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Extracellular Vesicles and Nanoparticles

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

Deadline for manuscript submissions: 30 April 2024 | Viewed by 12102

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Prof. Dr. Djuro Josic

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Faculty of Medicine, University Juraj Dobrila of Pula, 52100 Pula, Croatia
Interests: proteomics; foodborne pathogens; mechanisms of bacterial resistance; extracellular vesicles
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Dear Colleagues,

After their discovery, extracellular vesicles (EVs – also called “microparticles”) end of 1960s as a product of platelets, they were considered to be degradation products of limited importance. Evs first came in the focus of research about forty years later, and in the year 2012 the first volume in prestigious Journal was issued. This Special Issue of IJMS is to give an additional view in this field. These submicron size vesicles are shed not only from various cell types of multicellular organisms, but also by unicellular ones like Gram positive and Gram negative bacteria. As the product of most eucariotic cells, exosomes are the the most frequently investigated EVs, and they have multiple function, like cell-cell communication, cellular signaling, blood coagulation and homeostasis. However, they seem to be also involved in many pathological processes like tumor growth and invasion, hypertension and vascular injury. EVs that are shed by bacteria and other unicellular organisms were neglected for longer time, and the existence of EVs shed by Gram positive bacteria was even questioned. Now, EVs that are shed by pathogens like bacteria are in the focus of many investigations, especially regarding their role in human diseases.

In this Special Issue, the manuscripts dealing with the new aspects of EVs investigations, especially regarding their isolation and analytics for identification of new disease biomarkers, the role of exosomes and EVs in signal transduction in targeted therapy of several diseases (especially cancer) and in the interaction between the pathogen and host organism. The next point of interest are the microvesicles shed by bacteria and other pathogens and their role in infection and resistance, carrying of toxins and biofilm formation.

Prof. Dr. Djuro Josic
Guest Editor

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Keywords

extracellular vesicles
exosomes
bacterial toxins
viruses
biomarkers
signal transduction
targeted therapy
exososmes in cancer
exosomes and extracellular vesicles host-pathogen interaction
extracellular vesicles of gram positive bacteria
extracellular vesicles of gram negative bacteria
extracellular vesicles and biofilm formation

Published Papers (7 papers)

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Research

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23 pages, 9373 KiB

Open AccessArticle

Hsp70 and Calcitonin Receptor Protein in Extracellular Vesicles from Glioblastoma Multiforme: Biomarkers with Putative Roles in Carcinogenesis and Potential for Differentiating Tumor Types

by Giusi Alberti, Christian M. Sánchez-López, Antonio Marcilla, Rosario Barone, Celeste Caruso Bavisotto, Francesca Graziano, Everly Conway de Macario, Alberto J. L. Macario, Fabio Bucchieri, Francesco Cappello, Claudia Campanella and Francesca Rappa

Int. J. Mol. Sci. 2024, 25(6), 3415; https://doi.org/10.3390/ijms25063415 - 18 Mar 2024

Viewed by 664

Abstract

Glioblastoma multiforme (GBM) is a malignancy of bad prognosis, and advances in early detection and treatment are needed. GBM is heterogenous, with varieties differing in malignancy within a tumor of a patient and between patients. Means are needed to distinguish these GMB forms, so that specific strategies can be deployed for patient management. We study the participation of the chaperone system (CS) in carcinogenesis. The CS is dynamic, with its members moving around the body in extracellular vesicles (EVs) and interacting with components of other physiological systems in health and disease, including GBM. Here, we describe the finding of high amounts of Hsp70 (HSPA1A) and the calcitonin receptor protein (CTR) in EVs in patients with GBM. We present a standardized protocol for collecting, purifying, and characterizing EVs carrying Hsp70 and CTR in plasma-derived EVs from patients with GBM. EVs from GBM patients were obtained just before tumor ablative surgery (T0) and 7 days afterwards (T1); Hsp70 was highly elevated at T0 and less so at T1, and CTR was greatly increased at T0 and reduced to below normal values at T1. Our results encourage further research to assess Hsp70 and CTR as biomarkers for differentiating tumor forms and to determine their roles in GBM carcinogenesis. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Nanoparticles)

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12 pages, 2151 KiB

Open AccessArticle

Comparison of Methods for Quantifying Extracellular Vesicles of Gram-Negative Bacteria

by Chanel A. Mosby, Natalia Perez Devia and Melissa K. Jones

Int. J. Mol. Sci. 2023, 24(20), 15096; https://doi.org/10.3390/ijms242015096 - 11 Oct 2023

