant. As a consequence, they have a role in information transmission and in the modulation of the biological function of recipient cells. Among other things, they are involved in antigen presentation and the induction of secretion events by immune cells. Thus, extracellular vesicles participate in the regulation of immune responses during infections. We will discuss their potential as effectors and disease biomarkers concerning only mycobacterial infections.

Diversity and heterogeneity of extracellular RNA in human plasma

Extracellular RNAs (exRNAs) are secreted by nearly all cell types and are now known to play multiple physiological roles. In humans, exRNA populations are found in nearly any physiological liquid and are attracting growing interest as a potential source for biomarker discovery. Human plasma, a readily available sample for biomedical analysis, reported to contain various subpopulations of exRNA, some of which are most likely components of plasma ribonucleoproteins (RNPs), while others are encapsulated into extracellular vesicles (EVs) of different size, origin and composition. This variation explains the extreme complexity of the human exRNA fraction in plasma. In this work, we aimed to characterize exRNA species from blood samples of healthy human donors to achieve the most comprehensive overview of the species, sizes and origins of the exRNA present in plasma fractions. Unbiased analysis of exRNA composition was performed with prefractionation of plasma exRNA followed by library preparation, sequencing and bioinformatics analysis. Our results demonstrate that, in addition to "mature", adaptor ligation-competent RNA species (5'-P/3'-OH), human plasma contains a substantial proportion of degraded RNA fragments (5'-OH/3'-P or cycloP), which can be made competent for ligation using appropriate treatments. These degraded RNAs represent the major fraction in the overall population and mostly correspond to rRNA, in contrast to mature products, which mostly contain miRNAs and hY4 RNA fragments. Precipitation polyethylene glycol (PEG)-based kits for EV isolation yield a fraction that is highly contaminated by large RNPs and by RNA loosely bound to EVs. Purer EV preparations are obtained by using proteinase K and RNase A treatment, as well as by size-exclusion chromatography (SEC). These samples have rather distinct RNA compositions compared to PEG-precipitated EV preparations and contain a substantial proportion of exRNA of non-human origin, arising from human skin and gut microbiota, including viral microbiota. These exogenous exRNAs represent up to 75-80% of total RNA reads in highly purified extracellular vesicles, paving the way for biomedical exploitation of these non-human biomarkers.

Isolation and Characterization of Small Extracellular Vesicles from Porcine Blood Plasma, Cerebrospinal Fluid, and Seminal Plasma

Extracellular vesicles (EVs) are a highly attractive subject of biomedical research as possible carriers of nucleic acid and protein biomarkers. EVs released to body fluids enable indirect access to inner organs by so-called "liquid biopsies". Obtaining a high-quality EV sample with minimum contaminants is crucial for proteomic analyses using LC-MS/MS or other techniques. However, the EV content in various body fluids largely differs, which may hamper subsequent analyses. Here, we present a comparison of extracellular vesicle yields from blood plasma, cerebrospinal fluid, and seminal plasma using an experimental pig model. Pigs are widely used in biomedical research as large animal models with anatomy and physiology close to those of humans and enable studies (e.g., of the nervous system) that are unfeasible in humans. EVs were isolated from body fluids by differential centrifugation followed by ultracentrifugation. EVs were characterized according to protein yields and to the quality of the isolated vesicles (e.g., size distribution, morphology, positivity for exosome markers). In our experimental setting, substantial differences in EV amounts were identified among body fluids, with the seminal plasma being the richest EV source. The yields of pellet proteins from ultracentrifugation of 1 mL of porcine body fluids may help to estimate body fluid input volumes to obtain sufficient samples for subsequent proteomic analyses.

The role of extracellular vesicles in cancer microenvironment and metastasis: myths and challenges

The concept of vesicles or cell debris released by cancer cells to promote metastasis is not new, but the mechanisms used to currently ascribe their impact in metastasis are of intense debate. A significant increase in reports describing the role of cancer-derived EVs in cancer metastasis has been followed by a growing amount of uncertainty behind these claims. This review will delve into the role of EVs in promoting cancer metastasis by relying on a balanced perspective that looks at challenges faced previously by extracellular vesicle biologists, current technical limitations in the field, and overlooked physiologic mechanisms that may play a confounding role. This review will also discuss how certain experimental approaches are misleading which ultimately lead to overly optimistic mechanisms that have minimally contributed to the pathophysiology of metastasis.

