Proteomes of Extracellular Vesicles

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (15 April 2019) | Viewed by 51622

Special Issue Editors


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Guest Editor
Maria Sklodowska-Curie Institute-Oncology Center, Gliwice Branch, 44-101 Gliwice, Poland
Interests: cancer biomarkers; cellular signaling; clinical proteomics; clinical metabolomics; mass spectrometry imaging; stress response

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Guest Editor
1. UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
2. Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
Interests: clinical cancer immunology; cancer immunotherapy; extracellular vesicles; immuno-oncology; immune suppression in cancer; regulatory T cells; tumor-derived exosomes; tumor microenvironment
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Guest Editor
Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Branch in Gliwice, 44-101 Gliwice, Poland
Interests: clinical proteomics; extracellular vesicles; immunoproteomics; mass spectrometry; radiobiology; radioproteomics; stress response

Special Issue Information

Most cells release different types of vesicles into the extracellular microenvironment, both in vivo and in vitro, which are known under the general term of “extracellular vesicles (EVs)”. Recently, much attention has been paid to a subset of small EVs called exosomes, because of their role in cell-to-cell communication and involvement in disease-related processes. Exosomes are 30–150nm in size and are membrane-enclosed structures. They are actively secreted by cells via the mechanisms involving multivesicular bodies (MVBs). They transmit complex molecular and genetic information, including signals for cell death, survival, and differentiation, from exosome-secreting cells to multiple types of neighboring or distant recipient cells. The functional role of EVs depends on their molecular cargo, including their proteome content. EVs present in blood and other physiological fluids have a large potential for liquid biopsy and are an emerging source of disease biomarkers. However, the isolation and characterization of EVs, including the analysis of their proteome cargo, remains a challenge and represents an important limitation in this field of research.

We invite you to contribute original research, technical notes, methods papers, and reviews on the subject of the “Proteomes of Extracellular Vesicles”. Papers that cover advances in the methods of isolation and analysis of these vesicles by mass spectrometry approaches as well as their implementation both in basic research and the translational field of disease proteomics will be appreciated by our readership and will be highlighted as important and significant advancements of proteomic science.

Prof. Piotr Widlak
Prof. Theresa L. Whiteside
Prof. Monika Pietrowska
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomarkers
  • cancer cell biology
  • exosomes
  • extracellular vesicles
  • human proteome
  • immune cell regulation
  • liquid biopsy
  • mass spectrometry
  • stress response

Published Papers (8 papers)

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Editorial

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4 pages, 174 KiB  
Editorial
Proteomic Analysis of Plasma-Derived Exosomes in Defining Their Role as Biomarkers of Disease Progression, Response to Therapy and Outcome
by Theresa L. Whiteside
Proteomes 2019, 7(3), 27; https://doi.org/10.3390/proteomes7030027 - 30 Jun 2019
Cited by 10 | Viewed by 4347
Abstract
Extracellular vesicles (EVs) have recently emerged as an intercellular communication system that plays an important role in health and becomes dysfunctional in disease [...] Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)

