Ultrasensitive protein detection technologies for extracellular vesicle measurements

Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson's disease

Accurate diagnosis of early Parkinson's disease requires platforms suitable for detecting minute amounts of neuronally derived biomarkers in the massive protein excess of easily accessible biofluids such as blood. Here, we describe an on-chip droplet-confined fluorescence reporting assay that identified α-synuclein on the membrane of L1CAM+ extracellular vesicles (EVs) immunocaptured from human serum and corroborate this finding by super-resolution direct stochastic optical reconstruction microscopy (dSTORM) microscopy. Using conditioned media from neuroblastoma cells expressing α-synuclein mutants or patient-derived induced pluripotent stem cell (iPSC) neurons with α-synuclein gene triplication, we found that association of α-synuclein with the L1CAM+ EV surface is increased under pathological conditions. Accordingly, this readout, as measured by the droplet-based assay, is an improved predictive biomarker in the prodromal phase (area under the receiver operating characteristic curve [AUC] = 0.93) or diagnostic biomarker in the clinical phase (AUC = 0.95) of Parkinson's disease. More broadly, our platform will simplify the assessment of EV membrane proteins and facilitate their application as diagnostic biomarkers across diverse clinical indications.

Proteomics of Extracellular Vesicles: Recent Updates, Challenges and Limitations

Extracellular vesicles (EVs) are lipid-bound vesicles secreted by cells, including exosomes, microvesicles, and apoptotic bodies. Proteomic analyses of EVs, particularly in relation to cancer, reveal specific biomarkers crucial for diagnosis and therapy. However, isolation techniques such as ultracentrifugation, size-exclusion chromatography, and ultrafiltration face challenges regarding purity, contamination, and yield. Contamination from other proteins complicates downstream processing, leading to difficulties in identifying biomarkers and interpreting results. Future research will focus on refining EV characterization for diagnostic and therapeutic applications, improving proteomics tools for greater accuracy, and exploring the use of EVs in drug delivery and regenerative medicine. In this review, we provide a bird's eye view of various challenges, starting with EV isolation methods, yield, purity, and limitations in the proteome analysis of EVs for identifying protein targets.

Emerging roles of noncoding RNAs in cardiovascular pathophysiology

This review comprehensively examines the diverse roles of noncoding RNAs (ncRNAs) in the pathogenesis and treatment of cardiovascular disease (CVD), focusing on microRNA (miRNA), long noncoding RNA (lncRNA), piwi-interacting RNA (piRNA), small-interfering RNA (siRNA), circular RNA (circRNA), and vesicle-associated RNAs. These ncRNAs are integral regulators of key cellular processes, including gene expression, inflammation, and fibrosis, and they hold great potential as both diagnostic biomarkers and therapeutic targets. The review highlights novel insights into how these RNA species, particularly miRNAs, lncRNAs, and piRNAs, contribute to various CVDs such as hypertension, atherosclerosis, and myocardial infarction. In addition, it explores the emerging role of extracellular vesicles (EVs) in intercellular communication and their therapeutic potential in cardiovascular health. The review underscores the need for continued research into ncRNAs and RNA-based therapies, with a focus on advancing delivery systems and expanding personalized medicine approaches to improve cardiovascular outcomes.

Toward Identification of Markers for Brain-Derived Extracellular Vesicles in Cerebrospinal Fluid: A Large-Scale, Unbiased Analysis Using Proximity Extension Assays

Extracellular vesicles (EVs) captured in biofluids have opened a new frontier for liquid biopsies. To enrich for vesicles coming from a particular cell type or tumour, scientists utilize antibodies to transmembrane proteins that are relatively unique to the cell type of interest. However, recent evidence has called into question the basic assumption that all transmembrane proteins measured in biofluids are, in fact, EV-associated. To identify both candidate markers for brain-derived EV immunocapture and cargo proteins to validate the EVs' cell of origin, we conducted an unbiased Olink screen, measuring 5416 unique proteins in cerebrospinal fluid after size exclusion chromatography. We identified proteins that demonstrated a clear EV fractionation pattern and created a searchable dataset of candidate EV-associated markers-both proteins that are cell type-specific within the brain, and proteins found across multiple cell types for use as general EV markers. We further implemented the DeepTMHMM deep learning model to differentiate predicted cytosolic, transmembrane, and external proteins and found that intriguingly, only 10% of the predicted transmembrane proteins have a clear EV fractionation pattern based on our stringent criteria. This dataset further bolsters the critical importance of verifying EV association of candidate proteins using methods such as size exclusion chromatography before downstream use of the targets for EV analysis.