CNS-derived extracellular vesicles from superoxide dismutase 1 (SOD1)G93A ALS mice originate from astrocytes and neurons and carry misfolded SOD1

Extracellular vesicles (EVs) are secreted by myriad cells in culture and also by unicellular organisms, and their identification in mammalian fluids suggests that EV release also occurs at the organism level. However, although it is clearly important to better understand EVs' roles in organismal biology, EVs in solid tissues have received little attention. Here, we modified a protocol for EV isolation from primary neural cell culture to collect EVs from frozen whole murine and human neural tissues by serial centrifugation and purification on a sucrose gradient. Quantitative proteomics comparing brain-derived EVs from nontransgenic (NTg) and a transgenic amyotrophic lateral sclerosis (ALS) mouse model, superoxide dismutase 1 (SOD1)^G93A, revealed that these EVs contain canonical exosomal markers and are enriched in synaptic and RNA-binding proteins. The compiled brain EV proteome contained numerous proteins implicated in ALS, and EVs from SOD1^G93A mice were significantly depleted in myelin-oligodendrocyte glycoprotein compared with those from NTg animals. We observed that brain- and spinal cord-derived EVs, from NTg and SOD1^G93A mice, are positive for the astrocyte marker GLAST and the synaptic marker SNAP25, whereas CD11b, a microglial marker, was largely absent. EVs from brains and spinal cords of the SOD1^G93A ALS mouse model, as well as from human SOD1 familial ALS patient spinal cord, contained abundant misfolded and nonnative disulfide-cross-linked aggregated SOD1. Our results indicate that CNS-derived EVs from an ALS animal model contain pathogenic disease-causing proteins and suggest that brain astrocytes and neurons, but not microglia, are the main EV source.

Exosomes of malignant tumors: prospects of omiсs diagnostics

The main problems in the diagnostics and treatment of malignant tumors are early detection of the disease, prediction of the course of the disease and response to therapy. The solution may be associated with identification of biomarkers secreted by tumor cells within extracellular vesicles, known as exosomes. The study of exosome proteins attracts special attention, because their molecular composition can have information about tumor identity, and also represent a set of signaling molecules that regulate the processes of tumor progression and growth. In addition, the analysis of exosomes secreted into the extracellular space corresponds to the promising concept of a liquid biopsy. In this review, we have summarized the current experience in the molecular study of exosomes in various types of malignant tumors, including colorectal cancer, lung cancer, ovaries, prostate and breast cancer, with special emphasis on omics methods and outlined the prospects for their use in diagnosis.

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

Exploring Small Extracellular Vesicles for Precision Medicine in Prostate Cancer

Tumor microenvironment constitutes a complex network in which tumor cells communicate among them and with stromal and immune cells. It has been shown that cancer cells are able to exchange genetic materials through small extracellular vesicles (EVs), a heterogeneous group of vesicles with different size and shape, cargo content, and function. The importance to investigate populations of circulating EVs would be of great importance as prostate cancer (PCa) biomarkers. In several neoplasms as well as in PCa, nanometer-sized EVs of endosomal origin are implicated in supporting tumor growth and metastatic spread by both altering local stroma cells and creating a protumor environment that favors the formation of pre-metastatic niches. Several techniques are applicable for the isolation and analysis of PCa-derived small EVs and are illustrated in this article. Due to the high sensitivity and specificity of these techniques, small EVs have become ideal candidates for early diagnosis. Moreover, we discuss the role of small EVs during PCa carcinogenesis, as well as in modulating the development of drug resistance to hormonal therapy and chemotherapy, thus underlining the potential of EV-tailored strategies in PCa patients.

Extracellular Vesicles in Prostate Cancer Carcinogenesis, Diagnosis, and Management