Research

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17 pages, 2825 KiB  
Article
Comparison of Proteome Composition of Serum Enriched in Extracellular Vesicles Isolated from Polycythemia Vera Patients and Healthy Controls
by Anna Fel, Aleksandra E. Lewandowska, Petro E. Petrides and Jacek R. Wiśniewski
Proteomes 2019, 7(2), 20; https://doi.org/10.3390/proteomes7020020 - 6 May 2019
Cited by 21 | Viewed by 5584
Abstract
Extracellular vesicles (EVs), e.g., exosomes and microvesicles, are one of the main networks of intercellular communication. In myeloproliferative neoplasms, such as polycythemia vera (PV), excess of EVs originating from overabundant blood cells can directly contribute to thrombosis through their procoagulant activity. However, the [...] Read more.
Extracellular vesicles (EVs), e.g., exosomes and microvesicles, are one of the main networks of intercellular communication. In myeloproliferative neoplasms, such as polycythemia vera (PV), excess of EVs originating from overabundant blood cells can directly contribute to thrombosis through their procoagulant activity. However, the proteomic composition of these vesicles in PV patients has not been investigated before. In this work, we examined the proteomic composition of serum EVs of PV patients in comparison to healthy controls. We processed EV-enriched serum samples using the Multiple Enzyme Filter Aided Sample Preparation approach (MED-FASP), conducted LC-MS/MS measurements on a Q-Exactive HF-X mass spectrometer, and quantitatively analyzed the absolute concentrations of identified proteins by the Total Protein Approach (TPA). Thirty-eight proteins were present at statistically significant different concentrations between PV patients’ study group and healthy controls’ group. The main protein components deregulated in PV were primarily related to excessive amounts of cells, increased platelet activation, elevated immune and inflammatory response, and high concentrations of procoagulant and angiogenic agents. Our study provides the first quantitative analysis of the serum EVs’ proteome in PV patients. This new knowledge may contribute to a better understanding of the secondary systemic effects of PV disease and further development of diagnostic or therapeutic procedures. Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)
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12 pages, 1152 KiB  
Article
Proteome Profiling of Exosomes Purified from a Small Amount of Human Serum: The Problem of Co-Purified Serum Components
by Mateusz Smolarz, Monika Pietrowska, Natalia Matysiak, Łukasz Mielańczyk and Piotr Widłak
Proteomes 2019, 7(2), 18; https://doi.org/10.3390/proteomes7020018 - 28 Apr 2019
Cited by 67 | Viewed by 8924
Abstract
Untargeted proteomics analysis of extracellular vesicles (EVs) isolated from human serum or plasma remains a technical challenge due to the contamination of these vesicles with lipoproteins and other abundant serum components. Here we aimed to test a simple method of EV isolation from [...] Read more.
Untargeted proteomics analysis of extracellular vesicles (EVs) isolated from human serum or plasma remains a technical challenge due to the contamination of these vesicles with lipoproteins and other abundant serum components. Here we aimed to test a simple method of EV isolation from a small amount of human serum (<1 mL) using the size-exclusion chromatography (SEC) standalone for the discovery of vesicle-specific proteins by the untargeted LC–MS/MS shotgun approach. We selected the SEC fraction containing vesicles with the size of about 100 nm and enriched with exosome markers CD63 and CD81 (but not CD9 and TSG101) and analyzed it in a parallel to the subsequent SEC fraction enriched in the lipoprotein vesicles. In general, there were 267 proteins identified by LC–MS/MS in exosome-containing fraction (after exclusion of immunoglobulins), yet 94 of them might be considered as serum proteins. Hence, 173 exosome-related proteins were analyzed, including 92 proteins absent in lipoprotein-enriched fraction. In this set of exosome-related proteins, there were 45 species associated with the GO cellular compartment term “extracellular exosome”. Moreover, there were 31 proteins associated with different immune-related functions in this set, which putatively reflected the major role of exosomes released by immune cells present in the blood. We concluded that identified set of proteins included a bona fide exosomes components, yet the coverage of exosome proteome was low due to co-purified high abundant serum proteins. Nevertheless, the approach proposed in current work outperformed other comparable protocols regarding untargeted identification of exosome proteins and could be recommended for pilot exploratory studies when a small amount of a serum/plasma specimen is available. Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)
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14 pages, 4422 KiB  
Article
Isolation and Characterization of Small Extracellular Vesicles from Porcine Blood Plasma, Cerebrospinal Fluid, and Seminal Plasma
by Helena Kupcova Skalnikova, Bozena Bohuslavova, Karolina Turnovcova, Jana Juhasova, Stefan Juhas, Marie Rodinova and Petr Vodicka
Proteomes 2019, 7(2), 17; https://doi.org/10.3390/proteomes7020017 - 25 Apr 2019
Cited by 33 | Viewed by 8967
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)
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13 pages, 1918 KiB  
Communication
Extracellular Vesicle Integrins Distinguish Unique Cancers
by Stephanie N. Hurwitz and David G. Meckes, Jr.
Proteomes 2019, 7(2), 14; https://doi.org/10.3390/proteomes7020014 - 11 Apr 2019
Cited by 46 | Viewed by 6029
Abstract
The proteomic profile of extracellular vesicles (EVs) has been of increasing interest, particularly in understanding cancer growth, drug resistance, and metastatic behavior. Emerging data suggest that cancer-derived EVs carry an array of oncogenic cargo, including certain integrin proteins that may, in turn, promote [...] Read more.
The proteomic profile of extracellular vesicles (EVs) has been of increasing interest, particularly in understanding cancer growth, drug resistance, and metastatic behavior. Emerging data suggest that cancer-derived EVs carry an array of oncogenic cargo, including certain integrin proteins that may, in turn, promote cell detachment, migration, and selection of future metastatic sites. We previously reported a large comparison of secreted vesicle protein cargo across sixty diverse human cancer cell lines. Here, we analyze the distinct integrin profiles of these cancer EVs. We further demonstrate the enrichment of integrin receptors in cancer EVs compared to vesicles secreted from benign epithelial cells. The total EV integrin levels, including the quantity of integrins α6, αv, and β1 correlate with tumor stage across a variety of epithelial cancer cells. In particular, integrin α6 also largely reflects breast and ovarian progenitor cell expression, highlighting the utility of this integrin protein as a potential circulating biomarker of certain primary tumors. This study provides preliminary evidence of the value of vesicle-associated integrin proteins in detecting the presence of cancer cells and prediction of tumor stage. Differential expression of integrins across cancer cells and selective packaging of integrins into EVs may contribute to further understanding the development and progression of tumor growth and metastasis across a variety of cancer types. Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)
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Review