Analysis of small extracellular vesicles from dried blood spots

This protocol paper describes how to extract small extracellular vesicles (sEVs) from dried blood spots (DBS). The methodology is described in detail and offers further evidence that the extracted particles are sEVs using western blotting (anti-CD9, CD63 and CD81) and fluorescence nanoparticle tracking analysis (fNTA). In addition, we present evidence that approximately 40% of the sEVs were recovered from DBS compared with EVs analyzed from plasma directly. The protocol proves to be robust, reliable and displays very interesting performances even after several weeks (up to 3 weeks) of storage of the DBS when analyzing the sEVs using protein microarray for the presence of the markers CD9, CD63, CD81, EpCAM, Flotilin-1, CD62E/P, CD142 and CD235a. These findings have important implications for using sEVs as future potential diagnostic tools by supporting the validity of less-invasive methods that can be implemented within vulnerable populations or in the field.

Four-dimensional trapped ion mobility spectrometry proteomics reveals circulating extracellular vesicles encapsulated drivers of nasopharyngeal carcinoma distant dissemination

Nasopharyngeal carcinoma (NPC) is a head and neck cancer with a high propensity for early metastatic spread. Emerging evidence shows that extracellular vesicles (EVs) are key players in cancer metastasis, but their role in NPC metastasis remains poorly understood. We here present the first description of the proteomic and functional profiles of serum-derived circulating small EVs in metastatic NPC patients. To enhance the capture of low-abundance signaling proteins in EVs, timsTOF-based four-dimensional label-free quantitative proteomics was employed. We found that metastatic NPC patients (M-NPC-EVs) exhibited the highest serum EV levels compared to locoregional patients (L-NPC-EVs) and healthy subjects (Normal-EVs). The proteome of M-NPC-EVs differed substantially from L-NPC-EVs and was functionally enriched in pathways regulating cell polarity and motility, glucose metabolism, and angiogenesis. Functional assays testing individual EV samples demonstrated that M-NPC-EVs pronouncedly enhanced NPC cell migration, invasion, and the formation of lamellipodia and filopodia in vitro, and promoted angiogenesis in subcutaneous Matrigel plugs in vivo. In silico analyses suggested that PTPRA, TPI1 and GPI highly enriched in M-NPC-EVs were putative drivers underlying the motogenic and angiogenic activities of M-NPC-EVs, and their high expression levels were associated with a poor prognosis of NPC patients. The increased expression of PTPRA, TPI1 and GPI in M-NPC-EVs was then validated in an independent cohort consisting of 175 NPC patients (locoregional n = 114; metastatic n = 61). Together, utilizing patient-derived EVs, we mimicked the potential pro-metastatic functions of EVs in NPC patients in vitro and in vivo and provided novel insights into their bioactive cargoes.

Approaches and Challenges in Characterizing the Molecular Content of Extracellular Vesicles for Biomarker Discovery

Extracellular vesicles (EVs) are lipid bilayer nanoparticles released from all known cells and are involved in cell-to-cell communication via their molecular content. EVs have been found in all tissues and body fluids, carrying a variety of biomolecules, including DNA, RNA, proteins, metabolites, and lipids, offering insights into cellular and pathophysiological conditions. Despite the emergence of EVs and their molecular contents as important biological indicators, it remains difficult to explore EV-mediated biological processes due to their small size and heterogeneity and the technical challenges in characterizing their molecular content. EV-associated small RNAs, especially microRNAs, have been extensively studied. However, other less characterized RNAs, including protein-coding mRNAs, long noncoding RNAs, circular RNAs, and tRNAs, have also been found in EVs. Furthermore, the EV-associated proteins can be used to distinguish different types of EVs. The spectrum of EV-associated RNAs, as well as proteins, may be associated with different pathophysiological conditions. Therefore, the ability to comprehensively characterize EVs' molecular content is critical for understanding their biological function and potential applications in disease diagnosis. Here, we set out to provide an overview of EV-associated RNAs and proteins as well as approaches currently being used to characterize them.