Extracellular vesicles (EVs), especially exosomes, are now well recognized as major ways by which cancer cells interact with each other and stromal cells. The meaningful messages transmitted by the EVs are carried by all components of the EVs, i.e., the membrane lipids and the cargo (DNAs, RNAs, microRNAs, long non-coding RNAs, proteins). They are clearly part of the armed arsenal by which cancer cells obtain and share more and more advantages to grow and conquer new spaces. Identification of these messages offers a significant opportunity to better understand how a cancer occurs and then develops both locally and distantly. But it also provides a powerful means by which cancer progression can be detected and monitored. In the last few years, significant research efforts have been made to precisely identify how the EV trafficking is modified in cancer cells as compared to normal cells and how this trafficking is altered during cancer progression. Prostate cancer has not escaped this trend. The aim of this review is to describe the results obtained when assessing the meaningful content of prostate cancer- and stromal-derived EVs in terms of a better comprehension of the cellular and molecular mechanisms underlying prostate cancer occurrence and development. This review also deals with the use of EVs as powerful tools to diagnose non-indolent prostate cancer as early as possible and to accurately define, in a personalized approach, its present and potential aggressiveness, its response to treatment (androgen deprivation, chemotherapy, radiation, surgery), and the overall patients’ prognosis.

Ceramide and Exosomes: A Novel Target in Cancer Biology and Therapy

Exosomes are secreted extracellular vesicles (EVs) that carry micro RNAs and other factors to reprogram cancer cells and tissues affected by cancer. Exosomes are exchanged between cancer cells and other tissues, often to prepare a premetastatic niche, escape immune surveillance, or spread multidrug resistance. Only a few studies investigated the function of lipids in exosomes although their lipid composition is different from that of the secreting cells. Ceramide is one of the lipids critical for exosome formation, and it is also enriched in these EVs. New research suggests that lipids in the exosomal membrane may organize and transmit "mobile rafts" that turn exosomes into extracellular signalosomes spreading activation of cell signaling pathways in oncogenesis and metastasis. Ceramide may modulate the function of mobile rafts and their effect on these cell signaling pathways. The critical role of lipids and, in particular, ceramide for formation, secretion, and function of exosomes may lead to a radically new understanding of cancer biology and therapy.

Non-alcoholic steatohepatitis pathogenesis: sublethal hepatocyte injury as a driver of liver inflammation

A subset of patients with non-alcoholic fatty liver disease develop an inflammatory condition, termed non-alcoholic steatohepatitis (NASH). NASH is characterised by hepatocellular injury, innate immune cell-mediated inflammation and progressive liver fibrosis. The mechanisms whereby hepatic inflammation occurs in NASH remain incompletely understood, but appear to be linked to the proinflammatory microenvironment created by toxic lipid-induced hepatocyte injury, termed lipotoxicity. In this review, we discuss the signalling pathways induced by sublethal hepatocyte lipid overload that contribute to the pathogenesis of NASH. Furthermore, we will review the role of proinflammatory, proangiogenic and profibrotic hepatocyte-derived extracellular vesicles as disease biomarkers and pathogenic mediators during lipotoxicity. We also review the potential therapeutic strategies to block the feed-forward loop between sublethal hepatocyte injury and liver inflammation.

Isolation of anti-extra-cellular vesicle single-domain antibodies by direct panning on vesicle-enriched fractions

Background

The thorough understanding of the physiological and pathological processes mediated by extracellular vesicles (EVs) is challenged by purification methods which are cumbersome, not reproducible, or insufficient to yield homogeneous material. Chromatography based on both ion-exchange and immune-capture can represent an effective method to improve EV purification and successive analysis.

Methods

Cell culture supernatant was used as a model sample for assessing the capacity of anion-exchange chromatography to separate distinct EV fractions and to isolate nanobodies by direct panning on whole EVs to recover binders specific for the native conformation of EV-surface epitopes and suitable to develop EV immune-capture reagents.

Results

Anion-exchange chromatography of cell culture supernatant separated distinct protein-containing fractions and all of them were positive for CD9, a biomarker associated to some EVs. This suggested the existence of several EV fractions but did not help in separating EVs from other contaminants. We further isolated several nanobodies instrumental for implementing immune-affinity protocols. These were able to immobilize EVs from both cell culture supernatant and biological samples, to be used in ELISA, flow-cytometry, and immune-purification.

Conclusions

Here we report the first successful isolation of anti-EV nanobodies for the use in immunoaffinity-based EV capture by panning a phage library directly on partially purified EVs. This achievement paves the way for the application of direct EV panning for the discovery of novel antibody-vesicle surface biomarker pairs and represents the preliminary requirement for the development of selective immune-capture that, in combination with anion-exchange chromatography, can simplify the systematic stratification of EV sub-populations and their individual characterization.

Electronic supplementary material

The online version of this article (10.1186/s12934-017-0856-9) contains supplementary material, which is available to authorized users.