Viewed by 1165

Abstract

There are a variety of methods employed by laboratories for quantifying extracellular vesicles isolated from bacteria. As a result, the ability to compare results across published studies can lead to questions regarding the suitability of methods and buffers for accurately quantifying these vesicles. Within the literature, there are several common methods for vesicle quantification. These include lipid quantification using the lipophilic dye FM 4-64, protein quantification using microBCA, Qubit, and NanoOrange assays, or direct vesicle enumeration using nanoparticle tracking analysis. In addition, various diluents and lysis buffers are also used to resuspend and treat vesicles. In this study, we directly compared the quantification of a bacterial outer membrane vesicle using several commonly used methods. We also tested the impact of different buffers, buffer age, lysis method, and vesicle diluent on vesicle quantification. The results showed that buffer age had no significant effect on vesicle quantification, but the lysis method impacted the reliability of measurements using Qubit and NanoOrange. The microBCA assay displayed the least variability in protein concentration values and was the most consistent, regardless of the buffer or diluent used. MicroBCA also demonstrated the strongest correlation to the NTA-determined particle number across a range of vesicle concentrations. Overall, these results indicate that with appropriate diluent and buffer choice, microBCA vs. NTA standard curves could be generated and the microBCA assay used to estimate the particle number when NTA instrumentation is not readily available. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Nanoparticles)

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17 pages, 3823 KiB

Open AccessArticle

High Recovery Chromatographic Purification of mRNA at Room Temperature and Neutral pH

by Rok Miklavčič, Polona Megušar, Špela Meta Kodermac, Blaž Bakalar, Darko Dolenc, Rok Sekirnik, Aleš Štrancar and Urh Černigoj

Int. J. Mol. Sci. 2023, 24(18), 14267; https://doi.org/10.3390/ijms241814267 - 19 Sep 2023

Cited by 1 | Viewed by 1936

Abstract

Messenger RNA (mRNA) is becoming an increasingly important therapeutic modality due to its potential for fast development and platform production. New emerging RNA modalities, such as circular RNA, drive the need for the development of non-affinity purification approaches. Recently, the highly efficient chromatographic purification of mRNA was demonstrated with multimodal monolithic chromatography media (CIM^® PrimaS), where efficient mRNA elution was achieved with an ascending pH gradient approach at pH 10.5. Here, we report that a newly developed chromatographic material enables the elution of mRNA at neutral pH and room temperature. This material demonstrates weak anion-exchanging properties and an isoelectric point of 5.3. It enables the baseline separation of mRNA (at least up to 10,000 nucleotides (nt) in size) from parental plasmid DNA (regardless of isoform composition) with both a NaCl gradient and ascending pH gradient approach, while mRNA elution is achieved in a pH range of 5–7. In addition, the basic structure of the novel material is a chromatographic monolith, enabling convection-assisted mass transfer of large RNA molecules to and from the active surface. This facilitates the elution of mRNA in 3–7 column volumes with more than 80% elution recovery and uncompromised integrity. This is demonstrated by the purification of a model mRNA (size 995 nt) from an in vitro transcription reaction mixture. The purified mRNA is stable for at least 34 days, stored in purified H₂O at room temperature. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Nanoparticles)

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25 pages, 8771 KiB

Open AccessArticle

Characterization and Proteomic Analysis of Plasma EVs Recovered from Healthy and Diseased Dogs with Canine Leishmaniosis

by Sofia Esteves, Clara Lima, Inês Costa, Hugo Osório, Carmen Fernandez-Becerra, Nuno Santarém and Anabela Cordeiro-da-Silva

Int. J. Mol. Sci. 2023, 24(6), 5490; https://doi.org/10.3390/ijms24065490 - 13 Mar 2023

Cited by 3 | Viewed by 1498

Abstract

Dogs are highly valued companions and work animals that are susceptible to many life-threatening conditions such as canine leishmaniosis (CanL). Plasma-derived extracellular vesicles (EVs), exploited extensively in biomarker discovery, constitute a mostly untapped resource in veterinary sciences. Thus, the definition of proteins associated with plasma EVs recovered from healthy and diseased dogs with a relevant pathogen would be important for biomarker development. For this, we recovered, using size-exclusion chromatography (SEC), EVs from 19 healthy and 20 CanL dogs’ plasma and performed proteomic analysis by LC-MS/MS to define their core proteomic composition and search for CanL-associated alterations. EVs-specific markers were identified in all preparations and also non-EVs proteins. Some EVs markers such as CD82 were specific to the healthy animals, while others, such as the Integrin beta 3 were identified in most samples. The EVs-enriched preparations allowed the identification of 529 canine proteins that were identified in both groups, while 465 and 154 were only identified in healthy or CanL samples, respectively. A GO enrichment analysis revealed few CanL-specific terms. Leishmania spp. protein identifications were also found, although with only one unique peptide. Ultimately, CanL-associated proteins of interest were identified and a core proteome was revealed that will be available for intra- and inter-species comparisons. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Nanoparticles)

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15 pages, 3494 KiB

Open AccessArticle

Identification of Novel Senescent Markers in Small Extracellular Vesicles

by Tomoka Misawa, Kazuhiro Hitomi, Kenichi Miyata, Yoko Tanaka, Risa Fujii, Masatomo Chiba, Tze Mun Loo, Aki Hanyu, Hiroko Kawasaki, Hisaya Kato, Yoshiro Maezawa, Koutaro Yokote, Asako J. Nakamura, Koji Ueda, Nobuo Yaegashi and Akiko Takahashi