Brain white matter damage biomarkers

White matter (WM), constituting nearly half of the human brain's mass, is pivotal for the rapid transmission of neural signals across different brain regions, significantly influencing cognitive processes like learning, memory, and problem-solving. The integrity of WM is essential for brain function, and its damage, which can occur due to conditions such as multiple sclerosis (MS), stroke, and traumatic brain injury, results in severe neurological deficits and cognitive decline. The primary objective of this book chapter is to discuss the clinical significance of fluid biomarkers in assessing WM damage within the central nervous system (CNS). It explores the biological underpinnings and pathological changes in WM due to various neurological conditions and details how alterations can be detected and quantified through fluid biomarkers. By examining biomarkers like Myelin Basic Protein (MBP), Neurofilament light chain (NFL), and others, the chapter highlights their role in enhancing diagnostic precision, monitoring disease progression, and guiding therapeutic interventions, thus providing crucial insights into maintaining WM integrity and preventing cognitive and physical disabilities.

Astrocyte Dysfunction Reflected in Ischemia-Induced Astrocyte-Derived Extracellular Vesicles: A Pilot Study on Acute Ischemic Stroke Patients

Extracellular vesicles (EVs) secreted by astrocytes (ADEVs) mediate numerous biological processes, providing insights into damage, repair, and protection following ischemic stroke (IS). This pilot study aimed to broaden the current knowledge on the astrocyte response to ischemia by dynamically assessing the aquaporin-4 (AQP4) and glial cell line-derived neurotrophic factor (GDNF) as cargo proteins of these vesicles in eighteen acute IS patients and nine controls. EV proteins were detected by Western blotting and followed 24 h (D1), 7 days (D7), and one month (M1) after symptoms onset. The post-ischemic ADEV AQP4 and GDNF levels were higher at D1 compared to the control group (p = 0.006 and p = 0.023). Significant differences were observed in ADEV AQP4 during the three evaluated time points (n = 12, p = 0.013) and between D1 and D7 (z = 2.858, p = 0.012), but not in EV GDNF. There was a positive relationship between the severity of stroke at D1 according to the National Institutes of Health Stroke Scale, and ADEV AQP4 at D1 (r = 0.50, p = 0.031), as well as ADEV GDNF at D1 and D7 (r = 0.49, p = 0.035 and r = 0.53, p = 0.021, respectively). The release of EVs with distinct protein profiles can be an attractive platform for the development of biomarkers in IS.

Lysis of Extracellular Vesicles and Multiplexed Protein Detection via a Reverse Phase Immunoassay Using a Gold-Nanoparticle-Embedded Membrane Platform

Extracellular vesicles (EVs) are cell-derived membrane-bound particles with molecular cargo reflective of their cell of origin. Analysis of disease-related EVs and associated cargo from biofluids is a promising tool for disease management. To facilitate the analysis of intravesicular molecules, EV lysis is needed. Moreover, highly sensitive and multiplexed detection methods are required to achieve early diagnostics. While cell lysis approaches have been well studied, the analysis of EV lysis methods and their effects on downstream molecular detection is lacking. In this work, we analyzed chemical, thermal, and mechanical EV lysis methods and determined their efficiency based on EV particle concentration and immunoassay activity. We, for the first time, discovered that vortex was an efficient EV lysis method and used it for detection of surface and intravesicular markers in a highly sensitive multiplexed reverse phase immunoassay on a gold-nanoparticle-embedded membrane. In phosphate-buffered saline, detection limits up to 3 orders of magnitude lower than enzyme-linked immunosorbent assay were achieved. In spiked human plasma, detection limits as low as 7.27 × 104 EVs/mL were achieved, making it suitable for early diagnostics. These results demonstrated an effective pipeline for lysing and molecular analysis of EVs from complex biofluids, paving the way for their broad applications in biomedicine.

Simultaneous Protein and RNA Analysis in Single Extracellular Vesicles, Including Viruses

The individual detection of human immunodeficiency virus (HIV) virions and resolution from extracellular vesicles (EVs) during analysis is a difficult challenge. Infectious enveloped virions and nonviral EVs are released simultaneously by HIV-infected host cells, in addition to hybrid viral EVs containing combinations of HIV and host components but lacking replicative ability. Complicating the issue, EVs and enveloped virions are both delimited by a lipid bilayer and share similar size and density. The feature that distinguishes infectious virions from host and hybrid EVs is the HIV genomic RNA (gRNA), which allows the virus to replicate. Single-particle analysis techniques, which provide snapshots of single biological nanoparticles, could resolve infectious virions from EVs. However, current single-particle analysis techniques focus mainly on protein detection, which fail to resolve hybrid EVs from infectious virions. A method to simultaneously detect viral protein and internal gRNA in the same particle would allow resolution of infectious HIV from EVs and noninfectious virions. Here, we introduce SPIRFISH, a high-throughput method for single-particle protein and RNA analysis, combining single particle interferometric reflectance imaging sensor with single-molecule fluorescence in situ hybridization. Using SPIRFISH, we detect HIV-1 envelope protein gp120 and genomic RNA within single infectious virions, allowing resolution against EV background and noninfectious virions. We further show that SPIRFISH can be used to detect specific RNAs within EVs. This may have major utility for EV therapeutics, which are increasingly focused on EV-mediated RNA delivery. SPIRFISH should enable single particle analysis of a broad class of RNA-containing nanoparticles.