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10 pages, 693 KiB  
Review
Different Types of Cellular Stress Affect the Proteome Composition of Small Extracellular Vesicles: A Mini Review
by Agata Abramowicz, Piotr Widłak and Monika Pietrowska
Proteomes 2019, 7(2), 23; https://doi.org/10.3390/proteomes7020023 - 23 May 2019
Cited by 30 | Viewed by 5192
Abstract
Extracellular vesicles (EVs) are well-known mediators of the cellular response to different stress factors, yet the exact mechanism of their action remains unclear. Hence, the characterization of their cargo, consisting of proteins, nucleic acids, and different classes of metabolites, helps to elucidate an [...] Read more.
Extracellular vesicles (EVs) are well-known mediators of the cellular response to different stress factors, yet the exact mechanism of their action remains unclear. Hence, the characterization of their cargo, consisting of proteins, nucleic acids, and different classes of metabolites, helps to elucidate an understanding of their function in stress-related communication. The unexpected diversity and complexity of these vesicles requires the incorporation of multiple technologically advanced approaches in EV-oriented studies. This mini review focuses on the invaluable role of proteomics, especially mass spectrometry-based tools, in the investigation of the role of small EVs in their response to stress. Though relatively few experimental works address this issue to date, the available data indicate that stress conditions would affect the composition of protein cargo of vesicles released by stressed cells, as evidenced by the functional importance of such changes in the context of the response of recipient cells. Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)
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12 pages, 253 KiB  
Review
Challenges in the Isolation and Proteomic Analysis of Cancer Exosomes—Implications for Translational Research
by Jadwiga Jablonska, Monika Pietrowska, Sonja Ludwig, Stephan Lang and Basant Kumar Thakur
Proteomes 2019, 7(2), 22; https://doi.org/10.3390/proteomes7020022 - 15 May 2019
Cited by 21 | Viewed by 5650
Abstract
Exosomes belong to the group of extracellular vesicles (EVs) that derive from various cell populations and mediate intercellular communication in health and disease. Like hormones or cytokines, exosomes released by cells can play a potent role in the communication between the cell of [...] Read more.
Exosomes belong to the group of extracellular vesicles (EVs) that derive from various cell populations and mediate intercellular communication in health and disease. Like hormones or cytokines, exosomes released by cells can play a potent role in the communication between the cell of origin and distant cells in the body to maintain homeostatic or pathological processes, including tumorigenesis. The nucleic acids, and lipid and protein cargo present in the exosomes are involved in a myriad of carcinogenic processes, including cell proliferation, tumor angiogenesis, immunomodulation, and metastasis formation. The ability of exosomal proteins to mediate direct functions by interaction with other cells qualifies them as tumor-specific biomarkers and targeted therapeutic approaches. However, the heterogeneity of plasma-derived exosomes consistent of (a) exosomes derived from all kinds of body cells, including cancer cells and (b) contamination of exosome preparation with other extracellular vesicles, such as apoptotic bodies, makes it challenging to obtain solid proteomics data for downstream clinical application. In this manuscript, we review these challenges beginning with the choice of different isolation methods, through the evaluation of obtained exosomes and limitations in the process of proteome analysis of cancer-derived exosomes to identify novel protein targets with functional impact in the context of translational oncology. Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)
16 pages, 744 KiB  
Review
Melanoma-Derived Extracellular Vesicles: Focus on Their Proteome
by Magdalena Surman, Ewa Stępień and Małgorzata Przybyło
Proteomes 2019, 7(2), 21; https://doi.org/10.3390/proteomes7020021 - 13 May 2019
Cited by 21 | Viewed by 6214
Abstract
Malignant melanoma is one of the most aggressive types of cancer, and its incidence is increasing rapidly each year. Despite the extensive research into improved diagnostic and treatment methods, early detection and disease constraint still present significant challenges. As successful isolation protocols have [...] Read more.
Malignant melanoma is one of the most aggressive types of cancer, and its incidence is increasing rapidly each year. Despite the extensive research into improved diagnostic and treatment methods, early detection and disease constraint still present significant challenges. As successful isolation protocols have been developed, extracellular vesicles (EVs) have become the subject of extensive investigation in terms of their role in cancer progression and as a possible source of disease biomarkers. Besides functional studies, quantitative and qualitative proteomics have recently emerged as promising tools for the advancement of melanoma biomarkers. Nevertheless, the amount of data concerning the proteome of melanoma-derived EVs is still very limited. In this review we cover the current knowledge on protein content of melanoma-derived EVs, with a focus on their potential role in the development and progression of melanomas. Full article
(This article belongs to the Special Issue Proteomes of Extracellular Vesicles)
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