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Characterization of Extracellular Vesicles in Disease
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Characterization of Extracellular Vesicles in Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 December 2024 | Viewed by 11625

Special Issue Editor

Dr. Verena Tretter

E-Mail Website
Guest Editor
Department of Anesthesia and General Intensive Care, Clinical Department of Anesthesia, Medizinische Universität Wien, Vienna, Austria
Interests: cell biology of the lung and heart; organ protection; signaling transduction in the lung; experimental anesthesiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Extracellular vesicles (EVs) are entities known to be released from all cell types, which contain signaling components such as proteins and nucleic acids enclosed by a lipid membrane. What was initially believed to be an unspecific secretion product has turned out to be a cell-type specific means of inter-cellular communication. The population of EVs is heterogenous with regard to the mode of biogenesis, size and cargo. Cargo signatures and their dependence on the (patho-)physiological status of the cell of origin as well as the mechanisms of specific detection of the recipient tissue are currently being investigated with the aim of defining EV-biomarkers and better understanding this communication route. In order to make progress in this field, analytical techniques are refined and frequently employ -omics technologies, such as proteomics and next-generation sequencing of RNAs.

This Special Issue invites contributions from this exciting research field with a special emphasis on the molecular characterization of extracellular vesicles depending on the physiological state of the secreting cell type and the recipient tissues.

Dr. Verena Tretter
Guest Editor

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Keywords

  • extracellular vesicle
  • exosomes
  • microvesicles
  • vesicle cargo

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Published Papers (6 papers)