Extracellular vesicles proteins for early cancer diagnosis: From omics to biomarkers

Extracellular vesicles (EVs) are a promising source of early biomarkers for cancer diagnosis. They are enriched with diverse molecular content, such as proteins, DNA, mRNA, miRNA, lipids, and metabolites. EV proteins have been widely investigated as potential biomarkers since they reflect specific patient conditions. However, although many markers have been validated and confirmed using external cohorts of patients and different analytical approaches, no EV protein markers are approved for diagnostic use. This review presents the primary strategies adopted using mass spectrometry and immune-based techniques to identify and validate EV protein biomarkers. We report and discuss recent scientific research focusing on cancer biomarker discovery through EVs, emphasizing their significant potential for the tempestive diagnosis of several cancer typologies. Finally, recent advancements in the standardization of EV isolation and quantitation through the development of easy-to-use and high-throughput kits for sample preparation-that should make protein EV biomarkers more reliable and accessible-are presented. The data reported here showed that there are still several challenges to be addressed before a protein vesicle marker becomes an essential tool in diagnosing cancer.

Biomarkers for Early Cancer Detection: A Landscape View of Recent Advancements, Spotlighting Pancreatic and Liver Cancers

Cancer is one of the leading causes of death worldwide. Early cancer detection is critical because it can significantly improve treatment outcomes, thus saving lives, reducing suffering, and lessening psychological and economic burdens. Cancer biomarkers provide varied information about cancer, from early detection of malignancy to decisions on treatment and subsequent monitoring. A large variety of molecular, histologic, radiographic, or physiological entities or features are among the common types of cancer biomarkers. Sizeable recent methodological progress and insights have promoted significant developments in the field of early cancer detection biomarkers. Here we provide an overview of recent advances in the knowledge related to biomolecules and cellular entities used for early cancer detection. We examine data from the CAS Content Collection, the largest human-curated collection of published scientific information, as well as from the biomarker datasets at Excelra, and analyze the publication landscape of recent research. We also discuss the evolution of key concepts and cancer biomarkers development pipelines, with a particular focus on pancreatic and liver cancers, which are known to be remarkably difficult to detect early and to have particularly high morbidity and mortality. The objective of the paper is to provide a broad overview of the evolving landscape of current knowledge on cancer biomarkers and to outline challenges and evaluate growth opportunities, in order to further efforts in solving the problems that remain. The merit of this review stems from the extensive, wide-ranging coverage of the most up-to-date scientific information, allowing unique, unmatched breadth of landscape analysis and in-depth insights.

Advances in extracellular vesicle isolation methods: a path towards cell-type specific EV isolation

Extracellular vesicles are small, heterogenous, phospholipid-rich vesicles that are secreted by all cells into the extracellular space. They play a key role in intercellular communication because they can transport a variety of biomolecules such as proteins, lipids, and nucleic acids between cells. As categorized by the International Society of Extracellular Vesicles (ISEV), the term EV encompasses different sub-types, including exosomes, microvesicles, and apoptotic bodies, which differ in their size, origin, and cargo. EVs can be isolated from biological fluids such as blood, urine, and cerebrospinal fluid, and their biomolecular content can be analyzed to monitor the progression of certain diseases. Therefore, EVs can be used as a new source of liquid biomarkers for advancing novel diagnostic and therapeutic tools. Isolating and analyzing EVs can be challenging due to their nanoscopic size and low abundance. Several techniques have been developed for the isolation and characterization of EVs, including ultracentrifugation, density gradient separation, size-exclusion chromatography, microfluidics, and magnetic bead-based/affinity methods. This review highlights advances in EV isolation techniques in the last decade and provides a perspective on their advantages, limitations, and potential application to cell-type specific EV isolation in the future.