Int. J. Mol. Sci. 2023, 24(3), 2421; https://doi.org/10.3390/ijms24032421 - 26 Jan 2023

Cited by 7 | Viewed by 2696

Abstract

Senescent cells exhibit several typical features, including the senescence-associated secretory phenotype (SASP), promoting the secretion of various inflammatory proteins and small extracellular vesicles (EVs). SASP factors cause chronic inflammation, leading to age-related diseases. Recently, therapeutic strategies targeting senescent cells, known as senolytics, have gained attention; however, noninvasive methods to detect senescent cells in living organisms have not been established. Therefore, the goal of this study was to identify novel senescent markers using small EVs (sEVs). sEVs were isolated from young and senescent fibroblasts using three different methods, including size-exclusion chromatography, affinity column for phosphatidylserine, and immunoprecipitation using antibodies against tetraspanin proteins, followed by mass spectrometry. Principal component analysis revealed that the protein composition of sEVs released from senescent cells was significantly different from that of young cells. Importantly, we identified ATP6V0D1 and RTN4 as novel markers that are frequently upregulated in sEVs from senescent and progeria cells derived from patients with Werner syndrome. Furthermore, these two proteins were significantly enriched in sEVs from the serum of aged mice. This study supports the potential use of senescent markers from sEVs to detect the presence of senescent cells in vivo. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Nanoparticles)

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Review

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23 pages, 1186 KiB

Open AccessReview

Extracellular Vesicles in the Central Nervous System: A Novel Mechanism of Neuronal Cell Communication

by Francesca Martina Filannino, Maria Antonietta Panaro, Tarek Benameur, Ilaria Pizzolorusso and Chiara Porro

Int. J. Mol. Sci. 2024, 25(3), 1629; https://doi.org/10.3390/ijms25031629 - 28 Jan 2024

Viewed by 1197

Abstract

Cell-to-cell communication is essential for the appropriate development and maintenance of homeostatic conditions in the central nervous system. Extracellular vesicles have recently come to the forefront of neuroscience as novel vehicles for the transfer of complex signals between neuronal cells. Extracellular vesicles are membrane-bound carriers packed with proteins, metabolites, and nucleic acids (including DNA, mRNA, and microRNAs) that contain the elements present in the cell they originate from. Since their discovery, extracellular vesicles have been studied extensively and have opened up new understanding of cell–cell communication; they may cross the blood–brain barrier in a bidirectional way from the bloodstream to the brain parenchyma and vice versa, and play a key role in brain–periphery communication in physiology as well as pathology. Neurons and glial cells in the central nervous system release extracellular vesicles to the interstitial fluid of the brain and spinal cord parenchyma. Extracellular vesicles contain proteins, nucleic acids, lipids, carbohydrates, and primary and secondary metabolites. that can be taken up by and modulate the behaviour of neighbouring recipient cells. The functions of extracellular vesicles have been extensively studied in the context of neurodegenerative diseases. The purpose of this review is to analyse the role extracellular vesicles extracellular vesicles in central nervous system cell communication, with particular emphasis on the contribution of extracellular vesicles from different central nervous system cell types in maintaining or altering central nervous system homeostasis. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Nanoparticles)

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29 pages, 2151 KiB

Open AccessReview

Nanoparticles in Medicine: Current Status in Cancer Treatment

by Krešimir Pavelić, Sandra Kraljević Pavelić, Aleksandar Bulog, Andrea Agaj, Barbara Rojnić, Miroslav Čolić and Dragan Trivanović

Int. J. Mol. Sci. 2023, 24(16), 12827; https://doi.org/10.3390/ijms241612827 - 15 Aug 2023

Cited by 4 | Viewed by 2173

Abstract

Cancer is still a leading cause of deaths worldwide, especially due to those cases diagnosed at late stages with metastases that are still considered untreatable and are managed in such a way that a lengthy chronic state is achieved. Nanotechnology has been acknowledged as one possible solution to improve existing cancer treatments, but also as an innovative approach to developing new therapeutic solutions that will lower systemic toxicity and increase targeted action on tumors and metastatic tumor cells. In particular, the nanoparticles studied in the context of cancer treatment include organic and inorganic particles whose role may often be expanded into diagnostic applications. Some of the best studied nanoparticles include metallic gold and silver nanoparticles, quantum dots, polymeric nanoparticles, carbon nanotubes and graphene, with diverse mechanisms of action such as, for example, the increased induction of reactive oxygen species, increased cellular uptake and functionalization properties for improved targeted delivery. Recently, novel nanoparticles for improved cancer cell targeting also include nanobubbles, which have already demonstrated increased localization of anticancer molecules in tumor tissues. In this review, we will accordingly present and discuss state-of-the-art nanoparticles and nano-formulations for cancer treatment and limitations for their application in a clinical setting. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Nanoparticles)

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