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Research

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15 pages, 2684 KiB  
Article
Effect of Unfractionated Heparin Dose on Complement Activation and Selected Extracellular Vesicle Populations during Extracorporeal Membrane Oxygenation
by Johannes Zipperle, Laurenz Vock, Gerhard Fritsch, Johannes Grillari, Marcin F. Osuchowski, Wolfgang Holnthoner, Herbert Schöchl, Rebecca Halbgebauer, Markus Huber-Lang, Nikolaus Hofmann, Vincenz Scharner, Mauro Panigada, Johannes Gratz and Giacomo Iapichino
Int. J. Mol. Sci. 2024, 25(20), 11166; https://doi.org/10.3390/ijms252011166 - 17 Oct 2024
Viewed by 1044
Abstract
Extracorporeal membrane oxygenation (ECMO) provides critical support for patients with severe cardiopulmonary dysfunction. Unfractionated heparin (UFH) is used for anticoagulation to maintain circuit patency and avoid thrombotic complications, but it increases the risk of bleeding. Extracellular vesicles (EVs), nano-sized subcellular spheres with potential [...] Read more.
Extracorporeal membrane oxygenation (ECMO) provides critical support for patients with severe cardiopulmonary dysfunction. Unfractionated heparin (UFH) is used for anticoagulation to maintain circuit patency and avoid thrombotic complications, but it increases the risk of bleeding. Extracellular vesicles (EVs), nano-sized subcellular spheres with potential pro-coagulant properties, are released during cellular stress and may serve as potential targets for monitoring anticoagulation, particularly in thromboinflammation. We investigated the impact of UFH dose during ECMO therapy at the coagulation–inflammation interface level, focusing on complement activation and changes in circulating large EV (lEV) subsets. In a post hoc analysis of a multicenter randomized controlled trial comparing two anticoagulation management algorithms, we examined lEV levels and complement activation in 23 veno-venous-ECMO patients stratified by UFH dose. Blood samples were collected at different time points and grouped into three phases of ECMO therapy: initiation (day 1), mid (days 3–4), and late (days 6–7). Immunoassays detected complement activation, and flow cytometry analyzed lEV populations with an emphasis on mitochondria-carrying subsets. Patients receiving <15 IU/kg/h UFH exhibited higher levels of the complement activation product C5a and soluble terminal complement complex (sC5b-9). Lower UFH doses were linked to increased endothelial-derived lEVs, while higher doses were associated with elevated RBC-derived and mitochondria-positive lEVs. Our findings suggest the potential theranostic relevance of EV detection at the coagulation–inflammation interface. Further research is needed to standardize EV detection methods and validate these findings in larger ECMO patient cohorts. Full article
(This article belongs to the Special Issue Characterization of Extracellular Vesicles in Disease)
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14 pages, 3085 KiB  
Article
SILAC-Based Characterization of Plasma-Derived Extracellular Vesicles in Patients Undergoing Partial Hepatectomy
by Ulrike Resch, Hubert Hackl, David Pereyra, Jonas Santol, Laura Brunnthaler, Joel Probst, Anna Sofie Jankoschek, Monika Aiad, Hendrik Nolte, Marcus Krueger, Patrick Starlinger and Alice Assinger
Int. J. Mol. Sci. 2024, 25(19), 10685; https://doi.org/10.3390/ijms251910685 - 4 Oct 2024
Viewed by 922
Abstract
Post-hepatectomy liver failure (PHLF) remains a significant risk for patients undergoing partial hepatectomy (PHx). Reliable prognostic markers and treatments to enhance liver regeneration are lacking. Plasma nanoparticles, including lipoproteins, exosomes, and extracellular vesicles (EVs), can reflect systemic and tissue-wide proteostasis and stress, potentially [...] Read more.
Post-hepatectomy liver failure (PHLF) remains a significant risk for patients undergoing partial hepatectomy (PHx). Reliable prognostic markers and treatments to enhance liver regeneration are lacking. Plasma nanoparticles, including lipoproteins, exosomes, and extracellular vesicles (EVs), can reflect systemic and tissue-wide proteostasis and stress, potentially aiding liver regeneration. However, their role in PHLF is still unknown. Methods: Our study included nine patients with hepatocellular carcinoma (HCC) undergoing PHx: three patients with PHLF, three patients undergoing the associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) procedure, and three matched controls without complications after PHx. Patient plasma was collected before PHx as well as 1 and 5 days after. EVs were isolated by ultracentrifugation, and extracted proteins were subjected to quantitative mass spectrometry using a super-SILAC mix prepared from primary and cancer cell lines. Results: We identified 2625 and quantified 2570 proteins in the EVs of PHx patients. Among these, 53 proteins were significantly upregulated and 32 were downregulated in patients with PHLF compared to those without PHLF. Furthermore, 110 proteins were upregulated and 78 were downregulated in PHLF patients compared to those undergoing ALPPS. The EV proteomic signature in PHLF indicates significant disruptions in protein translation, proteostasis, and intracellular vesicle biogenesis, as well as alterations in proteins involved in extracellular matrix (ECM) remodelling and the metabolic and cell cycle pathways, already present before PHx. Conclusions: Longitudinal proteomic analysis of the EVs circulating in the plasma of human patients undergoing PHx uncovers proteomic signatures associated with PHLF, which reflect dying hepatocytes and endothelial cells and were already present before PHx. Full article
(This article belongs to the Special Issue Characterization of Extracellular Vesicles in Disease)
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15 pages, 6163 KiB  
Article
Proteomic Characterization of Corneal Epithelial and Stromal Cell-Derived Extracellular Vesicles
by Vincent Yeung, Nikolay Boychev, Levi N. Kanu, Veronica Ng, Amy E. Ross, Audrey E. K. Hutcheon and Joseph B. Ciolino
Int. J. Mol. Sci. 2024, 25(19), 10338; https://doi.org/10.3390/ijms251910338 - 26 Sep 2024
Viewed by 739
Abstract
Communication between the different layers of the cornea (epithelium and stroma) is a complex, yet crucial element in the corneal healing process. Upon corneal injury, it has been reported that the bi-directional cross talk between the epithelium and stroma via the vesicular secretome, [...] Read more.
Communication between the different layers of the cornea (epithelium and stroma) is a complex, yet crucial element in the corneal healing process. Upon corneal injury, it has been reported that the bi-directional cross talk between the epithelium and stroma via the vesicular secretome, namely, extracellular vesicles (EVs), can lead to accelerated wound closure upon injury. However, the distinct protein markers of EVs derived from human corneal epithelial (HCE) cells, keratocytes (HCKs), fibroblasts (HCFs), and myofibroblasts (HCMs) remain poorly understood. All EVs were enriched for CD81 and showed increased expression levels of ITGAV and FN1 in HCM-EVs compared to HCE- and HCF-EVs. All EVs were negative for GM130 and showed minimal differences in biophysical properties (particle concentration, median particle size, and zeta potential). At the proteomic level, we show that HCM-EVs are enriched with proteins associated with fibrosis pathways, such as COL6A1, COL6A2, MMP1, MMP2, TIMP1, and TIMP2, compared to HCE-, HCK-, and HCF-EVs. Interestingly, HCE-EVs express proteins involved with the EIF-2 signaling pathway (stress-induced signals to regulate mRNA translation), such as RPS21, RALB, EIF3H, RALA, and others, compared to HCK-, HCF-, and HCM-EVs. In this study, we isolated EVs from cell-conditioned media from HCE, HCKs, HCFs, and HCMs and characterized their biophysical and protein composition by Western blot, nanoparticle tracking analysis, and proteomics. This study supports the view that EVs from the corneal epithelium and stroma have a distinct molecular composition and may provide novel protein markers to distinguish the difference between HCE-, HCK-, HCF-, and HCM-EVs. Full article
(This article belongs to the Special Issue Characterization of Extracellular Vesicles in Disease)
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22 pages, 4073 KiB  
Article
The Proteome of Extracellular Vesicles Released from Pulmonary Microvascular Endothelium Reveals Impact of Oxygen Conditions on Biotrauma
by Wolfgang Schaubmayr, Beatrix Hochreiter, Eva Hunyadi-Gulyas, Louise Riegler, Katy Schmidt, Akos Tiboldi, Bernhard Moser, Klaus U. Klein, Katharina Krenn, Gisela Scharbert, Thomas Mohr, Johannes A. Schmid, Andreas Spittler and Verena Tretter
Int. J. Mol. Sci. 2024, 25(4), 2415; https://doi.org/10.3390/ijms25042415 - 19 Feb 2024
Cited by 1 | Viewed by 1714
Abstract
The lung can experience different oxygen concentrations, low as in hypoxia, high as under supplemental oxygen therapy, or oscillating during intermittent hypoxia as in obstructive sleep apnea or intermittent hypoxia/hyperoxia due to cyclic atelectasis in the ventilated patient. This study aimed to characterize [...] Read more.
The lung can experience different oxygen concentrations, low as in hypoxia, high as under supplemental oxygen therapy, or oscillating during intermittent hypoxia as in obstructive sleep apnea or intermittent hypoxia/hyperoxia due to cyclic atelectasis in the ventilated patient. This study aimed to characterize the oxygen-condition-specific protein composition of extracellular vesicles (EVs) released from human pulmonary microvascular endothelial cells in vitro to decipher their potential role in biotrauma using quantitative proteomics with bioinformatic evaluation, transmission electron microscopy, flow cytometry, and non-activated thromboelastometry (NATEM). The release of vesicles enriched in markers CD9/CD63/CD81 was enhanced under intermittent hypoxia, strong hyperoxia and intermittent hypoxia/hyperoxia. Particles with exposed phosphatidylserine were increased under intermittent hypoxia. A small portion of vesicles were tissue factor-positive, which was enhanced under intermittent hypoxia and intermittent hypoxia/hyperoxia. EVs from treatment with intermittent hypoxia induced a significant reduction of Clotting Time in NATEM analysis compared to EVs isolated after normoxic exposure, while after intermittent hypoxia/hyperoxia, tissue factor in EVs seems to be inactive. Gene set enrichment analysis of differentially expressed genes revealed that EVs from individual oxygen conditions potentially induce different biological processes such as an inflammatory response under strong hyperoxia and intermittent hypoxia/hyperoxia and enhancement of tumor invasiveness under intermittent hypoxia. Full article
(This article belongs to the Special Issue Characterization of Extracellular Vesicles in Disease)
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Review

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12 pages, 1257 KiB  
Review
Acute Kidney Injury by Ischemia/Reperfusion and Extracellular Vesicles
by Mikkel Ørnfeldt Nørgård and Per Svenningsen
Int. J. Mol. Sci. 2023, 24(20), 15312; https://doi.org/10.3390/ijms242015312 - 18 Oct 2023
Cited by 8 | Viewed by 3397
Abstract
Acute kidney injury (AKI) is often caused by ischemia-reperfusion injury (IRI). IRI significantly affects kidney metabolism, which elicits pro-inflammatory responses and kidney injury. The ischemia/reperfusion of the kidney is associated with transient high mitochondrial-derived reactive oxygen species (ROS) production rates. Excessive mitochondrial-derived ROS [...] Read more.
Acute kidney injury (AKI) is often caused by ischemia-reperfusion injury (IRI). IRI significantly affects kidney metabolism, which elicits pro-inflammatory responses and kidney injury. The ischemia/reperfusion of the kidney is associated with transient high mitochondrial-derived reactive oxygen species (ROS) production rates. Excessive mitochondrial-derived ROS damages cellular components and, together with other pathogenic mechanisms, elicits a range of acute injury mechanisms that impair kidney function. Mitochondrial-derived ROS production also stimulates epithelial cell secretion of extracellular vesicles (EVs) containing RNAs, lipids, and proteins, suggesting that EVs are involved in AKI pathogenesis. This literature review focuses on how EV secretion is stimulated during ischemia/reperfusion and how cell-specific EVs and their molecular cargo may modify the IRI process. Moreover, critical pitfalls in the analysis of kidney epithelial-derived EVs are described. In particular, we will focus on how the release of kidney epithelial EVs is affected during tissue analyses and how this may confound data on cell-to-cell signaling. By increasing awareness of methodological pitfalls in renal EV research, the risk of false negatives can be mitigated. This will improve future EV data interpretation regarding EVs contribution to AKI pathogenesis and their potential as biomarkers or treatments for AKI. Full article
(This article belongs to the Special Issue Characterization of Extracellular Vesicles in Disease)
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18 pages, 358 KiB  
Review
Engineered Extracellular Vesicles: Emerging Therapeutic Strategies for Translational Applications
by Jessica N. Ziegler and Changhai Tian
Int. J. Mol. Sci. 2023, 24(20), 15206; https://doi.org/10.3390/ijms242015206 - 15 Oct 2023
Cited by 6 | Viewed by 2768
Abstract
Extracellular vesicles (EVs) are small, membrane-bound vesicles used by cells to deliver biological cargo such as proteins, mRNA, and other biomolecules from one cell to another, thus inducing a specific response in the target cell and are a powerful method of cell to [...] Read more.
Extracellular vesicles (EVs) are small, membrane-bound vesicles used by cells to deliver biological cargo such as proteins, mRNA, and other biomolecules from one cell to another, thus inducing a specific response in the target cell and are a powerful method of cell to cell and organ to organ communication, especially during the pathogenesis of human disease. Thus, EVs may be utilized as prognostic and diagnostic biomarkers, but they also hold therapeutic potential just as mesenchymal stem cells have been used in therapeutics. However, unmodified EVs exhibit poor targeting efficacy, leading to the necessity of engineered EVS. To highlight the advantages and therapeutic promises of engineered EVs, in this review, we summarized the research progress on engineered EVs in the past ten years, especially in the past five years, and highlighted their potential applications in therapeutic development for human diseases. Compared to the existing stem cell-derived EV-based therapeutic strategies, engineered EVs show greater promise in clinical applications: First, engineered EVs mediate good targeting efficacy by exhibiting a targeting peptide that allows them to specifically target a specific organ or even cell type, thus avoiding accumulation in undesired locations and increasing the potency of the treatment. Second, engineered EVs can be artificially pre-loaded with any necessary biomolecular cargo or even therapeutic drugs to treat a variety of human diseases such as cancers, neurological diseases, and cardiovascular ailments. Further research is necessary to improve logistical challenges in large-scale engineered EV manufacturing, but current developments in engineered EVs prove promising to greatly improve therapeutic treatment for traditionally difficult to treat diseases. Full article
(This article belongs to the Special Issue Characterization of Extracellular Vesicles in Disease)
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